wip

build_mosaic.sh

@@ -33,7 +33,7 @@ if [ -z "$end_date" ] || [ -z "$data_dir" ] || [ -z "$offset" ]; then
     exit 1
 fi
 
-echo 2_CI_data_prep.R $end_date $offset $data_dir
+echo mosaic_creation.R $end_date $offset $data_dir
 
 cd ../r_app
-Rscript 2_CI_data_prep.R $end_date $offset $data_dir
+Rscript mosaic_creation.R $end_date $offset $data_dir

build_report.sh

@@ -6,9 +6,6 @@ for arg in "$@"; do
         --filename=*)
             filename="${arg#*=}"
             ;;
-        --weeks_ago=*)
-            weeks_ago="${arg#*=}"
-            ;;
         --report_date=*)
             report_date="${arg#*=}"
             ;;
@@ -23,14 +20,13 @@ for arg in "$@"; do
 done
 
 # Check if required arguments are set
-if [ -z "$filename" ] || [ -z "$weeks_ago" ] || [ -z "$report_date" ] || [ -z "$data_dir" ]; then
+if [ -z "$filename" ] || [ -z "$report_date" ] || [ -z "$data_dir" ]; then
-    echo "Missing arguments. Use: build_reports.sh --filename=hello.txt --weeks_ago=3 --report_date=2020-01-01 --data_dir=chemba"
+    echo "Missing arguments. Use: build_reports.sh --filename=hello.txt --report_date=2020-01-01 --data_dir=chemba"
     exit 1
 fi
 
 # Script logic here
 echo "Filename: $filename"
-echo "Weeks ago: $weeks_ago"
 echo "Report date: $report_date"
 echo "Data directory: $data_dir"
 

laravel_app/app/Jobs/ProjectInterpolateGrowthModelJob.php

@@ -31,7 +31,7 @@ public function __construct(Project $project)
     public function handle(): void
     {
         $command = [
-            sprintf('%interpolate_growth_model.sh', base_path('../')),
+            sprintf('%s/interpolate_growth_model.sh', base_path('../')),
             sprintf('--project_dir=%s', $this->project->download_path),
         ];
 

laravel_app/app/Jobs/ProjectMosiacGeneratorJob.php

@@ -80,6 +80,10 @@ public static function handleFor(Project $project,Carbon $endDate, int $offset):
             logger("ProjecMosaicGeneratorJob::handleFor(end_date: $endDate, offset: $offset): InvalidMosaic.");
             return new NullJob();
         }
+
+        $week = $endDate->clone()->next($project->mail_day)->week;
+        $year = $endDate->clone()->next($project->mail_day)->year;
+
         /**
          * @var ProjectMosaic $mosaic
          */
@@ -89,11 +93,11 @@ public static function handleFor(Project $project,Carbon $endDate, int $offset):
                 'offset' => $offset,
             ],
             [
-                'name'   => sprintf('Period %s - %s', $endDate->format('Y-m-d'), $endDate->copy()->subDays($offset)->format('Y-m-d')),
+                'name'   => sprintf('Week_%s_%s', $week, $year),
                 'path'   => sprintf('%s/%s/%s',
                     $project->download_path,
                     'mosaics',
-                    ProjectMosaic::getFilenameByPeriod($endDate,$offset)
+                    sprintf('week_%s_%s.tif', $week, $year)
                 ),
                 'end_date' => $endDate->format('Y-m-d'),
                 'offset' => $offset,

laravel_app/app/Jobs/ProjectReportGeneratorJob.php

@@ -36,14 +36,11 @@ public function __construct(ProjectReport $projectReport, $sendMail = false)
     public function handle()
     {
         // TODO check the changements due to migration
-        //$this->projectReport->weeksAgo();
-
         $projectFolder = base_path('../');
 
