Merge remote-tracking branch 'origin/development' into development

DESCRIPTION

@@ -9,7 +9,7 @@ URL:
  https://landr.predictiveecology.org,
  https://github.com/PredictiveEcology/LandR
 Date: 2023-10-13
-Version: 1.1.0.9068
+Version: 1.1.0.9069
 Authors@R: c(
  person("Eliot J B", "McIntire", email = "[email protected]",
  role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6914-8316")),

NAMESPACE

@@ -14,6 +14,7 @@ export(FireDisturbance)
 export(FireDisturbancePM)
 export(LANDISDisp)
 export(NAcover2zero)
+export(PeatlandThermokarst)
 export(Ward)
 export(addNoPixel2CohortData)
 export(addPixels2CohortData)
@@ -29,7 +30,7 @@ export(assertERGs)
 export(assertFireToleranceDif)
 export(assertPixelCohortData)
 export(assertPixelCohortDataValid)
-export(assertPostFireDist)
+export(assertPostPartialDist)
 export(assertRepsAllCohortData)
 export(assertRstLCChange)
 export(assertSpeciesEcoregionCohortDataMatch)
@@ -62,6 +63,7 @@ export(equivalentName)
 export(equivalentNameColumn)
 export(extractMaxB)
 export(fasterizeFromSp)
+export(fitNLMModels)
 export(genPGsPostDisturbance)
 export(generatePixelGroups)
 export(genericExtract)
@@ -93,6 +95,7 @@ export(modifySpeciesAndSpeciesEcoregionTable)
 export(nonForestedPixels)
 export(overlayLCCs)
 export(overlayStacks)
+export(partialggplotMLL_maxB)
 export(partitionBiomass)
 export(pixelFate)
 export(plantNewCohorts)

R/assertions.R

@@ -651,26 +651,26 @@ assertSppVectors <- function(sppEquiv = NULL, sppNameVector = NULL, sppColorVect
 #'
 #' @return NULL
 #' @export
-assertPostFireDist <- function(cohortDataOrig, pixelGroupMapOrig, cohortDataNew, pixelGroupMapNew,
- postFirePixelCohortData, burnedPixelCohortData, doAssertion = getOption("LandR.assertions", TRUE)) {
+assertPostPartialDist <- function(cohortDataOrig, pixelGroupMapOrig, cohortDataNew, pixelGroupMapNew,
+ postDistPixelCohortData, distrbdPixelCohortData, doAssertion = getOption("LandR.assertions", TRUE)) {
  if (doAssertion) {
  oldPCohortData <- addPixels2CohortData(cohortDataOrig, pixelGroupMapOrig, doAssertion = FALSE)
  newPCohortData <- addPixels2CohortData(cohortDataNew, pixelGroupMapNew)
 
- testPGs <- oldPCohortData[pixelGroup %in% postFirePixelCohortData$pixelGroup, pixelGroup]
- testPIs <- postFirePixelCohortData[pixelGroup %in% testPGs, pixelIndex]
+ testPGs <- oldPCohortData[pixelGroup %in% postDistPixelCohortData$pixelGroup, pixelGroup]
+ testPIs <- postDistPixelCohortData[pixelGroup %in% testPGs, pixelIndex]
 
  cols <- c("pixelIndex", "speciesCode", "age")
  test1 <- unique(newPCohortData[pixelIndex %in% testPIs, ..cols])
- test2 <- unique(postFirePixelCohortData[pixelIndex %in% testPIs, ..cols])
+ test2 <- unique(postDistPixelCohortData[pixelIndex %in% testPIs, ..cols])
  setorderv(test1, cols)
  setorderv(test2, cols)
 
  if (!identical(test1, test2)) {
  stop("Post-fire disturbances miscalculated: missing survivor/regenerated cohorts")
  }
 
- test3 <- unique(burnedPixelCohortData[B == 0, ..cols])
+ test3 <- unique(distrbdPixelCohortData[B == 0, ..cols])
  test4 <- unique(newPCohortData[, ..cols])
  if (nrow(newPCohortData[test3, on = cols, nomatch = 0L])) {
  stop("Killed cohorts are still in cohortData table")

