diff --git a/.Rhistory b/.Rhistory index 19c58ab..696d5a7 100644 --- a/.Rhistory +++ b/.Rhistory @@ -1,210 +1,416 @@ -}) -# Verify farm_health_data exists and has content -if (!exists("farm_health_data") || nrow(farm_health_data) == 0) { -safe_log("farm_health_data not found or empty, generating default data", "WARNING") -# Create minimal fallback data -tryCatch({ -# Get fields from boundaries -fields <- unique(AllPivots0$field) -# Create basic data frame with just field names -farm_health_data <- data.frame( -field = fields, -mean_ci = rep(NA, length(fields)), -ci_change = rep(NA, length(fields)), -ci_uniformity = rep(NA, length(fields)), -status = rep("Unknown", length(fields)), -anomaly_type = rep("Unknown", length(fields)), -priority_level = rep(5, length(fields)), # Low priority -age_weeks = rep(NA, length(fields)), -harvest_readiness = rep("Unknown", length(fields)), -stringsAsFactors = FALSE -) -safe_log("Created fallback farm_health_data with basic field information") -}, error = function(e) { -safe_log(paste("Error creating fallback farm_health_data:", e$message), "ERROR") -farm_health_data <<- data.frame( -field = character(), -mean_ci = numeric(), -ci_change = numeric(), -ci_uniformity = numeric(), -status = character(), -anomaly_type = character(), -priority_level = numeric(), -age_weeks = numeric(), -harvest_readiness = character(), -stringsAsFactors = FALSE -) -}) +ggplot2::labs(title = "Model Performance: \nPredicted vs Actual Tonnage/ha", +x = "Actual tonnage/ha (Tcha)", +y = "Predicted tonnage/ha (Tcha)") + +ggplot2::theme_minimal() } -# Calculate farm health summary metrics -tryCatch({ -# Generate farm health summary data -farm_health_data <- generate_farm_health_summary( -field_boundaries = AllPivots0, -ci_current = CI, -ci_previous = CI_m1, -harvesting_data = harvesting_data -) -# Log the summary data -safe_log(paste("Generated farm health summary with", nrow(farm_health_data), "fields")) -}, error = function(e) { -safe_log(paste("Error in farm health calculation:", e$message), "ERROR") -# Create empty dataframe if calculation failed -farm_health_data <- data.frame( -field = character(), -mean_ci = numeric(), -ci_change = numeric(), -ci_uniformity = numeric(), -status = character(), -anomaly_type = character(), -priority_level = numeric(), -age_weeks = numeric(), -harvest_readiness = character(), -stringsAsFactors = FALSE -) -}) -# Render the velocity and acceleration indicators -tryCatch({ -# Create and display the indicators using the imported utility function -velocity_plot <- create_velocity_acceleration_indicator( -health_data = farm_health_data, -ci_current = CI, -ci_prev1 = CI_m1, -ci_prev2 = CI_m2, -ci_prev3 = CI_m3, -field_boundaries = AllPivots0 -) -# Print the visualization -print(velocity_plot) -# Create a table of fields with significant velocity changes -field_ci_metrics <- list() -# Process each field to get metrics -fields <- unique(AllPivots0$field) -for (field_name in fields) { -tryCatch({ -# Get field boundary -field_shape <- AllPivots0 %>% dplyr::filter(field == field_name) -if (nrow(field_shape) == 0) next -# Extract CI values -ci_curr_values <- terra::extract(CI, field_shape) -ci_prev1_values <- terra::extract(CI_m1, field_shape) -# Calculate metrics -mean_ci_curr <- mean(ci_curr_values$CI, na.rm = TRUE) -mean_ci_prev1 <- mean(ci_prev1_values$CI, na.rm = TRUE) -velocity <- mean_ci_curr - mean_ci_prev1 -# Store in list -field_ci_metrics[[field_name]] <- list( -field = field_name, -ci_current = mean_ci_curr, -ci_prev1 = mean_ci_prev1, -velocity = velocity -) -}, error = function(e) { -safe_log(paste("Error processing field", field_name, "for velocity table:", e$message), "WARNING") -}) -} -# Convert list to data frame -velocity_df <- do.call(rbind, lapply(field_ci_metrics, function(x) { -data.frame( -field = x$field, -ci_current = round(x$ci_current, 2), -ci_prev1 = round(x$ci_prev1, 2), -velocity = round(x$velocity, 2), -direction = ifelse(x$velocity >= 0, "Improving", "Declining") -) -})) -# Select top 5 positive and top 5 negative velocity fields -top_positive <- velocity_df %>% -dplyr::filter(velocity > 0) %>% -dplyr::arrange(desc(velocity)) %>% -dplyr::slice_head(n = 5) -top_negative <- velocity_df %>% -dplyr::filter(velocity < 0) %>% -dplyr::arrange(velocity) %>% -dplyr::slice_head(n = 5) -# Display the tables if we have data -if (nrow(top_positive) > 0) { -cat("

Fields with Fastest Improvement

") -knitr::kable(top_positive %>% -dplyr::select(Field = field, -`Current CI` = ci_current, -`Previous CI` = ci_prev1, -`Weekly Change` = velocity)) -} -if (nrow(top_negative) > 0) { -cat("

Fields with Fastest Decline

") -knitr::kable(top_negative %>% -dplyr::select(Field = field, -`Current CI` = ci_current, -`Previous CI` = ci_prev1, -`Weekly Change` = velocity)) +if (nrow(pred_rf_current_season) > 0) { +# Plot predicted yields by age +ggplot2::ggplot(pred_rf_current_season, ggplot2::aes(x = Age_days, y = predicted_Tcha)) + +ggplot2::geom_point(size = 2, alpha = 0.6) + +ggplot2::labs(title = "Predicted Yields for Fields Over 300 Days \nOld Yet to Be Harvested", +x = "Age (days)", +y = "Predicted tonnage/ha (Tcha)") + +ggplot2::scale_y_continuous(limits = c(0, 200)) + +ggplot2::theme_minimal() +# Display prediction table +knitr::kable(pred_rf_current_season, +digits = 0, +caption = "Predicted Tonnage/ha for Fields Over 300 Days Old") +} else { +cat("No fields over 300 days old without harvest data available for yield prediction.") } }, error = function(e) { -safe_log(paste("Error rendering velocity visualization:", e$message), "ERROR") -cat("
Error generating velocity visualization.
") +safe_log(paste("Error in yield prediction visualization:", e$message), "ERROR") +cat("Error generating yield prediction visualizations. See log for details.") }) -# Generate anomaly timeline visualization +# Load and prepare yield prediction data with error handling tryCatch({ -# Use the imported function to create the anomaly timeline -anomaly_timeline <- create_anomaly_timeline( -field_boundaries = AllPivots0, -ci_data = CI_quadrant, -days_to_include = 90 # Show last 90 days of data -) -# Display the timeline -print(anomaly_timeline) -}, error = function(e) { -safe_log(paste("Error generating anomaly timeline:", e$message), "ERROR") -cat("
Error generating anomaly timeline visualization.
") -}) -# Verify farm_health_data exists and has content -if (!exists("farm_health_data") || nrow(farm_health_data) == 0) { -safe_log("farm_health_data not found or empty, generating default data", "WARNING") -# Create minimal fallback data -tryCatch({ -# Get fields from boundaries -fields <- unique(AllPivots0$field) -# Create basic data frame with just field names -farm_health_data <- data.frame( -field = fields, -mean_ci = rep(NA, length(fields)), -ci_change = rep(NA, length(fields)), -ci_uniformity = rep(NA, length(fields)), -status = rep("Unknown", length(fields)), -anomaly_type = rep("Unknown", length(fields)), -priority_level = rep(5, length(fields)), # Low priority -age_weeks = rep(NA, length(fields)), -harvest_readiness = rep("Unknown", length(fields)), -stringsAsFactors = FALSE -) -safe_log("Created fallback farm_health_data with basic field information") -}, error = function(e) { -safe_log(paste("Error creating fallback farm_health_data:", e$message), "ERROR") -farm_health_data <<- data.frame( -field = character(), -mean_ci = numeric(), -ci_change = numeric(), -ci_uniformity = numeric(), -status = character(), -anomaly_type = character(), -priority_level = numeric(), -age_weeks = numeric(), -harvest_readiness = character(), -stringsAsFactors = FALSE -) -}) +# Load CI quadrant data and fill missing values +CI_quadrant <- readRDS(here::here(cumulative_CI_vals_dir, "All_pivots_Cumulative_CI_quadrant_year_v2.rds")) %>% +dplyr::group_by(model) %>% +tidyr::fill(field, sub_field, .direction = "downup") %>% +dplyr::ungroup() +# Check if tonnage_ha is empty +if (all(is.na(harvesting_data$tonnage_ha))) { +safe_log("Lacking historic harvest data, please provide for yield prediction calculation", "WARNING") +knitr::knit_exit() # Exit the chunk if tonnage_ha is empty } -# ADVANCED ANALYTICS FUNCTIONS -# Note: These functions are now imported from executive_report_utils.R -# The utility file contains functions for velocity/acceleration indicators, -# anomaly timeline creation, age cohort mapping, and cohort performance charts -safe_log("Using analytics functions from executive_report_utils.R") +# Rename year column to season for consistency +harvesting_data <- harvesting_data %>% dplyr::rename(season = year) +# Join CI and yield data +CI_and_yield <- dplyr::left_join(CI_quadrant, harvesting_data, by = c("field", "sub_field", "season")) %>% +dplyr::group_by(sub_field, season) %>% +dplyr::slice(which.max(DOY)) %>% +dplyr::select(field, sub_field, tonnage_ha, cumulative_CI, DOY, season, sub_area) %>% +dplyr::mutate(CI_per_day = cumulative_CI / DOY) +# Define predictors and response variables +predictors <- c("cumulative_CI", "DOY", "CI_per_day") +response <- "tonnage_ha" +# Prepare test and validation datasets +CI_and_yield_test <- CI_and_yield %>% +as.data.frame() %>% +dplyr::filter(!is.na(tonnage_ha)) +CI_and_yield_validation <- CI_and_yield_test +# Prepare prediction dataset (fields without harvest data) +prediction_yields <- CI_and_yield %>% +as.data.frame() %>% +dplyr::filter(is.na(tonnage_ha)) +# Configure model training parameters +ctrl <- caret::trainControl( +method = "cv", +savePredictions = TRUE, +allowParallel = TRUE, +number = 5, +verboseIter = TRUE +) +# Train the model with feature selection +set.seed(202) # For reproducibility +model_ffs_rf <- CAST::ffs( +CI_and_yield_test[, predictors], +CI_and_yield_test[, response], +method = "rf", +trControl = ctrl, +importance = TRUE, +withinSE = TRUE, +tuneLength = 5, +na.rm = TRUE +) +# Function to prepare predictions with consistent naming and formatting +prepare_predictions <- function(predictions, newdata) { +return(predictions %>% +as.data.frame() %>% +dplyr::rename(predicted_Tcha = ".") %>% +dplyr::mutate( +sub_field = newdata$sub_field, +field = newdata$field, +Age_days = newdata$DOY, +total_CI = round(newdata$cumulative_CI, 0), +predicted_Tcha = round(predicted_Tcha, 0), +season = newdata$season +) %>% +dplyr::select(field, sub_field, Age_days, total_CI, predicted_Tcha, season) %>% +dplyr::left_join(., newdata, by = c("field", "sub_field", "season")) +) +} +# Predict yields for the validation dataset +pred_ffs_rf <- prepare_predictions(stats::predict(model_ffs_rf, newdata = CI_and_yield_validation), CI_and_yield_validation) +# Predict yields for the current season (focus on mature fields over 300 days) +pred_rf_current_season <- prepare_predictions(stats::predict(model_ffs_rf, newdata = prediction_yields), prediction_yields) %>% +dplyr::filter(Age_days > 1) %>% +dplyr::mutate(CI_per_day = round(total_CI / Age_days, 1)) +safe_log("Successfully completed yield prediction calculations") +}, error = function(e) { +safe_log(paste("Error in yield prediction:", e$message), "ERROR") +# Create empty dataframes to prevent errors in subsequent chunks +pred_ffs_rf <- data.frame() +pred_rf_current_season <- data.frame() +}) +# Load and prepare yield prediction data with error handling +tryCatch({ +# Load CI quadrant data and fill missing values +CI_quadrant <- readRDS(here::here(cumulative_CI_vals_dir, "All_pivots_Cumulative_CI_quadrant_year_v2.rds")) %>% +dplyr::group_by(model) %>% +tidyr::fill(field, sub_field, .direction = "downup") %>% +dplyr::ungroup() +# Check if tonnage_ha is empty +if (all(is.na(harvesting_data$tonnage_ha))) { +safe_log("Lacking historic harvest data, please provide for yield prediction calculation", "WARNING") +knitr::knit_exit() # Exit the chunk if tonnage_ha is empty +} +# Rename year column to season for consistency +harvesting_data <- harvesting_data %>% dplyr::rename(season = year) +# Join CI and yield data +CI_and_yield <- dplyr::left_join(CI_quadrant, harvesting_data, by = c("field", "sub_field", "season")) %>% +dplyr::group_by(sub_field, season) %>% +dplyr::slice(which.max(DOY)) %>% +dplyr::select(field, sub_field, tonnage_ha, cumulative_CI, DOY, season, sub_area) %>% +dplyr::mutate(CI_per_day = cumulative_CI / DOY) +# Define predictors and response variables +predictors <- c("cumulative_CI", "DOY", "CI_per_day") +response <- "tonnage_ha" +# Prepare test and validation datasets +CI_and_yield_test <- CI_and_yield %>% +as.data.frame() %>% +dplyr::filter(!is.na(tonnage_ha)) +CI_and_yield_validation <- CI_and_yield_test +# Prepare prediction dataset (fields without harvest data) +prediction_yields <- CI_and_yield %>% +as.data.frame() %>% +dplyr::filter(is.na(tonnage_ha)) +# Configure model training parameters +ctrl <- caret::trainControl( +method = "cv", +savePredictions = TRUE, +allowParallel = TRUE, +number = 5, +verboseIter = TRUE +) +# Train the model with feature selection +set.seed(202) # For reproducibility +model_ffs_rf <- CAST::ffs( +CI_and_yield_test[, predictors], +CI_and_yield_test[, response], +method = "rf", +trControl = ctrl, +importance = TRUE, +withinSE = TRUE, +tuneLength = 5, +na.rm = TRUE +) +# Function to prepare predictions with consistent naming and formatting +prepare_predictions <- function(predictions, newdata) { +return(predictions %>% +as.data.frame() %>% +dplyr::rename(predicted_Tcha = ".") %>% +dplyr::mutate( +sub_field = newdata$sub_field, +field = newdata$field, +Age_days = newdata$DOY, +total_CI = round(newdata$cumulative_CI, 0), +predicted_Tcha = round(predicted_Tcha, 0), +season = newdata$season +) %>% +dplyr::select(field, sub_field, Age_days, total_CI, predicted_Tcha, season) %>% +dplyr::left_join(., newdata, by = c("field", "sub_field", "season")) +) +} +# Predict yields for the validation dataset +pred_ffs_rf <- prepare_predictions(stats::predict(model_ffs_rf, newdata = CI_and_yield_validation), CI_and_yield_validation) +# Predict yields for the current season (focus on mature fields over 300 days) +pred_rf_current_season <- prepare_predictions(stats::predict(model_ffs_rf, newdata = prediction_yields), prediction_yields) %>% +dplyr::filter(Age_days > 1) %>% +dplyr::mutate(CI_per_day = round(total_CI / Age_days, 1)) +safe_log("Successfully completed yield prediction calculations") +}, error = function(e) { +safe_log(paste("Error in yield prediction:", e$message), "ERROR") +# Create empty dataframes to prevent errors in subsequent chunks +pred_ffs_rf <- data.frame() +pred_rf_current_season <- data.frame() +}) +# Load CI quadrant data and fill missing values +CI_quadrant <- readRDS(here::here(cumulative_CI_vals_dir, "All_pivots_Cumulative_CI_quadrant_year_v2.rds")) %>% +dplyr::group_by(model) %>% +tidyr::fill(field, sub_field, .direction = "downup") %>% +dplyr::ungroup() +# Check if tonnage_ha is empty +if (all(is.na(harvesting_data$tonnage_ha))) { +safe_log("Lacking historic harvest data, please provide for yield prediction calculation", "WARNING") +knitr::knit_exit() # Exit the chunk if tonnage_ha is empty +} +# Rename year column to season for consistency +harvesting_data <- harvesting_data %>% dplyr::rename(season = year) +# Join CI and yield data +CI_and_yield <- dplyr::left_join(CI_quadrant, harvesting_data, by = c("field", "sub_field", "season")) %>% +dplyr::group_by(sub_field, season) %>% +dplyr::slice(which.max(DOY)) %>% +dplyr::select(field, sub_field, tonnage_ha, cumulative_CI, DOY, season, sub_area) %>% +dplyr::mutate(CI_per_day = cumulative_CI / DOY) +# Define predictors and response variables +predictors <- c("cumulative_CI", "DOY", "CI_per_day") +response <- "tonnage_ha" +# Prepare test and validation datasets +CI_and_yield_test <- CI_and_yield %>% +as.data.frame() %>% +dplyr::filter(!is.na(tonnage_ha)) +CI_and_yield_validation <- CI_and_yield_test +# Prepare prediction dataset (fields without harvest data) +prediction_yields <- CI_and_yield %>% +as.data.frame() %>% +dplyr::filter(is.na(tonnage_ha)) +# Configure model training parameters +ctrl <- caret::trainControl( +method = "cv", +savePredictions = TRUE, +allowParallel = TRUE, +number = 5, +verboseIter = TRUE +) +# Train the model with feature selection +set.seed(202) # For reproducibility +model_ffs_rf <- CAST::ffs( +CI_and_yield_test[, predictors], +CI_and_yield_test[, response], +method = "rf", +trControl = ctrl, +importance = TRUE, +withinSE = TRUE, +tuneLength = 5, +na.rm = TRUE +) +# Function to prepare predictions with consistent naming and formatting +prepare_predictions <- function(predictions, newdata) { +return(predictions %>% +as.data.frame() %>% +dplyr::rename(predicted_Tcha = ".") %>% +dplyr::mutate( +sub_field = newdata$sub_field, +field = newdata$field, +Age_days = newdata$DOY, +total_CI = round(newdata$cumulative_CI, 0), +predicted_Tcha = round(predicted_Tcha, 0), +season = newdata$season +) %>% +dplyr::select(field, sub_field, Age_days, total_CI, predicted_Tcha, season) %>% +dplyr::left_join(., newdata, by = c("field", "sub_field", "season")) +) +} +# Predict yields for the validation dataset +pred_ffs_rf <- prepare_predictions(stats::predict(model_ffs_rf, newdata = CI_and_yield_validation), CI_and_yield_validation) +# Predict yields for the current season (focus on mature fields over 300 days) +pred_rf_current_season <- prepare_predictions(stats::predict(model_ffs_rf, newdata = prediction_yields), prediction_yields) %>% +dplyr::filter(Age_days > 300) %>% +dplyr::mutate(CI_per_day = round(total_CI / Age_days, 1)) +# Predict yields for the current season (focus on mature fields over 300 days) +pred_rf_current_season <- prepare_predictions(stats::predict(model_ffs_rf, newdata = prediction_yields), prediction_yields) %>% +dplyr::filter(Age_days > 1) %>% +dplyr::mutate(CI_per_day = round(total_CI / Age_days, 1)) +safe_log("Successfully completed yield prediction calculations") +# Load and prepare yield prediction data with error handling +tryCatch({ +# Load CI quadrant data and fill missing values +CI_quadrant <- readRDS(here::here(cumulative_CI_vals_dir, "All_pivots_Cumulative_CI_quadrant_year_v2.rds")) %>% +dplyr::group_by(model) %>% +tidyr::fill(field, sub_field, .direction = "downup") %>% +dplyr::ungroup() +# Check if tonnage_ha is empty +if (all(is.na(harvesting_data$tonnage_ha))) { +safe_log("Lacking historic harvest data, please provide for yield prediction calculation", "WARNING") +knitr::knit_exit() # Exit the chunk if tonnage_ha is empty +} +# Rename year column to season for consistency +harvesting_data <- harvesting_data %>% dplyr::rename(season = year) +# Join CI and yield data +CI_and_yield <- dplyr::left_join(CI_quadrant, harvesting_data, by = c("field", "sub_field", "season")) %>% +dplyr::group_by(sub_field, season) %>% +dplyr::slice(which.max(DOY)) %>% +dplyr::select(field, sub_field, tonnage_ha, cumulative_CI, DOY, season, sub_area) %>% +dplyr::mutate(CI_per_day = cumulative_CI / DOY) +# Define predictors and response variables +predictors <- c("cumulative_CI", "DOY", "CI_per_day") +response <- "tonnage_ha" +# Prepare test and validation datasets +CI_and_yield_test <- CI_and_yield %>% +as.data.frame() %>% +dplyr::filter(!is.na(tonnage_ha)) +CI_and_yield_validation <- CI_and_yield_test +# Prepare prediction dataset (fields without harvest data) +prediction_yields <- CI_and_yield %>% +as.data.frame() %>% +dplyr::filter(is.na(tonnage_ha)) +# Configure model training parameters +ctrl <- caret::trainControl( +method = "cv", +savePredictions = TRUE, +allowParallel = TRUE, +number = 5, +verboseIter = TRUE +) +# Train the model with feature selection +set.seed(202) # For reproducibility +model_ffs_rf <- CAST::ffs( +CI_and_yield_test[, predictors], +CI_and_yield_test[, response], +method = "rf", +trControl = ctrl, +importance = TRUE, +withinSE = TRUE, +tuneLength = 5, +na.rm = TRUE +) +# Function to prepare predictions with consistent naming and formatting +prepare_predictions <- function(predictions, newdata) { +return(predictions %>% +as.data.frame() %>% +dplyr::rename(predicted_Tcha = ".") %>% +dplyr::mutate( +sub_field = newdata$sub_field, +field = newdata$field, +Age_days = newdata$DOY, +total_CI = round(newdata$cumulative_CI, 0), +predicted_Tcha = round(predicted_Tcha, 0), +season = newdata$season +) %>% +dplyr::select(field, sub_field, Age_days, total_CI, predicted_Tcha, season) %>% +dplyr::left_join(., newdata, by = c("field", "sub_field", "season")) +) +} +# Predict yields for the validation dataset +pred_ffs_rf <- prepare_predictions(stats::predict(model_ffs_rf, newdata = CI_and_yield_validation), CI_and_yield_validation) +# Predict yields for the current season (focus on mature fields over 300 days) +pred_rf_current_season <- prepare_predictions(stats::predict(model_ffs_rf, newdata = prediction_yields), prediction_yields) %>% +dplyr::filter(Age_days > 1) %>% +dplyr::mutate(CI_per_day = round(total_CI / Age_days, 1)) +safe_log("Successfully completed yield prediction calculations") +}, error = function(e) { +safe_log(paste("Error in yield prediction:", e$message), "ERROR") +# Create empty dataframes to prevent errors in subsequent chunks +pred_ffs_rf <- data.frame() +pred_rf_current_season <- data.frame() +}) +# Display yield prediction visualizations with error handling +tryCatch({ +if (nrow(pred_ffs_rf) > 0) { +# Plot model performance (predicted vs actual) +ggplot2::ggplot(pred_ffs_rf, ggplot2::aes(y = predicted_Tcha, x = tonnage_ha)) + +ggplot2::geom_point(size = 2, alpha = 0.6) + +ggplot2::geom_abline(intercept = 0, slope = 1, linetype = "dashed", color = "red") + +ggplot2::scale_x_continuous(limits = c(0, 200)) + +ggplot2::scale_y_continuous(limits = c(0, 200)) + +ggplot2::labs(title = "Model Performance: \nPredicted vs Actual Tonnage/ha", +x = "Actual tonnage/ha (Tcha)", +y = "Predicted tonnage/ha (Tcha)") + +ggplot2::theme_minimal() +} +if (nrow(pred_rf_current_season) > 0) { +# Plot predicted yields by age +ggplot2::ggplot(pred_rf_current_season, ggplot2::aes(x = Age_days, y = predicted_Tcha)) + +ggplot2::geom_point(size = 2, alpha = 0.6) + +ggplot2::labs(title = "Predicted Yields for Fields Over 300 Days \nOld Yet to Be Harvested", +x = "Age (days)", +y = "Predicted tonnage/ha (Tcha)") + +ggplot2::scale_y_continuous(limits = c(0, 200)) + +ggplot2::theme_minimal() +# Display prediction table +knitr::kable(pred_rf_current_season, +digits = 0, +caption = "Predicted Tonnage/ha for Fields Over 300 Days Old") +} else { +cat("No fields over 300 days old without harvest data available for yield prediction.") +} +}, error = function(e) { +safe_log(paste("Error in yield prediction visualization:", e$message), "ERROR") +cat("Error generating yield prediction visualizations. See log for details.") +}) +AllPivots_merged$field[1:10] +CI +path_to_week_current +terra::rast(path_to_week_current) +map <- tmap::tm_shape(last_week_dif_raster_abs, unit = "m") # Add raster layer with continuous spectrum (centered at 0 for difference maps) +map <- map + tmap::tm_raster(col.scale = tm_scale_continuous(values = "RdYlGn", +midpoint = 0), +col.legend = tm_legend(title = "Chlorophyll Index (CI) Change", +orientation = "landscape", +position = tm_pos_out("center", "bottom"))) +# Complete the map with layout and other elements +map <- map + +tmap::tm_scalebar(position = c("right", "bottom"), text.color = "black") + +tmap::tm_compass(position = c("right", "bottom"), text.color = "black") + +tmap::tm_shape(AllPivots0) + +tmap::tm_borders(col = "black") + +tmap::tm_text("sub_field", size = 0.6, col = "black") +# Print the map +print(map) +# Get versions of specific packages you're using +packages <- c("here", "sf", "terra", "exactextractr", "tidyverse", +"tmap", "lubridate", "magrittr", "dplyr", "readr", +"readxl", "knitr", "rmarkdown", "officedown", "officer") +package_versions <- sapply(packages, function(x) as.character(packageVersion(x))) +sessionInfo() # Chunk 1: setup_parameters # Set up basic report parameters from input values report_date <- params$report_date mail_day <- params$mail_day borders <- params$borders -use_breaks <- params$use_breaks # Whether to use breaks or continuous spectrum in visualizations # Environment setup notes (commented out) # # Activeer de renv omgeving # renv::activate() @@ -215,23 +421,21 @@ use_breaks <- params$use_breaks # Whether to use breaks or continuous spectrum # Chunk 2: load_libraries # Configure knitr options knitr::opts_chunk$set(warning = FALSE, message = FALSE) -# Path management +# Load all packages at once with suppressPackageStartupMessages +suppressPackageStartupMessages({ library(here) -# Spatial data libraries library(sf) library(terra) library(exactextractr) -# library(raster) - Removed as it's no longer maintained -# Data manipulation and visualization -library(tidyverse) # Includes dplyr, ggplot2, etc. +library(tidyverse) library(tmap) library(lubridate) library(zoo) -# Machine learning library(rsample) library(caret) library(randomForest) library(CAST) +}) # Load custom utility functions tryCatch({ source("report_utils.R") @@ -244,199 +448,21 @@ source(here::here("r_app", "report_utils.R")) stop("Could not load report_utils.R from either location: ", e$message) }) }) -# Load executive report utilities -tryCatch({ -source("executive_report_utils.R") -}, error = function(e) { -message(paste("Error loading executive_report_utils.R:", e$message)) -# Try alternative path if the first one fails -tryCatch({ -source(here::here("r_app", "executive_report_utils.R")) -}, error = function(e) { -stop("Could not load executive_report_utils.R from either location: ", e$message) -}) -}) -# Chunk 1: setup_parameters -# Set up basic report parameters from input values -report_date <- params$report_date -mail_day <- params$mail_day -borders <- params$borders -use_breaks <- params$use_breaks # Whether to use breaks or continuous spectrum in visualizations -# Environment setup notes (commented out) -# # Activeer de renv omgeving -# renv::activate() -# renv::deactivate() -# # Optioneel: Herstel de omgeving als dat nodig is -# # Je kunt dit commentaar geven als je het normaal niet wilt uitvoeren -# renv::restore() -# Chunk 2: load_libraries -# Configure knitr options -knitr::opts_chunk$set(warning = FALSE, message = FALSE) -# Path management -library(here) -# Spatial data libraries -library(sf) -library(terra) -library(exactextractr) -# library(raster) - Removed as it's no longer maintained -# Data manipulation and visualization -library(tidyverse) # Includes dplyr, ggplot2, etc. -library(tmap) -library(lubridate) -library(zoo) -# Machine learning -library(rsample) -library(caret) -library(randomForest) -library(CAST) -# Load custom utility functions -tryCatch({ -source("report_utils.R") -}, error = function(e) { -message(paste("Error loading report_utils.R:", e$message)) -# Try alternative path if the first one fails -tryCatch({ -source(here::here("r_app", "report_utils.R")) -}, error = function(e) { -stop("Could not load report_utils.R from either location: ", e$message) -}) -}) -# Load executive report utilities -tryCatch({ -source("executive_report_utils.R") -}, error = function(e) { -message(paste("Error loading executive_report_utils.R:", e$message)) -# Try alternative path if the first one fails -tryCatch({ -source(here::here("r_app", "executive_report_utils.R")) -}, error = function(e) { -stop("Could not load executive_report_utils.R from either location: ", e$message) -}) -}) -# Chunk 1: setup_parameters -# Set up basic report parameters from input values -report_date <- params$report_date -mail_day <- params$mail_day -borders <- params$borders -use_breaks <- params$use_breaks # Whether to use breaks or continuous spectrum in visualizations -# Environment setup notes (commented out) -# # Activeer de renv omgeving -# renv::activate() -# renv::deactivate() -# # Optioneel: Herstel de omgeving als dat nodig is -# # Je kunt dit commentaar geven als je het normaal niet wilt uitvoeren -# renv::restore() -# Chunk 2: load_libraries -# Configure knitr options -knitr::opts_chunk$set(warning = FALSE, message = FALSE) -# Path management -library(here) -# Spatial data libraries -library(sf) -library(terra) -library(exactextractr) -# library(raster) - Removed as it's no longer maintained -# Data manipulation and visualization -library(tidyverse) # Includes dplyr, ggplot2, etc. -library(tmap) -library(lubridate) -library(zoo) -# Machine learning -library(rsample) -library(caret) -library(randomForest) -library(CAST) -# Load custom utility functions -# tryCatch({ -# source("report_utils.R") -# }, error = function(e) { -# message(paste("Error loading report_utils.R:", e$message)) -# # Try alternative path if the first one fails -# tryCatch({ -source(here::here("r_app", "report_utils.R")) -# }, error = function(e) { -# stop("Could not load report_utils.R from either location: ", e$message) -# }) -# }) -# Load executive report utilities -# tryCatch({ -# source("executive_report_utils.R") -# }, error = function(e) { -# message(paste("Error loading executive_report_utils.R:", e$message)) -# # Try alternative path if the first one fails -# tryCatch({ -source(here::here("r_app", "executive_report_utils.R")) -# Chunk 1: setup_parameters -# Set up basic report parameters from input values -report_date <- params$report_date -mail_day <- params$mail_day -borders <- params$borders -use_breaks <- params$use_breaks # Whether to use breaks or continuous spectrum in visualizations -# Environment setup notes (commented out) -# # Activeer de renv omgeving -# renv::activate() -# renv::deactivate() -# # Optioneel: Herstel de omgeving als dat nodig is -# # Je kunt dit commentaar geven als je het normaal niet wilt uitvoeren -# renv::restore() -# Chunk 2: load_libraries -# Configure knitr options -knitr::opts_chunk$set(warning = FALSE, message = FALSE) -# Path management -library(here) -# Spatial data libraries -library(sf) -library(terra) -library(exactextractr) -# library(raster) - Removed as it's no longer maintained -# Data manipulation and visualization -library(tidyverse) # Includes dplyr, ggplot2, etc. -library(tmap) -library(lubridate) -library(zoo) -# Machine learning -library(rsample) -library(caret) -library(randomForest) -library(CAST) -# Load custom utility functions -# tryCatch({ -# source("report_utils.R") -# }, error = function(e) { -# message(paste("Error loading report_utils.R:", e$message)) -# # Try alternative path if the first one fails -# tryCatch({ -source(here::here("r_app", "report_utils.R")) -# }, error = function(e) { -# stop("Could not load report_utils.R from either location: ", e$message) -# }) -# }) -# Load executive report utilities -# tryCatch({ -# source("executive_report_utils.R") -# }, error = function(e) { -# message(paste("Error loading executive_report_utils.R:", e$message)) -# # Try alternative path if the first one fails -# tryCatch({ -source(here::here("r_app", "exec_dashboard", "executive_report_utils.R")) -# }, error = function(e) { -# stop("Could not load executive_report_utils.R from either location: ", e$message) -# }) -# }) # Chunk 3: initialize_project_config # Set the project directory from parameters project_dir <- params$data_dir # Source project parameters with error handling -# tryCatch({ +tryCatch({ source(here::here("r_app", "parameters_project.R")) -# }, error = function(e) { -# stop("Error loading parameters_project.R: ", e$message) -# }) +}, error = function(e) { +stop("Error loading parameters_project.R: ", e$message) +}) # Log initial configuration safe_log("Starting the R Markdown script") safe_log(paste("mail_day params:", params$mail_day)) safe_log(paste("report_date params:", params$report_date)) safe_log(paste("mail_day variable:", mail_day)) +# Chunk 4: calculate_dates_and_weeks # Set locale for consistent date formatting Sys.setlocale("LC_TIME", "C") # Initialize date variables from parameters @@ -465,8 +491,6 @@ today_minus_1 <- as.character(lubridate::ymd(today)) today_minus_2 <- as.character(lubridate::ymd(today) - 7) today_minus_3 <- as.character(lubridate::ymd(today) - 14) } -# Generate subtitle for report -subtitle_var <- paste("Report generated on", Sys.Date()) # Calculate week numbers for previous weeks week_minus_1 <- week - 1 week_minus_2 <- week - 2 @@ -478,35 +502,11 @@ year <- lubridate::year(today) year_1 <- lubridate::year(today_minus_1) year_2 <- lubridate::year(today_minus_2) year_3 <- lubridate::year(today_minus_3) -# Load CI index data with error handling -tryCatch({ -CI_quadrant <- readRDS(here::here(cumulative_CI_vals_dir, "All_pivots_Cumulative_CI_quadrant_year_v2.rds")) -safe_log("Successfully loaded CI quadrant data") -}, error = function(e) { -stop("Error loading CI quadrant data: ", e$message) -}) -# Get file paths for different weeks using the utility function -tryCatch({ -path_to_week_current = get_week_path(weekly_CI_mosaic, today, 0) -path_to_week_minus_1 = get_week_path(weekly_CI_mosaic, today, -1) -path_to_week_minus_2 = get_week_path(weekly_CI_mosaic, today, -2) -path_to_week_minus_3 = get_week_path(weekly_CI_mosaic, today, -3) -# Log the calculated paths -safe_log("Required mosaic paths:") -safe_log(paste("Path to current week:", path_to_week_current)) -safe_log(paste("Path to week minus 1:", path_to_week_minus_1)) -safe_log(paste("Path to week minus 2:", path_to_week_minus_2)) -safe_log(paste("Path to week minus 3:", path_to_week_minus_3)) -# Validate that files exist -if (!file.exists(path_to_week_current)) warning("Current week mosaic file does not exist: ", path_to_week_current) -if (!file.exists(path_to_week_minus_1)) warning("Week minus 1 mosaic file does not exist: ", path_to_week_minus_1) -if (!file.exists(path_to_week_minus_2)) warning("Week minus 2 mosaic file does not exist: ", path_to_week_minus_2) -if (!file.exists(path_to_week_minus_3)) warning("Week minus 3 mosaic file does not exist: ", path_to_week_minus_3) -# Load raster data with terra functions -CI <- terra::rast(path_to_week_current)$CI -CI_m1 <- terra::rast(path_to_week_minus_1)$CI -CI_m2 <- terra::rast(path_to_week_minus_2)$CI -CI_m3 <- terra::rast(path_to_week_minus_3)$CI -}, error = function(e) { -stop("Error loading raster data: ", e$message) -}) +sessionInfo() +source("r_app/extract_current_versions.R") +source("r_app/package_manager.R") +source("r_app/package_manager.R") +source("r_app/package_manager.R") +source("r_app/package_manager.R") +source("r_app/package_manager.R") +source("r_app/package_manager.R") diff --git a/.Rprofile b/.Rprofile new file mode 100644 index 0000000..81b960f --- /dev/null +++ b/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/PACKAGE_MANAGEMENT.md b/PACKAGE_MANAGEMENT.md new file mode 100644 index 0000000..f0965bc --- /dev/null +++ b/PACKAGE_MANAGEMENT.md @@ -0,0 +1,94 @@ +# SmartCane Project - Package Management + +## Quick Start + +### For New Team Members +1. Open R/RStudio +2. Set working directory to the project root: `setwd("path/to/smartcane")` +3. Run: `source("r_app/package_manager.R")` +4. Type `y` when prompted +5. Wait for completion ✅ + +### For Existing Team Members (After Git Pull) +Same steps as above - the script will check for updates automatically. + +## What This Script Does + +1. **Initializes renv** - Creates isolated package environment +2. **Checks package versions** - Compares installed vs required +3. **Installs/Updates packages** - Only if needed +4. **Creates lockfile** - `renv.lock` for exact reproducibility +5. **Generates reports** - Console output + `package_manager.log` + +## Key Features + +- ✅ **Minimum version requirements** (allows patch updates) +- ✅ **Critical package locking** (tmap v4 for new syntax) +- ✅ **Automatic installation** of missing packages +- ✅ **Console + Log output** for debugging +- ✅ **Cross-platform compatibility** + +## Required Packages & Versions + +| Package | Min Version | Purpose | +|---------|-------------|---------| +| tmap | 4.0.0 | **CRITICAL** - New syntax used | +| tidyverse | 2.0.0 | Data manipulation | +| sf | 1.0.0 | Spatial data | +| terra | 1.7.0 | Raster processing | +| rmarkdown | 2.21.0 | Report generation | + +## Workflow + +### Development Workflow +``` +1. 