- added input argument type for main functions

- added documentation to repository

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R/Lib_CheckConvertData.R

@@ -13,7 +13,7 @@
 #' converts a raster into BIL format as expected by DivMapping codes
 #'
 #' @param Raster_Path character. Full path for the raster to be converted
-#' @param Sensor character. Name of the sensor
+#' @param Sensor character. Name of the sensor. a .hdr template for the sensor should be provided in extdata/HDR
 #' @param Convert_Integer boolean. Should data be converted into integer ?
 #' @param Multiplying_Factor numeric. Multiplying factor (eg convert real reflectance values between 0 and 1 into integer between 0 and 10000).
 #' @param Output_Dir character. Path to output directory.
@@ -154,9 +154,10 @@ raster2BIL <- function(Raster_Path, Sensor = "unknown", Output_Dir = FALSE, Conv
 
 #' Checks if the data to be processed has the format type expected
 #'
-#' @param Raster_Path full path for the raster to be converted
-#' @param Mask is the raster a mask?
+#' @param Raster_Path character. full path for the raster to be converted
+#' @param Mask boolean. Set true if the raster is a mask
 #'
+#' @return
 #' @export
 check_data <- function(Raster_Path, Mask = FALSE) {
   HDR_Path <- get_HDR_name(Raster_Path)

R/Lib_FilterData.R

@@ -11,16 +11,16 @@
 
 #' Performs radiometric filtering based on three criteria: NDVI, NIR reflectance, Blue reflectance
 #'
-#' @param Image_Path Path of the image to be processed
-#' @param Mask_Path Path of the mask corresponding to the image
-#' @param Output_Dir output directory
-#' @param TypePCA Type of PCA: "PCA" or "SPCA"
-#' @param NDVI_Thresh NDVI threshold applied to produce a mask (select pixels with NDVI>NDVI_Thresh)
-#' @param Blue_Thresh Blue threshold applied to produce a mask (select pixels with Blue refl < Blue_Thresh --> filter clouds) refl expected between 0 and 10000
-#' @param NIR_Thresh NIR threshold applied to produce a mask (select pixels with NIR refl < NIR_Thresh) refl expected between 0 and 10000
-#' @param Blue central wavelength corresponding to the blue spectral band (in nanometers)
-#' @param Red central wavelength corresponding to the red spectral band (in nanometers)
-#' @param NIR central wavelength corresponding to the NIR spectral band (in nanometers)
+#' @param Image_Path character. Path of the image to be processed
+#' @param Mask_Path character. Path of the mask corresponding to the image
+#' @param Output_Dir character. Path for output directory
+#' @param TypePCA character. Type of PCA: choose either "PCA" or "SPCA"
+#' @param NDVI_Thresh numeric. NDVI threshold applied to produce a mask (select pixels with NDVI>NDVI_Thresh)
+#' @param Blue_Thresh numeric. Blue threshold applied to produce a mask (select pixels with Blue refl < Blue_Thresh --> filter clouds) refl expected between 0 and 10000
+#' @param NIR_Thresh numeric. NIR threshold applied to produce a mask (select pixels with NIR refl < NIR_Thresh) refl expected between 0 and 10000
+#' @param Blue numeric. central wavelength corresponding to the blue spectral band (in nanometers)
+#' @param Red numeric. central wavelength corresponding to the red spectral band (in nanometers)
+#' @param NIR numeric. central wavelength corresponding to the NIR spectral band (in nanometers)
 #'
 #' @return ImPathShade = updated shademask file
 #' @export

R/Lib_MapSpectralSpecies.R

@@ -13,11 +13,11 @@
 
 #' maps spectral species based on PCA file computed previously
 #'
-#' @param Input_Image_File Path and name of the image to be processed
-#' @param Output_Dir output directory
-#' @param TypePCA Type of PCA: "PCA" or "SPCA"
-#' @param PCA_Files path for PCA file
-#' @param ImPathShade path for shade file (= mask)
+#' @param Input_Image_File character. Path of the image to be processed
+#' @param Output_Dir character. Path for output directory
+#' @param TypePCA character. Type of PCA: choose either "PCA" or "SPCA"
+#' @param PCA_Files character. Path of the PCA image
+#' @param ImPathShade character. Path of the mask corresponding to the image
 #' @param Pix_Per_Partition number of pixels for each partition
 #' @param nb_partitions number of partition
 #' @param nbCPU numeric. Number of CPUs to use in parallel.

R/Lib_PerformPCA.R

@@ -11,13 +11,13 @@
 
 #' Performs PCA for all images and create PCA file with either all or a selection of PCs
 #'
-#' @param ImPath Path and name of the image to be processed
-#' @param ImPathShade correponding shade mask
-#' @param Output_Dir output directory
-#' @param Continuum_Removal boolean: should continuum removal be applied?
-#' @param TypePCA Type of PCA: "PCA" or "SPCA"
-#' @param FilterPCA boolean. If TRUE 2nd filtering based on PCA
-#' @param Excluded_WL boolean. Water Vapor Absorption domains (in nanometers). Can also be used to exclude spectific domains
+#' @param ImPath character. Path of the image to be processed
+#' @param ImPathShade character. Path of the mask corresponding to the image
+#' @param Output_Dir character. Path for output directory
+#' @param Continuum_Removal boolean. Set to TRUE if continuum removal should be applied
+#' @param TypePCA character. Type of PCA: choose either "PCA" or "SPCA"
+#' @param FilterPCA boolean. Set to TRUE if 2nd filtering based on PCA is required
+#' @param Excluded_WL  numeric. Water Vapor Absorption domains (in nanometers, min and max WL). Can also be used to exclude spectific domains. dims = N x 2 (N = number of domains to be eliminated)
 #' @param nb_partitions numeric. Number of repetitions to estimate diversity from the raster (averaging repetitions).
 #' @param nbCPU numeric. Number fo CPUs in use.
 #' @param MaxRAM numeric. Maximum size of chunk in GB to limit RAM allocation when reading image file.
@@ -482,11 +482,11 @@ define_pixels_per_iter <- function(ImNames, nb_partitions = nb_partitions) {
 
 #' Check if principal components are properly selected as expected by the method
 #'
-#' @param Output_Dir output directory
-#' @param Input_Image_File path for image to be processed
-#' @param PCA_Files path of PCA files
-#' @param TypePCA Type of PCA: "PCA" or "SPCA"
-#' @param File_Open Boolean. automatically opens file if TRUE
+#' @param Input_Image_File character. Path of the image to be processed
+#' @param Output_Dir character. Path for output directory
+#' @param PCA_Files character. Path of the PCA image
+#' @param TypePCA character. Type of PCA: choose either "PCA" or "SPCA"
+#' @param File_Open Boolean. Set to TRUE for file to open automatically
 #'
 #' @return nothing
 #' @importFrom utils file.edit