M demuzaere review3

.Rbuildignore

@@ -8,4 +8,7 @@
 .github$
 ^CITATION\.cff$
 ^\\.gitignore$
-.gitignore$
+.gitignore$
+^CODE_OF_CONDUCT\.md$
+^CONTRIBUTING\.md$
+^bdtopo_2_2_osm\.csv$

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: lczexplore
 Title: lczexplore
-Version: 0.0.1.0002
+Version: 0.0.1.0003
 Authors@R: c(
     person("Matthieu", "Gousseff", , "matthieu.gousseff@univ-ubs.fr", role = c("aut", "cre")),
     person(, "Centre National de la Recherche Scientifique, Lab-Sticc", role = "cph", comment = c(ORCID = "0000-0002-7106-2677"))
   )
-Description: This lczexplore package automatize the comparison of sets of local climate zone classifications. It was developed thanks to the project PAENDORA2 (Pour la gestion du confort estival : Données, Outils et Recherche-Action) (2022 -2025), funded by ADEME.
+Description: This lczexplore package automatize the comparison of sets of local climate zone classifications. It was developed thanks to the project PAENDORA2 (Pour la gestion du confort estival : Donnees, Outils et Recherche-Action) (2022 -2025), funded by ADEME.
 License: LGPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

R/confidSensib.R

@@ -6,7 +6,7 @@
 #' @param inputDf is an R file with geom IDs, (LCZ) classifications and
 #' a confidence value granted for the (LCZ) classifications values of each geom. Ignored if filePath is not empty.
 #' @param filePath is the path to a csv file containing geom IDs, LCZ classifications and
-#' a confidence value granted for the LCZ value of each geom.
+#' a confidence value granted for the LCZ value of each geom. Set it to "" if inputDf is specified (recommanded)
 #' @param nPoints is the number of points (quantiles) of confidence for which
 #' the average agreement between classifications will be computed
 #' @param wf1 is the name of the workflow used to produce the first LCZ
@@ -27,14 +27,16 @@
 #' @export
 #'
 #' @examples
-#' mainPath<-system.file("extdata", package = "lczexplore")
-#' testSourceFact<-read.csv(paste0(mainPath,"/bdtopo_2_2_osm.csv"),
-#' sep=";",header=TRUE,stringsAsFactors = TRUE)
-#' confidSensib(inputDf=testSourceFact, filePath="",
+#' # creation of the comparison data on which to perform the analysis
+#' redonCompare<-compareLCZ(sf1=redonBDT, wf1="bdt", geomID1 = "ID_RSU", column1 ="LCZ_PRIMARY",
+#'                         confid1 = "LCZ_UNIQUENESS_VALUE",
+#'                         sf2=redonOSM, wf2="osm",geomID2 = "ID_RSU", column2="LCZ_PRIMARY",
+#'                         confid2 ="LCZ_UNIQUENESS_VALUE", exwrite=FALSE, plot=FALSE, saveG="")
+#' confidSensib(inputDf=redonCompare$data,
 #' nPoints=5, wf1="bdtopo_2_2", wf2="osm",
 #' geomID1="ID_RSU", column1="LCZ_PRIMARY", confid1="LCZ_UNIQUENESS_VALUE",
 #' geomID2="ID_RSU.1",column2="LCZ_PRIMARY.1", confid2="LCZ_UNIQUENESS_VALUE.1",
-#' sep=";", repr="standard", plot=TRUE, saveG=mainPath)
+#' sep=";", repr="standard", plot=TRUE, saveG="")
 confidSensib<-function(inputDf="", filePath="", nPoints=5,
                        wf1="bdtopo_2_2", wf2="osm",
                        geomID1="ID_RSU", column1="LCZ_PRIMARY", confid1="LCZ_UNIQUENESS_VALUE",
@@ -74,7 +76,7 @@ confidSensib<-function(inputDf="", filePath="", nPoints=5,
   # between LCZ classifications
 
   echIntConf<-subset(echInt,!is.na(echInt$confidMin))
-  # print("séparation");(print(nrow(echIntNoconf)));(print(nrow(echIntConf)));(print(nrow(echInt)))
+
 
   #############################################################################################
   # All LCZ levels treated together
@@ -163,7 +165,7 @@ confidSensib<-function(inputDf="", filePath="", nPoints=5,
   }
 
   if(saveG!=""){
-        plotName<-paste0(saveG,"/GeneralUniquenessSensib.jpg")
+        plotName<-paste0(saveG,"/GeneralUniquenessSensib.png")
     png(filename = plotName,width=1200,height=900)
     print(allLCZ$ctPlot)
     dev.off()
@@ -216,7 +218,7 @@ typeLevels<-unique(echIntConf[,column1]) %>% as.vector
  }
 
  if(saveG!=""){
-   plotName<-paste0(saveG,"/byLCZUniquenessSensib.jpg")
+   plotName<-paste0(saveG,"/byLCZUniquenessSensib.png")
    png(filename = plotName,width=1200,height=900)
    print(byLCZPLot)
    dev.off()

