SciCodePile/SciCode-Domain-Code
DATA1: Domain-Specific Code Dataset Dataset Overview DATA1 is a large-scale domain-specific code dataset focusing on code samples from interdisciplinary fields such as biology, chemistry, materials science, and related areas. The dataset is collected and organized from GitHub repositories, covering 178 different domain topics with over 1.1 billion lines of code. Dataset Statistics Total Datasets: 178 CSV files Total Data Size: ~115 GB Total Lines… See the full description on the dataset page: https://huggingface.co/datasets/SciCodePile/SciCode-Domain-Code.
41.3k
1"keyword","repo_name","file_path","file_extension","file_size","line_count","content","language"
2"Pathogens","pat-s/pathogen-modeling","exec-drake.R",".R","945","30","## make targets3 4r_make(r_args = list(show = TRUE))5 6# visualize7 8r_vis_drake_graph(group = ""stage"", clusters = c(""data"", ""task"", ""learner"",9 ""mlr_settings"",10 ""prediction""),11 targets_only = TRUE, show_output_files = FALSE)12# see outdated13 14r_outdated(r_args = list(show = TRUE))15 16# Misc17r_predict_runtime(r_args = list(show = TRUE))18 19r_predict_workers()20 21 22# Manually ----------------------------------------------------------------23 24make(plan, verbose = 2, targets = c(""maps_debugging_diplodia_no_temp""),25 cache_log_file = ""log/cache_log.txt"",26 console_log_file = ""log/drake.log"",27 lazy_load = ""promise"", caching = ""worker"",28 memory_strategy = ""memory"",29 template = list(log_file = ""log/worker%a.log"", n_cpus= 5, memory = 20000),30 garbage_collection = TRUE, jobs = 2, parallelism = ""clustermq"")31","R"
32"Pathogens","pat-s/pathogen-modeling","tic.R",".R","77","2","do_package_checks(error_on = ""error"", args = c(""--no-tests"", ""--no-manual""))33","R"
34"Pathogens","pat-s/pathogen-modeling","LICENSE.md",".md","1074","22","# MIT License35 36Copyright (c) 2019 Patrick Schratz37 38Permission is hereby granted, free of charge, to any person obtaining a copy39of this software and associated documentation files (the ""Software""), to deal40in the Software without restriction, including without limitation the rights41to use, copy, modify, merge, publish, distribute, sublicense, and/or sell42copies of the Software, and to permit persons to whom the Software is43furnished to do so, subject to the following conditions:44 45The above copyright notice and this permission notice shall be included in all46copies or substantial portions of the Software.47 48THE SOFTWARE IS PROVIDED ""AS IS"", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR49IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,50FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE51AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER52LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,53OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE54SOFTWARE.55","Markdown"
56"Pathogens","pat-s/pathogen-modeling","_drake.R",".R","3358","83","# Plans -----------------------------------------------------------57source(""code/99-packages.R"")58sourceDirectory(""R/"")59 60data_plan = code_to_plan(""code/01-data/data.R"")61task_plan = code_to_plan(""code/01-data/task.R"")62learners_plan = code_to_plan(""code/02-mlr-settings/learner.R"")63resampling_plan = code_to_plan(""code/02-mlr-settings/resampling.R"")64param_set_plan = code_to_plan(""code/02-mlr-settings/param-set.R"")65tune_ctrl_plan = code_to_plan(""code/02-mlr-settings/tune_ctrl_mbo.R"")66tuning_wrapper_plan = code_to_plan(""code/02-mlr-settings/tuning.R"")67source(""code/03-benchmark/aggregate-results.R"")68source(""code/03-benchmark/benchmark.R"")69source(""code/04-prediction/prediction.R"")70visualization_plan = code_to_plan(""code/05-visualization/vis-partitions.R"")71dataset_tables_plan = code_to_plan(""code/05-visualization/create_dataset_tables.R"")72source(""code/06-reports.R"")73 74source(""https://raw.githubusercontent.com/mlr-org/mlr-extralearner/master/R/RLearner_classif_gam.R"")75 76# grouping for visualization77data_plan$stage = ""data""78task_plan$stage = ""data""79learners_plan$stage = ""learner""80resampling_plan$stage = ""mlr_settings""81param_set_plan$stage = ""mlr_settings""82tune_ctrl_plan$stage = ""mlr_settings""83tuning_wrapper_plan$stage = ""learner""84benchmark_plan$stage = ""benchmark""85bmr_aggr_path_resamp_plan$stage = ""benchmark""86bmr_aggr_model_resamp_plan$stage = ""benchmark""87no_extract_plan$stage = ""benchmark""88bm_all_pathogens_plan$stage = ""benchmark""89prediction_prob_plan$stage = ""prediction""90prediction_maps_plan$stage = ""prediction""91reports_plan$stage = ""reports""92visualization_plan$stage = ""visualization""93dataset_tables_plan$stage = ""visualization""94 95# Combine all -------------------------------------------------------------96 97plan = bind_plans(data_plan, task_plan, learners_plan, resampling_plan,98 param_set_plan, tune_ctrl_plan, tuning_wrapper_plan,99 100 bmr_aggr_path_resamp_plan,101 bmr_aggr_model_resamp_plan,102 bm_all_pathogens_plan,103 no_extract_plan,104 benchmark_plan,105 106 prediction_prob_plan,107 prediction_maps_plan,108 reports_plan,109 visualization_plan,110 dataset_tables_plan)111 112plan %<>% mutate(stage = as.factor(stage))113 114options(clustermq.scheduler = ""slurm"",115 clustermq.template = ""~/papers/2018-model-comparison/slurm_clustermq.tmpl"")116 117 118### Show log in console119# watch -n .1 tail -n 40 ~/git/pathogen-modeling/drake.log120 121drake_config(plan,122 verbose = 2,123 targets = c(""pathogen_maps_debugging"", ""prediction_pathogens""),124 lazy_load = ""promise"",125 console_log_file = ""log/drake.log"",126 caching = ""worker"",127 template = list(log_file = ""log/worker%a.log"", n_cpus = 16, memory = 60000,128 job_name = ""paper1""),129 prework = list(quote(set.seed(1, ""L'Ecuyer-CMRG"")),130 quote(future::plan(future.callr::callr, workers = 10)),131 quote(parallelStart(132 mode = ""multicore"", cpus = ignore(16), level = ""mlr.resample""133 ))134 ),135 garbage_collection = TRUE, jobs = 3, parallelism = ""clustermq"",136 lock_envir = FALSE, keep_going = TRUE137)138","R"
139"Pathogens","pat-s/pathogen-modeling","inst/rsync-jupiter.sh",".sh","2660","50","#! /bin/bash140 141########142# LIFE143########144 145# `pathogen-prediction-maps` --------------- copy pathogen infection prediction PNG maps to LIFE146rsync -rlptDvzog --chown=www-data:www-data --fake-super \147 /mnt/cluster/home/patrick/papers/2018-model-comparison/docs/figure/prediction-pathogens.Rmd/prediction-map* \148 -e ssh patrick@jupiter.geogr.uni-jena.de:/home/www/life-healthy-forest/action-B1-spatial-mapping/pathogen-infection-maps/149 150# `pathogen_prediction_report` ------------ copy pathogen infection report to LIFE151rsync -rlptDvzog --chown=www-data:www-data --fake-super \152 /mnt/cluster/home/patrick/papers/2018-model-comparison/analysis/rmd/pathogens-prediction.html \153 -e ssh patrick@jupiter.geogr.uni-jena.de:/home/www/life-healthy-forest/action-B1-spatial-mapping/154 155# `benchmark_all_pathogens`-------- copy benchmark report all pathogens to LIFE156rsync -rlptDvzog --chown=www-data:www-data --fake-super \157 /mnt/cluster/home/patrick/papers/2018-model-comparison/analysis/rmd/pathogens-performance.html \158 -e ssh patrick@jupiter.geogr.uni-jena.de:/home/www/life-healthy-forest/action-B1-spatial-mapping/159 160########161# paper ""2018-model-comparison""162########163 164# `benchmark_diplodia` ----------- copy benchmark report DIPLODIA to patrick165rsync -rlptDvzog --chown=www-data:www-data --fake-super \166 /mnt/cluster/home/patrick/papers/2018-model-comparison/analysis/rmd/pathogens-performance-diplodia.html \167 -e ssh patrick@jupiter.geogr.uni-jena.de:/home/patrick/2018-model-comparison/168 169# `visualize_partitions` -------------- copy visualization of partitions to patrick170rsync -rlptDvzog --chown=www-data:www-data --fake-super \171 /mnt/cluster/home/patrick/papers/2018-model-comparison/analysis/rmd/visualize-partitions.html \172 -e ssh patrick@jupiter.geogr.uni-jena.de:/home/patrick/2018-model-comparison/173 174# `vis_opt_paths` -------------- copy visualization of optimization paths to patrick175 176rsync -rlptDvzog --chown=www-data:www-data --fake-super \177 /mnt/cluster/home/patrick/papers/2018-model-comparison/analysis/rmd/vis-opt-paths.html \178 -e ssh patrick@jupiter.geogr.uni-jena.de:/home/patrick/2018-model-comparison/179 180# `vis_tuning_effects` -------------- copy visualization of tuning effects to patrick181rsync -rlptDvzog --chown=www-data:www-data --fake-super \182 /mnt/cluster/home/patrick/papers/2018-model-comparison/analysis/rmd/vis-tuning-effects.html \183 -e ssh patrick@jupiter.geogr.uni-jena.de:/home/patrick/2018-model-comparison/184 185# rsync -rlptDvzog --chown=www-data:www-data --fake-super \186# /mnt/geoinf_web/bi28yuv/LIFE-Healthy-Forest/* \187# -e ssh patrick@jupiter.geogr.uni-jena.de:/home/www/life-healthy-forest/action-A2-predictor-database/188","Shell"
