SAP

R/geojson_imagery.R

@@ -0,0 +1,43 @@
+# THIS IS THE MERGE BETWEEN geom_stat and geom_boxplot
+
+#' Basic statistics on GeoJSON file like lists or charts
+#'
+#' @name geojson_stat
+#'
+#' @description Basic descriptive statistics on GeoJSON file. This function is used by `geojson_format_path()` and is the front counterpart of `ref_hps()` for a Postgres query.
+#'
+#' @param stat.name name of output file. Default "stat".
+#' @param geojson.path path of GeoJSON file. Default 'caravanserail.geojson'
+#' @param concept.name name of field used to store IDs. Default `hp.id`.
+#' @param stat type of statistic that will be computed. Default `list_fields` (list the fields). Other options are: `list_ids` list EAMENA IDs. Use `stat` to diplay charts like pie chart or histograms, etc., see option `chart.type`
+#' @param chart.type either "`pie`" for pie chart, or "`hist`" for histogram, "`radar`" for radar diagrams. Only useful if the option `stat` is set to `stats` (`stat = "stats"`).
+#' @param field.names field name on which statistic will be performed. Only useful if the option `stat` is set to `stats` (`stat = "stats"`).
+#' @param name of field on which paths will be grouped. For example "route". Will create as many plots as there are different categories. Default NA.
+#' @param color.set the RBrewer color set. Default "Set1".
+#' @param fig.width,fig.height size of output chart.
+#' @param fig.dev format of image: "png" (default), "jpg", "svg", etc.
+#' @param export.stat if TRUE return stats to be stored in new variable
+#' @param export.plot if TRUE, export tats in new file, if FALSE will only display it
+#' @param dirOut folder where outputs will be saved. Default: '/results'. If it doesn't exist, will be created. Only useful is export.plot is TRUE.
+#' @param verbose if TRUE (by default), print messages.
+#'
+#' @return Show or export basic statistics on GeoJSON file
+#'
+#' @examples
+#'
+#' # list HP names
+#' geojson_stat(stat.name = "geojson_fields", stat = "list_ids")
+#'
+#'
+#' @export
+geojson_imagery <- function(geojson.path = paste0(system.file(package = "eamenaR"),
+                                                  "/extdata/caravanserail.geojson"),
+                            export.plot = FALSE,
+                            dirOut = paste0(system.file(package = "eamenaR"),
+                                            "/results/"),
+                            verbose = TRUE){
+  pass
+}
+
+geojson.path <- "C:/Users/Thomas Huet/Desktop/Sistan/data/sistan_part1_hps.geojson"
+geojson_imagery(geojson.path)

