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Run RDA

rda_run.Rd

Run RDA

Usage

rda_run(
  gen,
  env,
  coords = NULL,
  model = "full",
  correctGEO = FALSE,
  correctPC = FALSE,
  nPC = 3,
  Pin = 0.05,
  R2permutations = 1000,
  R2scope = T
)

Arguments

gen

genotype dosage matrix (rows = individuals & columns = SNPs) or vcfR object

env

dataframe with environmental data or a Raster* type object from which environmental values for the coordinates can be extracted

coords

dataframe with coordinates (only needed if correctGEO = TRUE) or if env is a Raster* from which values should be extracted

model

whether to fit the model with all variables ("full") or to perform variable selection to determine the best set of variables ("best"); defaults to "full"

correctGEO

whether to condition on geographic coordinates

correctPC

whether to condition on PCs from PCA of genotypes

nPC

number of PCs to use if correctPC = TRUE (defaults to 3); if set to "manual" a selection option with a terminal prompt will be provided

Pin

if model = "best", limits of permutation P-values for adding (Pin) a term to the model, or dropping (Pout) from the model. Term is added if P <= Pin, and removed if P > Pout (see ordiR2step) (defaults to 0.05)

R2permutations

if model = "best", number of permutations used in the estimation of adjusted R2 for cca using RsquareAdj (see ordiR2step) (defaults to 1000)

R2scope

if model = "best" and set to TRUE (default), use adjusted R2 as the stopping criterion: only models with lower adjusted R2 than scope are accepted (see ordiR2step)

Value

RDA model

See also

Other RDA functions: rda_cor(), rda_do_everything(), rda_getoutliers(), rda_plot(), rda_table(), rda_varpart(), rda_varpart_table()