change main functions name to respect standard

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
 S3method(split,line)
-export(Check.Data.Format)
-export(Convert.Raster2BIL)
-export(Get.Diversity.From.Plots)
-export(Get.List.Shp)
-export(Get.Projection)
-export(Map.Alpha.Diversity)
-export(Map.Beta.Diversity)
 export(Map.Spectral.Species)
 export(Perform.PCA.Image)
 export(Perform.Radiometric.Filtering)
 export(Select.Components)
+export(check_data)
+export(diversity_from_plots)
+export(list.shp)
+export(map_alpha_div)
+export(map_beta_div)
+export(projection.file)
+export(raster2BIL)
 import(raster)
 import(tools)
 importFrom(dissUtils,diss)
@@ -23,6 +23,9 @@ importFrom(future.apply,future_lapply)
 importFrom(labdsv,pco)
 importFrom(matlab,padarray)
 importFrom(matrixStats,rowSds)
+importFrom(raster,projection)
+importFrom(raster,raster)
+importFrom(raster,shapefile)
 importFrom(raster,writeRaster)
 importFrom(rgdal,readOGR)
 importFrom(snow,splitRows)

R/Lib_CheckConvertData.R

@@ -174,7 +174,7 @@ check_data <- function(Raster.Path, Mask = FALSE) {
       message("Current Image format")
       print(HDR$interleave)
       message("Please run the function named ")
-      print("Convert.Raster2BIL")
+      print("raster2BIL")
       message("in order to convert your raster data")
       message("or use appropriate software")
       message("*********************************************************")
@@ -223,7 +223,7 @@ check_data <- function(Raster.Path, Mask = FALSE) {
     message("ENVI hdr file with band interleaved by line (BIL) file format")
     message("")
     message("Please run the function named ")
-    print("Convert.Raster2BIL")
+    print("raster2BIL")
     message("in order to convert your raster data")
     message("*********************************************************")
     message("")

R/Lib_MapAlphaDiversity.R

@@ -26,7 +26,7 @@
 #' @param Index.Alpha character. Either 'Shannon', 'Simpson' or 'Fisher'.
 #'
 #' @export
-alpha_div <- function(Input.Image.File, Output.Dir, Spatial.Unit,
+map_alpha_div <- function(Input.Image.File, Output.Dir, Spatial.Unit,
                                 TypePCA = "SPCA", nbclusters = 50,
                                 MinSun = 0.25, pcelim = 0.02,
                                 Index.Alpha = "Shannon", FullRes = TRUE,

R/Lib_MapBetaDiversity.R

@@ -29,7 +29,7 @@
 #' @param pcelim numeric. Minimum contribution (in \%) required for a spectral species
 #'
 #' @export
-Map.Beta.Diversity <- function(Input.Image.File, Output.Dir, Spatial.Unit,
+map_beta_div <- function(Input.Image.File, Output.Dir, Spatial.Unit,
                                TypePCA = "SPCA", nbclusters = 50,
                                Nb.Units.Ordin = 2000, MinSun = 0.25,
                                pcelim = 0.02, scaling = "PCO", FullRes = TRUE,

R/Lib_Validation_biodivMapR.R

@@ -192,7 +192,7 @@ diversity_from_plots = function(Raster, Plots,NbClusters = 50,Name.Plot = FALSE)
     if (file.exists(paste(file_path_sans_ext(File.Vector),'.shp',sep=''))){
       Plot                = readOGR(Dir.Vector,Name.Vector[[ip]],verbose = FALSE)
       # check if vector and rasters are in teh same referential
-      Projection.Plot     = Get.Projection(File.Vector,'vector')
+      Projection.Plot     = projection.file(File.Vector,'vector')
       # if not, convert vector file
       if (!Projection.Raster==Projection.Plot){
         if (!file.exists(File.Vector.reproject)){

examples/example_script.R

@@ -28,10 +28,10 @@
 # path (absolute or relative) for the image to process
 # expected to be in ENVI HDR format, BIL interleaved
 Input.Image.File  = system.file('extdata', 'RASTER', 'S2A_T33NUD_20180104_Subset', package = 'biodivMapR')
-Check.Data.Format(Input.Image.File)
+check_data(Input.Image.File)
 
 # convert the image using Convert.Raster2BIL if not in the proper format
-Input.Image.File  = Convert.Raster2BIL(Raster.Path = Input.Image.File,
+Input.Image.File  = raster2BIL(Raster.Path = Input.Image.File,
                                        Sensor = 'SENTINEL_2A',
                                        Convert.Integer = TRUE,
                                        Output.Directory = '~/test')
@@ -59,7 +59,7 @@ FilterPCA         = TRUE
 ################################################################################
 ##      Check if the image format is compatible with codes (ENVI BIL)         ##
 ################################################################################
-Check.Data.Format(Input.Image.File)
+check_data(Input.Image.File)
 
