Apply Variance Inflation Factor (VIF) calculation.
Usage
vif_predictors(pred, area = "all", th = 0.5, maxobservations = 5000, variables_selected =
NULL)
vif_summary(i)Arguments
- pred
A
input_sdmorpredictorsobject.- area
Character. Which area should be used in vif selection? Standard is
"all". Alternativelly, set it to"occurrences"to perform VIF only in the occurrence records.- th
Threshold to be applied in VIF routine. See ?usdm::vifcor.
- maxobservations
Max observations to use to calculate the VIF.
- variables_selected
If there is a subset of predictors that should be used in this function, it can be informed using this parameter. If set to
NULL(standard) all variables are used.- i
A
input_sdmto retrieve information from.
Examples
# Create sdm_area object:
sa <- sdm_area(parana, cell_size = 25000, output_crs = 6933)
#> ! Making grid over study area is an expensive task. Please, be patient!
#> ℹ Using GDAL to make the grid and resample the variables.
# Include predictors:
sa <- add_predictors(sa, bioc) |> select_predictors(c("bio1", "bio4", "bio12"))
#> ! Making grid over the study area is an expensive task. Please, be patient!
#> ℹ Using GDAL to make the grid and resample the variables.
# Include scenarios:
sa <- add_scenarios(sa, scen)
#> ! Making grid over the study area is an expensive task. Please, be patient!
#> ℹ Using GDAL to make the grid and resample the variables.
#> ! Making grid over the study area is an expensive task. Please, be patient!
#> ℹ Using GDAL to make the grid and resample the variables.
#> ! Making grid over the study area is an expensive task. Please, be patient!
#> ℹ Using GDAL to make the grid and resample the variables.
#> ! Making grid over the study area is an expensive task. Please, be patient!
#> ℹ Using GDAL to make the grid and resample the variables.
# Create occurrences:
oc <- occurrences_sdm(occ, occ_crs = 6933)
# Create input_sdm:
i <- input_sdm(oc, sa)
#> Warning: Some records from `occ` do not fall in `pred`.
#> ℹ 2 elements from `occ` were excluded.
#> ℹ If this seems too much, check how `occ` and `pred` intersect.
# VIF calculation:
i <- vif_predictors(i)
i
#> caretSDM
#> ................................
#> Class : input_sdm
#>
#> =========== Overview ===========
#> Focal Taxon : Araucaria angustifolia
#> Spatial extent : -5276744.44724281, -3295036.62222337, -4626744.44724281, -2795036.62222337 (xmin,xmax,ymin,ymax)
#> Temporal extent (inferred) : 2090 - 2090
#> Observation type : Presence-only
#> Predictor names : bio1, bio4, bio12
#>
#> ============= Data =============
#> -- Biodiversity data --
#> Taxon names : Araucaria angustifolia
#> Sample size : 417
#> -- Predictor variables --
#> Number of predictors : 3
#> Predictor names : bio1, bio4, bio12
#> Spatial extent : -5276744.44724281, -3295036.62222337, -4626744.44724281, -2795036.62222337 (xmin,xmax,ymin,ymax)
#> Spatial resolution : (25000, 25000)
#> Coordinate reference system : WGS 84 / NSIDC EASE- ( EPSG: 6933 )
#> -- Transfer data --
#> Number of scenarios : 5
#> Scenario names : ca_ssp245_2090, ca_ssp585_2090, mi_ssp245_2090, mi_ssp585_2090, current
#> Temporal extent (inferred) : 2090 - 2090
#>
#> ============= Model ============
#> -- Multicollinearity --
#> Variable selection method : vif
#> Selected variables : bio1, bio4
#>
#> ========== Assessment ==========
# Retrieve information about vif:
vif_summary(i)
#> 1 variables from the 3 input variables have collinearity problem:
#>
#> bio12
#>
#> After excluding the collinear variables, the linear correlation coefficients ranges between:
#> min correlation ( bio4 ~ bio1 ): -0.3182326
#> max correlation ( bio4 ~ bio1 ): -0.3182326
#>
#> ---------- VIFs of the remained variables --------
#> Variables VIF
#> 1 bio1 1.112684
#> 2 bio4 1.112684
selected_variables(i)
#> [1] "bio1" "bio4"