more internalization

R/RcppExports.R

@@ -2,11 +2,13 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 #' @rdname aspwb
+#' @keywords internal
 aspwbInput <- function(crop_factor, control, soil) {
  .Call(`_medfate_aspwbInput`, crop_factor, control, soil)
 }
 
 #' @rdname aspwb
+#' @keywords internal
 aspwb_day <- function(x, date, meteovec, latitude, elevation, slope = NA_real_, aspect = NA_real_, runon = 0.0, lateralFlows = NULL, waterTableDepth = NA_real_, modifyInput = TRUE) {
  .Call(`_medfate_aspwb_day`, x, date, meteovec, latitude, elevation, slope, aspect, runon, lateralFlows, waterTableDepth, modifyInput)
 }
@@ -65,6 +67,7 @@ aspwb_day <- function(x, date, meteovec, latitude, elevation, slope = NA_real_,
 #' S <- aspwb(x, examplemeteo, latitude = 41.82592, elevation = 100)
 #' 
 #' @name aspwb
+#' @keywords internal
 aspwb <- function(x, meteo, latitude, elevation, slope = NA_real_, aspect = NA_real_, waterTableDepth = NA_real_) {
  .Call(`_medfate_aspwb`, x, meteo, latitude, elevation, slope, aspect, waterTableDepth)
 }
@@ -542,91 +545,109 @@ fire_necrosisHeight <- function(Ib_surf, t_res, thermal_factor, T_air = 25.0, rh
 #' plant_ID(exampleforest, SpParamsMED)
 #' 
 #' @name plant_values
+#' @keywords internal
 plant_ID <- function(x, SpParams, treeOffset = 0L, shrubOffset = 0L) {
  .Call(`_medfate_cohortIDs`, x, SpParams, treeOffset, shrubOffset)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_basalArea <- function(x, SpParams) {
  .Call(`_medfate_cohortBasalArea`, x, SpParams)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_largerTreeBasalArea <- function(x, SpParams, self_proportion = 0.5) {
  .Call(`_medfate_cohortLargerTreeBasalArea`, x, SpParams, self_proportion)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_cover <- function(x, SpParams) {
  .Call(`_medfate_cohortCover`, x, SpParams)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_species <- function(x, SpParams) {
  .Call(`_medfate_cohortSpecies`, x, SpParams)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_speciesName <- function(x, SpParams) {
  .Call(`_medfate_cohortSpeciesName`, x, SpParams)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_density <- function(x, SpParams) {
  .Call(`_medfate_cohortDensity`, x, SpParams)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_height <- function(x, SpParams) {
  .Call(`_medfate_cohortHeight`, x, SpParams)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_individualArea <- function(x, SpParams) {
  .Call(`_medfate_cohortIndividualArea`, x, SpParams)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_crownRatio <- function(x, SpParams) {
  .Call(`_medfate_cohortCrownRatio`, x, SpParams)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_crownBaseHeight <- function(x, SpParams) {
  .Call(`_medfate_cohortCrownBaseHeight`, x, SpParams)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_crownLength <- function(x, SpParams) {
  .Call(`_medfate_cohortCrownLength`, x, SpParams)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_foliarBiomass <- function(x, SpParams, gdd = NA_real_) {
  .Call(`_medfate_cohortFoliarBiomass`, x, SpParams, gdd)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_fuelLoading <- function(x, SpParams, gdd = NA_real_, includeDead = TRUE) {
  .Call(`_medfate_cohortFuelLoading`, x, SpParams, gdd, includeDead)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_equilibriumLeafLitter <- function(x, SpParams, AET = 800) {
  .Call(`_medfate_cohortEquilibriumLeafLitter`, x, SpParams, AET)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_equilibriumSmallBranchLitter <- function(x, SpParams, smallBranchDecompositionRate = 0.81) {
  .Call(`_medfate_cohortEquilibriumSmallBranchLitter`, x, SpParams, smallBranchDecompositionRate)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_phytovolume <- function(x, SpParams) {
  .Call(`_medfate_cohortPhytovolume`, x, SpParams)
 }
 
