Partial RDA variance partitioning

Partial RDA variance partitioning

Usage

rda_varpart(gen, env, coords, Pin, R2permutations, R2scope, nPC)

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

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)

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

Value

df with relevant statistics from variance partitioning analysis

See also

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