errors when `GC$NonLinearModel == NULL`

[CeresBarros]

Here's a reprex.

Many species have a non-error/non-character GC, with tables full of NA's, but GC$NonLinearModel == NULL

repos <- c("predictiveecology.r-universe.dev", getOption("repos"))
install.packages(c("SpaDES.project"), repos = repos)
library(SpaDES.project)

out <- setupProject(
  ## INPUT OBJECTS -----------------------------------
  ## these need to come *before* any formal arguments, as they are needed for params.R
  sppEquivCol = "Boreal",
  vegLeadingProportion = 0,
  successionTimestep = 10L,
  eventCaching = c(".inputObjects", "init"),
  useParallel = FALSE,
  paths = list("packagePath" = "packages/",
               "projectPath" = "~/tutos/LandRDemo_coreVeg"),
  packages = c(
    ## these are needed but don't load
    "PredictiveEcology/SpaDES.experiment@development (HEAD)",
    "terra"  
  ),
  options = list(
    "reproducible.destinationPath" = paths$inputPath,
    "spades.inputPath" = paths$inputPath,
    "spades.moduleCodeChecks" = FALSE
  ),
  modules = c(
    # "PredictiveEcology/Biomass_speciesData@development",
    # "PredictiveEcology/Biomass_borealDataPrep@development",
    # "PredictiveEcology/Biomass_speciesParameters@development",
    # "PredictiveEcology/Biomass_core@development",
    # "PredictiveEcology/Biomass_validationKNN@development"
    "Biomass_speciesData",
    "Biomass_borealDataPrep",
    "Biomass_speciesParameters",
    "Biomass_core",
    "Biomass_validationKNN"
  ),
  ## SIMULATION SETUP ------------------------------------
  times = list(start = 2001, end = 2031),
  params = "PredictiveEcology/PredictiveEcology.org@training-book/tutos/LandRDemo_coreVeg/params.R",
  ## (more) INPUT OBJECTS -----------------------------------
  ## these come after, so that we don't need to pre-install/load LandR
  ## species lists/traits
  sppEquiv = {
    data("sppEquivalencies_CA", package = "LandR")
    sppEquivalencies_CA[grep("Pin", LandR), `:=`(EN_generic_short = "Pine",
                                                 EN_generic_full = "Pine",
                                                 Leading = "Pine leading")]
    sppEquivalencies_CA[grep("Betu_pap", LandR), `:=`(EN_generic_short = "Birch",
                                                      EN_generic_full = "Birch",
                                                      Leading = "Birch leading")]
    ## all Popu will be merged
    sppEquivalencies_CA[grep("Popu_", LandR), `:=`(EN_generic_short = "Poplar",
                                                   EN_generic_full = "Poplar",
                                                   Leading = "Poplar leading")]
    sppEquivalencies_CA[grep("Popu_", LandR), Boreal := "Popu_Spp"]

    ## define spp column to use for model
    sppEquivalencies_CA <- sppEquivalencies_CA[!"", on = sppEquivCol]
    sppEquivalencies_CA <- na.omit(sppEquivalencies_CA, sppEquivCol)
    sppEquivalencies_CA
  },
  speciesParams = {
    list(
      "shadetolerance" = list(
        Betu_Pap = 1
        , Lari_Lar = 1
        , Pice_Gla = 2
        , Pice_Mar = 3
        , Pinu_Ban = 1.5
        , Popu_Spp = 1
      )
    )
  },
  studyArea = {
    originalcrs <- "+proj=longlat +datum=NAD83 +no_defs +ellps=GRS80 +towgs84=0,0,0"
    Biomass_corecrs <- "+proj=lcc +lat_1=49 +lat_2=77 +lat_0=0 +lon_0=-95 +x_0=0 +y_0=0 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0"

    smallExtent <- c(xmin = -104.757, xmax = -104.48835, ymin = 55.68663, ymax = 55.94491)
    studyAreaS <- terra::vect(terra::ext(smallExtent))
    studyAreaS <-  terra::vect(terra::geom(studyAreaS), "polygons", crs = originalcrs, atts = data.frame(id = 1:length(studyAreaS)))
    studyAreaS <- terra::project(studyAreaS, Biomass_corecrs)
    studyAreaS
  },
  studyAreaLarge = {
    originalcrs <- "+proj=longlat +datum=NAD83 +no_defs +ellps=GRS80 +towgs84=0,0,0"
    Biomass_corecrs <- "+proj=lcc +lat_1=49 +lat_2=77 +lat_0=0 +lon_0=-95 +x_0=0 +y_0=0 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0"
    largeExtent <- c(xmin = -104.757, xmax = -104.2197, ymin = 55.68663, ymax = 56.20319)

    studyAreaL <- terra::vect(terra::ext(largeExtent))
    studyAreaL <-  terra::vect(terra::geom(studyAreaL), "polygons", crs = originalcrs, atts = data.frame(id = 1:length(studyAreaL)))
    studyAreaL <- terra::project(studyAreaL, Biomass_corecrs)
    studyAreaL
  }
)

out$modules <- out$modules[out$modules != "Biomass_validationKNN"]  

## initialise simulation and cache
simInitOut <- do.call(SpaDES.core::simInit, out) |>
  reproducible::Cache(useCache = "overwrite")

simOut <- SpaDES.core::spades(simInitOut)

[CeresBarros]

proposed fix #42 , but maybe worth checking why GC$NonLinearModel is NULL, rather than class error

[CeresBarros]

fixed in #42