189"Pathogens","pat-s/pathogen-modeling","inst/99-funs.R",".R","1250","37","##### my.pairs env190the.col.hist <- ""cyan""191 192 193panel.hist <- function(x, col.hist=the.col.hist,194 cex.cor=NULL,digits=NULL,col=NULL,pch=NULL,cex=NULL,...)195{196 dummy <- is.character(cex.cor) | is.numeric(digits) | is.character(cex) | is.character(pch) | is.character(col)197 usr <- par(""usr""); on.exit(par(usr))198 par(usr = c(usr[1:2], 0, 1.5) )199 h <- hist(x, plot = FALSE)200 breaks <- h$breaks; nB <- length(breaks)201 y <- h$counts; y <- y/max(y)202 rect(breaks[-nB], 0, breaks[-1], y, col=col.hist, ...)203}204 205panel.cor <- function(x, y, digits=2, prefix="""", cex.cor=NULL,206 col.hist=NULL,207 col=NULL,pch=NULL,cex=NULL,...)208{209 dummy <- is.character(col.hist) | is.character(cex) | is.character(pch) | is.character(col)210 usr <- par(""usr""); on.exit(par(usr))211 par(usr = c(0, 1, 0, 1))212 r <- abs(cor(x, y, use=""pairwise.complete.obs""))213 txt <- format(c(r, 0.123456789), digits=digits)[1]214 txt <- paste(prefix, txt, sep="""")215 if (is.null(cex.cor)) cex.cor <- 0.8/strwidth(txt)216 #text(0.5, 0.5, txt, cex = cex.cor * r)217 text(0.5, 0.5, txt, cex = cex.cor)218}219 220my_pairs <- function( x, ... )221{222 pairs( x, ...,223 upper.panel=panel.smooth, lower.panel=panel.cor, diag.panel=panel.hist )224}225","R"
226"Pathogens","pat-s/pathogen-modeling","inst/atlas-climatico-new.R",".R","1634","40","library(magrittr)227library(readr)228library(raster)229library(sf)230library(dplyr)231pr_1km_CAPV_Arakil <- read.table(file = ""data/02-pr/pr/pr_1km_CAPV_Arakil.csv"", sep = "","", dec = ""."", header = TRUE)232 233test = tidyr::gather(pr_1km_CAPV_Arakil, ""coord_id"", ""p_sum"", -YYYYMMDD, factor_key = F) %>%234 #dplyr::filter(coord_id != ""X22512"") %>%235 dplyr::rename(date = YYYYMMDD) %>%236 dplyr::mutate(date = as.character(date)) %>%237 dplyr::mutate(date = lubridate::as_date(date)) %>%238 dplyr::filter(date > ""2000-01-01"") %>%239 dplyr::mutate(coord_id = stringr::str_remove(coord_id, ""X"")) %>%240 dplyr::mutate(month = lubridate::month(date)) %>% # create month column (includes all years)241 dplyr::group_by(month, coord_id) %>%242 dplyr::summarise_at(""p_sum"", mean) # get the summarised p_sum for the respective grouping243 244coordinates = readr::read_table2(""data/01_grid_1km_cuencas/grid_1km_cuencas_etrs89/stations_Arakil_etrs89.txt"",245 col_type = readr::cols(station_id = col_character()))246 247df_bind = dplyr::left_join(test, coordinates, by = c(""coord_id"" = ""station_id""))248 249df_bind %<>%250 dplyr::rename(x = UTMXetrs89) %>%251 dplyr::rename(y = UTMYetrs89) %>%252 dplyr::mutate(month = as.factor(as.character(month))) %>%253 dplyr::select(x, y, p_sum, month)254 255#df_month = split(df_bind, df_bind$month, drop = FALSE)256 257x = df_bind %>% group_split(month, keep = FALSE)258 259x = map(x, ~ as.data.frame(.x, xy = TRUE))260 261x_st = map(x, ~ st_as_sf(.x, coords = c(""x"", ""y""), crs = 25830))262x_sp = map(x_st, ~ as(.x, ""Spatial""))263x_spdf = map(x_sp, ~ SpatialPixelsDataFrame(.x, tolerance = 0.973816, .x@data))264x_ras = map(x_spdf, ~ raster(.x))265","R"
266"Pathogens","pat-s/pathogen-modeling","man-roxygen/learner.R",".R","50","2","#' @param learner Learner from [mlr::makeLearner]267","R"
268"Pathogens","pat-s/pathogen-modeling","man-roxygen/url.R",".R","52","2","#' @param url URL to download from (usually Zenodo)269","R"
270"Pathogens","pat-s/pathogen-modeling","man-roxygen/task.R",".R","24","2","#' @param task mlr task271","R"
272"Pathogens","pat-s/pathogen-modeling","man-roxygen/param_set.R",".R","34","2","#' @param param_set mlr Param Set273","R"
274"Pathogens","pat-s/pathogen-modeling","man-roxygen/tune_ctrl.R",".R","44","2","#' @param tune_ctrl mrl tune control object275","R"
276"Pathogens","pat-s/pathogen-modeling","man-roxygen/resampling.R",".R","36","2","#' @param resampling mlr resampling277","R"