 #' @rdname plant_values
+#' @keywords internal
 plant_LAI <- function(x, SpParams, gdd = NA_real_, bounded = TRUE) {
  .Call(`_medfate_cohortLAI`, x, SpParams, gdd, bounded)
 }
@@ -651,16 +672,19 @@ plant_LAI <- function(x, SpParams, gdd = NA_real_, bounded = TRUE) {
 #' @seealso \code{\link{spwb}}, \code{\link{forest}}, \code{\link{plant_basalArea}}, \code{\link{summary.forest}}
 #' 
 #' @name herb_values
+#' @keywords internal
 herb_foliarBiomass <- function(x, SpParams) {
  .Call(`_medfate_herbFoliarBiomass`, x, SpParams)
 }
 
 #' @rdname herb_values
+#' @keywords internal
 herb_fuelLoading <- function(x, SpParams) {
  .Call(`_medfate_herbFuelLoading`, x, SpParams)
 }
 
 #' @rdname herb_values
+#' @keywords internal
 herb_LAI <- function(x, SpParams) {
  .Call(`_medfate_herbLAI`, x, SpParams)
 }
@@ -711,21 +735,25 @@ herb_LAI <- function(x, SpParams) {
 #' species_parameter(c("Pinus halepensis", "Quercus ilex"), SpParamsMED, "Psi_Extract")
 #' 
 #' @name species_values
+#' @keywords internal
 species_basalArea <- function(x, SpParams) {
  .Call(`_medfate_speciesBasalArea`, x, SpParams)
 }
 
 #' @rdname species_values
+#' @keywords internal
 species_cover <- function(x, SpParams) {
  .Call(`_medfate_speciesCover`, x, SpParams)
 }
 
 #' @rdname species_values
+#' @keywords internal
 species_density <- function(x, SpParams) {
  .Call(`_medfate_speciesDensity`, x, SpParams)
 }
 
 #' @rdname species_values
+#' @keywords internal
 species_foliarBiomass <- function(x, SpParams, gdd = NA_real_) {
  .Call(`_medfate_speciesFoliarBiomass`, x, SpParams, gdd)
 }
@@ -751,16 +779,19 @@ stand_foliarBiomass <- function(x, SpParams, gdd = NA_real_) {
 }
 
 #' @rdname stand_values
+#' @keywords internal
 stand_fuelLoading <- function(x, SpParams, gdd = NA_real_, includeDead = TRUE) {
  .Call(`_medfate_standFuelLoading`, x, SpParams, gdd, includeDead)
 }
 
 #' @rdname stand_values
+#' @keywords internal
 stand_shrubVolume <- function(x, SpParams) {
  .Call(`_medfate_standShrubVolume`, x, SpParams)
 }
 
 #' @rdname stand_values
+#' @keywords internal
 stand_LAI <- function(x, SpParams, gdd = NA_real_, bounded = TRUE) {
  .Call(`_medfate_standLAI`, x, SpParams, gdd, bounded)
 }
@@ -3855,12 +3886,13 @@ plant_water <- function(x) {
 #' @param herbTranspiration Transpiration of herbaceous plants for \code{day} (mm).
 #' @param stepFunctions An integer to indicate a simulation step for which photosynthesis and profit maximization functions are desired.
 #' 
-#' 
+#' @keywords internal
 transp_transpirationSperry <- function(x, meteo, day, latitude, elevation, slope, aspect, canopyEvaporation = 0.0, snowMelt = 0.0, soilEvaporation = 0.0, herbTranspiration = 0.0, stepFunctions = NA_integer_, modifyInput = TRUE) {
  .Call(`_medfate_transpirationSperry`, x, meteo, day, latitude, elevation, slope, aspect, canopyEvaporation, snowMelt, soilEvaporation, herbTranspiration, stepFunctions, modifyInput)
 }
 
