sse.sample: Calculate Sample Specific Errors

In special-uor/fxTWAPLS: An Improved Version of WA-PLS

Calculate Sample Specific Errors

Description

Calculate Sample Specific Errors

Usage

sse.sample(
  modern_taxa,
  modern_climate,
  fossil_taxa,
  trainfun,
  predictfun,
  nboot,
  nPLS,
  nsig,
  usefx = FALSE,
  fx_method = "bin",
  bin = NA,
  cpus = 4,
  seed = NULL,
  test_mode = FALSE,
  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
fossil_taxa	Fossil taxa abundance data to reconstruct past climates, each row represents a site to be reconstructed, each column represents a taxon.
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.
nboot	The number of bootstrap cycles you want to use.
nPLS	The number of components to be extracted.
nsig	The significant number of components to use to reconstruct past climates, this can be obtained from the cross-validation results.
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.
seed	Seed for reproducibility.
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

The bootstrapped standard error for each site.

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]

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

## SSE
nboot <- 5 # Recommended 1000
nsig <- 3 # This should be got from the random t-test of the cross validation

sse_tf_Tmin2 <- fxTWAPLS::sse.sample(
  modern_taxa = taxa,
  modern_climate = modern_pollen$Tmin,
  fossil_taxa = core,
  trainfun = fxTWAPLS::TWAPLS.w2,
  predictfun = fxTWAPLS::TWAPLS.predict.w,
  nboot = nboot,
  nPLS = 5,
  nsig = nsig,
  usefx = TRUE,
  fx_method = "bin",
  bin = 0.02,
  cpus = 2,
  seed = 1
)

# Run with progress bar
`%>%` <- magrittr::`%>%`
sse_tf_Tmin2 <- fxTWAPLS::sse.sample(
  modern_taxa = taxa,
  modern_climate = modern_pollen$Tmin,
  fossil_taxa = core,
  trainfun = fxTWAPLS::TWAPLS.w2,
  predictfun = fxTWAPLS::TWAPLS.predict.w,
  nboot = nboot,
  nPLS = 5,
  nsig = nsig,
  usefx = TRUE,
  fx_method = "bin",
  bin = 0.02,
  cpus = 2,
  seed = 1
) %>% fxTWAPLS::pb()

## End(Not run)

special-uor/fxTWAPLS documentation built on June 30, 2024, 1:58 p.m.