Replace paste0 and fs::file_path with file.path for paths

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2: do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 export(LPDAACDataPool)
 export(clipLevel1B)
@@ -17,6 +17,7 @@ export(clipLevel2BPAVDProfile)
 export(clipLevel2BPAVDProfileGeometry)
 export(clipLevel2BVPM)
 export(clipLevel2BVPMGeometry)
+export(close)
 export(gediWFMetrics)
 export(gediWFSimulator)
 export(gedifinder)
@@ -42,8 +43,6 @@ exportClasses(gedi.level1b)
 exportClasses(gedi.level1bSim)
 exportClasses(gedi.level2a)
 exportClasses(gedi.level2b)
-exportMethods(close)
-exportMethods(plot)
 import(data.table)
 import(fs)
 import(ggplot2)

R/C_processExtractMetrics.R

@@ -135,11 +135,11 @@
 #'                            coords = c(xcenter_Savanna, ycenter_Savanna))
 #'
 #'# Extracting GEDI feull-waveform derived metrics
-#'wf_amazon_metrics<-gediWFMetrics(input=wf_amazon,outRoot=getwd())
-#'wf_cerrado_metrics<-gediWFMetrics(input=wf_cerrado,outRoot=getwd())
+#'wf_amazon_metrics<-gediWFMetrics(input=wf_amazon,outRoot=file.path(getwd(), "amazon"))
+#'wf_cerrado_metrics<-gediWFMetrics(input=wf_cerrado,outRoot=file.path(getwd(), "cerrado"))
 #'
-#'wf_amazon@h5$close()
-#'wf_cerrado@h5$close()
+#'close(wf_amazon)
+#'close(wf_cerrtado)
 #'
 #'metrics<-rbind(wf_amazon_metrics,wf_cerrado_metrics)
 #'rownames(metrics)<-c("Amazon","Cerrado")
@@ -404,7 +404,7 @@ gediWFMetrics = function(
   cleanInList(inputInList)
 
   if (res==0) {
-    output = paste0(outRoot, ".metric.txt")
+    output = fs::path_ext_set(outRoot, ".metric.txt")
     header = read.csv(output, sep=",", nrow=1, header = FALSE, as.is=TRUE)
     header[ncol(header)] = NULL
     header=gsub(" *\\d+ *([^,]*)", "\\1", header)

R/C_simulateFullWaveform.R

@@ -132,9 +132,9 @@
 #'plot(wf_Savanna, relative=TRUE, polygon=TRUE, type="l", lwd=2, col="green",
 #'     xlab="Waveform Amplitude (%)", ylab="Elevation (m)", ylim=c(815,835))
 #'grid()
-#'
-#'wf_Amazon@h5$close_all()
-#'wf_Savanna@h5$close_all()
+#' 
+#'close(wf_Amazon)
+#'close(wf_Amazon)
 #'}
 #'
 #' @import hdf5r
@@ -234,7 +234,7 @@ gediWFSimulator = function(
 
   inputInList = inputOrInList(input)
   if (fs::path_ext(output) != "h5") {
-    output = paste0(output, ".h5")
+    output = fs::path_ext_set(output, ".h5")
   }
 
   .Call("C_gediSimulator",

R/LPDAACDataPool.R

@@ -56,7 +56,7 @@ LPDAACDataPool<-function(filepath,outdir){
 
       cat(paste0("Downloading file ",filename," \n"))
       # Write file to disk (authenticating with netrc) using the current directory/filename
-      response <- httr::GET(files[i], httr::write_disk(paste0(outdir,"\\",filename), overwrite = TRUE), httr::progress(),
+      response <- httr::GET(files[i], httr::write_disk(file.path(outdir, "",filename), overwrite = TRUE), httr::progress(),
                             httr::config(netrc = TRUE, netrc_file = netrc), httr::set_cookies("LC" = "cookies"))
 
       # Check to see if file downloaded correctly

R/class.gedi.R

@@ -63,6 +63,7 @@ gedi.fullwaveform <- setClass(
 #'
 #'@param x An object of class "gedi.fullwaveform". (output of \code{\link[rGEDI:getLevel1BWF]{getLevel1BWF}} function)
 #'@param y: not used (inherited from R base)
+#'@param ...: will be passed to the main plot
 #'
 #'@param relative if TRUE, the Wavform Amplitude will be showed in percentage (\%)
 #'@param polygon if TRUE, polygon will be added to the plot
@@ -86,13 +87,13 @@ setGeneric("plot", function(x, y, ...)
 #'                     "https://github.com/carlos-alberto-silva/rGEDI/",
 #'                     "releases/download/examples/examples.zip"
 #'              ),
-#'              destfile=paste0(outdir,"/examples.zip"))
+#'              destfile=file.path(outdir, "examples.zip"))
 #'
 #'# unzip the file
-#'unzip(paste0(outdir,"\\examples.zip"))
+#'unzip(file.path(outdir, "examples.zip"))
 #'
 #'# specify the path to GEDI level1B data
-#'level1bpath = paste0(outdir,"\\GEDI01_B_2019108080338_O01964_T05337_02_003_01_sub.h5")
+#'level1bpath = file.path(outdir, "GEDI01'_B_2019108080338_O01964_T05337_02_003_01_sub.h5")
 #'
 #'# Reading GEDI level1B file
 #'level1b<-readLevel1b(gedilevel1b)

R/clipLevel2BVPM.R

@@ -100,13 +100,13 @@ clipLevel2BVPM = function(level2BVPM,xmin, xmax, ymin, ymax){
 #'                     "https://github.com/carlos-alberto-silva/rGEDI/",
 #'                     "releases/download/examples/examples.zip"
 #'              ),
-#'              destfile=paste0(outdir,"/examples.zip"))
+#'              destfile=file.path(outdir, "examples.zip"))
 #'
 #'# unzip the file
-#'unzip(paste0(outdir,"\\examples.zip"))
+#'unzip(file.path(outdir, "examples.zip"))
 #'
 #'# specify the path to GEDI level2B data
-#'level2bpath = paste0(outdir,"\\GEDI02_B_2019108080338_O01964_T05337_02_001_01_sub.h5")
+#'level2bpath = file.path(outdir, "GEDI02_B_2019108080338_O01964_T05337_02_001_01_sub.h5")
 #'
 #'# Reading GEDI level1B file
 #'level2b<-readLevel2b(gedilevel2b)

R/getLevel2BVPM.R

@@ -34,13 +34,13 @@
 #'                     "https://github.com/carlos-alberto-silva/rGEDI/",
 #'                     "releases/download/examples/examples.zip"
 #'              ),
-#'              destfile=paste0(outdir,"/examples.zip"))
+#'              destfile=file.path(outdir, "examples.zip"))
 #'
 #'# unzip the file
-#'unzip(paste0(outdir,"\\examples.zip"))
+#'unzip(file.path(outdir, "examples.zip"))
 #'
 #'# specify the path to GEDI level2B data
-#'level2bpath = paste0(outdir,"\\GEDI02_B_2019108080338_O01964_T05337_02_001_01_sub.h5")
+#'level2bpath = file.path(outdir, "GEDI02_B_2019108080338_O01964_T05337_02_001_01_sub.h5")
 #'
 #'# Reading GEDI level1B file
 #'level2b<-readLevel2b(gedilevel2b)