R/importLCZraster.R

@@ -1,19 +1,22 @@
-#' Imports the LCZ classifications produced on raster maps, mainly by the WUDAPT algorithm.
-#' For now, the function  import from the european tiff
-#' produced by WUDAPT. Users can DOWNLOAD the WUDAPT tiff file
-#' at the following url : https://figshare.com/articles/dataset/European_LCZ_map/13322450
-#' A future version may include the world data once a strategy is defined to deal with CRS.
+#' Imports the LCZ classifications produced on raster maps.  
+#' For now, the european tif map produced by WUDAP is used as a reference example. 
+#' Users can DOWNLOAD the WUDAPT tif file at the following url : 
+#' https://figshare.com/articles/dataset/European_LCZ_map/13322450
 #'
 #' @param dirPath is the path to the directory where the
-#' @param fileName is the name of the raster file (tif or geotif), by default \'EU_LCZ_map.tif\' . 
-#' Will be useful when other zones will be added
-#' @param column indicates the name of the column which will contain the LCZ in the output file
-#' @param typeLevels indicates a named vector of the unique values contained in column,
-#' @param zone set to europe by default, may include world once a strategy is defined
-#' @param bBox bBox is the bounding box needed to crop the raster tiff file.
-#' It can be produced by the importLCZvect function if one has a vect map o the same zone, 
-#' it can be a set of coordinates. It can either be of class bBox or of class sfc.
-#' @return an sf file containing the geom and LCZ levels from the raster within the bBox bounding box
+#' @param fileName is the name of the raster file (tif or geotif), by default \'EU_LCZ_map.tif\'.
+#' @param LCZband defines the band of the raster file which contains the LCZ types. 
+#' It can be a number or a band name (default = 1)
+#' @param LCZcolumn the name of the column of the output sf File in which the LCZ types will be stored
+#' (default = "LCZ")
+#' @param confidenceBand the band of the raster files which contains a measure of confidence. 
+#' Can be a number or a band name (default = "", that is no measure of confidence provided)
+#' @param confidenceColumn the name of the column of the output sf File in which the confidence values will be stored
+#' (default = "", no confidence value specified)
+#' @param typeLevels indicates a named vector of the unique values contained in LCZcolumn,
+#' @param bBox bBox is the bounding box needed to crop the raster file.
+#' It can be produced bu the importLCZvect function. It can either be of class bBox or of class sfc
+#' @return an sf file containing the geom and LCZ levels from theraster tiff within the bBox bounding box
 #' @import sf dplyr forcats
 #' @importFrom terra crop
 #' @importFrom terra rast
@@ -35,54 +38,56 @@
 #' # fileName="redonWudapt.tif",bBox=redonBbox)
 #' 
 #' # another way to get the bounding box when one doesn't want 
-#' # to compare to a vector map is to enter it's coordinates 
-#' # and feed them to st_bbox() of the sf package. 
+#' #to compare to a vector map is to enter it's coordinates 
+#' # and feed them to st_bbox() of the sf package.
 #' 
-#' # the following example can only be executed when user has downloaded 
-#' # CONUS-wide LCZ map and Training Areas on WUDAPT website
-#' # sanDiegobBoxCoord<-st_sf(a=1:2, geom=st_sfc(
-#' #    st_point(c(-117.175198,32.707289)),
-#' #    st_point(c(-117.112198,32.750900)),crs = 4326
-#' #))
-#' #sanDiegoBbox<-st_bbox(sanDiegobBoxCoord)
-#' #sanDiegoWudapt<-importLCZraster(
-#' #dirPath="path_of_the_tiff",
-#' #fileName="CONUS_LCZ_map_NLCD_v1.0_epsg4326.tif",
-#' #column="CONUS_LCZ_map_NLCD_v1.0_epsg4326"
-#' #  ,bBox=sanDiegoBbox)
-#' #showLCZ(sanDiegoWudapt, column="CONUS_LCZ_map_NLCD_v1.0_epsg4326")
-importLCZraster<-function(dirPath,zone="europe",bBox,fileName="EU_LCZ_map.tif", column='EU_LCZ_map',
+#' # imporLCZraster also allows to choose which band of a raster file to import
+#' redonWudapt<-importLCZraster(system.file("extdata", package = "lczexplore"),
+#' fileName="redonWudapt.tif",bBox=redonBbox, LCZband=1, LCZcolumn='EU_LCZ_map')
+importLCZraster<-function(dirPath, bBox, fileName="EU_LCZ_map.tif", LCZband=1, LCZcolumn='EU_LCZ_map',
+                          confidenceBand = "", confidenceColumn = "confidence",
+
                           typeLevels=c("1"="1","2"="2","3"="3","4"="4","5"="5","6"="6","7"="7","8"="8",
                            "9"="9","10"="10","101"="11","102"="12","103"="13","104"="14",
                             "105"="15", "106"="16","107"="17")){
 # internal import function used in two loops
-  effectiveImport<-function(fileName,bBox){
-    sfFile<-rast(fileName)
+  effectiveImport<-function(fileName,bBox,LCZband,confidenceBand,LCZcolumn, confidenceColumn){
+
+     if(confidenceBand=="") {
+    lyrs=list(LCZband)
+    sfFile<-do.call(rast, list(x=fileName, lyrs=lyrs))
+  } else if (confidenceBand!="") {
+    lyrs=list(LCZband,confidenceBand)
+    sfFile<-do.call(rast, list(x=fileName, lyrs=lyrs))
+  }
+
     if (sum(class(bBox)%in%c("sfc_POLYGON","sfc" ))==0) {
       bBox<-st_as_sfc(bBox)
     }
-    bBox<-st_transform(bBox,st_crs(sfFile,proj=T))
+    bBox<-st_transform(bBox, st_crs(sfFile,proj=TRUE))
 