 #' @rdname transp_modes
+#' @keywords internal
 transp_transpirationSureau <- function(x, meteo, day, latitude, elevation, slope, aspect, canopyEvaporation = 0.0, snowMelt = 0.0, soilEvaporation = 0.0, herbTranspiration = 0.0, modifyInput = TRUE) {
  .Call(`_medfate_transpirationSureau`, x, meteo, day, latitude, elevation, slope, aspect, canopyEvaporation, snowMelt, soilEvaporation, herbTranspiration, modifyInput)
 }
@@ -4048,6 +4080,7 @@ transp_transpirationSureau <- function(x, meteo, day, latitude, elevation, slope
 #' modifyInput = FALSE)
 #' 
 #' @name transp_modes
+#' @keywords internal
 transp_transpirationGranier <- function(x, meteo, day, latitude, elevation, slope, aspect, modifyInput = TRUE) {
  .Call(`_medfate_transpirationGranier`, x, meteo, day, latitude, elevation, slope, aspect, modifyInput)
 }

R/VerticalProfiles.R

@@ -47,6 +47,7 @@
 #' 
 #' vprofile_windExtinction(exampleforest, SpParamsMED)
 #' 
+#' @keywords internal
 #' @name vprofile_leafAreaDensity
 vprofile_leafAreaDensity<-function(x, SpParams = NULL, z = NULL, gdd = NA, 
  byCohorts = FALSE, bySpecies = FALSE, includeHerbs = FALSE,
@@ -117,6 +118,7 @@ vprofile_leafAreaDensity<-function(x, SpParams = NULL, z = NULL, gdd = NA,
 }
 
 #' @rdname vprofile_leafAreaDensity
+#' @keywords internal
 vprofile_rootDistribution<-function(x, SpParams, d = NULL, bySpecies = FALSE, 
  draw = TRUE, xlim = NULL) {
  if(is.null(d)){
@@ -145,6 +147,7 @@ vprofile_rootDistribution<-function(x, SpParams, d = NULL, bySpecies = FALSE,
 }
 
 #' @rdname vprofile_leafAreaDensity
+#' @keywords internal
 vprofile_fuelBulkDensity<-function(x, SpParams, z = NULL, gdd = NA,
  draw = TRUE, xlim = NULL) {
  if(is.null(z)) z <- seq(0, ceiling(max(plant_height(x, SpParams))/100)*100 +10, by=1)
@@ -163,6 +166,7 @@ vprofile_fuelBulkDensity<-function(x, SpParams, z = NULL, gdd = NA,
 }
 
 #' @rdname vprofile_leafAreaDensity
+#' @keywords internal
 vprofile_PARExtinction<-function(x, SpParams, z = NULL, gdd = NA, includeHerbs = FALSE, 
  draw = TRUE, xlim = c(0,100)) {
  if(is.null(z)) z <- seq(0, ceiling(max(plant_height(x, SpParams), na.rm = TRUE)/100)*100 +10, by=1)
@@ -181,6 +185,7 @@ vprofile_PARExtinction<-function(x, SpParams, z = NULL, gdd = NA, includeHerbs =
 }
 
 #' @rdname vprofile_leafAreaDensity
+#' @keywords internal
 vprofile_SWRExtinction<-function(x, SpParams, z = NULL, gdd = NA, includeHerbs = FALSE, 
  draw = TRUE, xlim = c(0,100)) {
  if(is.null(z)) z <- seq(0, ceiling(max(plant_height(x, SpParams))/100)*100 +10, by=1)
@@ -199,6 +204,7 @@ vprofile_SWRExtinction<-function(x, SpParams, z = NULL, gdd = NA, includeHerbs =
 }
 
