Merge pull request #110 from AgrDataSci/devel

fix-map-path
AgrDataSci · May 31, 2023 · 65a9f95 · 65a9f95
2 parents 2843b65 + e0d0ed0
commit 65a9f95
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Showing 7 changed files with 80 additions and 66 deletions.
diff --git a/.gitignore b/.gitignore
@@ -19,3 +19,4 @@ dev
 reportcm
 run-local/local
 tests
+tempmap
diff --git a/ClimMob.R b/ClimMob.R
@@ -69,7 +69,7 @@ try_data = tryCatch({
                          tidynames = FALSE, 
                          pivot.wider = TRUE)
 
-  rank_dat = organize_ranking_data(cmdatajson, 
+  rank_dat = organize_ranking_data(cmdata = cmdatajson, 
                                    pars, 
                                    groups, 
                                    option_label = option,
@@ -97,7 +97,7 @@ if (any_error(try_data)) {
 # 2. Organise quantitative data ####
 try_quanti_data = tryCatch({
 
-  quanti_dat = organize_quantitative_data(cmdatajson, 
+  quanti_dat = organize_quantitative_data(cmdata = cmdatajson, 
                                           pars, 
                                           groups = groups, 
                                           id = "id",
@@ -427,6 +427,10 @@ if (isTRUE(quanti_dat$quantitative)) {
 
 }
 
+if (isTRUE(trial_map$geoTRUE)) {
+  unlink(trial_map$mapDIR, recursive = TRUE)
+}
+
 # End of analysis
 
 
diff --git a/modules/00_check_packages.R b/modules/00_check_packages.R
@@ -8,7 +8,7 @@ pkg <- c('caret', 'climatrends', 'ClimMobTools', 'ggparty', 'ggplot2', 'gosset',
          'gridExtra', 'gtools', 'igraph', 'janitor', 'jsonlite', 'knitr', 'leaflet', 
          'mapview', 'multcompView', 'nasapower', 'partykit', 'patchwork', 
          'PlackettLuce', 'plotrix', 'pls', 'png', 'psychotools', 'qvcalc',
-         'remotes', 'rmarkdown')
+         'remotes', 'rmarkdown', 'lubridate')
 
 install.packages(pkg)
 

diff --git a/modules/01_functions.R b/modules/01_functions.R
@@ -32,6 +32,7 @@ library("plotrix")
 library("gridExtra")
 library("caret")
 library("janitor")
+library("lubridate")
 
 #'Get colour pallet
 #' @param x an integer

diff --git a/modules/05_spatial_overview.R b/modules/05_spatial_overview.R
@@ -30,43 +30,49 @@ get_testing_sites_map = function(cmdata, output_path, backward_path){
 
   geoTRUE = all(any(lon), any(lat))
 
-  if (isTRUE(geoTRUE)) {
-
-    # find the vector with most completeness 
-    less_nas = lapply(cmdata[lon], function(x){
-      sum(is.na(x))
-    })
-
-    lon = names(which.min(unlist(less_nas)))
-    lat = gsub("_longitude", "_latitude", lon)
-
-    lonlat = cmdata[, c(lon,lat)]
-
-    lonlat[1:2] = lapply(lonlat[1:2], as.numeric)
+  if (isFALSE(geoTRUE)) {
+    return(list(geoTRUE = FALSE))
+  }
+
+  # find the vector with most completeness 
+  less_nas = lapply(cmdata[lon], function(x){
+    sum(is.na(x))
+  })
+
+  lon = names(which.min(unlist(less_nas)))
+  lat = gsub("_longitude", "_latitude", lon)
+
+  lonlat = cmdata[, c(lon,lat)]
+
+  lonlat[1:2] = lapply(lonlat[1:2], as.numeric)
+
+  lonlat[,1] = ifelse(lonlat[,1] > 180 | lonlat[,1] < -180, NA, lonlat[,1])
+
+  lonlat[,2] = ifelse(lonlat[,2] > 70 | lonlat[,2] < -70, NA, lonlat[,2])
+
+  nlonlat = dim(lonlat)[[1]]
+
+  if (nlonlat > 0) {
 
-    lonlat[,1] = ifelse(lonlat[,1] > 180 | lonlat[,1] < -180, NA, lonlat[,1])
+    trial_map = plot_map(data = lonlat, 
+                         make.clusters = FALSE,
+                         xy = c(1, 2),
+                         minimap = TRUE, 
+                         map_provider = "OpenStreetMap.Mapnik")
 
-    lonlat[,2] = ifelse(lonlat[,2] > 70 | lonlat[,2] < -70, NA, lonlat[,2])
+    tempmap = paste0(getwd(), "/tempmap/")
 
-    nlonlat = dim(lonlat)[[1]]
+    dir.create(tempmap, recursive = TRUE, showWarnings = FALSE)
 
-    if (nlonlat > 0) {
-
-      trial_map = plot_map(data = lonlat, 
-                           make.clusters = FALSE,
-                           xy = c(1, 2),
-                           minimap = TRUE, 
-                           map_provider = "OpenStreetMap.Mapnik")
-
-      mapview::mapshot(trial_map, 
-                       url = paste0(output_path, "/trial_map.html"),
-                       file = paste0(output_path, "/trial_map.png"))
-
-    }
+    mapview::mapshot(trial_map, 
+                     url = paste0(tempmap, "/trial_map.html"),
+                     file = paste0(tempmap, "/trial_map.png"))
 
   }
 
-  result = list(map_path = paste0(output_path, "trial_map.png"),
+  result = list(geoTRUE = TRUE, 
+                mapDIR = tempmap,
+                map_path = paste0(tempmap, "/trial_map.png"),
                 map = trial_map,
                 coords = lonlat)
 
@@ -75,7 +81,8 @@ get_testing_sites_map = function(cmdata, output_path, backward_path){
 # .......................................
 # Error in data 
 # this is a file that is generated to be used in case of errors
-error_data_trial_map = list(map_path = "",
+error_data_trial_map = list(geoTRUE = FALSE, 
+                            map_path = "",
                             map = 0L,
                             coords = data.frame())
 
diff --git a/modules/09_agroclimatic_insights.R b/modules/09_agroclimatic_insights.R
@@ -59,7 +59,7 @@ get_agroclimatic_data = function(cmdata,
 
   dates = cmdata[dates[1]]
 
-  dates = climatrends:::.coerce2Date(dates[,1])
+  dates = lubridate::as_date(dates[,1])
 
   rain = rainfall(coords[noNAs, ],
                   day.one = dates[noNAs],
@@ -150,6 +150,8 @@ get_agroclimatic_data = function(cmdata,
                 rainfall = rain1,
                 temperature = temp1,
                 dates = dates,
+                window = c(min(dates, na.rm = TRUE),
+                           max(dates, na.rm = TRUE) + ndays),
                 noNAs = noNAs,
                 date_used = date_used)
-Original file line number
+Diff line change
@@ Expand Up / @@ -19,3 +19,4 @@ dev @@
     reportcm
     run-local/local
     tests
+    tempmap