fxTWAPLS: An Improved Version of WA-PLS

Overview

The goal of this package is to provide an improved version of WA-PLS by including the tolerances of taxa and the frequency of the sampled climate variable. This package also provides a way of leave-out cross-validation that removes both the test site and sites that are both geographically close and climatically close for each cycle, to avoid the risk of pseudo-replication.

Installation

You can install the released version of fxTWAPLS from CRAN with:

install.packages("fxTWAPLS")

And the development version from GitHub with:

install.packages("remotes")
remotes::install_github("special-uor/fxTWAPLS", "dev")

Publications

• Liu Mengmeng, Prentice Iain Colin, ter Braak Cajo J. F., Harrison Sandy P.. 2020 An improved statistical approach for reconstructing past climates from biotic assemblages. Proc. R. Soc. A. 476: 20200346. https://doi.org/10.1098/rspa.2020.0346 - fxTWAPLS v0.0.2

install.packages("remotes")
remotes::install_github("special-uor/fxTWAPLS@v0.0.2")

Notes

The following functions can be executed in parallel:

• cv.pr.w
• cv.w
• get_distance
• get_pseudo
• sse.sample

To do so, include the cpus parameter. For example:

# without fx
cv_Tmin <- fxTWAPLS::cv.w(taxa,
                          modern_pollen$Tmin,
                          nPLS = 5,
                          fxTWAPLS::WAPLS.w,
                          fxTWAPLS::WAPLS.predict.w,
                          cpus = 2)

Optionally, a progress bar can be displayed for long computations. Just “pipe” the function call to fxTWAPLS::pb().

# without fx
`%>%` <- magrittr::`%>%`
cv_Tmin <- fxTWAPLS::cv.w(taxa,
                          modern_pollen$Tmin,
                          nPLS = 5,
                          fxTWAPLS::WAPLS.w,
                          fxTWAPLS::WAPLS.predict.w,
                          cpus = 2) %>%
  fxTWAPLS::pb()

Alternatively, if you are not familiar with the “pipe” operator, you can run the following code:

# without fx
cv_Tmin <- fxTWAPLS::pb(fxTWAPLS::cv.w(taxa,
                                       modern_pollen$Tmin,
                                       nPLS = 5,
                                       fxTWAPLS::WAPLS.w,
                                       fxTWAPLS::WAPLS.predict.w,
                                       cpus = 2))