Merge branch 'development'

PredictiveEcology · Jul 15, 2020 · a3944cf · a3944cf
2 parents 7447fa3 + 5552b87
commit a3944cf
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Showing 17 changed files with 117 additions and 123 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -9,7 +9,7 @@ URL:
  http:https://landr.predictiveecology.org,
  https://github.com/PredictiveEcology/LandR
 Date: 2020-06-16
-Version: 0.0.6
+Version: 0.0.7
 Authors@R: c(
  person("Eliot J B", "McIntire", email = "[email protected]",
  role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6914-8316")),

diff --git a/R/assertions.R b/R/assertions.R
@@ -187,7 +187,7 @@ assertColumns <- function(obj, colClasses,
 #' @template cohortData
 #'
 #' @template pixelGroupMap
-#'
+#' @template cohortDefinitionCols
 #' @param sim If the \code{simList} is included, then the \code{browser()} call will be more useful.
 #'
 #' @param maxExpectedNumDiverge A numeric, length 1, indicating by how many they
@@ -197,7 +197,6 @@ assertColumns <- function(obj, colClasses,
 #' was called.
 #'
 #' @param verbose Controls message output. Defaults to \code{getOption("LandR.verbose")}
-#'
 #' @note
 #' TODO
 #'
@@ -207,7 +206,8 @@ assertColumns <- function(obj, colClasses,
 #' @rdname assertions
 assertCohortData <- function(cohortData, pixelGroupMap, sim, maxExpectedNumDiverge = 1,
  message = "", doAssertion = getOption("LandR.assertions", TRUE),
- verbose = getOption("LandR.verbose", TRUE)) {
+ verbose = getOption("LandR.verbose", TRUE),
+ cohortDefinitionCols = c("pixelGroup", "age", "speciesCode")) {
  if (doAssertion) {
  if (!isTRUE("pixelGroup" %in% names(cohortData))) {
  stop("cohortData must have pixelGroup")
@@ -219,7 +219,7 @@ assertCohortData <- function(cohortData, pixelGroupMap, sim, maxExpectedNumDiver
  test2 <- sum(!b %in% a)
 
  browser(expr = exists("aaaa"))
- cohortDataN <- cohortData[, .N, by = c("pixelGroup", "speciesCode", "age", "B")]
+ cohortDataN <- cohortData[, .N, by = cohortDefinitionCols]
  test3 <- which(cohortDataN$N != 1)
  if (test1 > maxExpectedNumDiverge || test2 > maxExpectedNumDiverge) {
  if (nchar(message) > 0) message(message)

diff --git a/R/cohorts.R b/R/cohorts.R
diff --git a/R/makeDummyInputs.R b/R/makeDummyInputs.R
@@ -91,7 +91,6 @@ makeDummyEcoregionFiles <- function(ecoregionMap, rstLCC, rasterToMatch) {
  ecoregionFiles <- Cache(ecoregionProducer,
  ecoregionMaps = list(ecoregionMap, rstLCC),
  ecoregionName = "ECODISTRIC",
- ecoregionActiveStatus = ecoregionstatus,
  rasterToMatch = rasterToMatch,
  userTags = "ecoregionFiles")
  return(ecoregionFiles)

diff --git a/man-roxygen/cohortDefinitionCols.R b/man-roxygen/cohortDefinitionCols.R
@@ -0,0 +1,2 @@
+#' @param cohortDefinitionCols the columns in \code{cohortData} that define unique cohorts
+#'
diff --git a/man/addNoPixel2CohortData.Rd b/man/addNoPixel2CohortData.Rd
diff --git a/man/addPixels2CohortData.Rd b/man/addPixels2CohortData.Rd
diff --git a/man/assertions.Rd b/man/assertions.Rd
diff --git a/man/columnsForPixelGroups.Rd b/man/columnsForPixelGroups.Rd
diff --git a/man/dot-speciesTableColNames.Rd b/man/dot-speciesTableColNames.Rd
diff --git a/man/landisIIrepo.Rd b/man/landisIIrepo.Rd
diff --git a/man/pkgEnv.Rd b/man/pkgEnv.Rd
diff --git a/man/rmMissingCohorts.Rd b/man/rmMissingCohorts.Rd
diff --git a/man/sppEquivalencies_CA.Rd b/man/sppEquivalencies_CA.Rd
diff --git a/man/uniqueDefinitions.Rd b/man/uniqueDefinitions.Rd
diff --git a/man/updateCohortData.Rd b/man/updateCohortData.Rd
diff --git a/man/updateCohortDataPostHarvest.Rd b/man/updateCohortDataPostHarvest.Rd