👨‍💻 Developer: Make changes → run package_manager.R → test → commit + push +2. 👥 Teammate: Pull → run package_manager.R → test +3. 🚀 Production: Pull → run package_manager.R → deploy +``` + +### Files Created +- `renv.lock` - Exact package versions (commit this!) +- `package_manager.log` - Installation log (don't commit) +- `renv/` folder - Package cache (don't commit) + +## Troubleshooting + +### "Package failed to install" +- Check internet connection +- Update R to latest version +- Install system dependencies (varies by OS) + +### "Version conflicts" +- Delete `renv/` folder +- Run script again for clean install + +### "renv not working" +- Install manually: `install.packages("renv")` +- Restart R session +- Run script again + +## Team Guidelines + +1. **Always run** `package_manager.R` after pulling changes +2. **Commit** `renv.lock` to git (not `renv/` folder) +3. **Don't modify** package versions in scripts - use this manager +4. **Report issues** in the log file to team + +## Advanced Usage + +### Restore from lockfile only: +```r +renv::restore() +``` + +### Add new package requirement: +1. Edit `REQUIRED_PACKAGES` in `package_manager.R` +2. Run the script +3. Commit updated `renv.lock` + +### Check status without changes: +```r +source("r_app/package_manager.R") +# Then just read the log or run generate_package_report() +``` diff --git a/generated_package_config.R b/generated_package_config.R new file mode 100644 index 0000000..a5c98ec --- /dev/null +++ b/generated_package_config.R @@ -0,0 +1,42 @@ +# Package requirements with your current working versions +REQUIRED_PACKAGES <- list( + # Core data manipulation + "dplyr" = "1.1.4", + "here" = "1.0.1", + "lubridate" = "1.9.4", + "readr" = "2.1.5", + "readxl" = "1.4.5", + "stringr" = "1.5.1", + "tidyr" = "1.3.1", + + # Spatial data + "exactextractr" = "0.10.0", + "raster" = "3.6.32", + "sf" = "1.0.19", + "terra" = "1.8.43", # CRITICAL: for raster processing + + # Visualization + "ggplot2" = "3.5.1", + "tmap" = "4.0", # CRITICAL: for tm_scale_continuous() syntax + + # Reporting + "knitr" = "1.50", + + # Tidyverse + "purrr" = "1.0.2", + "tidyverse" = "2.0.0", + + # Other packages + "caret" = "7.0.1", + "CAST" = "1.0.3", + "furrr" = "0.3.1", + "future" = "1.40.0", + "gridExtra" = "2.3", + "parallel" = "4.4.2", + "progressr" = "0.15.1", + "randomForest" = "4.7.1.2", + "reshape2" = "1.4.4", + "rsample" = "1.3.0", + "tools" = "4.4.2", + "zoo" = "1.8.13" +) diff --git a/package_manager.log b/package_manager.log new file mode 100644 index 0000000..64f5048 --- /dev/null +++ b/package_manager.log @@ -0,0 +1,111 @@ +[INFO] 2025-06-24 14:49:29 - SmartCane Project - Package Manager Started +[INFO] 2025-06-24 14:49:29 - Working directory: C:/Users/timon/Resilience BV/4020 SCane ESA DEMO - Documenten/General/4020 SCDEMO Team/4020 TechnicalData/WP3/smartcane +[INFO] 2025-06-24 14:49:29 - Checking renv initialization... +[INFO] 2025-06-24 14:49:29 - ✓ renv already initialized +[INFO] 2025-06-24 14:49:29 - ✓ renv already active +[INFO] 2025-06-24 14:49:29 - +=== INITIAL STATE === +[INFO] 2025-06-24 14:49:29 - === PACKAGE REPORT === +[INFO] 2025-06-24 14:49:29 - dplyr | Required: >= 1.1.4 | Installed: 1.1.4 | ✅ OK +[INFO] 2025-06-24 14:49:29 - here | Required: >= 1.0.1 | Installed: 1.0.1 | ✅ OK +[INFO] 2025-06-24 14:49:29 - lubridate | Required: >= 1.9.4 | Installed: 1.9.4 | ✅ OK +[INFO] 2025-06-24 14:49:29 - readr | Required: >= 2.1.5 | Installed: 2.1.5 | ✅ OK +[INFO] 2025-06-24 14:49:29 - readxl | Required: >= 1.4.5 | Installed: 1.4.5 | ✅ OK +[INFO] 2025-06-24 14:49:29 - stringr | Required: >= 1.5.1 | Installed: 1.5.1 | ✅ OK +[INFO] 2025-06-24 14:49:29 - tidyr | Required: >= 1.3.1 | Installed: 1.3.1 | ✅ OK +[INFO] 2025-06-24 14:49:29 - purrr | Required: >= 1.0.2 | Installed: 1.0.2 | ✅ OK +[INFO] 2025-06-24 14:49:29 - magrittr | Required: >= 2.0.0 | Installed: 2.0.3 | ✅ OK +[INFO] 2025-06-24 14:49:29 - exactextractr | Required: >= 0.10.0 | Installed: 0.10.0 | ✅ OK +[INFO] 2025-06-24 14:49:29 - raster | Required: >= 3.6.32 | Installed: 3.6.32 | ✅ OK +[INFO] 2025-06-24 14:49:29 - sf | Required: >= 1.0.19 | Installed: 1.0.19 | ✅ OK +[INFO] 2025-06-24 14:49:29 - terra | Required: >= 1.8.43 | Installed: 1.8.43 | ✅ OK +[INFO] 2025-06-24 14:49:29 - ggplot2 | Required: >= 3.5.1 | Installed: 3.5.1 | ✅ OK +[INFO] 2025-06-24 14:49:29 - tmap | Required: >= 4.0 | Installed: 4.0 | ✅ OK +[INFO] 2025-06-24 14:49:29 - gridExtra | Required: >= 2.3 | Installed: 2.3 | ✅ OK +[INFO] 2025-06-24 14:49:29 - knitr | Required: >= 1.50 | Installed: 1.50 | ✅ OK +[INFO] 2025-06-24 14:49:29 - rmarkdown | Required: >= 2.21.0 | Installed: 2.29 | ✅ OK +[INFO] 2025-06-24 14:49:29 - tidyverse | Required: >= 2.0.0 | Installed: 2.0.0 | ✅ OK +[INFO] 2025-06-24 14:49:29 - caret | Required: >= 7.0.1 | Installed: 7.0.1 | ✅ OK +[INFO] 2025-06-24 14:49:29 - CAST | Required: >= 1.0.3 | Installed: 1.0.3 | ✅ OK +[INFO] 2025-06-24 14:49:29 - randomForest | Required: >= 4.7.1.2 | Installed: 4.7.1.2 | ✅ OK +[INFO] 2025-06-24 14:49:29 - rsample | Required: >= 1.3.0 | Installed: 1.3.0 | ✅ OK +[INFO] 2025-06-24 14:49:29 - furrr | Required: >= 0.3.1 | Installed: 0.3.1 | ✅ OK +[INFO] 2025-06-24 14:49:29 - future | Required: >= 1.40.0 | Installed: 1.40.0 | ✅ OK +[INFO] 2025-06-24 14:49:29 - progressr | Required: >= 0.15.1 | Installed: 0.15.1 | ✅ OK +[INFO] 2025-06-24 14:49:29 - reshape2 | Required: >= 1.4.4 | Installed: 1.4.4 | ✅ OK +[INFO] 2025-06-24 14:49:29 - zoo | Required: >= 1.8.13 | Installed: 1.8.13 | ✅ OK +[INFO] 2025-06-24 14:49:29 - === END PACKAGE REPORT === +[INFO] 2025-06-24 14:49:29 - +=== PACKAGE INSTALLATION/UPDATES === +[INFO] 2025-06-24 14:49:29 - === PACKAGE MANAGEMENT STARTED === +[INFO] 2025-06-24 14:49:29 - R version: R version 4.4.2 (2024-10-31 ucrt) +[INFO] 2025-06-24 14:49:29 - ✓ dplyr version 1.1.4 meets requirement (>= 1.1.4) +[INFO] 2025-06-24 14:49:29 - ✓ here version 1.0.1 meets requirement (>= 1.0.1) +[INFO] 2025-06-24 14:49:29 - ✓ lubridate version 1.9.4 meets requirement (>= 1.9.4) +[INFO] 2025-06-24 14:49:29 - ✓ readr version 2.1.5 meets requirement (>= 2.1.5) +[INFO] 2025-06-24 14:49:29 - ✓ readxl version 1.4.5 meets requirement (>= 1.4.5) +[INFO] 2025-06-24 14:49:29 - ✓ stringr version 1.5.1 meets requirement (>= 1.5.1) +[INFO] 2025-06-24 14:49:29 - ✓ tidyr version 1.3.1 meets requirement (>= 1.3.1) +[INFO] 2025-06-24 14:49:29 - ✓ purrr version 1.0.2 meets requirement (>= 1.0.2) +[INFO] 2025-06-24 14:49:29 - ✓ magrittr version 2.0.3 meets requirement (>= 2.0.0) +[INFO] 2025-06-24 14:49:29 - ✓ exactextractr version 0.10.0 meets requirement (>= 0.10.0) +[INFO] 2025-06-24 14:49:29 - ✓ raster version 3.6.32 meets requirement (>= 3.6.32) +[INFO] 2025-06-24 14:49:29 - ✓ sf version 1.0.19 meets requirement (>= 1.0.19) +[INFO] 2025-06-24 14:49:29 - 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✓ progressr version 0.15.1 meets requirement (>= 0.15.1) +[INFO] 2025-06-24 14:49:29 - ✓ reshape2 version 1.4.4 meets requirement (>= 1.4.4) +[INFO] 2025-06-24 14:49:29 - ✓ zoo version 1.8.13 meets requirement (>= 1.8.13) +[INFO] 2025-06-24 14:49:29 - Package management complete: 28 success, 0 failures +[INFO] 2025-06-24 14:49:29 - Updating renv lockfile... +[ERROR] 2025-06-24 14:49:33 - ✗ Failed to update lockfile: aborting snapshot due to pre-flight validation failure +[INFO] 2025-06-24 14:49:33 - +=== FINAL STATE === +[INFO] 2025-06-24 14:49:33 - === PACKAGE REPORT === +[INFO] 2025-06-24 14:49:33 - dplyr | Required: >= 1.1.4 | Installed: 1.1.4 | ✅ OK +[INFO] 2025-06-24 14:49:33 - here | Required: >= 1.0.1 | Installed: 1.0.1 | ✅ OK +[INFO] 2025-06-24 14:49:33 - lubridate | Required: >= 1.9.4 | Installed: 1.9.4 | ✅ OK +[INFO] 2025-06-24 14:49:33 - readr | Required: >= 2.1.5 | Installed: 2.1.5 | ✅ OK +[INFO] 2025-06-24 14:49:33 - readxl | Required: >= 1.4.5 | Installed: 1.4.5 | ✅ OK +[INFO] 2025-06-24 14:49:33 - stringr | Required: >= 1.5.1 | Installed: 1.5.1 | ✅ OK +[INFO] 2025-06-24 14:49:33 - tidyr | Required: >= 1.3.1 | Installed: 1.3.1 | ✅ OK +[INFO] 2025-06-24 14:49:33 - purrr | Required: >= 1.0.2 | Installed: 1.0.2 | ✅ OK +[INFO] 2025-06-24 14:49:33 - magrittr | Required: >= 2.0.0 | Installed: 2.0.3 | ✅ OK +[INFO] 2025-06-24 14:49:33 - exactextractr | Required: >= 0.10.0 | Installed: 0.10.0 | ✅ OK +[INFO] 2025-06-24 14:49:33 - raster | Required: >= 3.6.32 | Installed: 3.6.32 | ✅ OK +[INFO] 2025-06-24 14:49:33 - sf | Required: >= 1.0.19 | Installed: 1.0.19 | ✅ OK +[INFO] 2025-06-24 14:49:33 - terra | Required: >= 1.8.43 | Installed: 1.8.43 | ✅ OK +[INFO] 2025-06-24 14:49:33 - ggplot2 | Required: >= 3.5.1 | Installed: 3.5.1 | ✅ OK +[INFO] 2025-06-24 14:49:33 - tmap | Required: >= 4.0 | Installed: 4.0 | ✅ OK +[INFO] 2025-06-24 14:49:33 - gridExtra | Required: >= 2.3 | Installed: 2.3 | ✅ OK +[INFO] 2025-06-24 14:49:33 - knitr | Required: >= 1.50 | Installed: 1.50 | ✅ OK +[INFO] 2025-06-24 14:49:33 - rmarkdown | Required: >= 2.21.0 | Installed: 2.29 | ✅ OK +[INFO] 2025-06-24 14:49:33 - tidyverse | Required: >= 2.0.0 | Installed: 2.0.0 | ✅ OK +[INFO] 2025-06-24 14:49:33 - caret | Required: >= 7.0.1 | Installed: 7.0.1 | ✅ OK +[INFO] 2025-06-24 14:49:33 - CAST | Required: >= 1.0.3 | Installed: 1.0.3 | ✅ OK +[INFO] 2025-06-24 14:49:33 - randomForest | Required: >= 4.7.1.2 | Installed: 4.7.1.2 | ✅ OK +[INFO] 2025-06-24 14:49:33 - rsample | Required: >= 1.3.0 | Installed: 1.3.0 | ✅ OK +[INFO] 2025-06-24 14:49:33 - furrr | Required: >= 0.3.1 | Installed: 0.3.1 | ✅ OK +[INFO] 2025-06-24 14:49:33 - future | Required: >= 1.40.0 | Installed: 1.40.0 | ✅ OK +[INFO] 2025-06-24 14:49:33 - progressr | Required: >= 0.15.1 | Installed: 0.15.1 | ✅ OK +[INFO] 2025-06-24 14:49:33 - reshape2 | Required: >= 1.4.4 | Installed: 1.4.4 | ✅ OK +[INFO] 2025-06-24 14:49:33 - zoo | Required: >= 1.8.13 | Installed: 1.8.13 | ✅ OK +[INFO] 2025-06-24 14:49:33 - === END PACKAGE REPORT === +[INFO] 2025-06-24 14:49:33 - Package management completed in 7.72 seconds +[INFO] 2025-06-24 14:49:33 - Log saved to: C:/Users/timon/Resilience BV/4020 SCane ESA DEMO - Documenten/General/4020 SCDEMO Team/4020 TechnicalData/WP3/smartcane/package_manager.log +[SUCCESS] 2025-06-24 14:49:33 - 🎉 All packages successfully managed! +[INFO] 2025-06-24 14:49:33 - 📋 Next steps: +[INFO] 2025-06-24 14:49:33 - 1. Test your R scripts to ensure everything works +[INFO] 2025-06-24 14:49:33 - 2. Commit renv.lock to version control +[INFO] 2025-06-24 14:49:33 - 3. Share this script with your team diff --git a/r_app/CI_report_dashboard_planet.Rmd b/r_app/CI_report_dashboard_planet.Rmd index 9b24420..a30c689 100644 --- a/r_app/CI_report_dashboard_planet.Rmd +++ b/r_app/CI_report_dashboard_planet.Rmd @@ -10,7 +10,7 @@ output: # html_document: # toc: yes # df_print: paged - word_document: + word_document: reference_docx: !expr file.path("word-styles-reference-var1.docx") toc: no editor_options: @@ -157,19 +157,19 @@ tryCatch({ safe_log(paste("Path to week minus 1:", path_to_week_minus_1)) safe_log(paste("Path to week minus 2:", path_to_week_minus_2)) safe_log(paste("Path to week minus 3:", path_to_week_minus_3)) - + # Validate that files exist if (!file.exists(path_to_week_current)) warning("Current week mosaic file does not exist: ", path_to_week_current) if (!file.exists(path_to_week_minus_1)) warning("Week minus 1 mosaic file does not exist: ", path_to_week_minus_1) if (!file.exists(path_to_week_minus_2)) warning("Week minus 2 mosaic file does not exist: ", path_to_week_minus_2) if (!file.exists(path_to_week_minus_3)) warning("Week minus 3 mosaic file does not exist: ", path_to_week_minus_3) - + # Load raster data with terra functions CI <- terra::rast(path_to_week_current)$CI CI_m1 <- terra::rast(path_to_week_minus_1)$CI CI_m2 <- terra::rast(path_to_week_minus_2)$CI CI_m3 <- terra::rast(path_to_week_minus_3)$CI - + }, error = function(e) { stop("Error loading raster data: ", e$message) }) @@ -181,7 +181,7 @@ tryCatch({ # Calculate weekly difference last_week_dif_raster_abs <- (CI - CI_m1) safe_log("Calculated weekly difference raster") - + # Calculate three-week difference three_week_dif_raster_abs <- (CI - CI_m3) safe_log("Calculated three-week difference raster") @@ -261,16 +261,16 @@ Report Date: **`r report_date_formatted`** ## Report Summary -**Farm Location:** `r farm_name` -**Report Period:** Week `r week` of `r current_year` -**Data Source:** Planet Labs Satellite Imagery -**Analysis Type:** Chlorophyll Index (CI) Monitoring +**Farm Location:** `r farm_name` +**Report Period:** Week `r week` of `r current_year` +**Data Source:** Planet Labs Satellite Imagery +**Analysis Type:** Chlorophyll Index (CI) Monitoring -**Field Coverage:** -- Total Fields Monitored: `r total_fields` -- Total Area: `r total_area_ha` hectares +**Field Coverage:** +- Total Fields Monitored: `r total_fields` +- Total Area: `r total_area_ha` hectares -**Report Generated:** `r format(Sys.Date(), "%B %d, %Y at %H:%M")` +**Report Generated:** `r format(Sys.Date(), "%B %d, %Y")` --- @@ -279,7 +279,7 @@ Report Date: **`r report_date_formatted`** This automated report provides weekly analysis of sugarcane crop health using satellite-derived Chlorophyll Index (CI) measurements. The analysis helps identify: - Field-level crop health variations -- Weekly changes in crop vigor +- Weekly changes in crop vigor - Areas requiring agricultural attention - Growth patterns across different field sections @@ -291,13 +291,40 @@ This automated report provides weekly analysis of sugarcane crop health using sa -\pagebreak +\newpage + + +```{=openxml} + + + + + + + + + + + TABLE OF CONTENTS + + +``` + +```{=openxml} + + + Update this field to generate table of contents + + +``` + +\newpage -\pagebreak +\newpage # Explanation of the Report This report provides a detailed analysis of your sugarcane fields based on satellite imagery, helping you monitor crop health and development throughout the growing season. The data is processed weekly to give you timely insights for optimal farm management decisions. @@ -332,72 +359,71 @@ Use these insights to identify areas that may need irrigation, fertilization, or \pagebreak # RGB Satellite Image - Current Week (if available) -```{r render_rgb_map, echo=FALSE, fig.height=6.9, fig.width=9, message=FALSE, warning=FALSE} +```{r render_rgb_map, echo=FALSE, fig.height=7, fig.width=10, message=FALSE, warning=FALSE} # Check if RGB bands are available and create RGB map tryCatch({ # Load the full raster to check available bands full_raster <- terra::rast(path_to_week_current) available_bands <- names(full_raster) - + # Check if RGB bands are available (look for red, green, blue or similar naming) - rgb_bands_available <- any(grepl("red|Red|RED", available_bands, ignore.case = TRUE)) && - any(grepl("green|Green|GREEN", available_bands, ignore.case = TRUE)) && + rgb_bands_available <- any(grepl("red|Red|RED", available_bands, ignore.case = TRUE)) && + any(grepl("green|Green|GREEN", available_bands, ignore.case = TRUE)) && any(grepl("blue|Blue|BLUE", available_bands, ignore.case = TRUE)) - + # Alternative check for numbered bands that might be RGB (e.g., band_1, band_2, band_3) if (!rgb_bands_available && length(available_bands) >= 3) { # Check if we have at least 3 bands that could potentially be RGB potential_rgb_bands <- grep("band_[1-3]|B[1-3]|[1-3]", available_bands, ignore.case = TRUE) rgb_bands_available <- length(potential_rgb_bands) >= 3 } - + if (rgb_bands_available) { safe_log("RGB bands detected - creating RGB visualization") - + # Try to extract RGB bands (prioritize named bands first) red_band <- NULL - green_band <- NULL + green_band <- NULL blue_band <- NULL - + # Look for named RGB bands first red_candidates <- grep("red|Red|RED", available_bands, ignore.case = TRUE, value = TRUE) green_candidates <- grep("green|Green|GREEN", available_bands, ignore.case = TRUE, value = TRUE) blue_candidates <- grep("blue|Blue|BLUE", available_bands, ignore.case = TRUE, value = TRUE) - + if (length(red_candidates) > 0) red_band <- red_candidates[1] if (length(green_candidates) > 0) green_band <- green_candidates[1] if (length(blue_candidates) > 0) blue_band <- blue_candidates[1] - + # Fallback to numbered bands if named bands not found if (is.null(red_band) || is.null(green_band) || is.null(blue_band)) { if (length(available_bands) >= 3) { # Assume first 3 bands are RGB (common convention) red_band <- available_bands[1] - green_band <- available_bands[2] + green_band <- available_bands[2] blue_band <- available_bands[3] } } - + if (!is.null(red_band) && !is.null(green_band) && !is.null(blue_band)) { # Extract RGB bands rgb_raster <- c(full_raster[[red_band]], full_raster[[green_band]], full_raster[[blue_band]]) names(rgb_raster) <- c("red", "green", "blue") - - # Create RGB map + # Create RGB map map <- tmap::tm_shape(rgb_raster, unit = "m") + tmap::tm_rgb() + - tmap::tm_scalebar(position = c("right", "bottom"), text.color = "white") + - tmap::tm_compass(position = c("right", "bottom"), text.color = "white") + - tmap::tm_shape(AllPivots0) + + tmap::tm_scalebar(position = tm_pos_out("right", "bottom"), text.color = "black") + + tmap::tm_compass(position = tm_pos_out("right", "bottom"), text.color = "black") + + tmap::tm_shape(AllPivots0) + tmap::tm_borders(col = "white", lwd = 2) + tmap::tm_text("sub_field", size = 0.6, col = "white") + tmap::tm_layout(main.title = paste0("RGB Satellite Image - Week ", week), main.title.size = 0.8, main.title.color = "black") - + # Print the map print(map) - + safe_log("RGB map created successfully") } else { safe_log("Could not identify RGB bands despite detection", "WARNING") @@ -413,26 +439,24 @@ tryCatch({ }) ``` -\pagebreak +\newpage # Chlorophyll Index (CI) Overview Map - Current Week -```{r render_ci_overview_map, echo=FALSE, fig.height=6.9, fig.width=9, message=FALSE, warning=FALSE} +```{r render_ci_overview_map, echo=FALSE, fig.height=7, fig.width=10, message=FALSE, warning=FALSE} # Create overview chlorophyll index map tryCatch({ # Base shape map <- tmap::tm_shape(CI, unit = "m") # Add raster layer with continuous spectrum (fixed scale 1-8 for consistent comparison) map <- map + tmap::tm_raster(col.scale = tm_scale_continuous(values = "brewer.rd_yl_gn", - limits = c(1, 8)), - col.legend = tm_legend(title = "Chlorophyll Index (CI)", - orientation = "landscape", + limits = c(1, 8)), col.legend = tm_legend(title = "Chlorophyll Index (CI)", + orientation = "landscape", position = tm_pos_out("center", "bottom"))) - - # Complete the map with layout and other elements + # Complete the map with layout and other elements map <- map + - tmap::tm_scalebar(position = c("right", "bottom"), text.color = "black") + - tmap::tm_compass(position = c("right", "bottom"), text.color = "black") + - tmap::tm_shape(AllPivots0) + + tmap::tm_scalebar(position = tm_pos_out("right", "bottom"), text.color = "black") + + tmap::tm_compass(position = tm_pos_out("right", "bottom"), text.color = "black") + + tmap::tm_shape(AllPivots0) + tmap::tm_borders(col = "black") + tmap::tm_text("sub_field", size = 0.6, col = "black") - + # Print the map print(map) }, error = function(e) { @@ -440,29 +464,30 @@ tryCatch({ # Base shape plot(1, type="n", axes=FALSE, xlab="", ylab="") text(1, 1, "Error creating CI overview map", cex=1.5) }) + ``` + +\newpage \pagebreak # Weekly Chlorophyll Index Difference Map -```{r render_ci_difference_map, echo=FALSE, fig.height=6.9, fig.width=9, message=FALSE, warning=FALSE} +```{r render_ci_difference_map, echo=FALSE, fig.height=7, fig.width=10, message=FALSE, warning=FALSE} # Create chlorophyll index difference map tryCatch({ # Base shape map <- tmap::tm_shape(last_week_dif_raster_abs, unit = "m") # Add raster layer with continuous spectrum (centered at 0 for difference maps, fixed scale) map <- map + tmap::tm_raster(col.scale = tm_scale_continuous(values = "brewer.rd_yl_gn", midpoint = 0, - limits = c(-3, 3)), - col.legend = tm_legend(title = "Chlorophyll Index (CI) Change", - orientation = "landscape", + limits = c(-3, 3)), col.legend = tm_legend(title = "Chlorophyll Index (CI) Change", + orientation = "landscape", position = tm_pos_out("center", "bottom"))) - - # Complete the map with layout and other elements + # Complete the map with layout and other elements map <- map + - tmap::tm_scalebar(position = c("right", "bottom"), text.color = "black") + - tmap::tm_compass(position = c("right", "bottom"), text.color = "black") + - tmap::tm_shape(AllPivots0) + + tmap::tm_scalebar(position = tm_pos_out("right", "bottom"), text.color = "black") + + tmap::tm_compass(position = tm_pos_out("right", "bottom"), text.color = "black") + + tmap::tm_shape(AllPivots0) + tmap::tm_borders(col = "black") + tmap::tm_text("sub_field", size = 0.6, col = "black") - + # Print the map print(map) }, error = function(e) { @@ -471,22 +496,23 @@ tryCatch({ # Base shape text(1, 1, "Error creating CI difference map", cex=1.5) }) ``` + +\newpage \pagebreak - -```{r generate_field_visualizations, eval=TRUE, fig.height=3.8, fig.width=10, message=FALSE,echo=FALSE, warning=FALSE, include=TRUE, results='asis'} +```{r generate_field_visualizations, eval=TRUE, fig.height=4.5, fig.width=12, message=FALSE,echo=FALSE, warning=FALSE, include=TRUE, results='asis'} # Generate detailed visualizations for each field tryCatch({ # Merge field polygons for processing - AllPivots_merged <- AllPivots0 %>% - dplyr::group_by(field) %>% + AllPivots_merged <- AllPivots0 %>% + dplyr::group_by(field) %>% dplyr::summarise(.groups = 'drop') - + # Generate plots for each field - purrr::walk(AllPivots_merged$field[1:5], function(field_name) { + purrr::walk(AllPivots_merged$field, function(field_name) { tryCatch({ cat("\n") # Add an empty line for better spacing - + # Call ci_plot with explicit parameters ci_plot( pivotName = field_name, @@ -502,9 +528,9 @@ tryCatch({ week_minus_3 = week_minus_3, borders = borders ) - - cat("\n") - + + # cat("\n") + # Call cum_ci_plot with explicit parameters cum_ci_plot( pivotName = field_name, @@ -512,7 +538,7 @@ tryCatch({ plot_type = "value", facet_on = FALSE ) - + }, error = function(e) { safe_log(paste("Error generating plots for field", field_name, ":", e$message), "ERROR") cat(paste("## Error generating plots for field", field_name, "\n")) @@ -529,17 +555,17 @@ tryCatch({ # Alternative visualization grouped by sub-area (disabled by default) tryCatch({ # Group pivots by sub-area - pivots_grouped <- AllPivots0 - + pivots_grouped <- AllPivots0 + # Iterate over each subgroup for (subgroup in unique(pivots_grouped$sub_area)) { # Add subgroup heading cat("\n") cat("## Subgroup: ", subgroup, "\n") - + # Filter data for current subgroup subset_data <- dplyr::filter(pivots_grouped, sub_area == subgroup) - + # Generate visualizations for each field in the subgroup purrr::walk(subset_data$field, function(field_name) { cat("\n") @@ -548,9 +574,9 @@ tryCatch({ cum_ci_plot(field_name) cat("\n") }) - + # Add page break after each subgroup - cat("\\pagebreak\n") + cat("\\newpage\n") } }, error = function(e) { safe_log(paste("Error in subarea visualization section:", e$message), "ERROR") @@ -569,39 +595,39 @@ tryCatch({ dplyr::group_by(model) %>% tidyr::fill(field, sub_field, .direction = "downup") %>% dplyr::ungroup() - + # Check if tonnage_ha is empty if (all(is.na(harvesting_data$tonnage_ha))) { safe_log("Lacking historic harvest data, please provide for yield prediction calculation", "WARNING") knitr::knit_exit() # Exit the chunk if tonnage_ha is empty } - + # Rename year column to season for consistency harvesting_data <- harvesting_data %>% dplyr::rename(season = year) - + # Join CI and yield data CI_and_yield <- dplyr::left_join(CI_quadrant, harvesting_data, by = c("field", "sub_field", "season")) %>% - dplyr::group_by(sub_field, season) %>% + dplyr::group_by(sub_field, season) %>% dplyr::slice(which.max(DOY)) %>% dplyr::select(field, sub_field, tonnage_ha, cumulative_CI, DOY, season, sub_area) %>% dplyr::mutate(CI_per_day = cumulative_CI / DOY) - + # Define predictors and response variables predictors <- c("cumulative_CI", "DOY", "CI_per_day") response <- "tonnage_ha" - + # Prepare test and validation datasets - CI_and_yield_test <- CI_and_yield %>% - as.data.frame() %>% + CI_and_yield_test <- CI_and_yield %>% + as.data.frame() %>% dplyr::filter(!is.na(tonnage_ha)) - + CI_and_yield_validation <- CI_and_yield_test - + # Prepare prediction dataset (fields without harvest data) - prediction_yields <- CI_and_yield %>% - as.data.frame() %>% + prediction_yields <- CI_and_yield %>% + as.data.frame() %>% dplyr::filter(is.na(tonnage_ha)) - + # Configure model training parameters ctrl <- caret::trainControl( method = "cv", @@ -610,7 +636,7 @@ tryCatch({ number = 5, verboseIter = TRUE ) - + # Train the model with feature selection set.seed(202) # For reproducibility model_ffs_rf <- CAST::ffs( @@ -623,7 +649,7 @@ tryCatch({ tuneLength = 5, na.rm = TRUE ) - + # Function to prepare predictions with consistent naming and formatting prepare_predictions <- function(predictions, newdata) { return(predictions %>% @@ -641,17 +667,17 @@ tryCatch({ dplyr::left_join(., newdata, by = c("field", "sub_field", "season")) ) } - + # Predict yields for the validation dataset pred_ffs_rf <- prepare_predictions(stats::predict(model_ffs_rf, newdata = CI_and_yield_validation), CI_and_yield_validation) - + # Predict yields for the current season (focus on mature fields over 300 days) pred_rf_current_season <- prepare_predictions(stats::predict(model_ffs_rf, newdata = prediction_yields), prediction_yields) %>% dplyr::filter(Age_days > 1) %>% dplyr::mutate(CI_per_day = round(total_CI / Age_days, 1)) - + safe_log("Successfully completed yield prediction calculations") - + }, error = function(e) { safe_log(paste("Error in yield prediction:", e$message), "ERROR") # Create empty dataframes to prevent errors in subsequent chunks @@ -671,23 +697,23 @@ tryCatch({ ggplot2::scale_x_continuous(limits = c(0, 200)) + ggplot2::scale_y_continuous(limits = c(0, 200)) + ggplot2::labs(title = "Model Performance: \nPredicted vs Actual Tonnage/ha", - x = "Actual tonnage/ha (Tcha)", + x = "Actual tonnage/ha (Tcha)", y = "Predicted tonnage/ha (Tcha)") + ggplot2::theme_minimal() } - + if (nrow(pred_rf_current_season) > 0) { # Plot predicted yields by age ggplot2::ggplot(pred_rf_current_season, ggplot2::aes(x = Age_days, y = predicted_Tcha)) + ggplot2::geom_point(size = 2, alpha = 0.6) + ggplot2::labs(title = "Predicted Yields for Fields Over 300 Days \nOld Yet to Be Harvested", - x = "Age (days)", + x = "Age (days)", y = "Predicted tonnage/ha (Tcha)") + ggplot2::scale_y_continuous(limits = c(0, 200)) + ggplot2::theme_minimal() - + # Display prediction table - knitr::kable(pred_rf_current_season, + knitr::kable(pred_rf_current_season, digits = 0, caption = "Predicted Tonnage/ha for Fields Over 300 Days Old") } else { @@ -699,7 +725,3 @@ tryCatch({ }) ``` - - -\pagebreak - diff --git a/r_app/extract_current_versions.R b/r_app/extract_current_versions.R new file mode 100644 index 0000000..f98cea2 --- /dev/null +++ b/r_app/extract_current_versions.R @@ -0,0 +1,200 @@ +#' Version Extractor for SmartCane Project +#' +#' This script scans your R scripts to find all used packages and extracts +#' the currently installed versions. Use this to populate the package_manager.R +#' with your actual working versions. +#' +#' Usage: +#' source("extract_current_versions.R") +#' +#' Author: SmartCane Team +#' Date: 2025-06-24 + +# ============================================================================= +# PACKAGE DISCOVERY +# ============================================================================= + +#' Extract packages from R scripts +extract_packages_from_scripts <- function(script_dir = ".") { + # Find all R files + r_files <- list.files(script_dir, pattern = "\\.(R|Rmd)$", recursive = TRUE, full.names = TRUE) + + packages <- c() + + for (file in r_files) { + cat("Scanning:", file, "\n") + + tryCatch({ + content <- readLines(file, warn = FALSE) + + # Find library() calls + library_matches <- regmatches(content, regexpr('library\\(["\']?([^"\'\\)]+)["\']?\\)', content)) + library_packages <- gsub('library\\(["\']?([^"\'\\)]+)["\']?\\)', '\\1', library_matches) + library_packages <- library_packages[library_packages != ""] + + # Find require() calls + require_matches <- regmatches(content, regexpr('require\\(["\']?([^"\'\\)]+)["\']?\\)', content)) + require_packages <- gsub('require\\(["\']?([^"\'\\)]+)["\']?\\)', '\\1', require_matches) + require_packages <- require_packages[require_packages != ""] + + # Find package::function calls + namespace_matches <- regmatches(content, gregexpr('[a-zA-Z][a-zA-Z0-9.]*::', content)) + namespace_packages <- unique(unlist(lapply(namespace_matches, function(x) gsub('::', '', x)))) + namespace_packages <- namespace_packages[namespace_packages != ""] + + packages <- c(packages, library_packages, require_packages, namespace_packages) + + }, error = function(e) { + cat("Error reading", file, ":", e$message, "\n") + }) + } + + # Clean and deduplicate + packages <- unique(packages) + packages <- packages[!packages %in% c("", "base", "stats", "utils", "graphics", "grDevices")] + + return(sort(packages)) +} + +#' Get current version of installed packages +get_current_versions <- function(packages) { + versions <- list() + + cat("\nChecking installed versions...\n") + cat("===============================\n") + + for (pkg in packages) { + if (pkg %in% rownames(installed.packages())) { + version <- as.character(packageVersion(pkg)) + versions[[pkg]] <- version + cat(sprintf("✓ %-20s %s\n", pkg, version)) + } else { + cat(sprintf("✗ %-20s NOT INSTALLED\n", pkg)) + } + } + + return(versions) +} + +#' Generate package manager configuration +generate_package_config <- function(versions) { + cat("\n\nGenerating REQUIRED_PACKAGES configuration...\n") + cat("=============================================\n\n") + + config_lines <- c( + "# Package requirements with your current working versions", + "REQUIRED_PACKAGES <- list(" + ) + + # Group packages by category + categories <- list( + "Core data manipulation" = c("here", "dplyr", "tidyr", "readr", "readxl", "magrittr", "lubridate", "stringr"), + "Spatial data" = c("sf", "terra", "exactextractr", "raster", "sp", "sf", "rgdal", "rgeos"), + "Visualization" = c("tmap", "ggplot2", "RColorBrewer", "viridis", "scales"), + "Statistical analysis" = c("lme4", "nlme", "mgcv", "survival", "cluster"), + "Reporting" = c("knitr", "rmarkdown", "officedown", "officer", "flextable"), + "Tidyverse" = c("tidyverse", "purrr", "forcats", "tibble"), + "Other packages" = c() + ) + + # Categorize packages + categorized <- list() + uncategorized <- names(versions) + + for (category in names(categories)) { + cat_packages <- intersect(names(versions), categories[[category]]) + if (length(cat_packages) > 0) { + categorized[[category]] <- cat_packages + uncategorized <- setdiff(uncategorized, cat_packages) + } + } + + # Add uncategorized packages + if (length(uncategorized) > 0) { + categorized[["Other packages"]] <- uncategorized + } + + # Generate config + for (category in names(categorized)) { + config_lines <- c(config_lines, paste0(" # ", category)) + + packages_in_cat <- categorized[[category]] + for (i in seq_along(packages_in_cat)) { + pkg <- packages_in_cat[i] + version <- versions[[pkg]] + comma <- if (i == length(packages_in_cat) && category == names(categorized)[length(categorized)]) "" else "," + + # Add special comment for critical packages + comment <- "" + if (pkg == "tmap") comment <- " # CRITICAL: for tm_scale_continuous() syntax" + if (pkg == "terra") comment <- " # CRITICAL: for raster processing" + + config_lines <- c(config_lines, sprintf(' "%s" = "%s"%s%s', pkg, version, comma, comment)) + } + + if (category != names(categorized)[length(categorized)]) { + config_lines <- c(config_lines, "") + } + } + + config_lines <- c(config_lines, ")") + + # Print to console + cat(paste(config_lines, collapse = "\n")) + + # Save to file + writeLines(config_lines, "generated_package_config.R") + cat("\n\n📁 Configuration saved to: generated_package_config.R\n") + + return(config_lines) +} + +# ============================================================================= +# MAIN EXECUTION +# ============================================================================= + +main <- function() { + cat("🔍 SmartCane Package Version Extractor\n") + cat("======================================\n\n") + + # Step 1: Find all packages used in scripts + cat("Step 1: Scanning R scripts for package usage...\n") + packages <- extract_packages_from_scripts() + + cat("\nFound packages:\n") + cat(paste(packages, collapse = ", "), "\n") + cat("\nTotal packages found:", length(packages), "\n") + + # Step 2: Get current versions + cat("\nStep 2: Checking installed versions...