 #' @rdname vprofile_leafAreaDensity
+#' @keywords internal
 vprofile_windExtinction<-function(x, SpParams, u = 1, windMeasurementHeight = 200,
  boundaryLayerSize = 2000, target = "windspeed",
  z = NULL, gdd = NA, includeHerbs = FALSE,

R/dataset_documentation.R

@@ -1,3 +1,67 @@
+#' Description of the plant cohorts of a forest stand.
+#' 
+#' \code{exampleforest} is an example of forest stand description, whereas \code{exampleforest2} is an alternative forest description where leaf area index and crown ratio are supplied instead of structural (density, DBH and cover) parameters. 
+#' 
+#' @name forest
+#' @aliases exampleforest exampleforest2
+#' @docType data
+#' 
+#' @source DGCN (2005). Tercer Inventario Forestal Nacional (1997-2007): Catalunya. \enc{Dirección}{Direccion} General de \enc{Conservación}{Conservacion} de la Naturaleza, Ministerio de Medio Ambiente, Madrid.
+#' @seealso \code{\link{forest}}, \code{\link{spwb}}, \code{\link{spwbInput}}
+#' @format An object of class \code{forest} contains the description of the woody (tree or shrub) cohorts and herb layer of a forest patch.
+#' It has the following structure (see details):
+#' \itemize{
+#' \item{\code{treeData}: A data frame of tree cohorts (in rows) and the following columns:
+#' \itemize{
+#' \item{\code{Species}: String with species (taxon) name or a non-negative integer for tree species identity (i.e., 0,1,2,...) matching SpParams.}
+#' \item{\code{Height}: Total tree height (in cm).}
+#' \item{\code{DBH}: Tree diameter at breast height (in cm).}
+#' \item{\code{N}: Density (number of individuals/hectare) that the measured tree represents.}
+#' \item{\code{Z50}: Depth (in mm) corresponding to 50\% of fine roots.}
+#' \item{\code{Z95}: Depth (in mm) corresponding to 95\% of fine roots.}
+#' }
+#' }
+#' \item{\code{shrubData}: A data frame of shrub cohorts (in rows) and the following columns:
+#' \itemize{
+#' \item{\code{Species}: String with species (taxon) name or a non-negative integer for shrub species identity (i.e., 0,1,2,...) matching SpParams.}
+#' \item{\code{Height}: Average total height of plants (in cm).}
+#' \item{\code{Cover}: Percent cover.}
+#' \item{\code{Z50}: Depth (in mm) corresponding to 50\% of fine roots.}
+#' \item{\code{Z95}: Depth (in mm) corresponding to 95\% of fine roots.}
+#' }
+#' }
+#' \item{\code{herbCover}: Percent cover of the herb layer (optional).}
+#' \item{\code{herbHeight}: Mean height (in cm) of the herb layer (optional).}
+#' \item{\code{seedBank}: A data frame containing seed bank information with the following columns:
+#' \itemize{
+#' \item{\code{Species}: String with species (taxon) name or a non-negative integer for tree species identity (i.e., 0,1,2,...) matching SpParams.}
+#' \item{\code{Percent}: Amount of seeds in relation to full seed bank (in \%).}
+#' }
+#' }
+#' }
+#' @details
+#' The structure presented above for \code{forest} objects corresponds to the required data elements. 
+#' A \code{forest} object can contain additional information when this is available. Data frames \code{treeData} 
+#' and \code{shrubData} can contain additional columns:
+#' \itemize{
+#' \item{\code{LAI}: Leaf area index (m2/m2)}
+#' \item{\code{FoliarBiomass}: Standing dry biomass of leaves (kg/m2)}
+#' \item{\code{FuelLoading}: Fine fuel loading (kg/m2)}
+#' \item{\code{CrownRatio}: The ratio between crown length and total height (between 0 and 1)}
+#' }
+#' Similarly, one can define \code{forest} list elements \code{herbLAI}, \code{herbFoliarBiomass} or \code{herbFuelLoading}.
+#' All these values are used to override allometry-based estimates of those variables when initializing
+#' inputs for functions \code{\link{spwb}} or \code{\link{spwb_day}}. Note that leaf area index, foliar biomass and
+#' fuel loading are related entities, and they are treated as such in medfate. Therefore, users are expected to supply 
+#' one or the other, and not all of them at the same time.
+#' 
+#' @seealso \code{\link{summary.forest}}, \code{\link{emptyforest}}, \code{\link{plot.forest}}
+#' @examples
+#' data(exampleforest)
+#' data(exampleforest2)
+#' @keywords data
+NULL
+
 #' Example daily meteorology data
 #' 
 #' Example data set of meteorological input.