278"Pathogens","pat-s/pathogen-modeling","packrat/init.R",".R","8406","227","local({279 280 ## Helper function to get the path to the library directory for a281 ## given packrat project.282 getPackratLibDir <- function(projDir = NULL) {283 path <- file.path(""packrat"", ""lib"", R.version$platform, getRversion())284 285 if (!is.null(projDir)) {286 287 ## Strip trailing slashes if necessary288 projDir <- sub(""/+$"", """", projDir)289 290 ## Only prepend path if different from current working dir291 if (!identical(normalizePath(projDir), normalizePath(getwd())))292 path <- file.path(projDir, path)293 }294 295 path296 }297 298 ## Ensure that we set the packrat library directory relative to the299 ## project directory. Normally, this should be the working directory,300 ## but we also use '.rs.getProjectDirectory()' if necessary (e.g. we're301 ## rebuilding a project while within a separate directory)302 libDir <- if (exists("".rs.getProjectDirectory""))303 getPackratLibDir(.rs.getProjectDirectory())304 else305 getPackratLibDir()306 307 ## Unload packrat in case it's loaded -- this ensures packrat _must_ be308 ## loaded from the private library. Note that `requireNamespace` will309 ## succeed if the package is already loaded, regardless of lib.loc!310 if (""packrat"" %in% loadedNamespaces())311 try(unloadNamespace(""packrat""), silent = TRUE)312 313 if (suppressWarnings(requireNamespace(""packrat"", quietly = TRUE, lib.loc = libDir))) {314 315 # Check 'print.banner.on.startup' -- when NA and RStudio, don't print316 print.banner <- packrat::get_opts(""print.banner.on.startup"")317 if (print.banner == ""auto"" && is.na(Sys.getenv(""RSTUDIO"", unset = NA))) {318 print.banner <- TRUE319 } else {320 print.banner <- FALSE321 }322 return(packrat::on(print.banner = print.banner))323 }324 325 ## Escape hatch to allow RStudio to handle bootstrapping. This326 ## enables RStudio to provide print output when automagically327 ## restoring a project from a bundle on load.328 if (!is.na(Sys.getenv(""RSTUDIO"", unset = NA)) &&329 is.na(Sys.getenv(""RSTUDIO_PACKRAT_BOOTSTRAP"", unset = NA))) {330 Sys.setenv(""RSTUDIO_PACKRAT_BOOTSTRAP"" = ""1"")331 setHook(""rstudio.sessionInit"", function(...) {332 # Ensure that, on sourcing 'packrat/init.R', we are333 # within the project root directory334 if (exists("".rs.getProjectDirectory"")) {335 owd <- getwd()336 setwd(.rs.getProjectDirectory())337 on.exit(setwd(owd), add = TRUE)338 }339 source(""packrat/init.R"")340 })341 return(invisible(NULL))342 }343 344 ## Bootstrapping -- only performed in interactive contexts,345 ## or when explicitly asked for on the command line346 if (interactive() || ""--bootstrap-packrat"" %in% commandArgs(TRUE)) {347 348 needsRestore <- ""--bootstrap-packrat"" %in% commandArgs(TRUE)349 350 message(""Packrat is not installed in the local library -- "",351 ""attempting to bootstrap an installation..."")352 353 ## We need utils for the following to succeed -- there are calls to functions354 ## in 'restore' that are contained within utils. utils gets loaded at the355 ## end of start-up anyhow, so this should be fine356 library(""utils"", character.only = TRUE)357 358 ## Install packrat into local project library359 packratSrcPath <- list.files(full.names = TRUE,360 file.path(""packrat"", ""src"", ""packrat"")361 )362 363 ## No packrat tarballs available locally -- try some other means of installation364 if (!length(packratSrcPath)) {365 366 message(""> No source tarball of packrat available locally"")367 368 ## There are no packrat sources available -- try using a version of369 ## packrat installed in the user library to bootstrap370 if (requireNamespace(""packrat"", quietly = TRUE) && packageVersion(""packrat"") >= ""0.2.0.99"") {371 message(""> Using user-library packrat ("",372 packageVersion(""packrat""),373 "") to bootstrap this project"")374 }375 376 ## Couldn't find a user-local packrat -- try finding and using devtools377 ## to install378 else if (requireNamespace(""devtools"", quietly = TRUE)) {379 message(""> Attempting to use devtools::install_github to install "",380 ""a temporary version of packrat"")381 library(stats) ## for setNames382 devtools::install_github(""rstudio/packrat"")383 }384 385 ## Try downloading packrat from CRAN if available386 else if (""packrat"" %in% rownames(available.packages())) {387 message(""> Installing packrat from CRAN"")388 install.packages(""packrat"")389 }390 391 ## Fail -- couldn't find an appropriate means of installing packrat392 else {393 stop(""Could not automatically bootstrap packrat -- try running "",394 ""\""'install.packages('devtools'); devtools::install_github('rstudio/packrat')\"""",395 ""and restarting R to bootstrap packrat."")396 }397 398 # Restore the project, unload the temporary packrat, and load the private packrat399 if (needsRestore)400 packrat::restore(prompt = FALSE, restart = TRUE)401 402 ## This code path only reached if we didn't restart earlier403 unloadNamespace(""packrat"")404 requireNamespace(""packrat"", lib.loc = libDir, quietly = TRUE)405 return(packrat::on())406 407 }408 409 ## Multiple packrat tarballs available locally -- try to choose one410 ## TODO: read lock file and infer most appropriate from there; low priority because411 ## after bootstrapping packrat a restore should do the right thing412 if (length(packratSrcPath) > 1) {413 warning(""Multiple versions of packrat available in the source directory;"",414 ""using packrat source:\n- "", shQuote(packratSrcPath))415 packratSrcPath <- packratSrcPath[[1]]416 }417 418 419 lib <- file.path(""packrat"", ""lib"", R.version$platform, getRversion())420 if (!file.exists(lib)) {421 dir.create(lib, recursive = TRUE)422 }423 424 message(""> Installing packrat into project private library:"")425 message(""- "", shQuote(lib))426 427 surround <- function(x, with) {428 if (!length(x)) return(character())429 paste0(with, x, with)430 }431 432 433 ## Invoke install.packages() in clean R session434 peq <- function(x, y) paste(x, y, sep = "" = "")435 installArgs <- c(436 peq(""pkgs"", surround(packratSrcPath, with = ""'"")),437 peq(""lib"", surround(lib, with = ""'"")),438 peq(""repos"", ""NULL""),439 peq(""type"", surround(""source"", with = ""'""))440 )441 442 fmt <- ""utils::install.packages(%s)""443 installCmd <- sprintf(fmt, paste(installArgs, collapse = "", ""))444 445 ## Write script to file (avoid issues with command line quoting446 ## on R 3.4.3)447 installFile <- tempfile(""packrat-bootstrap"", fileext = "".R"")448 writeLines(installCmd, con = installFile)449 on.exit(unlink(installFile), add = TRUE)450 451 fullCmd <- paste(452 surround(file.path(R.home(""bin""), ""R""), with = ""\""""),453 ""--vanilla"",454 ""--slave"",455 ""-f"",456 surround(installFile, with = ""\"""")457 )458 system(fullCmd)459 460 ## Tag the installed packrat so we know it's managed by packrat461 ## TODO: should this be taking information from the lockfile? this is a bit awkward462 ## because we're taking an un-annotated packrat source tarball and simply assuming it's now463 ## an 'installed from source' version464 465 ## -- InstallAgent -- ##466 installAgent <- ""InstallAgent: packrat 0.5.0""467 468 ## -- InstallSource -- ##469 installSource <- ""InstallSource: source""470 471 packratDescPath <- file.path(lib, ""packrat"", ""DESCRIPTION"")472 DESCRIPTION <- readLines(packratDescPath)473 DESCRIPTION <- c(DESCRIPTION, installAgent, installSource)474 cat(DESCRIPTION, file = packratDescPath, sep = ""\n"")475 476 # Otherwise, continue on as normal477 message(""> Attaching packrat"")478 library(""packrat"", character.only = TRUE, lib.loc = lib)479 480 message(""> Restoring library"")481 if (needsRestore)482 packrat::restore(prompt = FALSE, restart = FALSE)483 484 # If the environment allows us to restart, do so with a call to restore485 restart <- getOption(""restart"")486 if (!is.null(restart)) {487 message(""> Packrat bootstrap successfully completed. "",488 ""Restarting R and entering packrat mode..."")489 return(restart())490 }491 492 # Callers (source-erers) can define this hidden variable to make sure we don't enter packrat mode493 # Primarily useful for testing494 if (!exists("".__DONT_ENTER_PACKRAT_MODE__."") && interactive()) {495 message(""> Packrat bootstrap successfully completed. Entering packrat mode..."")496 packrat::on()497 }498 499 Sys.unsetenv(""RSTUDIO_PACKRAT_BOOTSTRAP"")500 501 }502 503})504","R"
505"Pathogens","pat-s/pathogen-modeling","code/06-reports.R",".R","713","18","reports_plan = drake_plan(506 507 benchmark_diplodia = wflow_publish(knitr_in(""analysis/benchmark-diplodia.Rmd""), view = FALSE),508 509 benchmark_pathogens = wflow_publish(knitr_in(""analysis/benchmark-pathogens.Rmd""), view = FALSE),510 511 prediction_pathogens = wflow_publish(knitr_in(""analysis/prediction-pathogens.Rmd""), view = FALSE),512 513 pathogen_maps_debugging = wflow_publish(knitr_in(""analysis/pathogen-maps-debugging.Rmd""), view = FALSE),514 515 vis_partitions = wflow_publish(knitr_in(""analysis/vis-partitions.Rmd""), view = FALSE),516 517 vis_opt_paths = wflow_publish(knitr_in(""analysis/vis-opt-paths.Rmd""), view = FALSE),518 519 vis_tuning_effects = wflow_publish(knitr_in(""analysis/vis-tuning-effects.Rmd""), view = FALSE)520 521)522","R"
