test_wreg: Testing the relationship species attributes and sample...

In zdealveindy/weimea: Weighted Mean Analysis

Description

Function calculating the weightet linear regressions between CWM of species attributes (traits) and sample attributes (environmental variables) and between SNC of sample attributes and species attributes (sensu ter Braak et al. 2018), and testing them by parametric tests and their combination into max test.

Usage

test_wreg(
  env,
  com = NULL,
  traits = NULL,
  test = "all",
  parallel = NULL,
  p.adjust.method = p.adjust.methods,
  adjustP = FALSE
)

## S3 method for class 'testWREG'
print(
  x,
  digits = max(3, getOption("digits") - 3),
  missing.summary = FALSE,
  eps.Pvalue = 0.001,
  signif.stars = getOption("show.signif.stars"),
  ...
)

## S3 method for class 'testWREG'
coef(object, ...)

rescale_axis(x, var_re, var_st)

## S3 method for class 'testWREG'
plot(
  x,
  alpha = 0.05,
  line = NA,
  cex.lab = 1.5,
  par.mar = c(0.5, 0.5, 0.5, 0.5),
  box.col = c("blue", "red"),
  box.lwd = 2,
  ...
)

Arguments

env	Vector, matrix or data frame with sample attributes (environemntal variables).
com	Matrix of data frame with species composition data.
traits	Vector, matrix or data frame with species attributes (traits)
test	NEEDS FIX Vector of character values. Which test should be conducted? Partial match to 'rowbased' row-based permutation test (called Model 2 in the Legendre et al. 1997 and Dray & Legendre 2008), 'colbased' for column-based permutation test (Model 4), and 'max' for max test (selecting the higher from rowbased and colbased result, Model 6). 'all' includes all three tests. See Details.
parallel	NULL (default) or integer number. Number of cores for parallel calculation. Maximum number of cores should correspond to number of available cores on the processor.
p.adjust.method	A string indicating the method of P-value adjustement, see p.adjust.methods for possible choices.
adjustP	Logical, default FALSE. Should be the P-values adjusted? If adjustP = TRUE, the last column in the results is adjusted by method selected in p.adjust.method.
x, object	NEEDS FIX object of the class "cwm", generated by function cwm.
digits	number of digits reported by print method on object of "cwm" class (default is 3).
missing.summary	Logical; should be the summary of values missing in env, cwm and traits be printed along to the result of test_cwm analysis? Default is TRUE.
eps.Pvalue	Values of P below this threshold will be printed as < [eps] in the output.
signif.stars	Logical; if TRUE, P-values are additionally encoded visually as 'significance stars' in order to help scanning of long coefficient tables. It defaults to the show.signif.stars slot of options.
...	Other arguments for print, summary or coef functions (not implemented yet).
var_re, var_st	Parameters for scaling function rescale_axis
alpha, line, cex.lab, par.mar, box.col, box.lwd	Graphical parameters for plot function.

Details

In the current implementation, species with missing species attributes are removed from sample x species matrix prior to permutation of species attributes among species.

Value

Function test_wreg returns the list of the class "testWREG" (with print and summary methods), which contains the following items: NEEDS TO FIX

• call Function call.

• out Data frame with results of calculation; the first column contains the original fourth corner metric (r_fc); following columns contain some of the following results of parametric tests: P.row, P.col and P.max. If adjustP = TRUE, the last column contains P values adjusted by p.adjust function.

• miss List with missing values of env, traits or cwm (the last provided for compatibility with test_cwm function and refers to samples which, after removing missing traits values, do not contain any species.)

• param Setting of input parameters (perm and test).

See Also

cwm test_cwm

Examples

data (vltava)
vltava.env <- vltava$env[,c('pH', 'COVERE32')]
vltava.com <- vltava$herbs$spe
vltava.traits <- vltava$herbs$traits
wreg <- test_wreg (env = vltava.env, com = vltava.com, traits = vltava.traits)

zdealveindy/weimea documentation built on Sept. 21, 2021, 2:15 p.m.