R/biomodWrappers.R

@@ -27,11 +27,11 @@ utils::globalVariables(c(
 #' @param responseVarData a data.table or list of data.tables with environmental data.
 #' If a list, it should be named according to `sp`, for subsetting.#'
 #'
-#' @param dir.name passed to `biomod2::BIOMOD_FormatingData`
+#' @param dir.name passed to [biomod2::BIOMOD_FormatingData]
 #'
-#' @param BIOMOD_ModelingArgs a named list of arguments passed to `biomod2::BIOMOD_Modeling`
+#' @param BIOMOD_ModelingArgs a named list of arguments passed to [biomod2::BIOMOD_Modeling]
 #'
-#' @param ... further arguments passed to `reproducible::Cache`
+#' @param ... further arguments passed to [reproducible::Cache]
 #'
 #' @export
 biomodModelingWrapper <- function(sp, responseVar, responseVarData, predictorVars, predictorVarsData,
@@ -165,10 +165,10 @@ biomodModelingWrapper <- function(sp, responseVar, responseVarData, predictorVar
 }
 
 #' BIOMOD_EnsembleModeling wrapper
-#' @param bm.mod output of `biomod2::BIOMOD_Modeling`
-#' @param metric.select.thresh passed `biomod2::BIOMOD_EnsembleModeling`.
+#' @param bm.mod output of [biomod2::BIOMOD_Modeling]
+#' @param metric.select.thresh passed [biomod2::BIOMOD_EnsembleModeling].
 #' By default no thresholding is applied.
-#' @param ... passed to Cache
+#' @param ... passed to [reproducible::Cache]
 #'
 #' @export
 biomodEnsembleWrapper <- function(bm.mod, metric.select.thresh = NULL, ...) {
@@ -202,13 +202,13 @@ biomodEnsembleWrapper <- function(bm.mod, metric.select.thresh = NULL, ...) {
 
 #' BIOMOD_Projection wrapper
 #'
-#' @param bm.mod output of `biomod2::BIOMOD_Modeling`
-#' @param bm.mod passed to `biomod2::BIOMOD_Projection`. If not supplied
+#' @param bm.mod output of [biomod2::BIOMOD_Modeling]
+#' @param bm.mod passed to [biomod2::BIOMOD_Projection]. If not supplied
 #' the data used to fit the model will be used.
-#' @param proj.name passed to `biomod2::BIOMOD_Projection`
-#' @param new.env passed to `biomod2::BIOMOD_Projection`
-#' @param new.env.xy passed to `biomod2::BIOMOD_Projection`
-#' @param ... passed to Cache
+#' @param proj.name passed to [biomod2::BIOMOD_Projection]
+#' @param new.env passed to [biomod2::BIOMOD_Projection]
+#' @param new.env.xy passed to [biomod2::BIOMOD_Projection]
+#' @param ... passed to [reproducible::Cache]
 #'
 #' @export
 biomodProjWrapper <- function(bm.mod, proj.name = "testProj", new.env = NULL, new.env.xy = NULL, ...) {
@@ -248,21 +248,21 @@ biomodProjWrapper <- function(bm.mod, proj.name = "testProj", new.env = NULL, ne
 }
 
 
-#' Simple wrapper around `biomod2::BIOMOD_EnsembleForecasting()`
+#' Simple wrapper around [biomod2::BIOMOD_EnsembleForecasting()]
 #'
-#' @param bm.em output of `biomod2::BIOMOD_EnsembleModeling`
+#' @param bm.em output of [biomod2::BIOMOD_EnsembleModeling]
 #'
-#' @param bm.proj output of `biomod2::BIOMOD_Projection`
+#' @param bm.proj output of [biomod2::BIOMOD_Projection]
 #'
-#' @param proj.name passed to `biomod2::BIOMOD_Projection`
+#' @param proj.name passed to [biomod2::BIOMOD_Projection]
 #'
-#' @param new.env passed to `biomod2::BIOMOD_EnsembleForecasting`
+#' @param new.env passed to [biomod2::BIOMOD_EnsembleForecasting]
 #'
-#' @param new.env.xy passed to `biomod2::BIOMOD_EnsembleForecasting`
+#' @param new.env.xy passed to [biomod2::BIOMOD_EnsembleForecasting]
 #'
-#' @param keep.in.memory passed to `biomod2::BIOMOD_EnsembleForecasting`
+#' @param keep.in.memory passed to [biomod2::BIOMOD_EnsembleForecasting]
 #'
-#' @param ... passed to `reproducible::Cache`
+#' @param ... passed to [reproducible::Cache]
 #'
 #' @export
 biomodEnsembleFrcstWrapper <- function(bm.em, bm.proj = NULL, proj.name = NULL, new.env = NULL,