R/ref_hps_1.R

@@ -71,6 +71,7 @@
 #'              d = d,
 #'              stat = "hist",
 #'              stat.name = "Disturbance Cause Category Type",
+#'              stat.field = "Disturbance Cause Category Type",
 #'              max.num = 20,
 #'              export.data = TRUE,
 #'              dirOut = "C:/Rprojects/eamenaR/results/",
@@ -82,6 +83,7 @@
 #'              d = d,
 #'              stat = "pie",
 #'              stat.name = "Overall Condition State Type",
+#'              stat.field = "Overall Condition State Type",
 #'              export.data = TRUE,
 #'              dirOut = "C:/Rprojects/eamenaR/results/",
 #'              fig.width = 12,
@@ -92,6 +94,7 @@
 #'              d = d,
 #'              stat = "pie",
 #'              stat.name = "Overall Condition State Type",
+#'              stat.field = "Overall Condition State Type",
 #'              perc = TRUE,
 #'              rounded = 1,
 #'              export.data = TRUE,
@@ -104,6 +107,7 @@ ref_hps <- function(db.con = NA,
                     d = NA,
                     stat = c("spat"),
                     perc = FALSE,
+                    rounded = 1,
                     stat.name = "eamena_hps",
                     stat.field = "Overall Condition State Type",
                     stat.format = ".geojson",
@@ -303,15 +307,15 @@ ref_hps <- function(db.con = NA,
   }
   if("hist" %in% stat){
     # return, for example: # 34cfe9f5-c2c0-11ea-9026-02e7594ce0a0
-    field.name <- eamenaR::ref_ids(stat.field,
+    field.uuid <- eamenaR::ref_ids(stat.field,
                                    choice = "db.concept.uuid")
     # TODO: generalise the SQL for other categories. Currently it only deals with Disturbance Cause Category Type (UUID=34cfea68-c2c0-11ea-9026-02e7594ce0a0). Ex:
     sqll <- stringr::str_interp(
       "
     SELECT v.value AS categ_type, COUNT(v.value) AS nb
     FROM tiles t
-    JOIN values v ON t.tiledata ->> '${field.name}'::text IS NOT NULL
-    AND v.valueid = (t.tiledata ->> '${field.name}'::text)::uuid
+    JOIN values v ON t.tiledata ->> '${field.uuid}'::text IS NOT NULL
+    AND v.valueid = (t.tiledata ->> '${field.uuid}'::text)::uuid
     GROUP BY v.valueid
     ORDER BY nb DESC
     "
@@ -342,8 +346,8 @@ ref_hps <- function(db.con = NA,
           ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, vjust = 1, hjust = 1, size = 10),
                          axis.title.y = ggplot2::element_text(angle = 90),
                          plot.margin = ggplot2::margin(0, 0, 1, 1, "cm"),
-                         panel.spacing = unit(2, "lines"),
-                         plot.title = ggplot2::element_text(margin = margin(b = 20))
+                         panel.spacing = ggplot2::unit(2, "lines"),
+                         plot.title = ggplot2::element_text(margin = ggplot2::margin(b = 20))
           )
       }
       if(perc){
@@ -358,9 +362,13 @@ ref_hps <- function(db.con = NA,
           ) +
           ggplot2::ylab(paste(stat.name, '%')) +
           ggplot2::scale_x_discrete(labels = function(x) stringr::str_wrap(x, width = warp.at)) +
+          ggplot2::scale_y_continuous(expand = c(0, 0, .075, 0)) + # expand the top to uncut large bar labels
           ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, vjust = 1, hjust = 1, size = 10),
                          axis.title.y = ggplot2::element_text(angle = 90),
-                         plot.margin = ggplot2::margin(0, 0, 1, 1, "cm"))
+                         plot.margin = ggplot2::margin(0, 0, 1, 1, "cm"),
+                         panel.spacing = ggplot2::unit(2, "lines"),
+                         plot.title = ggplot2::element_text(margin = ggplot2::margin(b = 20))
+          )
       }
       if (export.data) {
         dir.create(dirOut, showWarnings = FALSE)
@@ -380,14 +388,14 @@ ref_hps <- function(db.con = NA,
   }
   if("pie" %in% stat){
     # TODO: generalise the SQL for other categories. Currently it only deals with Overall Condition State Type (UUID=34cfe9f5-c2c0-11ea-9026-02e7594ce0a0)
-    field.name <- eamenaR::ref_ids(stat.field,
+    field.uuid <- eamenaR::ref_ids(stat.field,
                                    choice = "db.concept.uuid")
     sqll <- stringr::str_interp(
       "
       SELECT v.value AS categ_type, COUNT(v.value) AS nb
       FROM tiles t
-      JOIN values v ON t.tiledata ->> '34cfe9f5-c2c0-11ea-9026-02e7594ce0a0'::text IS NOT NULL
-                   AND v.valueid = (t.tiledata ->> '34cfe9f5-c2c0-11ea-9026-02e7594ce0a0'::text)::uuid
+      JOIN values v ON t.tiledata ->> '${field.uuid}'::text IS NOT NULL
+                   AND v.valueid = (t.tiledata ->> '${field.uuid}'::text)::uuid
       GROUP BY v.valueid
       ORDER BY nb DESC
       "
@@ -484,7 +492,8 @@ db.con <- RPostgres::dbConnect(drv = RPostgres::Postgres(),
 d <- ref_hps(db.con = db.con,
              d = d,
              stat = "hist",
-             stat.name = "Disturbance Cause Category Type",
+             stat.name = "Threat Category",
+             stat.field = "Threat Category",
              perc = T,
              max.num = 20,
              export.data = TRUE,

README.md

@@ -25,11 +25,11 @@ Together with analysis functions, the package offers different methods to manage
 
 ```mermaid
 flowchart LR
-    subgraph ide1 [<b>F</b>indable, <b>A</b>ccessible]
+    subgraph ide1 ["<b>F</b>indable, <b>A</b>ccessible"]
     A[(EAMENA<br>DB)];
     end
     A[(EAMENA<br>DB)] <---> B{{"eamenaR"}}:::eamenaRpkg;
-    subgraph ide2 [<b>I</b>nteroperable, <b>R</b>eusable]
+    subgraph ide2 ["<b>I</b>nteroperable, <b>R</b>eusable"]
     B;
     end
     classDef eamenaRpkg fill:#e3c071;