fxTWAPLS (version 0.1.0)

WAPLS.w: WA-PLS training function

Description

WA-PLS training function, which can perform fx correction. 1/fx^2 correction will be applied at step 7.

Usage

WAPLS.w(
  modern_taxa,
  modern_climate,
  nPLS = 5,
  usefx = FALSE,
  fx_method = "bin",
  bin = NA
)

Arguments

modern_taxa

The modern taxa abundance data, each row represents a sampling site, each column represents a taxon.

modern_climate

The modern climate value at each sampling site.

nPLS

The number of components to be extracted.

usefx

Boolean flag on whether or not use fx correction.

fx_method

Binned or p-spline smoothed fx correction: if usefx = FALSE, this should be NA; otherwise, fx function will be used when choosing "bin"; fx_pspline function will be used when choosing "pspline".

bin

Binwidth to get fx, needed for both binned and p-splined method. if usefx = FALSE, this should be NA;

Value

A list of the training results, which will be used by the predict function. Each element in the list is described below:

fit

the fitted values using each number of components.

x

the observed modern climate values.

taxon_name

the name of each taxon.

optimum

the updated taxon optimum (u* in the WA-PLS paper).

comp

each component extracted (will be used in step 7 regression).

u

taxon optimum for each component (step 2).

z

a parameter used in standardization for each component (step 5).

s

a parameter used in standardization for each component (step 5).

orth

a list that stores orthogonalization parameters (step 4).

alpha

a list that stores regression coefficients (step 7).

meanx

mean value of the observed modern climate values.

nPLS

the total number of components extracted.

See Also

fx, TWAPLS.w, and WAPLS.predict.w

Examples

# NOT RUN {
# Load modern pollen data
modern_pollen <- read.csv("/path/to/modern_pollen.csv")
                                      
# Extract taxa
taxaColMin <- which(colnames(modern_pollen) == "taxa0")
taxaColMax <- which(colnames(modern_pollen) == "taxaN")
taxa <- modern_pollen[, taxaColMin:taxaColMax]

# MTCO
fit_Tmin <- fxTWAPLS::WAPLS.w(taxa, modern_pollen$Tmin, nPLS = 5)
fit_f_Tmin <- fxTWAPLS::WAPLS.w(taxa, 
                                modern_pollen$Tmin, 
                                nPLS = 5, 
                                usefx = TRUE, 
                                fx_method = "bin",
                                bin = 0.02)
# }
# NOT RUN {
# }