R/emptyforest.R

@@ -0,0 +1,40 @@
+#' Creation of an empty forest
+#' 
+#' Creates an empty \code{\link{forest}} object.
+#' 
+#' @param ntree,nshrub Number of tree and shrub cohorts, respectively.
+#' @param nseed Number of species in the seed bank.
+#' 
+#' @return An empty \code{\link{forest}} object.
+#' 
+#' @author Miquel De \enc{Cáceres}{Caceres} Ainsa, CREAF
+#' 
+#' @seealso \code{\link{forest}}, \code{\link{tree2forest}}, \code{\link{summary.forest}}, \code{\link{forest_mapWoodyTables}}, \code{\link{forest_mergeTrees}}, 
+#' \code{\link{plot.forest}}
+#' 
+#' @examples 
+#' # Initializes forest with 2 tree cohorts and 1 shrub cohort
+#' emptyforest(ntree = 2, nshrub = 1)
+#' 
+#' @name emptyforest
+emptyforest <- function(ntree = 0, nshrub = 0, nseed = 0) {
+ l <- list()
+ l$treeData <- data.frame(Species=as.character(rep(NA, ntree)),
+ DBH=as.numeric(rep(NA, ntree)), 
+ Height=as.numeric(rep(NA, ntree)), 
+ N=as.numeric(rep(NA, ntree)),
+ Z50 = as.numeric(rep(NA, ntree)), 
+ Z95=as.numeric(rep(NA, ntree)))
+ l$shrubData <- data.frame(Species=as.character(rep(NA, nshrub)), 
+ Height=as.numeric(rep(NA, nshrub)), 
+ Cover = as.numeric(rep(NA, nshrub)), 
+ Z50 = as.numeric(rep(NA, nshrub)), 
+ Z95=as.numeric(rep(NA, nshrub)))
+ l$herbCover <- NA;
+ l$herbHeight <- NA;
+ l$seedBank <- data.frame(Species = as.character(rep(NA, nseed)),
+ Percent = as.numeric(rep(NA, nseed)))
+ class(l)<-c("forest","list")
+ return(l)
+}
+

R/hydraulics_supplyFunctionPlot.R

@@ -8,6 +8,7 @@
 #' @param speciesNames A flag to indicate the use of species names instead of cohort names in plots.
 #' @param ylim Graphical parameter to override function defaults.
 #' 
+#' @keywords internal
 hydraulics_supplyFunctionPlot<-function(x, draw = TRUE, type="E", speciesNames = FALSE, ylim=NULL) {
 
  TYPES = c("E","dEdP","StemPsi","RootPsi","ERhizo")

R/hydraulics_vulnerabilityCurvePlot.R

@@ -11,6 +11,7 @@
 #' @param draw A flag to indicate whether the vulnerability curve should be drawn or just returned.
 #' @param ylim,xlab,ylab Graphical parameters to override function defaults.
 #' 
+#' @keywords internal
 hydraulics_vulnerabilityCurvePlot<-function(x, soil = NULL, type="leaf", vulnerabilityFunction = "Weibull",
  psiVec = seq(-0.1, -8.0, by =-0.01), 
  relative = FALSE, speciesNames = FALSE,