fxTWAPLS (version 0.1.2)

TWAPLS.predict.w: TWA-PLS predict function

Description

TWA-PLS predict function

Usage

TWAPLS.predict.w(TWAPLSoutput, fossil_taxa)

Value

A list of the reconstruction results. Each element in the list is described below:

fit

the fitted values using each number of components.

nPLS

the total number of components extracted.

Arguments

TWAPLSoutput

The output of the TWAPLS.w training function, either with or without fx correction.

fossil_taxa

Fossil taxa abundance data to reconstruct past climates, each row represents a site to be reconstructed, each column represents a taxon.

See Also

TWAPLS.w

Examples

if (FALSE) {
# 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]

# Load reconstruction data
Holocene <- read.csv("/path/to/Holocene.csv")
taxaColMin <- which(colnames(Holocene) == "taxa0")
taxaColMax <- which(colnames(Holocene) == "taxaN")
core <- Holocene[, taxaColMin:taxaColMax]

## Train
fit_t_Tmin <- fxTWAPLS::TWAPLS.w(taxa, modern_pollen$Tmin, nPLS = 5)
fit_tf_Tmin <- fxTWAPLS::TWAPLS.w(
  taxa,
  modern_pollen$Tmin,
  nPLS = 5,
  usefx = TRUE,
  fx_method = "bin",
  bin = 0.02
)
fit_t_Tmin2 <- fxTWAPLS::TWAPLS.w2(taxa, modern_pollen$Tmin, nPLS = 5)
fit_tf_Tmin2 <- fxTWAPLS::TWAPLS.w2(
  taxa,
  modern_pollen$Tmin,
  nPLS = 5,
  usefx = TRUE,
  fx_method = "bin",
  bin = 0.02
)

## Predict
fossil_t_Tmin <- fxTWAPLS::TWAPLS.predict.w(fit_t_Tmin, core)
fossil_tf_Tmin <- fxTWAPLS::TWAPLS.predict.w(fit_tf_Tmin, core)
fossil_t_Tmin2 <- fxTWAPLS::TWAPLS.predict.w(fit_t_Tmin2, core)
fossil_tf_Tmin2 <- fxTWAPLS::TWAPLS.predict.w(fit_tf_Tmin2, core)
}