plot_scn_diff: Plot differences in suitable areas between climatic scenarios

In HemingNM/ENMwizard: Advanced Techniques for Ecological Niche Modeling Made Easy

Plot differences in suitable areas between climatic scenarios

Description

Plot differences between a selected climatic scenario and all other climatic scenarios for each species. This function will plota and (optionally) save the figures on pdf files in the folder "Mdls.thrshld/figs".

Usage

plot_scn_diff(
  mcmp,
  mtp,
  mSel,
  ref.scn = "ncurrent",
  sp.nm = "species",
  basemap = NULL,
  save = FALSE,
  mfrow = c(0, 0),
  numCores = 1,
  msnm = c("AUC10", "AUCmtp", "OR10", "ORmtp"),
  msr = c("AUC (OR10p)", "AUC (ORlpt)", "OR10p (AUC)", "ORlpt (AUC)"),
  scnm = c("cc26bi70", "cc45bi70", "cc60bi70", "cc85bi70", "mp26bi70", "mp45bi70",
    "mp85bi70", "mr26bi70", "mr45bi70", "mr60bi50", "mr85bi70", "cclgmbi", "ccmidbi",
    "lig_30s_bio_", "melgmbi", "memidbi", "mrlgmbi", "mrmidbi", "ncurrent", "current"),
  scr = c("2070-CCSM4-rcp2.6", "2070-CCSM4-rcp4.5", "2070-CCSM4-rcp6.0",
    "2070-CCSM4-rcp8.5", "2070-MPI-ESM-LR-rcp2.6", "2070-MPI-ESM-LR-rcp4.5",
    "2070-MPI-ESM-LR-rcp8.5", "2070-MIROC-ESM-rcp2.6", "2070-MIROC-ESM-rcp4.5",
    "2070-MIROC-ESM-rcp6.0", "2070-MIROC-ESM-rcp8.5", "LGM-CCSM4", "MH-CCSM4",
    "LIG-CCSM3", "LGM-MPI-ESM-P", "MH-MPI-ESM-P", "LGM-MIROC-ESM", "MH-MIROC-ESM",
    "Near Current", "Near Current")
)

Arguments

mcmp	An object returned by proj_mdl, containing calibrated models and model projections for each species; or species "i" of a object returned by "proj_mdl_b", containing a list of calibrated models and model projections for each species
mtp	Stack or brick of thresholded predictions
mSel	Character vector. Which criteria to use when selecting model(s). Currently implemented: "AvgAIC", "LowAIC", "OR", "AUC"
ref.scn	Selected climatic scenario to compare with all others. Usually "ncurrent". any (row or col) is 0, it will draw the layout automatically.
sp.nm	Species name. Used to name the output folder
basemap	Shapefile to be plotted with. Usually a continent or country shapefile
save	Logical. If TRUE will save plots in pdf.
mfrow	Number of rows and cols to draw plot (see ?par for details). If
numCores	Number of cores to use for parallelization. If set to 1, no paralellization is performed
msnm	Character vector. Short names of model selection criteria to be replaced. Same as given in Model names (ex. AUC10, AUCmtp, OR10, ORmtp)
msr	Character vector. Long names of model selection criteria to replace the short names. Must be in same order of argument 'msnm'
scnm	Character vector. Short names of climatic scenarios to be replaced. Ex. "cc26bi70", "cc45bi70"
scr	Character vector. Long names of climatic scenarios to replace the short names. Must be in same order of argument 'scnm'. Ex. "2070-CCSM4-rcp2.6", "2070-CCSM4-rcp4.5"

Value

won't return any object. Will save pdf's with differences among model predictions (for multiple climatic scenarios)

See Also

plot_scn_diff_b

Examples

## Not run: 
plot_scn_diff(mcmp.l=mxnt.mdls.preds.lst, mtp.l=mods.thrshld.lst)

## End(Not run)

HemingNM/ENMwizard documentation built on Jan. 4, 2024, 3:24 p.m.