philipp-baumann

if (!require("rix")) {
  if (!require("remotes") install.packages("remotes")
  remotes::install_github("b-rodrigues/rix")
}

library("rix")
# make sure that only nix library paths in /nix/... are used to load R packages
rix_init()
# define `default.nix` in reproducible manner (will ping nixpkgs revision on GitHub)
rix(

philipp-baumann

CMake Warning:
  Manually-specified variables were not used by the project:

    BUILD_TESTING
    CMAKE_EXPORT_NO_PACKAGE_REGISTRY
    CMAKE_POLICY_DEFAULT_CMP0025
    QT_QMAKE_EXECUTABLE


-- Build files have been written to: /tmp/nix-build-RStudio-2023.09.0+463.drv-1/source/build

philipp-baumann

# This file was generated by the {rix} R package v0.4.1 on 2024-01-06
# with following call:
# >rix(r_ver = "63143ac2c9186be6d9da6035fa22620018c85932",
#  > r_pkgs = c("dplyr",
#  > "data.table"),
#  > overwrite = TRUE)
# It uses nixpkgs' revision 63143ac2c9186be6d9da6035fa22620018c85932 for reproducibility purposes
# which will install R version latest
# Report any issues to https://github.com/b-rodrigues/rix
let

philipp-baumann

# install_github("b-rodrigues/rix", ref = "71-with-nix")
library("rix")
library("dplyr")
library("data.table")

# fusen::load_flat_functions(flat_file = "dev/build_envs.Rmd")
# fusen::load_flat_functions(flat_file = "dev/get_os.Rmd")


library("rix")

philipp-baumann

snv_impl_base <- function(X) {
  X <- as.matrix(X)
  X <- sweep(X, 1L, rowMeans(X, na.rm = TRUE), `-`)
  X_sc <- sweep(X, 1L, apply(X, 1L, sd, na.rm = TRUE), `/`)
  return(X_sc)
}

snv_impl_base_mstats <- function(X) {
  X <- as.matrix(X)
  X <- sweep(X, 1L, matrixStats::rowMeans2(X, na.rm = TRUE), `-`)

philipp-baumann

#' @title Average spectra in list-column by entries in grouping column
#' @description Average spectra in list-column of spectra tibble (`spc_tbl`) by
#' groups given in group column.
#' @param spc_tbl Tibble data frame containing at least the grouping column
#' given in argument `by` and input spectra given in list-column `column_in`.
#' @param by Character vector of length 1L or name/symbol that specifies the
#' column by which groups of spectra are averaged. Default is `"sample_id"`.
#' @param column_in Character vector of length 1L or or name/symbol that
#' specifies the list-column that contains the inputs spectra to be averaged.
#' Default is `"spc_rs"`, which are resampled spectra (i.e., resulting after

philipp-baumann

## Wrangle results of nested group k-fold cross-validation =====================

# Add additional grouping IDs
cubist_nested_results_ids <- cubist_nested_add_ids(
  object = cubist_nested_results_repgroupcv, x_vars = "spc_pre",
  id_cols = c("site_id", "depth_cm"),
  y_vars = param_names,
  custom_spc_averaging = FALSE)

# Get predicted and observed values for each outer resample assessment set

philipp-baumann

## Load packages
pkgs <- c("here", "drake", "tidyverse", "data.table",
  "simplerspec", "caret", "Cubist", "rsample", "nls.multstart",
  "broom", # modeling
  "future", "future.apply", "doParallel", "doFuture", # asynchronous computation
  "gghighlight", "grid", "gridExtra", "cowplot", # graphics
  "xtable") # tables
purrr::walk(pkgs, library, character.only = TRUE)

funs <- list(

philipp-baumann

{
  "R": {
    "Version": "3.6.1",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://cloud.r-project.org"
      }
    ]
  },

philipp-baumann

{
  "renv": {
    "Version": "0.6.0-61"
  },
  "R": {
    "Version": "3.6.1",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://cloud.r-project.org"