 ################################################################################
 ##                    DEFINE PARAMETERS FOR METHOD                            ##
@@ -98,10 +98,10 @@ Map.Spectral.Species(Input.Image.File,Output.Dir,PCA.Files,nbCPU=nbCPU,MaxRAM=Ma
 print("MAP ALPHA DIVERSITY")
 # Index.Alpha   = c('Shannon','Simpson')
 Index.Alpha   = c('Shannon')
-Map.Alpha.Diversity(Input.Image.File,Output.Dir,Spatial.Res,nbCPU=nbCPU,MaxRAM=MaxRAM,Index.Alpha = Index.Alpha)
+map_alpha_div(Input.Image.File,Output.Dir,Spatial.Res,nbCPU=nbCPU,MaxRAM=MaxRAM,Index.Alpha = Index.Alpha)
 
 print("MAP BETA DIVERSITY")
-Map.Beta.Diversity(Input.Image.File,Output.Dir,Spatial.Res,nbCPU=nbCPU,MaxRAM=MaxRAM)
+map_beta_div(Input.Image.File,Output.Dir,Spatial.Res,nbCPU=nbCPU,MaxRAM=MaxRAM)
 
 ################################################################################
 ##          COMPUTE ALPHA AND BETA DIVERSITY FROM FIELD PLOTS                 ##
@@ -118,15 +118,15 @@ vect        = system.file('extdata', 'VECTOR', package = 'biodivMapR')
 Shannon.All = list()
 
 # list vector data
-Path.Vector         = Get.List.Shp(vect)
+Path.Vector         = list.shp(vect)
 Name.Vector         = tools::file_path_sans_ext(basename(Path.Vector))
 
 # read raster data including projection
 RasterStack         = stack(Path.Raster)
-Projection.Raster   = Get.Projection(Path.Raster,'raster')
+Projection.Raster   = projection.file(Path.Raster,'raster')
 
 # get alpha and beta diversity indicators corresponding to shapefiles
-Biodiv.Indicators           = Get.Diversity.From.Plots(Raster = Path.Raster, Plots = Path.Vector,NbClusters = nbclusters)
+Biodiv.Indicators           = diversity_from_plots(Raster = Path.Raster, Plots = Path.Vector,NbClusters = nbclusters)
 # if no name
 Biodiv.Indicators$Name.Plot = seq(1,length(Biodiv.Indicators$Shannon[[1]]),by = 1)
 Shannon.RS                  = c(Biodiv.Indicators$Shannon)[[1]]

man/Check.Data.Format.Rd → man/check_data.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/Lib_CheckConvertData.R
-\name{Check.Data.Format}
-\alias{Check.Data.Format}
+\name{check_data}
+\alias{check_data}
 \title{Checks if the data to be processed has the format type expected}
 \usage{
-Check.Data.Format(Raster.Path, Mask = FALSE)
+check_data(Raster.Path, Mask = FALSE)
 }
 \arguments{
 \item{Raster.Path}{full path for the raster to be converted}

man/Get.Diversity.From.Plots.Rd → man/diversity_from_plots.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/Lib_Validation_biodivMapR.R
-\name{Get.Diversity.From.Plots}
-\alias{Get.Diversity.From.Plots}
+\name{diversity_from_plots}
+\alias{diversity_from_plots}
 \title{gets alpha diversity indicators from plot}
 \usage{
-Get.Diversity.From.Plots(Raster, Plots, NbClusters = 50,
-  Name.Plot = FALSE)
+diversity_from_plots(Raster, Plots, NbClusters = 50, Name.Plot = FALSE)
 }
 \arguments{
 \item{Raster}{SpectralSpecies file computed from DiverstyMapping method}

man/Get.List.Shp.Rd → man/list.shp.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/Lib_Validation_biodivMapR.R
-\name{Get.List.Shp}
-\alias{Get.List.Shp}
+\name{list.shp}
+\alias{list.shp}
 \title{Get list of shapefiles in a directory}
 \usage{
-Get.List.Shp(Path.Shp)
+list.shp(x)
 }
 \arguments{
-\item{Path.Shp}{path of the directory containing shapefiles}
+\item{x}{character or list. Directory containing shapefiles}
 }
 \value{
 list of shapefiles names

man/Map.Alpha.Diversity.Rd → man/map_alpha_div.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/Lib_MapAlphaDiversity.R
-\name{Map.Alpha.Diversity}
-\alias{Map.Alpha.Diversity}
+\name{map_alpha_div}
+\alias{map_alpha_div}
 \title{maps alpha diversity indicators  based on prior selection of PCs}
 \usage{
-Map.Alpha.Diversity(Input.Image.File, Output.Dir, Spatial.Unit,
+map_alpha_div(Input.Image.File, Output.Dir, Spatial.Unit,
   TypePCA = "SPCA", nbclusters = 50, MinSun = 0.25, pcelim = 0.02,
   Index.Alpha = "Shannon", FullRes = TRUE, LowRes = FALSE,
   MapSTD = FALSE, nbCPU = FALSE, MaxRAM = FALSE)

man/Map.Beta.Diversity.Rd → man/map_beta_div.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/Lib_MapBetaDiversity.R
-\name{Map.Beta.Diversity}
-\alias{Map.Beta.Diversity}
+\name{map_beta_div}
+\alias{map_beta_div}
 \title{maps beta diversity indicator based on spectral species distribution}
 \usage{
-Map.Beta.Diversity(Input.Image.File, Output.Dir, Spatial.Unit,
+map_beta_div(Input.Image.File, Output.Dir, Spatial.Unit,
   TypePCA = "SPCA", nbclusters = 50, Nb.Units.Ordin = 2000,
   MinSun = 0.25, pcelim = 0.02, scaling = "PCO", FullRes = TRUE,
   LowRes = FALSE, nbCPU = 1, MaxRAM = 0.25)

man/Get.Projection.Rd → man/projection.file.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/Lib_Validation_biodivMapR.R
-\name{Get.Projection}
-\alias{Get.Projection}
+\name{projection.file}
+\alias{projection.file}
 \title{get projection of a raster or a vector}
 \usage{
-Get.Projection(Path.File, Type = "raster")
+projection.file(file, type = "raster")
 }
 \arguments{
-\item{Path.File}{path for a raster or vector (shapefile)}
+\item{file}{path for a raster or vector (shapefile)}
 
-\item{Type}{'raster' or 'vector'}
+\item{type}{'raster' or 'vector'}
 }
 \value{
 projection

man/Convert.Raster2BIL.Rd → man/raster2BIL.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/Lib_CheckConvertData.R
-\name{Convert.Raster2BIL}
-\alias{Convert.Raster2BIL}
+\name{raster2BIL}
+\alias{raster2BIL}
 \title{converts a raster into BIL format as expected by DivMapping codes}
 \usage{
-Convert.Raster2BIL(Raster.Path, Sensor = "unknown",
-  Output.Directory = FALSE, Convert.Integer = TRUE,
-  Multiplying.Factor = 1, Multiplying.Factor.Last = 1)
+raster2BIL(Raster.Path, Sensor = "unknown", Output.Directory = FALSE,
+  Convert.Integer = TRUE, Multiplying.Factor = 1,
+  Multiplying.Factor.Last = 1)
 }
 \arguments{
 \item{Raster.Path}{character. Full path for the raster to be converted}

vignettes/tutorial.Rmd

@@ -49,9 +49,9 @@ The output directory defined with `Output.Dir` will contain all the results. For
 
 ```{r Input / Output files}
 Input.Image.File  = system.file('extdata', 'RASTER', 'S2A_T33NUD_20180104_Subset', package = 'biodivMapR')
-Check.Data.Format(Input.Image.File)
+check_data(Input.Image.File)
 
-Input.Image.File  = Convert.Raster2BIL(Raster.Path = Input.Image.File,
+Input.Image.File  = raster2BIL(Raster.Path = Input.Image.File,
                                        Sensor = 'SENTINEL_2A',
                                        Convert.Integer = TRUE,
                                        Output.Directory = '~/test')
@@ -136,11 +136,11 @@ Map.Spectral.Species(Input.Image.File, Output.Dir, PCA.Files,
 print("MAP ALPHA DIVERSITY")
 # Index.Alpha   = c('Shannon','Simpson')
 Index.Alpha   = c('Shannon')
-Map.Alpha.Diversity(Input.Image.File, Output.Dir, Spatial.Res,
+map_alpha_div(Input.Image.File, Output.Dir, Spatial.Res,
                     nbCPU = nbCPU, MaxRAM = MaxRAM, Index.Alpha = Index.Alpha)
 
 print("MAP BETA DIVERSITY")
-Map.Beta.Diversity(Input.Image.File, Output.Dir, Spatial.Res,
+map_beta_div(Input.Image.File, Output.Dir, Spatial.Res,
                    nbCPU = nbCPU, MaxRAM = MaxRAM)
 ```
 
@@ -159,15 +159,15 @@ vect        = system.file('extdata', 'VECTOR', package = 'biodivMapR')
 Shannon.All = list() # ??
 
 # list vector data
-Path.Vector         = Get.List.Shp(vect)
+Path.Vector         = list.shp(vect)
 Name.Vector         = tools::file_path_sans_ext(basename(Path.Vector))
 
 # read raster data including projection
 RasterStack         = stack(Path.Raster)
-Projection.Raster   = Get.Projection(Path.Raster,'raster')
+Projection.Raster   = projection.file(Path.Raster,'raster')
 
 # get alpha and beta diversity indicators corresponding to shapefiles
-Biodiv.Indicators           = Get.Diversity.From.Plots(Raster = Path.Raster, Plots = Path.Vector,NbClusters = nbclusters)
+Biodiv.Indicators           = diversity_from_plots(Raster = Path.Raster, Plots = Path.Vector,NbClusters = nbclusters)
 # if no name
 Biodiv.Indicators$Name.Plot = seq(1,length(Biodiv.Indicators$Shannon[[1]]),by = 1)
 Shannon.RS                  = c(Biodiv.Indicators$Shannon)[[1]]