plotUncertainty_getsd: plotUncertainty_getsd : Get GDM sd at max height DEPRECATED

In allanecology/BetaDivMultifun: Testing effects of multitrophic beta-diversity and land-use intensity (LUI) on ecosystem multifunctionality

plotUncertainty_getsd : Get GDM sd at max height DEPRECATED

Description

*Depreciation note* : This function is no longer used, because (1) the new version of the package 'gdm' allows extracting output data from this function, and (2) because we need the uncertainty not only at the maximum value, but throughout the 200 x values.

Usage

plotUncertainty_getsd(
  spTable,
  sampleSites,
  bsIters,
  geo = FALSE,
  splines = NULL,
  knots = NULL,
  splineCol = "blue",
  errCol = "grey80",
  plot.linewidth = 2,
  plot.layout = c(2, 2),
  parallel = FALSE,
  cores = 2
)

Arguments

spTable	same as in gdm::plotUncertainty
sampleSites	same as in gdm::plotUncertainty. 0.3 was used in Gossner 2016.
bsIters	same as in gdm::plotUncertainty. 100 were used in Gossner 2016.
geo	same as in gdm::plotUncertainty
splines	same as in gdm::plotUncertainty

Details

To get an uncertainty at the maximum x value of a GDM model (corresponds to max y), the function 'plotUncertainty' from the 'gdm' package was slightly modified : all input stays the same. New : a table is generated which contains the estimate at maximum x and its standard deviation for each predictor separately. The plotting has been outcommented, as there is no plot output needed in this case. All edited placed are marked with '#EDIT' in the code

Value

a data.table with 3 columns : the names of the predictors, the maximum effect size and its standard deviation

Examples

# read in gdminput from `results_nonpublic.R`.
test <- plotUncertainty_getsd(gdminput, sampleSites = 0.3, bsIters = 5, geo = T)

allanecology/BetaDivMultifun documentation built on Nov. 9, 2023, 8:47 p.m.