Commit 4243b973 authored by jbferet's avatar jbferet
Browse files

regenerated documentation

parent 4072c872
# 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)
......
......@@ -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...).}
......
......@@ -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...).}
......
% 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{
......
% 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}
......
% 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)
}
......
% 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{
......
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