working rmd file, removed renv because it messed up my R and could not get it to work

.Rprofile

@@ -1 +0,0 @@
-source("renv/activate.R")

r_app/2_CI_data_prep.R

@@ -1,7 +1,7 @@
 # activeer de renv omgeving;
 
-renv::activate('~/smartCane/r_app')
-renv::restore()
+# renv::activate('~/smartCane/r_app')
+# renv::restore()
 
 
 

r_app/CI_report_dashboard_planet.Rmd

@@ -2,7 +2,7 @@
 params:
   ref: "word-styles-reference-var1.docx"
   output_file: CI_report.docx
-  report_date: "2023-12-12"
+  report_date: "2024-04-18"
   data_dir: "chemba"
 output:
  # html_document:
@@ -23,8 +23,8 @@ report_date <- params$report_date
 # 
 # 
 # # Activeer de renv omgeving
-renv::activate()
-
+# 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()
@@ -140,8 +140,8 @@ AllPivots <- merge(AllPivots0, harvesting_data, by = c("Field", "subField")) #%>
 #rename(Field = pivot, subField = pivot_quadrant) #%>% select(-pivot.y)
 head(AllPivots)
 
-AllPivots_merged <- AllPivots %>% 
-   group_by(Field) #%>% summarise(sub_area = first(sub_area))
+AllPivots_merged <- AllPivots %>% #dplyr::select(Field, subField, sub_area) %>% unique() %>%
+   group_by(Field) %>% summarise(sub_area = first(sub_area))
 
 AllPivots_merged <- st_transform(AllPivots_merged, crs = proj4string(CI))
 
@@ -313,7 +313,7 @@ cum_ci_plot <- function(pivotName){
 
   g <- ggplot(data= data_ci2 %>% filter(season %in% unique_seasons)) +
        #   facet_wrap(~Year, scales = "free_x") +
-          geom_line( aes(Date, mean_rolling10, col = Field)) +
+          geom_line( aes(Date, mean_rolling10, col = subField)) +
           # geom_line(data= perfect_pivot, aes(Date , mean_rolling10, col = "Model CI (p5.1 Data 2022, \n date x axis is fictive)"), lty="11",size=1) +
           labs(title = paste("14 day rolling MEAN CI rate - Pivot ", pivotName))+
           # scale_y_continuous(limits=c(0.5,3), breaks = seq(0.5, 3, 0.5))+
@@ -400,13 +400,13 @@ pivots_grouped <- AllPivots_merged %>%
 # Iterate over each subgroup
 for (subgroup in unique(pivots_grouped$sub_area)) {
   cat("\n")
-  cat("\n # Subgroup: ", subgroup, "\n")  # Add a title for the subgroup
+  cat("# Subgroup: ", subgroup, "\n")  # Add a title for the subgroup
   subset_data <- filter(pivots_grouped, sub_area == subgroup)
-  cat("\n")
-  walk(AllPivots_merged$Field, ~ {
+  cat('\\pagebreak')
+  walk(subset_data$Field, ~ {
     cat("\n")  # Add an empty line for better spacing
     ci_plot(.x)
-    cat("\n") 
+    cat("\n")
     cum_ci_plot(.x)
     cat("\n")
   })