         $command = [
             sprintf('%sbuild_report.sh', $projectFolder),
             sprintf('--filename=%s', $this->projectReport->getFullPathName()),
-            sprintf('--weeks_ago=%s', $this->projectReport->weeksAgo()),
             sprintf('--report_date=%s', $this->projectReport->getReportDate()),
             sprintf('--data_dir=%s', $this->projectReport->project->download_path),
         ];

laravel_app/app/Models/Project.php

@@ -281,7 +281,7 @@ public function hasInvalidMosaicFor(Carbon $endDate,int $offset): bool
         // parameters : $
         // check if the mail day happens the day before mosaic -> good
         $dayOfWeekIso = Carbon::parse($this->mail_day)->dayOfWeekIso;
-        $min_updated_at_date = $endDate
+        $min_updated_at_date = $endDate->copy()
             ->startOfWeek()
             ->addDays($dayOfWeekIso - 1)
             ->format('Y-m-d');
@@ -296,7 +296,7 @@ public function hasInvalidMosaicFor(Carbon $endDate,int $offset): bool
 
     public function scheduleReport(?Carbon $endDate = null, ?int $offset = null)
     {
-        if($endDate->isFuture() || $endDate->isToday() || $offset <= 0){
+        if($endDate?->isFuture() || $endDate?->isToday() || $offset <= 0){
             logger('EndDate is today or in the future.');
             $endDate = null;
             $offset = null;

laravel_app/app/Models/ProjectMosaic.php

@@ -27,14 +27,17 @@ class ProjectMosaic extends Model
     ];
 
 
-    public static function getFilenameByPeriod(Carbon $endDate,int $offset)
+    public static function getFilenameByPeriod(Carbon $endDate, int $offset)
     {
-        return sprintf('period_%s_%s.tif',(clone $endDate)->subdays($offset)->format('Y-m-d'),$endDate->format('Y-m-d'));
+        return sprintf('week_%s_%s.tif', (clone $endDate)->subdays($offset)->week, $endDate->year);
     }
 
-    public static function projectMosaicNameFormat(Carbon $endDate,int $offset):string
+    public static function projectMosaicNameFormat(Carbon $endDate, int $offset): string
     {
-        return 'Period '.$endDate->copy()->subDays($offset)->toDateString().' - '.$endDate->toDateString();
+        return sprintf('Week_%s_%s',
+            $endDate->clone()->subDays($offset)->week,
+            $endDate->clone()->subDays($offset)->year
+        );
     }
 
     public function project()

laravel_app/tests/Unit/Models/ProjectTest.php

@@ -159,13 +159,13 @@ public function when_getFileDownloadsFor_is_called_it_returns_a_collection_of_se
             'download_path' => 'project_download_path',
         ]);
 
-        $downloads = $project->getFileDownloadsFor(new Carbon('2024-06-18'),7);
+        $downloads = $project->getFileDownloadsFor(new Carbon('2024-06-18'), 7);
         $this->assertCount(28, $downloads);
         collect($downloads)->each(fn($job) => $this->assertInstanceOf(ProjectDownloadTiffJob::class, $job));
     }
 
     /** @test */
-    public function when_getMosaicsFor_is_called_it_returns_a_collection_of_seven_downloads_jobs()
+    public function when_getMosaicsFor_is_called_it_returns_a_collection_of_4_jobs()
     {
         /* @var Project $project */
         $project = Project::create([
@@ -178,10 +178,60 @@ public function when_getMosaicsFor_is_called_it_returns_a_collection_of_seven_do
         collect($mosaics)->each(fn($job) => $this->assertInstanceOf(ProjectMosiacGeneratorJob::class, $job));
     }
 
