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new functions for LCZ compare article
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| #' In a given list of directories the function looks for LCZ datafiles, return a datasets LCZ values for each geom and workflow | ||
| #' @param dirList the list of directories for which the different LCZ files will be intersected | ||
| #' @param workflowNames sets the names of workflows and define the name of the files which will be loaded and intersected | ||
| #' @param for each diretory from dirList, a location name must be fed to the function | ||
| #' @importFrom ggplot2 geom_sf guides ggtitle aes | ||
| #' @import sf dplyr cowplot forcats units tidyr RColorBrewer utils grDevices rlang | ||
| #' @return returns graphics of comparison and an object called matConfOut which contains : | ||
| #' matConfLong, a confusion matrix in a longer form, | ||
| #' matConfPlot is a ggplot2 object showing the confusion matrix. | ||
| #' percAgg is the general agreement between the two sets of LCZ, expressed as a percentage of the total area of the study zone | ||
| #' pseudoK is a heuristic estimate of a Cohen's kappa coefficient of agreement between classifications | ||
| #' If saveG is not an empty string, graphics are saved under "saveG.png" | ||
| #' @export | ||
| #' @examples | ||
| #' | ||
| concatIntersectedLocations<-function(dirList, locations, workflowNames = c("osm","bdt","iau","wudapt")){ | ||
| allLocAllWfSf<-matrix(ncol = 5, nrow = 0) | ||
| allLocAllWfSf<-as.data.frame(allLocAllWfSf) | ||
| names(allLocAllWfSf)<- c("lcz_primary", "location", "wf", "area", "geometry") | ||
| for( i in 1:length(dirList)){ | ||
| dirPath<-dirList[1] | ||
| aLocation<-locations[i] | ||
| sfList<-loadMultipleSf(dirPath = dirPath, | ||
| workflowNames = workflowNames , location = aLocation ) | ||
| if(substr(dirPath, nchar(dirPath), nchar(dirPath))!="/"){dirPath<-paste0(dirPath, "/")} | ||
| zoneSfPath<-paste0(dirPath,"zone.fgb") | ||
| zoneSf<-read_sf(zoneSfPath) | ||
| sfList<-repairRoadsIAU(sfList = sfList, zoneSf = zoneSf, location = location) | ||
| concatSf<-concatAlocationWorkflows(sfList = sfList, | ||
| location = location, refCrs = 1) | ||
| allLocAllWfSf<-rbind(allLocAllWfSf, concatSf) | ||
| } | ||
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| allLocAllWfSf<- st_as_sf(allLocAllWfSf) | ||
| } | ||
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| rootDir<-"/home/gousseff/Documents/3_data/data_article_LCZ_diff_algos/newDataTree" | ||
| setwd(rootDir) | ||
| allLCZDirNames <- list.dirs()[-1] | ||
| allLCZDirNames <- substr(allLCZDirNames, start = 2, stop = 1000) | ||
| allLocationsNames<-substr(allLCZDirNames, start = 2, stop = 1000) | ||
| allLCZDirNames<-paste0(rootDir, allLCZDirNames, "/") | ||
| allLocallWfs<-concatIntersectedLocations( | ||
| dirList = allLCZDirNames, locations = allLocationsNames , workflowNames = c("osm","bdt","iau","wudapt")) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,52 @@ | ||
| #' in a given directory, if several LCZ files are present, it plots the repartition of LCZ regarding of their source (workflow) | ||
| #' NOTE: to represent the map of LCZ for a given fil, use `showLCZ` function instead | ||
| #' @param workflownames is a vector of prefixes. The LCZ files must benames workflow_rsu.fgb | ||
| #' @param plotNow. If TRUE, the boxplot of the repartition will be printed | ||
| #' @param plotSave. If TRUE, the plot will be saved in the directory pointed by dirPath | ||
| #' @importFrom ggplot2 geom_sf guides ggtitle aes | ||
| #' @importFrom caret dummyVars | ||
| #' @import sf dplyr cowplot forcats units tidyr RColorBrewer utils grDevices rlang | ||
| #' @return Cramer's V between pairs of levels, in a matrix (cramerMatrix) or long form (cramerLong), | ||
| #' and a dataframe with the nbOutAssociation most significant association | ||
| #' @export | ||
| #' @examples | ||
| plotLCZaLocation<-function(dirPath, location, workflowNames = c("osm","bdt","iau","wudapt"), | ||
| plotNow = FALSE, plotSave = TRUE){ | ||
| colorMap<-c("#8b0101","#cc0200","#fc0001","#be4c03","#ff6602","#ff9856", | ||
| "#fbed08","#bcbcba","#ffcca7","#57555a","#006700","#05aa05", | ||
| "#648423","#bbdb7a","#010101","#fdf6ae","#6d67fd") | ||
| names(colorMap)<-c(1:10,101:107) | ||
| etiquettes<-c("LCZ 1: Compact high-rise","LCZ 2: Compact mid-rise","LCZ 3: Compact low-rise", | ||
| "LCZ 4: Open high-rise","LCZ 5: Open mid-rise","LCZ 6: Open low-rise", | ||
| "LCZ 7: Lightweight low-rise","LCZ 8: Large low-rise", | ||
| "LCZ 9: Sparsely built","LCZ 10: Heavy industry", | ||
| "LCZ A: Dense trees", "LCZ B: Scattered trees", | ||
| "LCZ C: Bush,scrub","LCZ D: Low plants", | ||
| "LCZ E: Bare rock or paved","LCZ F: Bare soil or sand","LCZ G: Water") | ||
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| sfList<-loadMultipleSf(dirPath = dirPath, | ||
| workflowNames = workflowNames , location = location ) | ||
| if(substr(dirPath, nchar(dirPath), nchar(dirPath))!="/"){dirPath<-paste0(dirPath, "/")} | ||
| zoneSfPath<-paste0(dirPath,"zone.fgb") | ||
| zoneSf<-read_sf(zoneSfPath) | ||
| sfList<-repairRoadsIAU(sfList = sfList, zoneSf = zoneSf, location = location) | ||
| concatSf<-concatAlocationWorkflows(sfList = sfList, | ||
| location = location, refCrs = 1) | ||
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| surfaces<-concatSf %>% | ||
| mutate(wf = factor(wf, levels = c("bdt", "osm", "wudapt", "iau"))) %>% | ||
| group_by(wf, lcz_primary) %>% summarise(area=sum(area), location=unique(location)) | ||
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| location<-unique(surfaces$location) | ||
| outPlot<-ggplot(surfaces, aes(fill=lcz_primary, y=area, x=wf)) + | ||
| geom_col() + | ||
| # scale_fill_viridis(discrete = T) + | ||
| scale_fill_manual(values=colorMap, breaks = names(colorMap), labels = etiquettes) + | ||
| ggtitle(paste0("LCZ repartition by workflow for ", location)) | ||
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| plotName<-paste0(dirPath, "LCZbyWfBoxplot.png") | ||
| if(plotSave){ggsave(plotName, outPlot)} | ||
| if (plotNow){print(outPlot)} | ||
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| return(outPlot) | ||
| } |
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