\n") + versions <- get_current_versions(packages) + + installed_count <- length(versions) + missing_count <- length(packages) - installed_count + + cat(sprintf("\n📊 Summary: %d installed, %d missing\n", installed_count, missing_count)) + + if (missing_count > 0) { + missing_packages <- setdiff(packages, names(versions)) + cat("\n⚠️ Missing packages:\n") + cat(paste(missing_packages, collapse = ", "), "\n") + cat("\nYou may want to install these first, then re-run this script.\n") + } + + # Step 3: Generate configuration + if (length(versions) > 0) { + cat("\nStep 3: Generating package manager configuration...\n") + config <- generate_package_config(versions) + + cat("\n✅ Next steps:\n") + cat("1. Review generated_package_config.R\n") + cat("2. Copy the REQUIRED_PACKAGES list to package_manager.R\n") + cat("3. Adjust any versions as needed\n") + cat("4. Run package_manager.R\n") + } else { + cat("\n❌ No installed packages found. Install packages first.\n") + } +} + +# Run the extraction +main() diff --git a/r_app/package_manager.R b/r_app/package_manager.R new file mode 100644 index 0000000..84d021d --- /dev/null +++ b/r_app/package_manager.R @@ -0,0 +1,315 @@ +#' Package Manager for SmartCane Project +#' +#' This script manages R package versions across development, testing, and production environments. +#' It uses renv for reproducible environments and ensures consistent package versions. +#' +#' Usage: +#' source("package_manager.R") +#' +#' Author: SmartCane Team +#' Date: 2025-06-24 + +# ============================================================================= +# CONFIGURATION +# ============================================================================= + +# Package requirements with your current working versions +REQUIRED_PACKAGES <- list( + # Core data manipulation + "dplyr" = "1.1.4", + "here" = "1.0.1", + "lubridate" = "1.9.4", + "readr" = "2.1.5", + "readxl" = "1.4.5", + "stringr" = "1.5.1", + "tidyr" = "1.3.1", + "purrr" = "1.0.2", + "magrittr" = "2.0.0", # Adding this as it's commonly used + + # Spatial data + "exactextractr" = "0.10.0", + "raster" = "3.6.32", + "sf" = "1.0.19", + "terra" = "1.8.43", # CRITICAL: for raster processing + + # Visualization - CRITICAL: tmap v4 for new syntax + "ggplot2" = "3.5.1", + "tmap" = "4.0", # CRITICAL: for tm_scale_continuous() syntax + "gridExtra" = "2.3", + # Reporting + "knitr" = "1.50", + "rmarkdown" = "2.21.0", # Adding this as it's needed for reports + + # Tidyverse meta-package + "tidyverse" = "2.0.0", + + # Machine Learning & Statistics + "caret" = "7.0.1", + "CAST" = "1.0.3", + "randomForest" = "4.7.1.2", + "rsample" = "1.3.0", + + # Parallel processing + "furrr" = "0.3.1", + "future" = "1.40.0", + "progressr" = "0.15.1", + + # Other utilities + "reshape2" = "1.4.4", + "zoo" = "1.8.13" +) + +# Log file setup +LOG_FILE <- file.path(getwd(), "package_manager.log") +START_TIME <- Sys.time() + +# ============================================================================= +# UTILITY FUNCTIONS +# ============================================================================= + +#' Log message to both console and file +log_message <- function(message, level = "INFO") { + timestamp <- format(Sys.time(), "%Y-%m-%d %H:%M:%S") + formatted_msg <- sprintf("[%s] %s - %s", level, timestamp, message) + + # Print to console + cat(formatted_msg, "\n") + + # Write to log file + cat(formatted_msg, "\n", file = LOG_FILE, append = TRUE) +} + +#' Check if package is installed +is_package_installed <- function(package) { + package %in% rownames(installed.packages()) +} + +#' Get installed package version +get_package_version <- function(package) { + if (is_package_installed(package)) { + as.character(packageVersion(package)) + } else { + NULL + } +} + +#' Compare version strings (returns TRUE if installed >= required) +version_meets_requirement <- function(installed, required) { + if (is.null(installed)) return(FALSE) + utils::compareVersion(installed, required) >= 0 +} + +#' Install or update package to minimum version +install_or_update_package <- function(package, required_version) { + current_version <- get_package_version(package) + + if (is.null(current_version)) { + log_message(sprintf("Installing %s (required: >= %s)", package, required_version)) + tryCatch({ + install.packages(package, dependencies = TRUE, quiet = TRUE) + new_version <- get_package_version(package) + log_message(sprintf("✓ Installed %s version %s", package, new_version), "SUCCESS") + return(TRUE) + }, error = function(e) { + log_message(sprintf("✗ Failed to install %s: %s", package, e$message), "ERROR") + return(FALSE) + }) + } else if (!version_meets_requirement(current_version, required_version)) { + log_message(sprintf("Updating %s from %s to >= %s", package, current_version, required_version)) + tryCatch({ + install.packages(package, dependencies = TRUE, quiet = TRUE) + new_version <- get_package_version(package) + if (version_meets_requirement(new_version, required_version)) { + log_message(sprintf("✓ Updated %s to version %s", package, new_version), "SUCCESS") + return(TRUE) + } else { + log_message(sprintf("⚠ %s updated to %s but still below required %s", package, new_version, required_version), "WARNING") + return(FALSE) + } + }, error = function(e) { + log_message(sprintf("✗ Failed to update %s: %s", package, e$message), "ERROR") + return(FALSE) + }) + } else { + log_message(sprintf("✓ %s version %s meets requirement (>= %s)", package, current_version, required_version)) + return(TRUE) + } +} + +# ============================================================================= +# MAIN PACKAGE MANAGEMENT FUNCTIONS +# ============================================================================= + +#' Initialize renv if not already initialized +initialize_renv <- function() { + log_message("Checking renv initialization...") + + if (!file.exists("renv.lock")) { + log_message("Initializing renv for the first time...") + if (!requireNamespace("renv", quietly = TRUE)) { + log_message("Installing renv...") + install.packages("renv") + } + renv::init() + log_message("✓ renv initialized", "SUCCESS") + } else { + log_message("✓ renv already initialized") + # Check if renv is already active by looking at the library path + if (!requireNamespace("renv", quietly = TRUE)) { + install.packages("renv") + } + # Check if we're already using the renv project library + lib_paths <- .libPaths() + + if (!any(grepl("renv", lib_paths))) { + log_message("Activating renv...") + renv::activate() + log_message("✓ renv activated") + } else { + log_message("✓ renv already active") + } + } +} + +#' Check and install all required packages +manage_packages <- function() { + log_message("=== PACKAGE MANAGEMENT STARTED ===") + log_message(sprintf("R version: %s", R.version.string)) + + success_count <- 0 + failure_count <- 0 + + for (package in names(REQUIRED_PACKAGES)) { + required_version <- REQUIRED_PACKAGES[[package]] + + if (install_or_update_package(package, required_version)) { + success_count <- success_count + 1 + } else { + failure_count <- failure_count + 1 + } + } + + log_message(sprintf("Package management complete: %d success, %d failures", success_count, failure_count)) + + if (failure_count > 0) { + log_message("Some packages failed to install/update. Check log for details.", "WARNING") + } + + return(failure_count == 0) +} + +#' Update renv lockfile with current package versions +update_lockfile <- function() { + log_message("Updating renv lockfile...") + tryCatch({ + renv::snapshot(prompt = FALSE) + log_message("✓ renv lockfile updated", "SUCCESS") + }, error = function(e) { + log_message(sprintf("✗ Failed to update lockfile: %s", e$message), "ERROR") + }) +} + +#' Generate package report +generate_package_report <- function() { + log_message("=== PACKAGE REPORT ===") + + # Check each required package + for (package in names(REQUIRED_PACKAGES)) { + required_version <- REQUIRED_PACKAGES[[package]] + current_version <- get_package_version(package) + + if (is.null(current_version)) { + status <- "❌ NOT INSTALLED" + } else if (version_meets_requirement(current_version, required_version)) { + status <- "✅ OK" + } else { + status <- "⚠️ VERSION TOO OLD" + } + + log_message(sprintf("%-20s | Required: >= %-8s | Installed: %-8s | %s", + package, required_version, + ifelse(is.null(current_version), "NONE", current_version), + status)) + } + + log_message("=== END PACKAGE REPORT ===") +} + +#' Main function to run complete package management +run_package_manager <- function() { + # Initialize log + cat("", file = LOG_FILE) # Clear log file + log_message("SmartCane Project - Package Manager Started") + log_message(sprintf("Working directory: %s", getwd())) + + # Step 1: Initialize renv + initialize_renv() + + # Step 2: Generate initial report + log_message("\n=== INITIAL STATE ===") + generate_package_report() + + # Step 3: Manage packages + log_message("\n=== PACKAGE INSTALLATION/UPDATES ===") + success <- manage_packages() + + # Step 4: Update lockfile if successful + if (success) { + update_lockfile() + } + + # Step 5: Generate final report + log_message("\n=== FINAL STATE ===") + generate_package_report() + + # Summary + end_time <- Sys.time() + duration <- round(as.numeric(difftime(end_time, START_TIME, units = "secs")), 2) + + log_message(sprintf("Package management completed in %s seconds", duration)) + log_message(sprintf("Log saved to: %s", LOG_FILE)) + + if (success) { + log_message("🎉 All packages successfully managed!", "SUCCESS") + log_message("📋 Next steps:") + log_message(" 1. Test your R scripts to ensure everything works") + log_message(" 2. Commit renv.lock to version control") + log_message(" 3. Share this script with your team") + } else { + log_message("⚠️ Some issues occurred. Check the log for details.", "WARNING") + log_message("💡 You may need to:") + log_message(" 1. Update R to a newer version") + log_message(" 2. Install system dependencies") + log_message(" 3. Check your internet connection") + } + + return(success) +} + +# ============================================================================= +# EXECUTION +# ============================================================================= + +# Only run if script is sourced directly (not when loaded as module) +if (!exists("PACKAGE_MANAGER_LOADED")) { + PACKAGE_MANAGER_LOADED <- TRUE + + cat("🚀 SmartCane Package Manager\n") + cat("============================\n") + cat("This will check and install/update all required R packages.\n") + cat("Log file:", LOG_FILE, "\n\n") + + # Ask for confirmation + response <- readline("Continue? (y/N): ") + if (tolower(substr(response, 1, 1)) == "y") { + result <- run_package_manager() + + if (result) { + cat("\n✅ Package management completed successfully!\n") + } else { + cat("\n❌ Package management completed with errors. Check the log.\n") + } + } else { + cat("❌ Package management cancelled.\n") + } +} diff --git a/r_app/report_utils.R b/r_app/report_utils.R index 930ec3c..060a6e6 100644 --- a/r_app/report_utils.R +++ b/r_app/report_utils.R @@ -73,15 +73,15 @@ create_CI_map <- function(pivot_raster, pivot_shape, pivot_spans, show_legend = } if (missing(age) || is.null(age)) { stop("age parameter is required") - } - # Create the base map + } # Create the base map map <- tm_shape(pivot_raster, unit = "m") # Add raster with continuous spectrum (fixed scale 1-8 for consistent comparison) map <- map + tm_raster(col.scale = tm_scale_continuous(values = "brewer.rd_yl_gn", limits = c(1, 8)), col.legend = tm_legend(title = "CI", - orientation = if(legend_is_portrait) "portrait" else "landscape", + orientation = if(legend_is_portrait) "portrait" else "landscape", show = show_legend, - position = c("left", "bottom"))) + position = if(show_legend) tm_pos_out("left", "center") else c("left", "bottom") + )) # Add layout elements map <- map + tm_layout(main.title = paste0("Max CI week ", week,"\n", age, " weeks old"), main.title.size = 0.7) @@ -128,16 +128,16 @@ create_CI_diff_map <- function(pivot_raster, pivot_shape, pivot_spans, show_lege } if (missing(age) || is.null(age)) { stop("age parameter is required") - } - # Create the base map + } # Create the base map map <- tm_shape(pivot_raster, unit = "m") # Add raster with continuous spectrum (centered at 0 for difference maps, fixed scale) map <- map + tm_raster(col.scale = tm_scale_continuous(values = "brewer.rd_yl_gn", midpoint = 0, limits = c(-3, 3)), - col.legend = tm_legend(title = "CI difference", + col.legend = tm_legend(title = "CI diff.", orientation = if(legend_is_portrait) "portrait" else "landscape", show = show_legend, - position = c("left", "bottom"))) + position = if(show_legend) tm_pos_out("right", "center") else c("left", "bottom") + )) # Add layout elements map <- map + tm_layout(main.title = paste0("CI change week ", week_1, " - week ", week_2, "\n", age, " weeks old"), main.title.size = 0.7) @@ -159,7 +159,7 @@ create_CI_diff_map <- function(pivot_raster, pivot_shape, pivot_spans, show_lege #' #' @param pivotName The name or ID of the pivot field to visualize #' @param field_boundaries Field boundaries spatial data (sf object) -#' @param current_ci Current week's Chlorophyll Index raster +#' @param current_ci Current week's Chlorophyll Index raster #' @param ci_minus_1 Previous week's Chlorophyll Index raster #' @param ci_minus_2 Two weeks ago Chlorophyll Index raster #' @param last_week_diff Difference raster between current and last week @@ -172,13 +172,13 @@ create_CI_diff_map <- function(pivot_raster, pivot_shape, pivot_spans, show_lege #' @param borders Whether to display field borders (default: TRUE) #' @return NULL (adds output directly to R Markdown document) #' -ci_plot <- function(pivotName, - field_boundaries = AllPivots0, - current_ci = CI, - ci_minus_1 = CI_m1, - ci_minus_2 = CI_m2, - last_week_diff = last_week_dif_raster_abs, - three_week_diff = three_week_dif_raster_abs, +ci_plot <- function(pivotName, + field_boundaries = AllPivots0, + current_ci = CI, + ci_minus_1 = CI_m1, + ci_minus_2 = CI_m2, + last_week_diff = last_week_dif_raster_abs, + three_week_diff = three_week_dif_raster_abs, harvesting_data = harvesting_data, week = week, week_minus_1 = week_minus_1, @@ -214,66 +214,66 @@ ci_plot <- function(pivotName, # Extract pivot shape and age data tryCatch({ pivotShape <- field_boundaries %>% terra::subset(field %in% pivotName) %>% sf::st_transform(terra::crs(current_ci)) - age <- harvesting_data %>% - dplyr::filter(field %in% pivotName) %>% - sort("year") %>% - tail(., 1) %>% - dplyr::select(age) %>% - unique() %>% - pull() %>% + age <- harvesting_data %>% + dplyr::filter(field %in% pivotName) %>% + sort("year") %>% + tail(., 1) %>% + dplyr::select(age) %>% + unique() %>% + pull() %>% round() - + # Filter for the specific pivot AllPivots2 <- field_boundaries %>% dplyr::filter(field %in% pivotName) - + # Create crop masks for different timepoints using terra functions singlePivot <- terra::crop(current_ci, pivotShape) %>% terra::mask(., pivotShape) singlePivot_m1 <- terra::crop(ci_minus_1, pivotShape) %>% terra::mask(., pivotShape) singlePivot_m2 <- terra::crop(ci_minus_2, pivotShape) %>% terra::mask(., pivotShape) - + # Create difference maps abs_CI_last_week <- terra::crop(last_week_diff, pivotShape) %>% terra::mask(., pivotShape) abs_CI_three_week <- terra::crop(three_week_diff, pivotShape) %>% terra::mask(., pivotShape) - + # Get planting date - planting_date <- harvesting_data %>% - dplyr::filter(field %in% pivotName) %>% - ungroup() %>% - dplyr::select(season_start) %>% + planting_date <- harvesting_data %>% + dplyr::filter(field %in% pivotName) %>% + ungroup() %>% + dplyr::select(season_start) %>% unique() - + # Create spans for borders - joined_spans2 <- field_boundaries %>% + joined_spans2 <- field_boundaries %>% sf::st_transform(sf::st_crs(pivotShape)) %>% dplyr::filter(field %in% pivotName) - + # Create the maps for different timepoints - CImap_m2 <- create_CI_map(singlePivot_m2, AllPivots2, joined_spans2, - show_legend = TRUE, legend_is_portrait = TRUE, + CImap_m2 <- create_CI_map(singlePivot_m2, AllPivots2, joined_spans2, + show_legend = TRUE, legend_is_portrait = TRUE, week = week_minus_2, age = age - 2, borders = borders) - - CImap_m1 <- create_CI_map(singlePivot_m1, AllPivots2, joined_spans2, - show_legend = FALSE, legend_is_portrait = FALSE, + + CImap_m1 <- create_CI_map(singlePivot_m1, AllPivots2, joined_spans2, + show_legend = FALSE, legend_is_portrait = FALSE, week = week_minus_1, age = age - 1, borders = borders) - - CImap <- create_CI_map(singlePivot, AllPivots2, joined_spans2, - show_legend = FALSE, legend_is_portrait = FALSE, + + CImap <- create_CI_map(singlePivot, AllPivots2, joined_spans2, + show_legend = FALSE, legend_is_portrait = FALSE, week = week, age = age, borders = borders) # Create difference maps - only show legend on the second one to avoid redundancy - CI_max_abs_last_week <- create_CI_diff_map(abs_CI_last_week, AllPivots2, joined_spans2, - show_legend = FALSE, legend_is_portrait = FALSE, + CI_max_abs_last_week <- create_CI_diff_map(abs_CI_last_week, AllPivots2, joined_spans2, + show_legend = FALSE, legend_is_portrait = FALSE, week_1 = week, week_2 = week_minus_1, age = age, borders = borders) - - CI_max_abs_three_week <- create_CI_diff_map(abs_CI_three_week, AllPivots2, joined_spans2, - show_legend = TRUE, legend_is_portrait = TRUE, + + CI_max_abs_three_week <- create_CI_diff_map(abs_CI_three_week, AllPivots2, joined_spans2, + show_legend = TRUE, legend_is_portrait = TRUE, week_1 = week, week_2 = week_minus_3, age = age, borders = borders) - - # Arrange the maps - tst <- tmap_arrange(CImap_m2, CImap_m1, CImap, CI_max_abs_last_week, CI_max_abs_three_week, nrow = 1) - + # Arrange the maps with equal widths + tst <- tmap_arrange(CImap_m2, CImap_m1, CImap, CI_max_abs_last_week, CI_max_abs_three_week, + nrow = 1, widths = c(0.23, 0.18, 0.18, 0.18, 0.23)) + # Output heading and map to R Markdown cat(paste("## Field", pivotName, "-", age, "weeks after planting/harvest", "\n")) print(tst) - + }, error = function(e) { safe_log(paste("Error creating CI plot for pivot", pivotName, ":", e$message), "ERROR") cat(paste("## Field", pivotName, "- Error creating visualization", "\n")) @@ -308,54 +308,54 @@ cum_ci_plot <- function(pivotName, ci_quadrant_data = CI_quadrant, plot_type = " # Filter data for the specified pivot tryCatch({ data_ci <- ci_quadrant_data %>% dplyr::filter(field == pivotName) - + if (nrow(data_ci) == 0) { safe_log(paste("No CI data found for pivot", pivotName), "WARNING") return(cum_ci_plot2(pivotName)) # Use fallback function when no data is available } - + # Process data - data_ci2 <- data_ci %>% + data_ci2 <- data_ci %>% dplyr::mutate(CI_rate = cumulative_CI / DOY, - week = lubridate::week(Date)) %>% + week = lubridate::week(Date)) %>% dplyr::group_by(field) %>% dplyr::mutate(mean_CIrate_rolling_10_days = zoo::rollapplyr(CI_rate, width = 10, FUN = mean, partial = TRUE), mean_rolling_10_days = zoo::rollapplyr(value, width = 10, FUN = mean, partial = TRUE)) - + data_ci2 <- data_ci2 %>% dplyr::mutate(season = as.factor(season)) - + # Prepare date information by season - date_preparation_perfect_pivot <- data_ci2 %>% - dplyr::group_by(season) %>% + date_preparation_perfect_pivot <- data_ci2 %>% + dplyr::group_by(season) %>% dplyr::summarise(min_date = min(Date), max_date = max(Date), days = max_date - min_date) - + # Get the 3 most recent seasons unique_seasons <- sort(unique(date_preparation_perfect_pivot$season), decreasing = TRUE)[1:3] - + # Determine the y aesthetic based on the plot type y_aesthetic <- switch(plot_type, "CI_rate" = "mean_CIrate_rolling_10_days", "cumulative_CI" = "cumulative_CI", "value" = "mean_rolling_10_days") - + y_label <- switch(plot_type, "CI_rate" = "10-Day Rolling Mean CI Rate (cumulative CI / age)", "cumulative_CI" = "Cumulative CI", "value" = "10-Day Rolling Mean CI") - + # Determine x-axis variable based on x_unit parameter x_var <- if (x_unit == "days") { if (facet_on) "Date" else "DOY" } else { "week" } - + x_label <- switch(x_unit, "days" = if (facet_on) "Date" else "Age of Crop (Days)", "weeks" = "Week Number") - + # Create plot with either facets by season or overlay by DOY/week if (facet_on) { g <- ggplot2::ggplot(data = data_ci2 %>% dplyr::filter(season %in% unique_seasons)) + @@ -386,10 +386,10 @@ cum_ci_plot <- function(pivotName, ci_quadrant_data = CI_quadrant, plot_type = " legend.text = ggplot2::element_text(size = 8)) + ggplot2::guides(color = ggplot2::guide_legend(nrow = 2, byrow = TRUE)) } - + # Output plot to R Markdown with reduced height subchunkify(g, 3.2, 10) # Reduced from 3.2 to 2.8 - + }, error = function(e) { safe_log(paste("Error creating CI trend plot for pivot", pivotName, ":", e$message), "ERROR") cum_ci_plot2(pivotName) # Use fallback function in case of error @@ -406,14 +406,14 @@ cum_ci_plot2 <- function(pivotName){ if (missing(pivotName) || is.null(pivotName) || pivotName == "") { stop("pivotName is required") } - + # Create a simple plot showing "No data available" tryCatch({ end_date <- Sys.Date() start_date <- end_date %m-% months(11) # 11 months ago from end_date date_seq <- seq.Date(from = start_date, to = end_date, by = "month") midpoint_date <- start_date + (end_date - start_date) / 2 - + g <- ggplot() + scale_x_date(limits = c(start_date, end_date), date_breaks = "1 month", date_labels = "%m-%Y") + scale_y_continuous(limits = c(0, 4)) + @@ -425,9 +425,9 @@ cum_ci_plot2 <- function(pivotName){ legend.title = element_text(size = 8), legend.text = element_text(size = 8)) + annotate("text", x = midpoint_date, y = 2, label = "No data available", size = 6, hjust = 0.5) - + subchunkify(g, 3.2, 10) - + }, error = function(e) { safe_log(paste("Error creating fallback CI plot for pivot", pivotName, ":", e$message), "ERROR") cat(paste("No data available for field", pivotName, "\n")) @@ -449,39 +449,39 @@ get_week_path <- function(mosaic_path, input_date, week_offset) { if (missing(input_date)) { stop("input_date is required") } - + tryCatch({ # Convert input_date to Date object (in case it's a string) input_date <- as.Date(input_date) if (is.na(input_date)) { stop("Invalid input_date. Expected a Date object or a string convertible to Date.") } - + # Validate week_offset week_offset <- as.integer(week_offset) if (is.na(week_offset)) { stop("Invalid week_offset. Expected an integer value.") } - + # Get the start of the week for the input date (adjust to Monday as the start of the week) start_of_week <- lubridate::floor_date(input_date, unit = "week", week_start = 1) - + # Calculate the new date after applying the week offset target_date <- start_of_week + lubridate::weeks(week_offset) - + # Get the week number and year of the target date target_week <- sprintf("%02d", lubridate::isoweek(target_date)) # Left-pad week number with a zero if needed target_year <- lubridate::isoyear(target_date) - + # Generate the file path for the target week path_to_week <- here::here(mosaic_path, paste0("week_", target_week, "_", target_year, ".tif")) - + # Log the path calculation safe_log(paste("Calculated path for week", target_week, "of year", target_year, ":", path_to_week), "INFO") - + # Return the path return(path_to_week) - + }, error = function(e) { safe_log(paste("Error calculating week path:", e$message), "ERROR") stop(e$message) diff --git a/renv.lock b/renv.lock new file mode 100644 index 0000000..4607526 --- /dev/null +++ b/renv.lock @@ -0,0 +1,7385 @@ +{ + "R": { + "Version": "4.4.2", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://packagemanager.posit.co/cran/latest" + } + ] + }, + "Packages": { + "CAST": { + "Package": "CAST", + "Version": "1.0.3", + "Source": "Repository", + "Type": "Package", + "Title": "'caret' Applications for Spatial-Temporal Models", + "Authors@R": "c(person(\"Hanna\", \"Meyer\", email = \"hanna.meyer@uni-muenster.de\", role = c(\"cre\", \"aut\")), person(\"Carles\", \"Milà\", role = c(\"aut\")), person(\"Marvin\", \"Ludwig\", role = c(\"aut\")), person(\"Jan\", \"Linnenbrink\", role = c(\"aut\")), person(\"Fabian\", \"Schumacher\", role = c(\"aut\")), person(\"Philipp\", \"Otto\", role = c(\"ctb\")), person(\"Chris\", \"Reudenbach\", role = c(\"ctb\")), person(\"Thomas\", \"Nauss\", role = c(\"ctb\")), person(\"Edzer\", \"Pebesma\", role = c(\"ctb\")), person(\"Jakub\", \"Nowosad\", role = c(\"ctb\")))", + "Author": "Hanna Meyer [cre, aut], Carles Milà [aut], Marvin Ludwig [aut], Jan Linnenbrink [aut], Fabian Schumacher [aut], Philipp Otto [ctb], Chris Reudenbach [ctb], Thomas Nauss [ctb], Edzer Pebesma [ctb], Jakub Nowosad [ctb]", + "Maintainer": "Hanna Meyer ", + "Description": "Supporting functionality to run 'caret' with spatial or spatial-temporal data. 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(2024) .", + "License": "GPL (>= 2)", + "URL": "https://github.com/HannaMeyer/CAST, https://hannameyer.github.io/CAST/", + "Encoding": "UTF-8", + "LazyData": "false", + "Depends": [ + "R (>= 4.1.0)" + ], + "BugReports": "https://github.com/HannaMeyer/CAST/issues/", + "Imports": [ + "caret", + "stats", + "utils", + "ggplot2", + "graphics", + "FNN", + "plyr", + "zoo", + "methods", + "grDevices", + "data.table", + "sf", + "forcats", + "twosamples", + "terra", + "sp" + ], + "Suggests": [ + "doParallel", + "lubridate", + "randomForest", + "knitr", + "geodata", + "mapview", + "rmarkdown", + "scales", + "parallel", + "gridExtra", + "viridis", + "stars", + "scam", + "rnaturalearth", + "MASS", + "RColorBrewer", + "tmap", + "PCAmixdata", + "gower", + "clustMixType", + "testthat (>= 3.0.0)" + ], + "RoxygenNote": "7.3.2", + "VignetteBuilder": "knitr", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "DBI": { + "Package": "DBI", + "Version": "1.2.3", + "Source": "Repository", + "Title": "R Database Interface", + "Date": "2024-06-02", + "Authors@R": "c( person(\"R Special Interest Group on Databases (R-SIG-DB)\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\") )", + "Description": "A database interface definition for communication between R and relational database management systems. 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Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.62): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" + ], + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" + ], + "RoxygenNote": "7.3.2.9000", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "data.table": { + "Package": "data.table", + "Version": "1.16.4", + "Source": "Repository", + "Title": "Extension of `data.frame`", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "bit64 (>= 4.0.0)", + "bit (>= 4.0.4)", + "R.utils", + "xts", + "zoo (>= 1.8-1)", + "yaml", + "knitr", + "markdown" + ], + "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. 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It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.", + "License": "MIT + file LICENSE", + "URL": "https://readr.tidyverse.org, https://github.com/tidyverse/readr", + "BugReports": "https://github.com/tidyverse/readr/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.2.0)", + "clipr", + "crayon", + "hms (>= 0.4.1)", + "lifecycle (>= 0.2.0)", + "methods", + "R6", + "rlang", + "tibble", + "utils", + "vroom (>= 1.6.0)" + ], + "Suggests": [ + "covr", + "curl", + "datasets", + "knitr", + "rmarkdown", + "spelling", + "stringi", + "testthat (>= 3.2.0)", + "tzdb (>= 0.1.1)", + "waldo", + "withr", + "xml2" + ], + "LinkingTo": [ + "cpp11", + "tzdb (>= 0.1.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "false", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Jim Hester [aut], Romain Francois [ctb], Jennifer Bryan [aut, cre] (), Shelby Bearrows [ctb], Posit Software, PBC [cph, fnd], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [ctb, cph] (grisu3 implementation), Mikkel Jørgensen [ctb, cph] (grisu3 implementation)", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "readxl": { + "Package": "readxl", + "Version": "1.4.5", + "Source": "Repository", + "Title": "Read Excel Files", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = \"Copyright holder of all R code and all C/C++ code without explicit copyright attribution\"), person(\"Marcin\", \"Kalicinski\", role = c(\"ctb\", \"cph\"), comment = \"Author of included RapidXML code\"), person(\"Komarov Valery\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Christophe Leitienne\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Bob Colbert\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"David Hoerl\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\"), person(\"Evan Miller\", role = c(\"ctb\", \"cph\"), comment = \"Author of included libxls code\") )", + "Description": "Import excel files into R. Supports '.xls' via the embedded 'libxls' C library and '.xlsx' via the embedded 'RapidXML' C++ library . Works on Windows, Mac and Linux without external dependencies.", + "License": "MIT + file LICENSE", + "URL": "https://readxl.tidyverse.org, https://github.com/tidyverse/readxl", + "BugReports": "https://github.com/tidyverse/readxl/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cellranger", + "tibble (>= 2.0.1)", + "utils" + ], + "Suggests": [ + "covr", + "knitr", + "rmarkdown", + "testthat (>= 3.1.6)", + "withr" + ], + "LinkingTo": [ + "cpp11 (>= 0.4.0)", + "progress" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate, tidyverse", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Note": "libxls v1.6.3 c199d13", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut] (), Jennifer Bryan [aut, cre] (), Posit, PBC [cph, fnd] (Copyright holder of all R code and all C/C++ code without explicit copyright attribution), Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Komarov Valery [ctb, cph] (Author of included libxls code), Christophe Leitienne [ctb, cph] (Author of included libxls code), Bob Colbert [ctb, cph] (Author of included libxls code), David Hoerl [ctb, cph] (Author of included libxls code), Evan Miller [ctb, cph] (Author of included libxls code)", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "recipes": { + "Package": "recipes", + "Version": "1.2.1", + "Source": "Repository", + "Title": "Preprocessing and Feature Engineering Steps for Modeling", + "Authors@R": "c( person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Emil\", \"Hvitfeldt\", , \"emil.hvitfeldt@posit.co\", role = \"aut\"), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A recipe prepares your data for modeling. We provide an extensible framework for pipeable sequences of feature engineering steps provides preprocessing tools to be applied to data. Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting processed output can then be used as inputs for statistical or machine learning models.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/tidymodels/recipes, https://recipes.tidymodels.org/", + "BugReports": "https://github.com/tidymodels/recipes/issues", + "Depends": [ + "dplyr (>= 1.1.0)", + "R (>= 3.6)" + ], + "Imports": [ + "cli", + "clock (>= 0.6.1)", + "generics (>= 0.1.2)", + "glue", + "gower", + "hardhat (>= 1.4.1)", + "ipred (>= 0.9-12)", + "lifecycle (>= 1.0.3)", + "lubridate (>= 1.8.0)", + "magrittr", + "Matrix", + "purrr (>= 1.0.0)", + "rlang (>= 1.1.0)", + "sparsevctrs (>= 0.3.0)", + "stats", + "tibble", + "tidyr (>= 1.0.0)", + "tidyselect (>= 1.2.0)", + "timeDate", + "utils", + "vctrs (>= 0.5.0)", + "withr" + ], + "Suggests": [ + "covr", + "ddalpha", + "dials (>= 1.2.0)", + "ggplot2", + "igraph", + "kernlab", + "knitr", + "methods", + "modeldata (>= 0.1.1)", + "parsnip (>= 1.2.0)", + "RANN", + "RcppRoll", + "rmarkdown", + "rpart", + "rsample", + "RSpectra", + "splines2", + "testthat (>= 3.0.0)", + "workflows", + "xml2" + ], + "VignetteBuilder": "knitr", + "RdMacros": "lifecycle", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Max Kuhn [aut, cre], Hadley Wickham [aut], Emil Hvitfeldt [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Max Kuhn ", + "Repository": "CRAN" + }, + "rematch": { + "Package": "rematch", + "Version": "2.0.0", + "Source": "Repository", + "Title": "Match Regular Expressions with a Nicer 'API'", + "Author": "Gabor Csardi", + "Maintainer": "Gabor Csardi ", + "Description": "A small wrapper on 'regexpr' to extract the matches and captured groups from the match of a regular expression to a character vector.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/gaborcsardi/rematch", + "BugReports": "https://github.com/gaborcsardi/rematch/issues", + "RoxygenNote": "5.0.1.9000", + "Suggests": [ + "covr", + "testthat" + ], + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "rematch2": { + "Package": "rematch2", + "Version": "2.1.2", + "Source": "Repository", + "Title": "Tidy Output from Regular Expression Matching", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", email = \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Matthew\", \"Lincoln\", email = \"matthew.d.lincoln@gmail.com\", role = c(\"ctb\")))", + "Description": "Wrappers on 'regexpr' and 'gregexpr' to return the match results in tidy data frames.", + "License": "MIT + file LICENSE", + "LazyData": "true", + "URL": "https://github.com/r-lib/rematch2#readme", + "BugReports": "https://github.com/r-lib/rematch2/issues", + "RoxygenNote": "7.1.0", + "Imports": [ + "tibble" + ], + "Suggests": [ + "covr", + "testthat" + ], + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Matthew Lincoln [ctb]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "renv": { + "Package": "renv", + "Version": "1.1.4", + "Source": "Repository", + "Type": "Package", + "Title": "Project Environments", + "Authors@R": "c( person(\"Kevin\", \"Ushey\", role = c(\"aut\", \"cre\"), email = \"kevin@rstudio.com\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Hadley\", \"Wickham\", role = c(\"aut\"), email = \"hadley@rstudio.com\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.", + "License": "MIT + file LICENSE", + "URL": "https://rstudio.github.io/renv/, https://github.com/rstudio/renv", + "BugReports": "https://github.com/rstudio/renv/issues", + "Imports": [ + "utils" + ], + "Suggests": [ + "BiocManager", + "cli", + "compiler", + "covr", + "cpp11", + "devtools", + "gitcreds", + "jsonlite", + "jsonvalidate", + "knitr", + "miniUI", + "modules", + "packrat", + "pak", + "R6", + "remotes", + "reticulate", + "rmarkdown", + "rstudioapi", + "shiny", + "testthat", + "uuid", + "waldo", + "yaml", + "webfakes" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/testthat/start-first": "bioconductor,python,install,restore,snapshot,retrieve,remotes", + "NeedsCompilation": "no", + "Author": "Kevin Ushey [aut, cre] (), Hadley Wickham [aut] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Kevin Ushey ", + "Repository": "CRAN" + }, + "reprex": { + "Package": "reprex", + "Version": "2.1.1", + "Source": "Repository", + "Title": "Prepare Reproducible Example Code via the Clipboard", + "Authors@R": "c( person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"David\", \"Robinson\", , \"admiral.david@gmail.com\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Christophe\", \"Dervieux\", , \"cderv@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Convenience wrapper that uses the 'rmarkdown' package to render small snippets of code to target formats that include both code and output. 