+    /** @test */
+    public function when_getMosaicsFor_is_called_it_returns_a_collection_of_4_jobs_with_correct_week_numbers()
+    {
+        /* @var Project $project */
+        $project = Project::create([
+            'name'          => 'project_name',
+            'download_path' => 'project_download_path',
+            'mail_day'      => 'Friday',
+        ]);
+
+        $mosaics = $project->getMosaicsFor(new Carbon('2024-07-02'));
+        $this->assertCount(4, $mosaics);
+        collect($mosaics)->each(fn($job) => $this->assertInstanceOf(ProjectMosiacGeneratorJob::class, $job));
+
+        $this->assertEquals([
+            "Week_27_2024",
+            "Week_26_2024",
+            "Week_25_2024",
+            "Week_24_2024",
+        ],
+            collect($mosaics)->map(function ($job) {
+                return $job->mosaic->name;
+            })->toArray());
+    }
+
+    /** @test */
+    public function when_getMosaicsFor_is_called_it_returns_a_collection_of_4_jobs_with_where_current_day_is_in_week_26_but_the_mail_day_is_in_week_27()
+    {
+        /* @var Project $project */
+        $project = Project::create([
+            'name'          => 'project_name',
+            'download_path' => 'project_download_path',
+            'mail_day'      => 'Friday',
+        ]);
+
+        $mosaics = $project->getMosaicsFor(new Carbon('2024-06-28'));
+        $this->assertCount(4, $mosaics);
+        collect($mosaics)->each(fn($job) => $this->assertInstanceOf(ProjectMosiacGeneratorJob::class, $job));
+
+        $this->assertEquals([
+            "Week_27_2024",
+            "Week_26_2024",
+            "Week_25_2024",
+            "Week_24_2024",
+        ],
+            collect($mosaics)->map(function ($job) {
+                return $job->mosaic->name;
+            })->toArray());
+    }
+
     /** @test */
     public function when_getReport_is_called_it_returns_a_jobs()
     {
-        /* @var Project $project*/
+        /* @var Project $project */
         $project = Project::create([
             'name'          => 'project_name',
             'download_path' => 'project_download_path',
@@ -195,14 +245,14 @@ public function when_getReport_is_called_it_returns_a_jobs()
     /** @test */
     public function it_can_create_a_chain_of_batches_that_result_in_a_report()
     {
-        /* @var Project $project*/
+        /* @var Project $project */
         $project = Project::create([
             'name'          => 'project_name',
             'download_path' => 'project_download_path',
         ]);
 
         Bus::fake();
-        $project->scheduleReport(new Carbon('2023-01-01'),7);
+        $project->scheduleReport(new Carbon('2023-01-01'), 7);
         Bus::assertChained([
             Bus::chainedBatch(function (PendingBatch $batch) {
                 $batch;
@@ -228,14 +278,15 @@ public function when_friday_and_first_week_it_should_schedule($date, $day, $resu
         Carbon::setTestNow(Carbon::parse($day));
         $project = Project::factory()->create([
             'mail_frequency' => 'weekly',
-            'mail_day' => 'Friday',
+            'mail_day'       => 'Friday',
         ]);
 
         $this->assertEquals($result, $project->shouldSchedule());
     }
 
-    public static function scheduleDayProvider(){
+    public static function scheduleDayProvider()
-        return  [
+    {
+        return [
             ['date' => '2024-03-01', 'day' => 'Friday', 'result' => true],
             ['date' => '2024-03-02', 'day' => 'Saturday', 'result' => false],
             ['date' => '2024-03-03', 'day' => 'Sunday', 'result' => false],

r_app/CI_report_dashboard_planet.Rmd

@@ -3,7 +3,7 @@ params:
   ref: "word-styles-reference-var1.docx"
   output_file: CI_report.docx
   report_date: "2024-04-18"
-  data_dir: "chemba"
+  data_dir: "Sony"
 output:
  # html_document:
  #   toc: yes
@@ -70,10 +70,10 @@ source(here("r_app", "parameters_project.R"))
 
