cv.pr.w: Pseudo-removed leave-out cross-validation

In fxTWAPLS: An Improved Version of WA-PLS

Pseudo-removed leave-out cross-validation

Description

Pseudo-removed leave-out cross-validation

Usage

cv.pr.w(
  modern_taxa,
  modern_climate,
  nPLS = 5,
  trainfun,
  predictfun,
  pseudo,
  usefx = FALSE,
  fx_method = "bin",
  bin = NA,
  cpus = 4,
  test_mode = TRUE,
  test_it = 5
)

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.
trainfun	Training function you want to use, either WAPLS.w or TWAPLS.w.
predictfun	Predict function you want to use: if trainfun is WAPLS.w, then this should be WAPLS.predict.w; if trainfun is TWAPLS.w, then this should be TWAPLS.predict.w.
pseudo	The geographically and climatically close sites to each test site, obtained from get_pseudo function.
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;
cpus	Number of CPUs for simultaneous iterations to execute, check parallel::detectCores() for available CPUs on your machine.
test_mode	Boolean flag to execute the function with a limited number of iterations, test_it, for testing purposes only.
test_it	Number of iterations to use in the test mode.

Value

Leave-one-out cross validation results.

See Also

fx, TWAPLS.w, TWAPLS.predict.w, WAPLS.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]

point <- modern_pollen[, c("Long", "Lat")]
test_mode <- TRUE # It should be set to FALSE before running
dist <- fxTWAPLS::get_distance(
  point,
  cpus = 2, # Remove the following line
  test_mode = test_mode
)
pseudo_Tmin <- fxTWAPLS::get_pseudo(
  dist,
  modern_pollen$Tmin,
  cpus = 2, # Remove the following line
  test_mode = test_mode
)

cv_pr_tf_Tmin2 <- fxTWAPLS::cv.pr.w(
  taxa,
  modern_pollen$Tmin,
  nPLS = 5,
  fxTWAPLS::TWAPLS.w2,
  fxTWAPLS::TWAPLS.predict.w,
  pseudo_Tmin,
  usefx = TRUE,
  fx_method = "bin",
  bin = 0.02,
  cpus = 2, # Remove the following line
  test_mode = test_mode
)

# Run with progress bar
`%>%` <- magrittr::`%>%`
cv_pr_tf_Tmin2 <- fxTWAPLS::cv.pr.w(
  taxa,
  modern_pollen$Tmin,
  nPLS = 5,
  fxTWAPLS::TWAPLS.w2,
  fxTWAPLS::TWAPLS.predict.w,
  pseudo_Tmin,
  usefx = TRUE,
  fx_method = "bin",
  bin = 0.02,
  cpus = 2, # Remove the following line
  test_mode = test_mode
) %>%
  fxTWAPLS::pb()

## End(Not run)

fxTWAPLS documentation built on Nov. 25, 2022, 5:06 p.m.