diff --git a/r_app/.gitignore b/r_app/.gitignore
index eac6522..c5916ee 100644
--- a/r_app/.gitignore
+++ b/r_app/.gitignore
@@ -16,4 +16,5 @@ renv
.Rprofile
# Ignore OSX files
.DS_Store
+CI_report_dashboard_planet_files
diff --git a/r_app/2_CI_data_prep.R b/r_app/2_CI_data_prep.R
index 1706267..dc320f4 100644
--- a/r_app/2_CI_data_prep.R
+++ b/r_app/2_CI_data_prep.R
@@ -11,7 +11,6 @@ library(lubridate)
library(exactextractr)
library(CIprep)
-source(here("r_app", "parameters_project.R"))
# Vang alle command line argumenten op
args <- commandArgs(trailingOnly = TRUE)
@@ -57,6 +56,8 @@ weekly_CI_mosaic <- here(laravel_storage_dir, "weekly_mosaic")
daily_vrt <- here(data_dir, "vrt")
harvest_dir <- here(data_dir, "HarvestData")
+source(here("r_app", "parameters_project.R"))
+
dir.create(here(laravel_storage_dir))
dir.create(here(data_dir))
dir.create(here(extracted_CI_dir))
@@ -134,6 +135,12 @@ create_mask_and_crop <- function(file, field_boundaries) {
vrt_list <- list()
+# for (file in raster_files) {
+# v_crop <- create_mask_and_crop(file, field_boundaries)
+# message(file, " processed")
+# gc()
+# }
+
for (file in filtered_files) {
v_crop <- create_mask_and_crop(file, field_boundaries)
emtpy_or_full <- global(v_crop, "notNA")
@@ -271,14 +278,14 @@ if (new_project_question == TRUE) {
pivot_stats <- extracted_values %>%
map(readRDS) %>% list_rbind() %>%
- group_by(pivot_quadrant) %>%
+ group_by(subField) %>%
summarise(across(everything(), ~ first(na.omit(.))))
saveRDS(pivot_stats, here(cumulative_CI_vals_dir,"combined_CI_data.rds")) #used to save the rest of the data into one file
pivot_stats2 <- pivot_stats
- print("All CI values extracted from allhistoric images")
+ print("All CI values extracted from all historic images")
} else {
print("combined_CI_data.rds exists, adding the latest image data to the table.")
@@ -309,15 +316,15 @@ if (new_project_question == TRUE) {
# gather data into long format for easier calculation and visualisation
pivot_stats_long <- pivot_stats2 %>%
- tidyr::gather("Date", value, -pivot_quadrant, -pivot ) %>%
+ tidyr::gather("Date", value, -Field, -subField, -sub_area ) %>%
mutate(Date = right(Date, 8),
Date = lubridate::ymd(Date)
) %>%
drop_na(c("value","Date")) %>%
mutate(value = as.numeric(value))%>%
filter_all(all_vars(!is.infinite(.))) %>%
- rename(Field = pivot_quadrant,
- subField = Field) %>%
+ # rename(Field = pivot_quadrant,
+ # subField = Field) %>%
unique()
diff --git a/r_app/CI_Report_dashboard_planet.html b/r_app/CI_Report_dashboard_planet.html
index 3ab3f97..f90065a 100644
--- a/r_app/CI_Report_dashboard_planet.html
+++ b/r_app/CI_Report_dashboard_planet.html
@@ -11,7 +11,7 @@
-CI dashboard week 40 - all pivots dashboard using 3x3 meter resolution
+CI_report_dashboard_planet.knit
+
+