 
     cropTry<-try(sfFile %>% crop(bBox))
-    if(is(cropTry,"try-error")){stop("The bounding box doesn't intersect with the Wudapt tiff : \n
-                                     maybe it's out of the Europe zone covered by this package. \n Future versions may include other zones.")}
+    if(is(cropTry,"try-error")) { 
+      stop("The bounding box doesn't intersect with the provided raster file.")}
     else{
-    sfFile<-sfFile %>% crop(bBox) %>% as.polygons(dissolve=F) %>%
+    sfFile<-sfFile %>% crop(bBox) %>% as.polygons(dissolve=FALSE) %>%
       st_as_sf() %>% st_intersection(bBox)
 
       if (length(typeLevels==1)){
     typeLevels<-c("1"="1","2"="2","3"="3","4"="4","5"="5","6"="6","7"="7","8"="8",
                "9"="9","10"="10","101"="11","102"="12","103"="13","104"="14",
                "105"="15", "106"="16","107"="17")}
     # typeLevels2<-as.character(c(1:10,101:107))
-
-    sfFile<-sfFile%>%
-        mutate(!!column:=fct_recode(factor(subset(sfFile,select=column,drop=T),levels=typeLevels),
+
+    names(sfFile)[names(sfFile)==LCZband]<-LCZcolumn
+    names(sfFile)[names(sfFile)==confidenceBand]<-confidenceColumn
+      print(str(sfFile))
+    sfFile<-sfFile%>% mutate(!!LCZcolumn:=fct_recode(factor(subset(sfFile,select=LCZcolumn,drop=T),levels=typeLevels),
                                     !!!typeLevels)) %>%
-        drop_na(column)
+        drop_na(LCZcolumn)
 
-    cat(levels(subset(sfFile,select=column,drop=T)))
+    cat(levels(subset(sfFile,select=LCZcolumn,drop=T)))
     #plot(sfFile)
     sfFile
     }
@@ -95,27 +100,25 @@ importLCZraster<-function(dirPath,zone="europe",bBox,fileName="EU_LCZ_map.tif",
   else{
     fileName<-paste0(dirPath,"/",fileName)
     print(fileName)
-    if (!file.exists(fileName)){
-      choice<-readline(prompt="The wudapt Europe map tiff file doesn't exist in the specified directory. \n
-              If you want lczexplore to try and download it type 1, else type 2 to exit and get the tiff map by yourself")
-      print("choice: "); print(choice)
-      if (choice==1){
-        url<-"https://figshare.com/ndownloader/files/35069446"
-        fetchTry<-try(download.file(url=url,method="auto",destfile=fileName))
-        if(is(fetchTry,"try-error")){
-          stop("The file couldn't be downloaded, maybe try to dowload another way.")
-        } else {
-          sfFile<-effectiveImport(fileName = fileName,bBox=bBox)
-          sfFile
+    if (!file.exists(fileName)) {
+        stop("The raster file doesn't exist in the specified directory")
+        } else  { # if the user specifies the number of the layer and not its name
+          if (is.numeric(LCZband) | is.numeric(confidenceBand)){
+            sfFile<-rast(fileName)
+            layerNames <- names(sfFile)
+            if (is.numeric(LCZband)) { LCZband<-layerNames[LCZband] }
+            if (is.numeric(confidenceBand)) { confidenceBand<-layerNames[confidenceBand] }
           }
-      }
-    }
-    else{
-      sfFile<-effectiveImport(fileName = fileName,bBox=bBox)
-      sfFile
-      }
+
+          sfFile<-effectiveImport(fileName  =  fileName,  bBox = bBox,  
+                                  LCZband = LCZband,  LCZcolumn = LCZcolumn, 
+                                  confidenceBand =  confidenceBand, 
+                                  confidenceColumn = confidenceColumn)
+          sfFile
+    } 
   }
 
-
+sfFile$geomID<-row.names(sfFile)
+  return(sfFile)
 
 }

R/produceAnalysis.R

@@ -29,7 +29,7 @@
 #'
 #' @examples
 #' produceAnalysis(location="Redon", outDir=paste0(system.file(package="lczexplore"),"/tinytest"),
-#' wf1="bdtopo_2_2", wf2="osm", refYear1="2022", refYear2="2022", repr="standard", saveG=location)
+#' wf1="bdtopo_2_2", wf2="osm", refYear1="2022", refYear2="2022", repr="standard", saveG="")
 produceAnalysis<-function(location="Redon",
                           outDir=getwd(),
                           wf1="bdtopo_2_2",