 
 ```{r week, message=FALSE, warning=FALSE, include=FALSE}
-# week <- 5
-#today = "2023-12-12"
 today <- as.character(report_date)
 week <- week(today)
+ week <- 25
+today = "2024-06-21"
 
 
 #today = as.character(Sys.Date())
@@ -115,7 +115,7 @@ This PDF-dashboard shows the status of your fields on a weekly basis. We will sh
 
 # remove_pivots <- c("1.1", "1.12", "1.8", "1.9", "1.11", "1.14")
 CI_quadrant <- readRDS(here(cumulative_CI_vals_dir,"All_pivots_Cumulative_CI_quadrant_year_v2.rds"))# %>%
- # rename(pivot_quadrant = Field)
+ # rename(pivot_quadrant = field)
 
 CI    <- brick(here(weekly_CI_mosaic, paste0("week_",week, "_", year, ".tif"))) %>% subset("CI")
 CI_m1 <- brick(here(weekly_CI_mosaic, paste0("week_",week_minus_1, "_", year_1, ".tif"))) %>% subset("CI")
@@ -140,16 +140,16 @@ AllPivots0 <- field_boundaries_sf
 # pivots_dates <- readRDS(here(harvest_dir, "harvest_data_new"))
 # pivots_dates$pivot  <- factor(pivots_dates$pivot, levels = c("1.1", "1.2", "1.3", "1.4", "1.6", "1.7", "1.8", "1.9", "1.10", "1.11", "1.12", "1.13", "1.14" , "1.16" , "1.17" , "1.18" ,"2.1", "2.2", "2.3" , "2.4", "2.5", "3.1", "3.2", "3.3", "4.1", "4.2", "4.3", "4.4", "4.5", "4.6", "5.1" ,"5.2", "5.3", "5.4", "6.1", "6.2", "DL1.1", "DL1.3"))
 
-AllPivots <- merge(AllPivots0, harvesting_data, by = c("Field", "subField")) #%>%
+#AllPivots <- merge(AllPivots0, harvesting_data, by = c("field", "sub_field")) #%>%
-#rename(Field = pivot, subField = pivot_quadrant) #%>% select(-pivot.y)
+#rename(field = pivot, sub_field = pivot_quadrant) #%>% select(-pivot.y)
-head(AllPivots)
+#head(AllPivots)
 
-AllPivots_merged <- AllPivots %>% #dplyr::select(Field, subField, sub_area) %>% unique() %>%
+#AllPivots_merged <- AllPivots %>% #dplyr::select(field, sub_field, sub_area) %>% unique() %>%
-   group_by(Field) %>% summarise(sub_area = first(sub_area))
+#   group_by(field) %>% summarise(sub_area = first(sub_area))
 
-AllPivots_merged <- st_transform(AllPivots_merged, crs = proj4string(CI))
+#AllPivots_merged <- st_transform(AllPivots_merged, crs = proj4string(CI))
 
-pivot_names <- unique(CI_quadrant$Field)
+#pivot_names <- unique(CI_quadrant$field)
 
 ```
 
@@ -220,7 +220,7 @@ create_CI_map <- function(pivot_raster, pivot_shape, pivot_spans, show_legend =
   tm_layout(main.title = paste0("\nMax CI week ", week,"\n",  age, " weeks old"),
             main.title.size = 0.7, legend.show = show_legend) +
   tm_shape(pivot_shape) +
-  tm_borders(lwd = 3) +  tm_text("subField", size = 1/2) +
+  tm_borders(lwd = 3) +  tm_text("sub_field", size = 1/2) +
   tm_shape(pivot_spans) + tm_borders(lwd = 0.5, alpha=0.5)
 }
 
@@ -230,16 +230,16 @@ create_CI_diff_map <- function(pivot_raster, pivot_shape, pivot_spans, show_lege
   tm_layout(main.title =  paste0("CI change week ", week_1, "- week ",week_2, "\n", age," weeks old"),
             main.title.size = 0.7, legend.show = show_legend) +
   tm_shape(pivot_shape) +
-  tm_borders(lwd = 3) +  tm_text("subField", size = 1/2) +
+  tm_borders(lwd = 3) +  tm_text("sub_field", size = 1/2) +
   tm_shape(pivot_spans) + tm_borders(lwd = 0.5, alpha=0.5)
 }
 
 ci_plot <- function(pivotName){
    # pivotName = "1.1"
-   pivotShape <- AllPivots_merged %>% terra::subset(Field %in% pivotName)  %>% st_transform(crs(CI))
+   pivotShape <- AllPivots0 %>% terra::subset(field %in% pivotName)  %>% st_transform(crs(CI))
-   age <- AllPivots %>% dplyr::filter(Field %in% pivotName) %>% st_drop_geometry() %>% dplyr::select(Age) %>% unique()
+   age <- harvesting_data %>% dplyr::filter(field %in% pivotName) %>% dplyr::select(age) %>% unique()
 