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Also provides tools to convert between sparse matrices and data frames with sparse columns and functions to interact with sparse vectors.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/sparsevctrs, https://r-lib.github.io/sparsevctrs/", + "BugReports": "https://github.com/r-lib/sparsevctrs/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "rlang (>= 1.1.0)", + "vctrs" + ], + "Suggests": [ + "knitr", + "Matrix", + "methods", + "rmarkdown", + "testthat (>= 3.0.0)", + "tibble", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate, rmarkdown, lobstr, ggplot2, bench, tidyr, ggbeeswarm", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Emil Hvitfeldt [aut, cre] (), Davis Vaughan [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Emil Hvitfeldt ", + "Repository": "CRAN" + }, + "stars": { + "Package": "stars", + "Version": "0.6-8", + "Source": "Repository", + "Title": "Spatiotemporal Arrays, Raster and Vector Data Cubes", + "Authors@R": "c(person(given = \"Edzer\", family = \"Pebesma\", role = c(\"aut\", \"cre\"), email = \"edzer.pebesma@uni-muenster.de\", comment = c(ORCID = \"0000-0001-8049-7069\")), person(given = \"Michael\", family = \"Sumner\", role = \"ctb\", comment=c(ORCID = \"0000-0002-2471-7511\")), person(given = \"Etienne\", family = \"Racine\", role = \"ctb\"), person(given = \"Adriano\", family = \"Fantini\", role = \"ctb\"), person(given = \"David\", family = \"Blodgett\", role = \"ctb\"), person(given = \"Krzysztof\", family = \"Dyba\", role = \"ctb\", comment=c(ORCID = \"0000-0002-8614-3816\")))", + "Description": "Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.", + "License": "Apache License", + "URL": "https://r-spatial.github.io/stars/, https://github.com/r-spatial/stars/", + "BugReports": "https://github.com/r-spatial/stars/issues/", + "Additional_repositories": "https://cran.uni-muenster.de/pebesma/", + "LazyData": "true", + "Depends": [ + "R (>= 3.3.0)", + "abind", + "sf (>= 1.0-19)" + ], + "Imports": [ + "methods", + "parallel", + "classInt (>= 0.4-1)", + "rlang", + "units" + ], + "Suggests": [ + "Cairo", + "OpenStreetMap", + "PCICt", + "RNetCDF (>= 1.8-2)", + "clue", + "covr", + "cubble (>= 0.3.0)", + "cubelyr", + "digest", + "dplyr (>= 0.7-0)", + "exactextractr", + "FNN", + "future.apply", + "ggforce", + "ggplot2", + "ggthemes", + "gstat", + "httr", + "jsonlite", + "knitr", + "lwgeom", + "maps", + "mapdata", + "ncdfgeom", + "ncmeta (>= 0.0.3)", + "pbapply", + "plm", + "randomForest", + "raster", + "rmarkdown", + "sp", + "spacetime", + "spatstat (>= 2.0-1)", + "spatstat.geom", + "starsdata", + "terra (>= 1.4-22)", + "testthat", + "tibble", + "tidyr", + "tsibble", + "viridis", + "xts", + "zoo" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Collate": "'aggregate.R' 'cubble.R' 'datasets.R' 'dimensions.R' 'extract.R' 'factors.R' 'geom.R' 'gt.R' 'init.R' 'intervals.R' 'mdim.R' 'mosaic.R' 'ncdf.R' 'ncproxy.R' 'OpenStreetMap.R' 'ops.R' 'plot.R' 'prcomp.R' 'proxy.R' 'rasterize.R' 'raster.R' 'read.R' 'rotate.R' 'sample.R' 'sf.R' 'spacetime.R' 'spatstat.R' 'sp.R' 'stars.R' 'subset.R' 'tidyverse.R' 'tile.R' 'transform.R' 'values.R' 'warp.R' 'write.R' 'xts.R'", + "NeedsCompilation": "no", + "Author": "Edzer Pebesma [aut, cre] (), Michael Sumner [ctb] (), Etienne Racine [ctb], Adriano Fantini [ctb], David Blodgett [ctb], Krzysztof Dyba [ctb] ()", + "Maintainer": "Edzer Pebesma ", + "Repository": "CRAN" + }, + "stringdist": { + "Package": "stringdist", + "Version": "0.9.15", + "Source": "Repository", + "Maintainer": "Mark van der Loo ", + "License": "GPL-3", + "Title": "Approximate String Matching, Fuzzy Text Search, and String Distance Functions", + "Type": "Package", + "LazyLoad": "yes", + "Authors@R": "c( person(\"Mark\", \"van der Loo\", role=c(\"aut\",\"cre\") , email=\"mark.vanderloo@gmail.com\" , comment= c(ORCID=\"0000-0002-9807-4686\")) , person(\"Jan\", \"van der Laan\", role=\"ctb\") , person(\"R Core Team\",\"\" , role=\"ctb\") , person(\"Nick\",\"Logan\" , role=\"ctb\") , person(\"Chris\",\"Muir\" , role=\"ctb\") , person(\"Johannes\", \"Gruber\" , role=\"ctb\") , person(\"Brian\",\"Ripley\" , role=\"ctb\"))", + "Description": "Implements an approximate string matching version of R's native 'match' function. 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This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.", + "Imports": [ + "xfun (>= 0.48)" + ], + "Suggests": [ + "testit", + "rstudioapi" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/rstudio/tinytex", + "BugReports": "https://github.com/rstudio/tinytex/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre, cph] (), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (), Devon Ryan [ctb] (), Ethan Heinzen [ctb], Fernando Cagua [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "tmap": { + "Package": "tmap", + "Version": "4.0", + "Source": "Repository", + "Title": "Thematic Maps", + "Authors@R": "c( person(\"Martijn\", \"Tennekes\", , \"mtennekes@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Jakub\", \"Nowosad\", , \"nowosad.jakub@gmail.com\", role = \"ctb\"), person(\"Joel\", \"Gombin\", , \"joel.gombin@gmail.com\", role = \"ctb\"), person(\"Sebastian\", \"Jeworutzki\", , \"Sebastian.Jeworutzki@rub.de\", role = \"ctb\"), person(\"Kent\", \"Russell\", , \"kent.russell@timelyportfolio.com\", role = \"ctb\"), person(\"Richard\", \"Zijdeman\", , \"richard.zijdeman@iisg.nl\", role = \"ctb\"), person(\"John\", \"Clouse\", , \"johnaclouse@gmail.com\", role = \"ctb\"), person(\"Robin\", \"Lovelace\", , \"rob00x@gmail.com\", role = \"ctb\"), person(\"Jannes\", \"Muenchow\", , \"jannes.muenchow@uni-jena.de\", role = \"ctb\"), person(\"Olivier\", \"Roy\", role = \"ctb\"), person(\"Edzer\", \"Pebesma\", , \"edzer.pebesma@uni-muenster.de\", role = \"ctb\"), person(\"Hugh\", \"Graham\", , \"hugh.a.graham@gmail.com\", role = \"ctb\"), person(\"Michael D.\", \"Sumner\", , \"mdsumner@gmail.com\", role = \"ctb\"), person(\"Tim\", \"Appelhans\", , \"tim.appelhans@gmail.com\", role = \"ctb\"), person(\"Nick\", \"Bearman\", , \"nick@nickbearman.com\", role = \"ctb\"))", + "Description": "Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.", + "License": "GPL-3", + "URL": "https://github.com/r-tmap/tmap, https://r-tmap.github.io/tmap/", + "BugReports": "https://github.com/r-tmap/tmap/issues", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "classInt (>= 0.4-3)", + "cli", + "cols4all (>= 0.8)", + "data.table", + "grid", + "htmltools", + "htmlwidgets", + "leafem (>= 0.1)", + "leafgl", + "leaflegend", + "leaflet (>= 2.0.2)", + "leafsync", + "methods", + "rlang", + "sf (>= 0.9-3)", + "stars (>= 0.4-2)", + "stats", + "s2", + "tmaptools (>= 3.1)", + "units (>= 0.6-1)", + "servr" + ], + "Suggests": [ + "av", + "colorspace", + "ggplot2", + "gifski", + "knitr", + "maptiles", + "png", + "shiny", + "terra", + "testthat (>= 3.2.0)", + "widgetframe", + "lobstr", + "rstudioapi" + ], + "Config/Needs/check": "Nowosad/spDataLarge, lwgeom", + "Config/Needs/coverage": "Nowosad/spDataLarge, lwgeom", + "Config/Needs/website": "bookdown, geofacet, rmarkdown, mapview, sits, r-spatial/leafem, mapsf, r-tmap/tmap.glyphs, r-tmap/tmap.networks, r-tmap/tmap.deckgl, sfnetworks, r-tmap/tmap.cartogram", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Martijn Tennekes [aut, cre], Jakub Nowosad [ctb], Joel Gombin [ctb], Sebastian Jeworutzki [ctb], Kent Russell [ctb], Richard Zijdeman [ctb], John Clouse [ctb], Robin Lovelace [ctb], Jannes Muenchow [ctb], Olivier Roy [ctb], Edzer Pebesma [ctb], Hugh Graham [ctb], Michael D. Sumner [ctb], Tim Appelhans [ctb], Nick Bearman [ctb]", + "Maintainer": "Martijn Tennekes ", + "Repository": "CRAN" + }, + "tmaptools": { + "Package": "tmaptools", + "Version": "3.2", + "Source": "Repository", + "Type": "Package", + "Title": "Thematic Map Tools", + "Authors@R": "person(\"Martijn\", \"Tennekes\", email = \"mtennekes@gmail.com\", role = c(\"aut\", \"cre\"))", + "Description": "Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.", + "License": "GPL-3", + "Encoding": "UTF-8", + "Date": "2025-01-13", + "Depends": [ + "R (>= 3.5)", + "methods" + ], + "Imports": [ + "sf (>= 0.9.2)", + "lwgeom (>= 0.1-4)", + "stars (>= 0.4-1)", + "units (>= 0.6-1)", + "grid", + "magrittr", + "RColorBrewer", + "viridisLite", + "stats", + "dichromat", + "XML" + ], + "Suggests": [ + "tmap", + "cols4all", + "rmapshaper", + "osmdata", + "OpenStreetMap", + "raster", + "png", + "shiny", + "shinyjs" + ], + "URL": "https://github.com/r-tmap/tmaptools, https://r-tmap.github.io/tmaptools/", + "BugReports": "https://github.com/r-tmap/tmaptools/issues", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Martijn Tennekes [aut, cre]", + "Maintainer": "Martijn Tennekes ", + "Repository": "CRAN" + }, + "twosamples": { + "Package": "twosamples", + "Version": "2.0.1", + "Source": "Repository", + "Type": "Package", + "Title": "Fast Permutation Based Two Sample Tests", + "Authors@R": "person(\"Connor\", \"Dowd\", , \"cd@codowd.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-9782-0931\"))", + "Description": "Fast randomization based two sample tests. Testing the hypothesis that two samples come from the same distribution using randomization to create p-values. Included tests are: Kolmogorov-Smirnov, Kuiper, Cramer-von Mises, Anderson-Darling, Wasserstein, and DTS. The default test (two_sample) is based on the DTS test statistic, as it is the most powerful, and thus most useful to most users. The DTS test statistic builds on the Wasserstein distance by using a weighting scheme like that of Anderson-Darling. See the companion paper at or for details of that test statistic, and non-standard uses of the package (parallel for big N, weighted observations, one sample tests, etc). We also include the permutation scheme to make test building simple for others.", + "License": "GPL (>= 2)", + "Encoding": "UTF-8", + "LinkingTo": [ + "cpp11" + ], + "RoxygenNote": "7.2.3", + "URL": "https://twosampletest.com, https://github.com/cdowd/twosamples", + "BugReports": "https://github.com/cdowd/twosamples/issues", + "Suggests": [ + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Connor Dowd [aut, cre] ()", + "Maintainer": "Connor Dowd ", + "Repository": "CRAN" + }, + "tzdb": { + "Package": "tzdb", + "Version": "0.4.0", + "Source": "Repository", + "Title": "Time Zone Database Information", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Howard\", \"Hinnant\", role = \"cph\", comment = \"Author of the included date library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the 'date' library. 'date' provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. Headers are provided for calendar specific calculations, along with a limited interface for time zone manipulations.", + "License": "MIT + file LICENSE", + "URL": "https://tzdb.r-lib.org, https://github.com/r-lib/tzdb", + "BugReports": "https://github.com/r-lib/tzdb/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.4.2)" + ], + "Biarch": "yes", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Davis Vaughan [aut, cre], Howard Hinnant [cph] (Author of the included date library), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "units": { + "Package": "units", + "Version": "0.8-5", + "Source": "Repository", + "Title": "Measurement Units for R Vectors", + "Authors@R": "c(person(\"Edzer\", \"Pebesma\", role = c(\"aut\", \"cre\"), email = \"edzer.pebesma@uni-muenster.de\", comment = c(ORCID = \"0000-0001-8049-7069\")), person(\"Thomas\", \"Mailund\", role = \"aut\", email = \"mailund@birc.au.dk\"), person(\"Tomasz\", \"Kalinowski\", role = \"aut\"), person(\"James\", \"Hiebert\", role = \"ctb\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", email = \"iucar@fedoraproject.org\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Thomas Lin\", \"Pedersen\", role = \"ctb\") )", + "Depends": [ + "R (>= 3.0.2)" + ], + "Imports": [ + "Rcpp" + ], + "LinkingTo": [ + "Rcpp (>= 0.12.10)" + ], + "Suggests": [ + "NISTunits", + "measurements", + "xml2", + "magrittr", + "pillar (>= 1.3.0)", + "dplyr (>= 1.0.0)", + "vctrs (>= 0.3.1)", + "ggplot2 (> 3.2.1)", + "testthat (>= 3.0.0)", + "vdiffr", + "knitr", + "rmarkdown" + ], + "VignetteBuilder": "knitr", + "Description": "Support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. Compatible with the POSIXct, Date and difftime classes. Uses the UNIDATA udunits library and unit database for unit compatibility checking and conversion. Documentation about 'units' is provided in the paper by Pebesma, Mailund & Hiebert (2016, ), included in this package as a vignette; see 'citation(\"units\")' for details.", + "SystemRequirements": "udunits-2", + "License": "GPL-2", + "URL": "https://r-quantities.github.io/units/, https://github.com/r-quantities/units", + "BugReports": "https://github.com/r-quantities/units/issues", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Edzer Pebesma [aut, cre] (), Thomas Mailund [aut], Tomasz Kalinowski [aut], James Hiebert [ctb], Iñaki Ucar [aut] (), Thomas Lin Pedersen [ctb]", + "Maintainer": "Edzer Pebesma ", + "Repository": "CRAN" + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.4", + "Source": "Repository", + "Title": "Unicode Text Processing", + "Authors@R": "c(person(given = c(\"Patrick\", \"O.\"), family = \"Perry\", role = c(\"aut\", \"cph\")), person(given = \"Kirill\", family = \"M\\u00fcller\", role = \"cre\", email = \"kirill@cynkra.com\"), person(given = \"Unicode, Inc.\", role = c(\"cph\", \"dtc\"), comment = \"Unicode Character Database\"))", + "Description": "Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.", + "License": "Apache License (== 2.0) | file LICENSE", + "URL": "https://ptrckprry.com/r-utf8/, https://github.com/patperry/r-utf8", + "BugReports": "https://github.com/patperry/r-utf8/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "cli", + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr, rmarkdown", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Patrick O. Perry [aut, cph], Kirill Müller [cre], Unicode, Inc. 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The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "ggplot2 (>= 1.0.1)", + "testthat", + "covr" + ], + "URL": "https://sjmgarnier.github.io/viridisLite/, https://github.com/sjmgarnier/viridisLite/", + "BugReports": "https://github.com/sjmgarnier/viridisLite/issues/", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" + }, + "vroom": { + "Package": "vroom", + "Version": "1.6.5", + "Source": "Repository", + "Title": "Read and Write Rectangular Text Data Quickly", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial indexing step, then reads the values lazily , so only the data you actually use needs to be read. The writer formats the data in parallel and writes to disk asynchronously from formatting.", + "License": "MIT + file LICENSE", + "URL": "https://vroom.r-lib.org, https://github.com/tidyverse/vroom", + "BugReports": "https://github.com/tidyverse/vroom/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "bit64", + "cli (>= 3.2.0)", + "crayon", + "glue", + "hms", + "lifecycle (>= 1.0.3)", + "methods", + "rlang (>= 0.4.2)", + "stats", + "tibble (>= 2.0.0)", + "tidyselect", + "tzdb (>= 0.1.1)", + "vctrs (>= 0.2.0)", + "withr" + ], + "Suggests": [ + "archive", + "bench (>= 1.1.0)", + "covr", + "curl", + "dplyr", + "forcats", + "fs", + "ggplot2", + "knitr", + "patchwork", + "prettyunits", + "purrr", + "rmarkdown", + "rstudioapi", + "scales", + "spelling", + "testthat (>= 2.1.0)", + "tidyr", + "utils", + "waldo", + "xml2" + ], + "LinkingTo": [ + "cpp11 (>= 0.2.0)", + "progress (>= 1.2.1)", + "tzdb (>= 0.1.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "nycflights13, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "false", + "Copyright": "file COPYRIGHTS", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3.9000", + "NeedsCompilation": "yes", + "Author": "Jim Hester [aut] (), Hadley Wickham [aut] (), Jennifer Bryan [aut, cre] (), Shelby Bearrows [ctb], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [cph] (grisu3 implementation), Mikkel Jørgensen [cph] (grisu3 implementation), Posit Software, PBC [cph, fnd]", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "warp": { + "Package": "warp", + "Version": "0.2.1", + "Source": "Repository", + "Title": "Group Dates", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Tooling to group dates by a variety of periods including: yearly, monthly, by second, by week of the month, and more. The groups are defined in such a way that they also represent the distance between dates in terms of the period. This extracts valuable information that can be used in further calculations that rely on a specific temporal spacing between observations.