diff --git a/build_mosaic.sh b/build_mosaic.sh index 81aad6a..a873366 100755 --- a/build_mosaic.sh +++ b/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 \ No newline at end of file +Rscript mosaic_creation.R $end_date $offset $data_dir \ No newline at end of file diff --git a/build_report.sh b/build_report.sh index 6cb4097..d811879 100755 --- a/build_report.sh +++ b/build_report.sh @@ -6,9 +6,6 @@ for arg in "$@"; 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 - echo "Missing arguments. Use: build_reports.sh --filename=hello.txt --weeks_ago=3 --report_date=2020-01-01 --data_dir=chemba" +if [ -z "$filename" ] || [ -z "$report_date" ] || [ -z "$data_dir" ]; then + 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" diff --git a/laravel_app/app/Jobs/ProjectInterpolateGrowthModelJob.php b/laravel_app/app/Jobs/ProjectInterpolateGrowthModelJob.php index 0e02540..4389baf 100644 --- a/laravel_app/app/Jobs/ProjectInterpolateGrowthModelJob.php +++ b/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), ]; diff --git a/laravel_app/app/Jobs/ProjectMosiacGeneratorJob.php b/laravel_app/app/Jobs/ProjectMosiacGeneratorJob.php index 179aded..7e634a3 100644 --- a/laravel_app/app/Jobs/ProjectMosiacGeneratorJob.php +++ b/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, diff --git a/laravel_app/app/Jobs/ProjectReportGeneratorJob.php b/laravel_app/app/Jobs/ProjectReportGeneratorJob.php index 731ff88..3a89011 100644 --- a/laravel_app/app/Jobs/ProjectReportGeneratorJob.php +++ b/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), ]; diff --git a/laravel_app/app/Models/Project.php b/laravel_app/app/Models/Project.php index 2dc31ae..ee19e51 100644 --- a/laravel_app/app/Models/Project.php +++ b/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; diff --git a/laravel_app/app/Models/ProjectMosaic.php b/laravel_app/app/Models/ProjectMosaic.php index db2298f..024ddbc 100644 --- a/laravel_app/app/Models/ProjectMosaic.php +++ b/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() diff --git a/laravel_app/tests/Unit/Models/ProjectTest.php b/laravel_app/tests/Unit/Models/ProjectTest.php index ba1bf44..7e8aa98 100644 --- a/laravel_app/tests/Unit/Models/ProjectTest.php +++ b/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, $project->shouldSchedule()); } - public static function scheduleDayProvider(){ - return [ + public static function scheduleDayProvider() + { + return [ ['date' => '2024-03-01', 'day' => 'Friday', 'result' => true], ['date' => '2024-03-02', 'day' => 'Saturday', 'result' => false], ['date' => '2024-03-03', 'day' => 'Sunday', 'result' => false], diff --git a/r_app/CI_report_dashboard_planet.Rmd b/r_app/CI_report_dashboard_planet.Rmd index 44eb7cf..4cda350 100644 --- a/r_app/CI_report_dashboard_planet.Rmd +++ b/r_app/CI_report_dashboard_planet.Rmd @@ -3,7 +3,7 @@ params: ref: "word-styles-reference-var1.docx" output_file: CI_report.docx report_date: "2024-04-18" - data_dir: "chemba" + data_dir: "Sony" output: # html_document: # toc: yes @@ -70,10 +70,10 @@ source(here("r_app", "parameters_project.R")) ```{r week, message=FALSE, warning=FALSE, include=FALSE} -# week <- 5 -#today = "2023-12-12" today <- as.character(report_date) week <- week(today) + week <- 25 +today = "2024-06-21" #today = as.character(Sys.Date()) @@ -115,7 +115,7 @@ This PDF-dashboard shows the status of your fields on a weekly basis. We will sh # remove_pivots <- c("1.1", "1.12", "1.8", "1.9", "1.11", "1.14") CI_quadrant <- readRDS(here(cumulative_CI_vals_dir,"All_pivots_Cumulative_CI_quadrant_year_v2.rds"))# %>% - # rename(pivot_quadrant = Field) + # rename(pivot_quadrant = field) CI <- brick(here(weekly_CI_mosaic, paste0("week_",week, "_", year, ".tif"))) %>% subset("CI") CI_m1 <- brick(here(weekly_CI_mosaic, paste0("week_",week_minus_1, "_", year_1, ".tif"))) %>% subset("CI") @@ -140,16 +140,16 @@ AllPivots0 <- field_boundaries_sf # pivots_dates <- readRDS(here(harvest_dir, "harvest_data_new")) # pivots_dates$pivot <- factor(pivots_dates$pivot, levels = c("1.1", "1.2", "1.3", "1.4", "1.6", "1.7", "1.8", "1.9", "1.10", "1.11", "1.12", "1.13", "1.14" , "1.16" , "1.17" , "1.18" ,"2.1", "2.2", "2.3" , "2.4", "2.5", "3.1", "3.2", "3.3", "4.1", "4.2", "4.3", "4.4", "4.5", "4.6", "5.1" ,"5.2", "5.3", "5.4", "6.1", "6.2", "DL1.1", "DL1.3")) -AllPivots <- merge(AllPivots0, harvesting_data, by = c("Field", "subField")) #%>% -#rename(Field = pivot, subField = pivot_quadrant) #%>% select(-pivot.y) -head(AllPivots) +#AllPivots <- merge(AllPivots0, harvesting_data, by = c("field", "sub_field")) #%>% +#rename(field = pivot, sub_field = pivot_quadrant) #%>% select(-pivot.y) +#head(AllPivots) -AllPivots_merged <- AllPivots %>% #dplyr::select(Field, subField, sub_area) %>% unique() %>% - group_by(Field) %>% summarise(sub_area = first(sub_area)) +#AllPivots_merged <- AllPivots %>% #dplyr::select(field, sub_field, sub_area) %>% unique() %>% +# group_by(field) %>% summarise(sub_area = first(sub_area)) -AllPivots_merged <- st_transform(AllPivots_merged, crs = proj4string(CI)) +#AllPivots_merged <- st_transform(AllPivots_merged, crs = proj4string(CI)) -pivot_names <- unique(CI_quadrant$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)) - age <- AllPivots %>% dplyr::filter(Field %in% pivotName) %>% st_drop_geometry() %>% dplyr::select(Age) %>% unique() + pivotShape <- AllPivots0 %>% terra::subset(field %in% pivotName) %>% st_transform(crs(CI)) + 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('

Pivot', pivotName, '- week', week, '-', age$Age, 'weeks after planting/harvest

') # 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_text("subField", size = .6, col = "black") + tm_shape(AllPivots0)+ tm_borders( 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_text("subField", size = .6, col = "black") + tm_shape(AllPivots0)+ tm_borders( 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, ~ { - cat("# Hello!!!") +walk(AllPivots0$field, ~ { + # cat("# Hello!!!") cat("\n") # Add an empty line for better spacing ci_plot(.x) + cat("\n") # cum_ci_plot(.x) +# cat("\n") + cum_ci_plot2(.x) }) ``` -```{r looping_over_sub_area, echo=FALSE, fig.height=3.8, fig.width=10, message=FALSE, warning=FALSE, results='asis', eval=TRUE} -pivots_grouped <- AllPivots_merged # %>% +```{r looping_over_sub_area, echo=FALSE, fig.height=3.8, fig.width=10, message=FALSE, warning=FALSE, results='asis', eval=FALSE} +pivots_grouped <- AllPivots0 # %>% # group_by(sub_area) %>% # arrange(sub_area) # Optional: arrange the groups alphabetically by sub_area @@ -401,7 +404,7 @@ print(" PRINT") # cat("# Subgroup: ", subgroup, "\n") # Add a title for the subgroup subset_data <- filter(pivots_grouped, sub_area == subgroup) # cat("\\pagebreak") - walk(subset_data$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) ``` diff --git a/r_app/Rplots.pdf b/r_app/Rplots.pdf index c58e7b4..e0f9a77 100644 Binary files a/r_app/Rplots.pdf and b/r_app/Rplots.pdf differ diff --git a/r_app/interpolate_growth_model.R b/r_app/interpolate_growth_model.R index dd6834e..907b74f 100644 --- a/r_app/interpolate_growth_model.R +++ b/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 ) # diff --git a/r_app/mosaic_creation.R b/r_app/mosaic_creation.R index b132c97..400d034 100644 --- a/r_app/mosaic_creation.R +++ b/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)) diff --git a/r_app/parameters_project.R b/r_app/parameters_project.R index 42ca9e1..23ed5a4 100644 --- a/r_app/parameters_project.R +++ b/r_app/parameters_project.R @@ -1,5 +1,5 @@ - +library('readxl') #chemba if(project_dir == "chemba"){ message("Yield data for Chemba")