-   AllPivots2 <- AllPivots %>% dplyr::filter(Field %in% pivotName)
+   AllPivots2 <- AllPivots0 %>% dplyr::filter(field %in% pivotName)
 
    singlePivot <- CI %>% crop(., pivotShape) %>% mask(., pivotShape)
 
@@ -250,9 +250,9 @@ ci_plot <- function(pivotName){
    abs_CI_last_week <- last_week_dif_raster_abs %>% crop(., pivotShape) %>% mask(., pivotShape)
    abs_CI_three_week <- three_week_dif_raster_abs %>% crop(., pivotShape) %>% mask(., pivotShape)
 
-   planting_date <- harvesting_data %>% dplyr::filter(Field %in% pivotName) %>% ungroup()  %>% dplyr::select(Season_start)  %>% unique()
+   planting_date <- harvesting_data %>% dplyr::filter(field %in% pivotName) %>% ungroup()  %>% dplyr::select(season_start)  %>% unique()
 
-   joined_spans2 <- joined_spans %>% st_transform(crs(pivotShape))  %>%  dplyr::filter(Field %in% pivotName) #%>% unique() %>% st_crop(., pivotShape)
+   joined_spans2 <- AllPivots0 %>% st_transform(crs(pivotShape))  %>%  dplyr::filter(field %in% pivotName) #%>% unique() %>% st_crop(., pivotShape)
 
    CImap_m2 <- create_CI_map(singlePivot_m2, AllPivots2,  joined_spans2, show_legend= T, legend_is_portrait = T, week = week_minus_2, age = age  -2)
    CImap_m1 <- create_CI_map(singlePivot_m1, AllPivots2,  joined_spans2, show_legend= F, legend_is_portrait = F, week = week_minus_1, age = age  -1)
@@ -264,7 +264,7 @@ ci_plot <- function(pivotName){
 
    tst <- tmap_arrange(CImap_m2, CImap_m1, CImap,CI_max_abs_last_week, CI_max_abs_three_week, nrow = 1)
 
-   cat(paste("## Pivot", pivotName, "-", age$Age[1], "weeks after planting/harvest", "\n"))
+   cat(paste("## Pivot", pivotName, "-", age, "weeks after planting/harvest", "\n"))
    # cat("\n")
    # cat('<h2> Pivot', pivotName, '- week', week, '-', age$Age, 'weeks after planting/harvest <h2>')
  # cat(paste("# Pivot",pivots$pivot[i],"\n"))
@@ -283,7 +283,7 @@ cum_ci_plot <- function(pivotName){
   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)) +
-    labs(title = paste("14 day rolling MEAN CI rate - Field ", pivotName),
+    labs(title = paste("14 day rolling MEAN CI rate - field ", pivotName),
          x = "Date", y = "CI Rate") +
     theme(axis.text.x = element_text(angle = 60, hjust = 1),
           legend.justification = c(1, 0), legend.position = c(1, 0),
@@ -297,9 +297,9 @@ cum_ci_plot <- function(pivotName){
 cum_ci_plot2 <- function(pivotName){
 
   # pivotName = "1.1"
-  data_ci <- CI_quadrant %>% filter(Field == pivotName)
+  data_ci <- CI_quadrant %>% filter(field == pivotName)
   data_ci2 <- data_ci  %>% mutate(CI_rate = cumulative_CI/DOY,
-                                  week = week(Date))%>% group_by(Field) %>%
+                                  week = week(Date))%>% group_by(field) %>%
     mutate(mean_rolling10 = rollapplyr(CI_rate  , width = 10, FUN = mean, partial = TRUE)) #%>%
 
   date_preperation_perfect_pivot <- data_ci2 %>% group_by(season)  %>% summarise(min_date = min(Date),
@@ -310,7 +310,7 @@ cum_ci_plot2 <- function(pivotName){
 
 
   g <- ggplot(data= data_ci2)  +
-          geom_line( aes(Date, mean_rolling10, col = subField)) +
+          geom_line( aes(Date, mean_rolling10, col = sub_field)) +
           # 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))+
@@ -338,7 +338,7 @@ tm_shape(RGB_raster, unit = "m") + tm_rgb(r=1, g=2, b=3, max.value = 255) +
     tm_scale_bar(position = c("right", "top"), text.color = "white") +
 
    tm_compass(position = c("right", "top"), text.color = "white") +
-  tm_shape(AllPivots)+ tm_borders( col = "white") +
+  tm_shape(AllPivots0)+ tm_borders( col = "white") +
     tm_text("pivot_quadrant", size = .6, col = "white")
 
 ```
@@ -351,8 +351,8 @@ tm_shape(CI, unit = "m")+
    tm_scale_bar(position = c("right", "top"), text.color = "black") +
 
    tm_compass(position = c("right", "top"), text.color = "black") +
-  tm_shape(AllPivots)+ tm_borders( col = "black") +
+  tm_shape(AllPivots0)+ tm_borders( col = "black") +
-    tm_text("subField", size = .6, col = "black")
+    tm_text("sub_field", size = .6, col = "black")
 
 ```
 \newpage
@@ -365,31 +365,34 @@ tm_shape(CI, unit = "m")+
     tm_scale_bar(position = c("right", "top"), text.color = "black") +
 
     tm_compass(position = c("right", "top"), text.color = "black") +
-   tm_shape(AllPivots)+ tm_borders( col = "black") +
+   tm_shape(AllPivots0)+ tm_borders( col = "black") +
-     tm_text("subField", size = .6, col = "black")
+     tm_text("sub_field", size = .6, col = "black")
 
 ```
 
 \newpage
-```{r plots_ci_estate, eval=FALSE, fig.height=3.8, fig.width=10, message=FALSE, warning=FALSE, include=FALSE, results='asis'}
+```{r plots_ci_estate, eval=TRUE, fig.height=3.8, fig.width=10, message=FALSE,echo=FALSE, warning=FALSE, include=TRUE, results='asis'}
 # # pivots <- AllPivots_merged %>% filter(pivot != c("1.1", "1.17"))
-pivots_estate <- AllPivots_merged  %>% filter(Field %in% c("6.2")) #, "1.2", "1.3", "1.4")) #, "1.6", "1.7", "1.8", "1.9", "1.10", "1.11", "1.12", "1.13", "1.14" , "1.16" , "1.17" , "1.18" , "6.1", "6.2", "DL1.1", "DL1.3")) %>% filter(pivot != "1.17")
+# pivots_estate <- AllPivots_merged  %>% filter(field %in% c("6.2")) #, "1.2", "1.3", "1.4")) #, "1.6", "1.7", "1.8", "1.9", "1.10", "1.11", "1.12", "1.13", "1.14" , "1.16" , "1.17" , "1.18" , "6.1", "6.2", "DL1.1", "DL1.3")) %>% filter(pivot != "1.17")
 
 
 # pivots <- AllPivots_merged %>% filter(pivot != c("1.1", "1.17"))
 # pivots_estate <- AllPivots_merged %>% filter(pivot %in% c("1.1", "1.2", "1.7")) %>% filter(pivot != "1.17")
 
 
-walk(pivots_estate$Field, ~ {
+walk(AllPivots0$field, ~ {
-  cat("# Hello!!!")
+ # cat("# Hello!!!")
   cat("\n")  # Add an empty line for better spacing
   ci_plot(.x)
+ cat("\n")
  # cum_ci_plot(.x)
+#  cat("\n")
+   cum_ci_plot2(.x)
 })
 ```
 
-```{r looping_over_sub_area,  echo=FALSE, fig.height=3.8, fig.width=10, message=FALSE, warning=FALSE, results='asis', eval=TRUE}
+```{r looping_over_sub_area,  echo=FALSE, fig.height=3.8, fig.width=10, message=FALSE, warning=FALSE, results='asis', eval=FALSE}
-pivots_grouped <- AllPivots_merged # %>%
+pivots_grouped <- AllPivots0 # %>%
 #  group_by(sub_area) %>%
 #  arrange(sub_area)  # Optional: arrange the groups alphabetically by sub_area
 