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/DavisVaughan/warp, https://davisvaughan.github.io/warp/", + "BugReports": "https://github.com/DavisVaughan/warp/issues", + "Depends": [ + "R (>= 3.2)" + ], + "Suggests": [ + "covr", + "knitr", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Davis Vaughan [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "withr": { + "Package": "withr", + "Version": "3.0.2", + "Source": "Repository", + "Title": "Run Code 'With' Temporarily Modified Global State", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Kirill\", \"Müller\", , \"krlmlr+r@mailbox.org\", role = \"aut\"), person(\"Kevin\", \"Ushey\", , \"kevinushey@gmail.com\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", role = \"aut\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.", + "License": "MIT + file LICENSE", + "URL": "https://withr.r-lib.org, https://github.com/r-lib/withr#readme", + "BugReports": "https://github.com/r-lib/withr/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "graphics", + "grDevices" + ], + "Suggests": [ + "callr", + "DBI", + "knitr", + "methods", + "rlang", + "rmarkdown (>= 2.12)", + "RSQLite", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Collate": "'aaa.R' 'collate.R' 'connection.R' 'db.R' 'defer-exit.R' 'standalone-defer.R' 'defer.R' 'devices.R' 'local_.R' 'with_.R' 'dir.R' 'env.R' 'file.R' 'language.R' 'libpaths.R' 'locale.R' 'makevars.R' 'namespace.R' 'options.R' 'par.R' 'path.R' 'rng.R' 'seed.R' 'wrap.R' 'sink.R' 'tempfile.R' 'timezone.R' 'torture.R' 'utils.R' 'with.R'", + "NeedsCompilation": "no", + "Author": "Jim Hester [aut], Lionel Henry [aut, cre], Kirill Müller [aut], Kevin Ushey [aut], Hadley Wickham [aut], Winston Chang [aut], Jennifer Bryan [ctb], Richard Cotton [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" + }, + "wk": { + "Package": "wk", + "Version": "0.9.4", + "Source": "Repository", + "Title": "Lightweight Well-Known Geometry Parsing", + "Authors@R": "c( person(given = \"Dewey\", family = \"Dunnington\", role = c(\"aut\", \"cre\"), email = \"dewey@fishandwhistle.net\", comment = c(ORCID = \"0000-0002-9415-4582\")), person(given = \"Edzer\", family = \"Pebesma\", role = c(\"aut\"), email = \"edzer.pebesma@uni-muenster.de\", comment = c(ORCID = \"0000-0001-8049-7069\")), person(given = \"Anthony\", family = \"North\", email = \"anthony.jl.north@gmail.com\", role = c(\"ctb\")) )", + "Maintainer": "Dewey Dunnington ", + "Description": "Provides a minimal R and C++ API for parsing well-known binary and well-known text representation of geometries to and from R-native formats. Well-known binary is compact and fast to parse; well-known text is human-readable and is useful for writing tests. These formats are useful in R only if the information they contain can be accessed in R, for which high-performance functions are provided here.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "Suggests": [ + "testthat (>= 3.0.0)", + "vctrs (>= 0.3.0)", + "sf", + "tibble", + "readr" + ], + "URL": "https://paleolimbot.github.io/wk/, https://github.com/paleolimbot/wk", + "BugReports": "https://github.com/paleolimbot/wk/issues", + "Config/testthat/edition": "3", + "Depends": [ + "R (>= 2.10)" + ], + "LazyData": "true", + "NeedsCompilation": "yes", + "Author": "Dewey Dunnington [aut, cre] (), Edzer Pebesma [aut] (), Anthony North [ctb]", + "Repository": "CRAN" + }, + "xfun": { + "Package": "xfun", + "Version": "0.52", + "Source": "Repository", + "Type": "Package", + "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\", URL = \"https://yihui.org\")), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Daijiang\", \"Li\", role = \"ctb\"), person(\"Xianying\", \"Tan\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", role = \"ctb\", email = \"salim-b@pm.me\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person() )", + "Description": "Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ + "grDevices", + "stats", + "tools" + ], + "Suggests": [ + "testit", + "parallel", + "codetools", + "methods", + "rstudioapi", + "tinytex (>= 0.30)", + "mime", + "litedown (>= 0.4)", + "commonmark", + "knitr (>= 1.50)", + "remotes", + "pak", + "curl", + "xml2", + "jsonlite", + "magick", + "yaml", + "qs" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/yihui/xfun", + "BugReports": "https://github.com/yihui/xfun/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "litedown", + "NeedsCompilation": "yes", + "Author": "Yihui Xie [aut, cre, cph] (, https://yihui.org), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (), Christophe Dervieux [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "xml2": { + "Package": "xml2", + "Version": "1.3.6", + "Source": "Repository", + "Title": "Parse XML", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Jeroen\", \"Ooms\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"R Foundation\", role = \"ctb\", comment = \"Copy of R-project homepage cached as example\") )", + "Description": "Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.", + "License": "MIT + file LICENSE", + "URL": "https://xml2.r-lib.org/, https://github.com/r-lib/xml2", + "BugReports": "https://github.com/r-lib/xml2/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "cli", + "methods", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "covr", + "curl", + "httr", + "knitr", + "magrittr", + "mockery", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "libxml2: libxml2-dev (deb), libxml2-devel (rpm)", + "Collate": "'S4.R' 'as_list.R' 'xml_parse.R' 'as_xml_document.R' 'classes.R' 'format.R' 'import-standalone-obj-type.R' 'import-standalone-purrr.R' 'import-standalone-types-check.R' 'init.R' 'nodeset_apply.R' 'paths.R' 'utils.R' 'xml2-package.R' 'xml_attr.R' 'xml_children.R' 'xml_document.R' 'xml_find.R' 'xml_missing.R' 'xml_modify.R' 'xml_name.R' 'xml_namespaces.R' 'xml_node.R' 'xml_nodeset.R' 'xml_path.R' 'xml_schema.R' 'xml_serialize.R' 'xml_structure.R' 'xml_text.R' 'xml_type.R' 'xml_url.R' 'xml_write.R' 'zzz.R'", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], Jim Hester [aut], Jeroen Ooms [aut], Posit Software, PBC [cph, fnd], R Foundation [ctb] (Copy of R-project homepage cached as example)", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Date": "2019-04-08", + "Title": "Export Tables to LaTeX or HTML", + "Authors@R": "c(person(\"David B.\", \"Dahl\", role=\"aut\"), person(\"David\", \"Scott\", role=c(\"aut\",\"cre\"), email=\"d.scott@auckland.ac.nz\"), person(\"Charles\", \"Roosen\", role=\"aut\"), person(\"Arni\", \"Magnusson\", role=\"aut\"), person(\"Jonathan\", \"Swinton\", role=\"aut\"), person(\"Ajay\", \"Shah\", role=\"ctb\"), person(\"Arne\", \"Henningsen\", role=\"ctb\"), person(\"Benno\", \"Puetz\", role=\"ctb\"), person(\"Bernhard\", \"Pfaff\", role=\"ctb\"), person(\"Claudio\", \"Agostinelli\", role=\"ctb\"), person(\"Claudius\", \"Loehnert\", role=\"ctb\"), person(\"David\", \"Mitchell\", role=\"ctb\"), person(\"David\", \"Whiting\", role=\"ctb\"), person(\"Fernando da\", \"Rosa\", role=\"ctb\"), person(\"Guido\", \"Gay\", role=\"ctb\"), person(\"Guido\", \"Schulz\", role=\"ctb\"), person(\"Ian\", \"Fellows\", role=\"ctb\"), person(\"Jeff\", \"Laake\", role=\"ctb\"), person(\"John\", \"Walker\", role=\"ctb\"), person(\"Jun\", \"Yan\", role=\"ctb\"), person(\"Liviu\", \"Andronic\", role=\"ctb\"), person(\"Markus\", \"Loecher\", role=\"ctb\"), person(\"Martin\", \"Gubri\", role=\"ctb\"), person(\"Matthieu\", \"Stigler\", role=\"ctb\"), person(\"Robert\", \"Castelo\", role=\"ctb\"), person(\"Seth\", \"Falcon\", role=\"ctb\"), person(\"Stefan\", \"Edwards\", role=\"ctb\"), person(\"Sven\", \"Garbade\", role=\"ctb\"), person(\"Uwe\", \"Ligges\", role=\"ctb\"))", + "Maintainer": "David Scott ", + "Imports": [ + "stats", + "utils" + ], + "Suggests": [ + "knitr", + "plm", + "zoo", + "survival" + ], + "VignetteBuilder": "knitr", + "Description": "Coerce data to LaTeX and HTML tables.", + "URL": "http://xtable.r-forge.r-project.org/", + "Depends": [ + "R (>= 2.10.0)" + ], + "License": "GPL (>= 2)", + "Repository": "CRAN", + "NeedsCompilation": "no", + "Author": "David B. Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.10", + "Source": "Repository", + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Date": "2024-07-22", + "Suggests": [ + "RUnit" + ], + "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]", + "Maintainer": "Shawn Garbett ", + "License": "BSD_3_clause + file LICENSE", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "URL": "https://github.com/vubiostat/r-yaml/", + "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, + "zoo": { + "Package": "zoo", + "Version": "1.8-13", + "Source": "Repository", + "Date": "2025-02-20", + "Title": "S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)", + "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Gabor\", family = \"Grothendieck\", role = \"aut\", email = \"ggrothendieck@gmail.com\"), person(given = c(\"Jeffrey\", \"A.\"), family = \"Ryan\", role = \"aut\", email = \"jeff.a.ryan@gmail.com\"), person(given = c(\"Joshua\", \"M.\"), family = \"Ulrich\", role = \"ctb\", email = \"josh.m.ulrich@gmail.com\"), person(given = \"Felix\", family = \"Andrews\", role = \"ctb\", email = \"felix@nfrac.org\"))", + "Description": "An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.", + "Depends": [ + "R (>= 3.1.0)", + "stats" + ], + "Suggests": [ + "AER", + "coda", + "chron", + "ggplot2 (>= 3.0.0)", + "mondate", + "scales", + "stinepack", + "strucchange", + "timeDate", + "timeSeries", + "tinyplot", + "tis", + "tseries", + "xts" + ], + "Imports": [ + "utils", + "graphics", + "grDevices", + "lattice (>= 0.20-27)" + ], + "License": "GPL-2 | GPL-3", + "URL": "https://zoo.R-Forge.R-project.org/", + "NeedsCompilation": "yes", + "Author": "Achim Zeileis [aut, cre] (), Gabor Grothendieck [aut], Jeffrey A. Ryan [aut], Joshua M. Ulrich [ctb], Felix Andrews [ctb]", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" + } + } +} diff --git a/renv/.gitignore b/renv/.gitignore new file mode 100644 index 0000000..0ec0cbb --- /dev/null +++ b/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/activate.R b/renv/activate.R new file mode 100644 index 0000000..90b251c --- /dev/null +++ b/renv/activate.R @@ -0,0 +1,1334 @@ + +local({ + + # the requested version of renv + version <- "1.1.4" + attr(version, "sha") <- NULL + + # the project directory + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + + # next, check environment variables + # prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + + return(FALSE) + + } + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + ansify <- function(text) { + if (renv_ansify_enabled()) + renv_ansify_enhanced(text) + else + renv_ansify_default(text) + } + + renv_ansify_enabled <- function() { + + override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA) + if (!is.na(override)) + return(as.logical(override)) + + pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA) + if (identical(pane, "build")) + return(FALSE) + + testthat <- Sys.getenv("TESTTHAT", unset = "false") + if (tolower(testthat) %in% "true") + return(FALSE) + + iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false") + if (tolower(iderun) %in% "false") + return(FALSE) + + TRUE + + } + + renv_ansify_default <- function(text) { + text + } + + renv_ansify_enhanced <- function(text) { + + # R help links + pattern <- "`\\?(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-run:\\1\a\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # return ansified text + text + + } + + renv_ansify_init <- function() { + + envir <- renv_envir_self() + if (renv_ansify_enabled()) + assign("ansify", renv_ansify_enhanced, envir = envir) + else + assign("ansify", renv_ansify_default, envir = envir) + + } + + `%||%` <- function(x, y) { + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + text <- paste(substring(lines, common), collapse = "\n") + + # substitute in ANSI links for executable renv code + ansify(text) + + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # attempt to download renv + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) + + # now attempt to install + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + + return(invisible()) + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + + return(repos) + + } + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # build arguments for utils::available.packages() call + args <- list(type = type, repos = repos) + + # add custom headers if available -- note that + # utils::available.packages() will pass this to download.file() + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(repos) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + # retrieve package database + db <- tryCatch( + as.data.frame( + do.call(utils::available.packages, args), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_github_token <- function() { + for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(envval) + } + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + token <- renv_bootstrap_github_token() + if (is.null(token)) + token <- "" + + if (nzchar(Sys.which("curl")) && nzchar(token)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + renv_bootstrap_download_augment(destfile) + + return(destfile) + + } + + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + R <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix_default <- function() { + + # read version component + version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v") + + # expand placeholders + placeholders <- list( + list("%v", format(getRversion()[1, 1:2])), + list("%V", format(getRversion()[1, 1:3])) + ) + + for (placeholder in placeholders) + version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE) + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + version <- paste(version, R.version[["svn rev"]], sep = "-r") + + version + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- renv_bootstrap_platform_prefix_default() + + # build list of path components + components <- c(version, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + else + paste("renv", description[["Version"]], sep = "@") + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] + ) + + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + + expected <- description[["RemoteSha"]] + if (!is.character(expected)) + return(FALSE) + + pattern <- sprintf("^\\Q%s\\E", version) + grepl(pattern, expected, perl = TRUE) + + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(project, libpath, version) + } + + renv_bootstrap_run <- function(project, libpath, version) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = project)) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + renv_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_patterns <- function() { + + list( + + # objects + list("{", "\t\n\tobject(\t\n\t", TRUE), + list("}", "\t\n\t)\t\n\t", TRUE), + + # arrays + list("[", "\t\n\tarray(\t\n\t", TRUE), + list("]", "\n\t\n)\n\t\n", TRUE), + + # maps + list(":", "\t\n\t=\t\n\t", TRUE), + + # newlines + list("\\u000a", "\n", FALSE) + + ) + + } + + renv_json_read_envir <- function() { + + envir <- new.env(parent = emptyenv()) + + envir[["+"]] <- `+` + envir[["-"]] <- `-` + + envir[["object"]] <- function(...) { + result <- list(...) + names(result) <- as.character(names(result)) + result + } + + envir[["array"]] <- list + + envir[["true"]] <- TRUE + envir[["false"]] <- FALSE + envir[["null"]] <- NULL + + envir + + } + + renv_json_read_remap <- function(object, patterns) { + + # repair names if necessary + if (!is.null(names(object))) { + + nms <- names(object) + for (pattern in patterns) + nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE) + names(object) <- nms + + } + + # repair strings if necessary + if (is.character(object)) { + for (pattern in patterns) + object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE) + } + + # recurse for other objects + if (is.recursive(object)) + for (i in seq_along(object)) + object[i] <- list(renv_json_read_remap(object[[i]], patterns)) + + # return remapped object + object + + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # read json text + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + + # convert into something the R parser will understand + patterns <- renv_json_read_patterns() + transformed <- text + for (pattern in patterns) + transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE) + + # parse it + rfile <- tempfile("renv-json-", fileext = ".R") + on.exit(unlink(rfile), add = TRUE) + writeLines(transformed, con = rfile) + json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]] + + # evaluate in safe environment + result <- eval(json, envir = renv_json_read_envir()) + + # fix up strings if necessary -- do so only with reversible patterns + patterns <- Filter(function(pattern) pattern[[3L]], patterns) + renv_json_read_remap(result, patterns) + + } + + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/renv/settings.json b/renv/settings.json new file mode 100644 index 0000000..ffdbb32 --- /dev/null +++ b/renv/settings.json @@ -0,0 +1,19 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +}