regenerated documentation

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
 S3method(split,line)
-export(map_spectral_species)
-export(perform_PCA)
-export(perform_radiometric_filtering)
-export(select_PCA_components)
 export(check_data)
 export(diversity_from_plots)
 export(list.shp)
 export(map_alpha_div)
 export(map_beta_div)
+export(map_spectral_species)
+export(perform_PCA)
+export(perform_radiometric_filtering)
 export(projection.file)
 export(raster2BIL)
+export(select_PCA_components)
 import(raster)
 import(tools)
 importFrom(dissUtils,diss)

man/map_alpha_div.Rd

@@ -4,7 +4,7 @@
 \alias{map_alpha_div}
 \title{maps alpha diversity indicators  based on prior selection of PCs}
 \usage{
-map_alpha_div(Input.Image.File, Output.Dir, Spatial.Unit,
+map_alpha_div(Input.Image.File, Output.Dir, window_size,
   TypePCA = "SPCA", nbclusters = 50, MinSun = 0.25, pcelim = 0.02,
   Index.Alpha = "Shannon", FullRes = TRUE, LowRes = FALSE,
   MapSTD = FALSE, nbCPU = FALSE, MaxRAM = FALSE)
@@ -14,7 +14,7 @@ map_alpha_div(Input.Image.File, Output.Dir, Spatial.Unit,
 
 \item{Output.Dir}{character. Output directory.}
 
-\item{Spatial.Unit}{numeric. Size of spatial units (in pixels) to compute diversity.}
+\item{window_size}{numeric. Size of spatial units (in pixels) to compute diversity.}
 
 \item{TypePCA}{character. Type of PCA (PCA, SPCA, NLPCA...).}
 

man/map_beta_div.Rd

@@ -4,17 +4,17 @@
 \alias{map_beta_div}
 \title{maps beta diversity indicator based on spectral species distribution}
 \usage{
-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)
+map_beta_div(Input.Image.File, Output.Dir, window_size, 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)
 }
 \arguments{
 \item{Input.Image.File}{character. Path and name of the image to be processed.}
 
 \item{Output.Dir}{character. Output directory.}
 
-\item{Spatial.Unit}{numeric. Dimensions of the spatial unit.}
+\item{window_size}{numeric. Dimensions of the spatial unit.}
 
 \item{TypePCA}{character. Type of PCA (PCA, SPCA, NLPCA...).}
 

man/Map.Spectral.Species.Rd → man/map_spectral_species.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/Lib_MapSpectralSpecies.R
-\name{Map.Spectral.Species}
-\alias{Map.Spectral.Species}
+\name{map_spectral_species}
+\alias{map_spectral_species}
 \title{maps spectral species based on PCA file computed previously}
 \usage{
-Map.Spectral.Species(Input.Image.File, Output.Dir, PCA.Files,
+map_spectral_species(Input.Image.File, Output.Dir, PCA.Files,
   TypePCA = "SPCA", nbclusters = 50, nbCPU = 1, MaxRAM = FALSE)
 }
 \arguments{

man/Perform.PCA.Image.Rd → man/perform_PCA.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/Lib_PerformPCA.R
-\name{Perform.PCA.Image}
-\alias{Perform.PCA.Image}
+\name{perform_PCA}
+\alias{perform_PCA}
 \title{Performs PCA for all images and create PCA file with either all or a selection of PCs}
 \usage{
-Perform.PCA.Image(ImPath, ImPathShade, Output.Dir,
-  Continuum.Removal = TRUE, TypePCA = "SPCA", FilterPCA = FALSE,
-  Excluded.WL = FALSE, NbIter = 20, nbCPU = 1, MaxRAM = 0.25)
+perform_PCA(ImPath, ImPathShade, Output.Dir, Continuum.Removal = TRUE,
+  TypePCA = "SPCA", FilterPCA = FALSE, Excluded.WL = FALSE,
+  NbIter = 20, nbCPU = 1, MaxRAM = 0.25)
 }
 \arguments{
 \item{Output.Dir}{output directory}

man/Perform.Radiometric.Filtering.Rd → man/perform_radiometric_filtering.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/Lib_FilterData.R
-\name{Perform.Radiometric.Filtering}
-\alias{Perform.Radiometric.Filtering}
+\name{perform_radiometric_filtering}
+\alias{perform_radiometric_filtering}
 \title{Performs radiometric filtering based on three criteria: NDVI, NIR reflectance, Blue reflectance}
 \usage{
-Perform.Radiometric.Filtering(Image.Path, Mask.Path, Output.Dir,
+perform_radiometric_filtering(Image.Path, Mask.Path, Output.Dir,
   TypePCA = "SPCA", NDVI.Thresh = 0.5, Blue.Thresh = 500,
   NIR.Thresh = 1500, Blue = 480, Red = 700, NIR = 835)
 }

man/Select.Components.Rd → man/select_PCA_components.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/Lib_PerformPCA.R
-\name{Select.Components}
-\alias{Select.Components}
+\name{select_PCA_components}
+\alias{select_PCA_components}
 \title{Check if principal components are properly selected as expected by the method}
 \usage{
-Select.Components(Input.Image.File, Output.Dir, PCA.Files,
+select_PCA_components(Input.Image.File, Output.Dir, PCA.Files,
   TypePCA = "SPCA", File.Open = FALSE)
 }
 \arguments{