@@ -401,7 +404,7 @@ print(" PRINT")
 #  cat("# Subgroup: ", subgroup, "\n")  # Add a title for the subgroup
   subset_data <- filter(pivots_grouped, sub_area == subgroup)
 #  cat("\\pagebreak")
-  walk(subset_data$Field, ~ {
+  walk(subset_data$field, ~ {
   #  cat("\n")  # Add an empty line for better spacing
     ci_plot(.x)
   #  cat("\n")
@@ -463,13 +466,13 @@ ggplot(data= CI_all2%>% filter(season =="Data_2022"), aes(DOY, cumulative_CI, co
 The below table shows estimates of the biomass if you would harvest them now.
 ```{r eval=FALSE, message=FALSE, warning=FALSE, include=FALSE}
 CI_quadrant <-  readRDS(here(cumulative_CI_vals_dir,"All_pivots_Cumulative_CI_quadrant_year_v2.rds")) %>%
-  rename( pivot_quadrant = Field)#All_pivots_Cumulative_CI.rds
+  rename( pivot_quadrant = field)#All_pivots_Cumulative_CI.rds
 ggplot(CI_quadrant %>% filter(pivot %in% "1.11")) +
   geom_line(aes(DOY, cumulative_CI, col = as.factor(season))) +
   facet_wrap(~pivot_quadrant)
 
 pivots_dates0 <- pivots_dates0 %>% ungroup() %>% unique() %>%
-  dplyr::select(Field, subField, Tcha_2021, Tcha_2022 )  %>%
+  dplyr::select(field, sub_field, Tcha_2021, Tcha_2022 )  %>%
   pivot_longer(cols = c("Tcha_2021", "Tcha_2022"), names_to = "Tcha_Year", values_to = "Tcha") %>%
   filter(Tcha > 50) %>%
   mutate(season = as.integer(str_extract(Tcha_Year, "\\d+")))
@@ -549,7 +552,7 @@ ggplot(pred_ffs_rf, aes(y = predicted_Tcha  , x = Tcha , col = pivot )) +
   labs(title = "Model trained and tested on historical results - RF")
 
 ggplot(pred_rf_2023, aes(total_CI , predicted_Tcha_2023 , col = pivot )) +
-  geom_point() + labs(title = "2023 data (still to be harvested) - Fields over 300 days old")
+  geom_point() + labs(title = "2023 data (still to be harvested) - fields over 300 days old")
 
 knitr::kable(pred_rf_2023)
 ```

r_app/interpolate_growth_model.R

@@ -72,7 +72,7 @@ pivot_stats_long <- pivot_stats2 %>%
 # pivot_select_model_Data_2023 <- harvesting_data %>% filter(year == 2023) %>% filter(!is.na(season_start))  %>% pull(sub_field)
 
 pivot_select_model_Data_2024 <- harvesting_data %>% filter(year == 2024)%>% filter(!is.na(season_start)) %>% pull(sub_field)
-
+print(pivot_select_model_Data_2024)
 # pivots_dates_Data_2022 <- pivots_dates0 %>% filter(!is.na(season_end_2022))
 # pivot_select_model_Data_2022 <- unique(pivots_dates_Data_2022$pivot_quadrant )
 #

r_app/mosaic_creation.R

@@ -62,7 +62,7 @@ daily_vrt <- here(data_dir, "vrt")
 harvest_dir <-  here(data_dir, "HarvestData")
 
 source("parameters_project.R")
-source("utils_1.R")
+source("mosaic_creation_utils.R")
 
 dir.create(here(laravel_storage_dir))
 dir.create(here(data_dir))

r_app/parameters_project.R

@@ -1,5 +1,5 @@
 
-
+library('readxl')
 #chemba
 if(project_dir == "chemba"){
   message("Yield data for Chemba")