automated non-forest covers, fix doc

DESCRIPTION

@@ -46,7 +46,6 @@ Imports:
 Suggests:
     cowplot,
     dplyr,
-    ggplot2,
     knitr,
     lintr,
     PtProcess,

NAMESPACE

@@ -162,6 +162,7 @@ importFrom(stats,dbinom)
 importFrom(stats,dnorm)
 importFrom(stats,glm)
 importFrom(stats,is.empty.model)
+importFrom(stats,kmeans)
 importFrom(stats,lm)
 importFrom(stats,median)
 importFrom(stats,model.matrix)

R/fuelClassPrep.R

@@ -1,30 +1,27 @@
 utils::globalVariables(c(
-  "burned", "burnprob", "cell", "lcc", "pixelIndex", "speciesCode", "YEAR", "yearRange",
-  "absCoef", "possGroups", "propB", "pvalue", "sig", "sim", "species", "above10PctRelB",
-  "assignedFuelClass", "B_MgHa", "coef"
+  "above10PctRelB", "absCoef", "assignedFuelClass", "B_MgHa", "burned", "burnprob",
+  "cell", "coef", "lcc", "pixelIndex", "newName", "possGroups", "propB",
+  "pvalue", "sig", "sim", "species","speciesCode", "YEAR", "yearRange"
 ))
 
 #' Calculate proportional burn of landcover and tree species
 #'
 #' @template pixelGroupMap
-#'
 #' @template cohortData
-#'
 #' @param rstLCC a landcover map
-#'
 #' @param nonflammableLCC nonflammable landcover in `rstLCC`
-#'
+#' @param nonforestLCC vector or list of vectors of flammable nonforest LCC
 #' @param fires a single `sf` or `SpatVector` object of fire polygons containing a `YEAR` column
-#'
 #' @param yearRange  the range of years represented by this landscape
 #'
 #' @return `data.table` with cell, biomass, tree species or lcc for non-forest, and year of fire
 #'
 #' @examples
 #' # fuelClassPrep(
 #' #   sim$pixelGroupMap2011, sim$cohortData2011, sim$rstLCC2011,
+#' #   rstLCC = sim$rstLCC2011, nonForestLCC = sim$nonForestLCCGroups,
 #' #   nonflammableLCC = P(sim)$nonflammableLCC,
-#' #   fires = TODO,
+#' #   fires = do.call(rbind, sim$spreadFirePolys),
 #' #   yearRange = c(2012, 2020)
 #' # )
 #'
@@ -65,6 +62,7 @@ fuelClassPrep <- function(pixelGroupMap, cohortData, rstLCC,
 #'
 #' @param fuel vector of tree species or lcc in landscape by which to subset
 #' @param landscape created by `fuelClassPrep`
+#' @param form the formula to use - as a character
 #' @importFrom stats glm binomial
 makeGLM <- function(fuel, landscape, form) {
 
@@ -76,12 +74,12 @@ makeGLM <- function(fuel, landscape, form) {
 #'
 #' @param landscape data.table created by `prepFuelClasses`
 #' @param fuelCol the column in `sppEquiv` with default fuel classes
-#' @param rstLCC a landcover map
 #' @template sppEquiv
 #' @template sppEquivCol
 #' @param targetNonForestClasses the number of non-forest fuel classes to generate
-#' @param targetFuelClasses target number of fuel classes to generate
-#' @param yearRange  the range of years represented by this landscape
+#' @param targetFuelClasses target number of treed fuel classes to generate
+#' @param nonforestLCC vector or list of vectors of non-forest fuel classes
+#' @param pValue for glm coef significance when deciding to merge fuel classes
 #' @importFrom data.table melt
 #' @importFrom stats coefficients binomial glm kmeans
 #' @export

tests/testthat/test-fuelClasses.R

@@ -12,7 +12,7 @@ test_that("combine_fuel_classes behaves reasonably", {
 
    #birch and aspen will be combined, fir will not be combined with Picea
    out <- combine_fuel_classes(tempDF)
-   expect_true("PopBrch" %in% out$assignedFuelClass)
+   expect_true("Bt_p.Pp_t" %in% out$assignedFuelClass)
    expect_true("Abie_las" %in% out$assignedFuelClass)
 
    #with birch positive instead of negative
@@ -41,7 +41,7 @@ test_that("combine_fuel_classes behaves reasonably", {
   #Abie_las should NOT be combined
   out <- combine_fuel_classes(tempDF3)
   expect_true("Abie_las" %in% out$assignedFuelClass)
-  expect_true("LdJkPine" %in% out$assignedFuelClass)
-  expect_true("PopBrch" %in% out$assignedFuelClass)
+  expect_true("Pn_b.Pn_c" %in% out$assignedFuelClass)
+  expect_true("Bt_p.Pp_t" %in% out$assignedFuelClass)
 
 })