523"Pathogens","pat-s/pathogen-modeling","code/99-packages.R",".R","1993","42","suppressPackageStartupMessages(library(drake))524suppressPackageStartupMessages(library(mlr))525suppressPackageStartupMessages(library(magrittr))526suppressPackageStartupMessages(library(mlrMBO))527suppressPackageStartupMessages(library(purrr))528suppressPackageStartupMessages(library(parallelMap))529suppressPackageStartupMessages(library(sf))530suppressPackageStartupMessages(library(dplyr))531suppressPackageStartupMessages(library(lwgeom))532suppressPackageStartupMessages(library(forcats))533suppressPackageStartupMessages(library(tibble))534suppressPackageStartupMessages(library(rgdal))535suppressPackageStartupMessages(library(viridis))536suppressPackageStartupMessages(library(rasterVis))537suppressPackageStartupMessages(library(lattice))538suppressPackageStartupMessages(library(latticeExtra))539suppressPackageStartupMessages(library(glue))540suppressPackageStartupMessages(library(RSAGA))541suppressPackageStartupMessages(library(stringr))542suppressPackageStartupMessages(library(GSIF))543suppressPackageStartupMessages(library(sp))544suppressPackageStartupMessages(library(R.utils))545suppressPackageStartupMessages(library(curl))546suppressPackageStartupMessages(library(fs))547suppressPackageStartupMessages(library(rgenoud))548suppressPackageStartupMessages(library(stringr))549suppressPackageStartupMessages(library(ggplot2))550suppressPackageStartupMessages(library(ggspatial))551suppressPackageStartupMessages(library(clustermq))552suppressPackageStartupMessages(library(ggsci))553suppressPackageStartupMessages(library(furrr))554suppressPackageStartupMessages(library(future.callr))555suppressPackageStartupMessages(library(ggpubr))556suppressPackageStartupMessages(library(hrbrthemes))557suppressPackageStartupMessages(library(cowplot))558suppressPackageStartupMessages(library(reporttools))559suppressPackageStartupMessages(library(ggrepel))560suppressPackageStartupMessages(library(ggExtra))561suppressPackageStartupMessages(library(kableExtra))562suppressPackageStartupMessages(library(here))563suppressPackageStartupMessages(library(workflowr))564","R"
565"Pathogens","pat-s/pathogen-modeling","code/04-prediction/prediction.R",".R","11567","244","args_pred = tibble(task = rlang::syms(c(""tasks_pred_no_ph"",566 ""tasks_pred_no_ph"",567 ""tasks_pred_no_ph"",568 ""tasks_pred_no_ph"",569 ""tasks_pred_no_ph"",570 571 ""diplodia_task_dummy_prediction_no_temp"",572 ""diplodia_task_dummy_prediction_no_precip"",573 ""diplodia_task_dummy_prediction_no_hail"",574 ""diplodia_task_dummy_prediction_no_ph"",575 ""diplodia_task_dummy_prediction_no_soil"",576 ""diplodia_task_dummy_prediction_no_lithology"",577 ""diplodia_task_dummy_prediction_no_slope"",578 ""diplodia_task_dummy_prediction_no_pisr"",579 580 ""diplodia_task_dummy_prediction_no_ph"",581 ""fusarium_task_dummy_prediction_no_ph"",582 ""armillaria_task_dummy_no_ph"",583 ""heterobasidion_task_dummy_no_ph"",584 ""tasks_pred_no_ph"")),585 learner = c(""lrn_rf"",586 ""lrn_svm"",587 ""lrn_xgboost"",588 ""lrn_kknn"",589 ""lrn_glm"",590 591 ""lrn_rf"", # debugging tasks592 ""lrn_rf"", # debugging tasks593 ""lrn_rf"", # debugging tasks594 ""lrn_rf"", # debugging tasks595 ""lrn_rf"", # debugging tasks596 ""lrn_rf"", # debugging tasks597 ""lrn_rf"", # debugging tasks598 ""lrn_rf"", # debugging tasks599 600 ""lrn_gam_diplodia_pred_no_ph"",601 ""lrn_gam_fusarium_pred_no_ph"",602 ""lrn_gam_armillaria_pred_no_ph"",603 ""lrn_gam_heterobasidion_pred_no_ph"",604 ""lrn_brt""),605 resampling = rlang::syms(rep(""spcv_inner_fiveF"", 18)),606 param_set = rlang::syms(c(""ps_rf"",607 ""ps_svm"",608 ""ps_xgboost"",609 ""ps_kknn"",610 ""NULL"",611 612 ""ps_rf"", # debugging tasks613 ""ps_rf"", # debugging tasks614 ""ps_rf"", # debugging tasks615 ""ps_rf"", # debugging tasks616 ""ps_rf"", # debugging tasks617 ""ps_rf"", # debugging tasks618 ""ps_rf"", # debugging tasks619 ""ps_rf"", # debugging tasks620 621 ""ps_gam_diplodia_fusarium_pred"",622 ""ps_gam_diplodia_fusarium_pred"",623 ""ps_gam_armillaria_heterobasidion"",624 ""ps_gam_armillaria_heterobasidion"",625 ""ps_brt"")),626 tune_ctrl = rlang::syms(c(""tune_ctrl_rf_100"",627 ""tune_ctrl_svm_100"",628 ""tune_ctrl_xgboost_100"",629 ""tune_ctrl_kknn_100"",630 ""NULL"",631 632 ""tune_ctrl_rf_100"", # debugging tasks633 ""tune_ctrl_rf_100"", # debugging tasks634 ""tune_ctrl_rf_100"", # debugging tasks635 ""tune_ctrl_rf_100"", # debugging tasks636 ""tune_ctrl_rf_100"", # debugging tasks637 ""tune_ctrl_rf_100"", # debugging tasks638 ""tune_ctrl_rf_100"", # debugging tasks639 ""tune_ctrl_rf_100"", # debugging tasks640 641 ""tune_ctrl_gam_100_diplodia_fusarium_pred"",642 ""tune_ctrl_gam_100_diplodia_fusarium_pred"",643 ""tune_ctrl_gam_100_armillaria_heterobasidion"",644 ""tune_ctrl_gam_100_armillaria_heterobasidion"",645 ""tune_ctrl_brt_100"")),646 prediction_data = c(rep(rlang::syms(""pred_data_no_ph""), 5),647 648 rlang::syms(""pred_data_no_temp""),649 rlang::syms(""pred_data_no_precip""),650 rlang::syms(""pred_data_no_hail""),651 rlang::syms(""pred_data_no_ph""),652 rlang::syms(""pred_data_no_soil""),653 rlang::syms(""pred_data_no_lithology""),654 rlang::syms(""pred_data_no_slope""),655 rlang::syms(""pred_data_no_pisr""),656 657 rep(rlang::syms(""pred_data_no_ph""), 5)),658 prediction_grid = rep(rlang::syms(""temperature_mean""), 18),659 desc_resampling = c(""spatial/spatial"",660 ""spatial/spatial"",661 ""spatial/spatial"",662 ""spatial/spatial"",663 ""spatial/no tuning"",664 665 ""spatial/spatial"", # debugging tasks666 ""spatial/spatial"", # debugging tasks667 ""spatial/spatial"", # debugging tasks668 ""spatial/spatial"", # debugging tasks669 ""spatial/spatial"", # debugging tasks670 ""spatial/spatial"", # debugging tasks671 ""spatial/spatial"", # debugging tasks672 ""spatial/spatial"", # debugging tasks673 674 ""spatial/spatial"",675 ""spatial/spatial"",676 ""spatial/spatial"",677 ""spatial/spatial"",678 ""spatial/spatial"")679)680args_pred$id = suppressWarnings(paste0(""prediction_"", str_split(args_pred$learner, ""_"", simplify = TRUE)[, 2]))681args_pred$learner = rlang::syms(args_pred$learner)682 683args_pred[6, ""id""] = ""prediction_debugging_diplodia_no_temp""684args_pred[7, ""id""] = ""prediction_debugging_diplodia_no_precip""685args_pred[8, ""id""] = ""prediction_debugging_diplodia_no_hail""686args_pred[9, ""id""] = ""prediction_debugging_diplodia_no_ph""687args_pred[10, ""id""] = ""prediction_debugging_diplodia_no_soil""688args_pred[11, ""id""] = ""prediction_debugging_diplodia_no_lithology""689args_pred[12, ""id""] = ""prediction_debugging_diplodia_no_slope""690args_pred[13, ""id""] = ""prediction_debugging_diplodia_no_pisr""691 692args_pred[14, ""id""] = ""prediction_gam_diplodia_no_ph""693args_pred[15, ""id""] = ""prediction_gam_fusarium_no_ph""694args_pred[16, ""id""] = ""prediction_gam_armillaria_no_ph""695args_pred[17, ""id""] = ""prediction_gam_heterobasidion_no_ph""696 697prediction_prob_plan = map_plan(args_pred, prediction_custom, trace = FALSE)698 699 700# prediction maps ---------------------------------------------------------701 702args_pred = tibble(prediction_raster = c(""prediction_glm"",703 704 ""prediction_gam_diplodia_no_ph"",705 ""prediction_gam_fusarium_no_ph"",706 ""prediction_gam_armillaria_no_ph"",707 ""prediction_gam_heterobasidion_no_ph"",708 709 ""prediction_svm"",710 711 ""prediction_rf"",712 713 ""prediction_kknn"",714 715 ""prediction_xgboost"",716 717 ""prediction_brt"",718 719 ""prediction_debugging_diplodia_no_temp"",720 ""prediction_debugging_diplodia_no_precip"",721 ""prediction_debugging_diplodia_no_hail"",722 ""prediction_debugging_diplodia_no_ph"",723 ""prediction_debugging_diplodia_no_soil"",724 ""prediction_debugging_diplodia_no_lithology"",725 ""prediction_debugging_diplodia_no_slope"",726 ""prediction_debugging_diplodia_no_pisr""727),728model_name = c(""glm"",729 730 ""gam"",731 ""gam"",732 ""gam"",733 ""gam"",734 735 ""svm"",736 737 ""rf"",738 739 ""kknn"",740 741 ""xgboost"",742 743 ""brt"",744 745 ""rf"",746 ""rf"",747 ""rf"",748 ""rf"",749 ""rf"",750 ""rf"",751 ""rf"",752 ""rf""753),754benchmark_object = c(""bm_sp_non_glm"",755 756 ""bm_sp_sp_diplodia_gam"",757 ""bm_sp_sp_fusarium_gam"",758 ""bm_sp_sp_armillaria_gam"",759 ""bm_sp_sp_heterobasidion_gam"",760 761 ""no_extract_bm_sp_sp_svm"",762 ""no_extract_bm_sp_sp_rf"",763 ""no_extract_bm_sp_sp_kknn"",764 ""no_extract_bm_sp_sp_xgboost"",765 ""no_extract_bm_sp_sp_brt"",766 767 ""no_extract_bm_sp_sp_brt"", # debugging768 ""no_extract_bm_sp_sp_brt"", # debugging769 ""no_extract_bm_sp_sp_brt"", # debugging770 ""no_extract_bm_sp_sp_brt"", # debugging771 ""no_extract_bm_sp_sp_brt"", # debugging772 ""no_extract_bm_sp_sp_brt"", # debugging773 ""no_extract_bm_sp_sp_brt"", # debugging774 ""no_extract_bm_sp_sp_brt"" # debugging775),776resampling = c(# glm777 ""spatial/no tuning"",778 779 # gam780 ""spatial/spatial"",781 ""spatial/spatial"",782 ""spatial/spatial"",783 ""spatial/spatial"",784 785 ""spatial/spatial"",786 ""spatial/spatial"",787 ""spatial/spatial"",788 ""spatial/spatial"",789 ""spatial/spatial"",790 791 ""NA"", # debugging792 ""NA"", # debugging793 ""NA"", # debugging794 ""NA"", # debugging795 ""NA"", # debugging796 ""NA"", # debugging797 ""NA"", # debugging798 ""NA"") # debugging799)800 801args_pred$id = suppressWarnings(paste0(""maps_"", gsub(""prediction_"", """", args_pred$prediction_raster)))802args_pred$prediction_raster = rlang::syms(args_pred$prediction_raster)803args_pred$benchmark_object = rlang::syms(args_pred$benchmark_object)804 805prediction_maps_plan = map_plan(args_pred, create_prediction_map, trace = FALSE)806 807rm(list=ls(pattern=""args_pred""))808","R"
809"Pathogens","pat-s/pathogen-modeling","code/01-data/task.R",".R","8428","170","810# tasks all predictors ----------------------------------------------------811 812heterobasidion_task_dummy <- task_custom(heterobasidion_data,813 ""heterobasidion"", ""heterobasi"",814 dummy_features = c(""lithology"", ""soil""),815 dummy.factors = TRUE816)817 818armillaria_task_dummy <- task_custom(armillaria_data,819 ""armillaria"", ""armillaria"",820 dummy_features = c(""lithology"", ""soil""),821 dummy.factors = TRUE822)823 824diplodia_task_dummy <- task_custom(diplodia_data,825 ""diplodia"", ""diplo01"",826 dummy_features = c(""lithology"", ""soil"", ""year""),827 dummy.factors = TRUE828)829 830diplodia_task <- task_custom(diplodia_data,831 ""diplodia"", ""diplo01"",832 dummy_features = c(""lithology"", ""soil"", ""year""),833 dummy.factors = FALSE834)835 836fusarium_task_dummy <- task_custom(fusarium_data,837 ""fusarium"", ""fus01"",838 dummy_features = c(""lithology"", ""soil"", ""year""),839 dummy.factors = TRUE840)841 842diplodia_task_dummy_prediction <- task_custom_prediction(diplodia_data,843 ""diplodia"", ""diplo01"",844 dummy_features = c(""lithology"", ""soil""),845 dummy.factors = TRUE,846 remove.vars = TRUE847)848 849fusarium_task_dummy_prediction <- task_custom_prediction(fusarium_data,850 ""fusarium"", ""fus01"",851 dummy_features = c(""lithology"", ""soil""),852 dummy.factors = TRUE,853 remove.vars = TRUE854)855 856# tasks no ph -------------------------------------------------------------857 858 859heterobasidion_task_dummy_no_ph <- task_custom(heterobasidion_data_no_ph,860 ""heterobasidion"", ""heterobasi"",861 dummy_features = c(""lithology"", ""soil""),862 dummy.factors = TRUE863)864 865armillaria_task_dummy_no_ph <- task_custom(armillaria_data_no_ph,866 ""armillaria"", ""armillaria"",867 dummy_features = c(""lithology"", ""soil""),868 dummy.factors = TRUE869)870 871diplodia_task_dummy_no_ph <- task_custom(diplodia_data_no_ph,872 ""diplodia"", ""diplo01"",873 dummy_features = c(""lithology"", ""soil"", ""year""),874 dummy.factors = TRUE875)876 877diplodia_task_no_ph <- task_custom(diplodia_data_no_ph,878 ""diplodia"", ""diplo01"",879 dummy_features = c(""lithology"", ""soil"", ""year""),880 dummy.factors = FALSE881)882 883fusarium_task_dummy_no_ph <- task_custom(fusarium_data_no_ph,884 ""fusarium"", ""fus01"",885 dummy_features = c(""lithology"", ""soil"", ""year""),886 dummy.factors = TRUE887)888 889diplodia_task_dummy_prediction_no_ph <- task_custom_prediction(diplodia_data_no_ph,890 ""diplodia"", ""diplo01"",891 dummy_features = c(""lithology"", ""soil""),892 dummy.factors = TRUE,893 remove.vars = TRUE894)895 896fusarium_task_dummy_prediction_no_ph <- task_custom_prediction(fusarium_data_no_ph,897 ""fusarium"", ""fus01"",898 dummy_features = c(""lithology"", ""soil""),899 dummy.factors = TRUE,900 remove.vars = TRUE901)902 903# Debugging tasks ---------------------------------------------------------904 905# We can't put them into a list because each one needs its own prediction task906 907diplodia_task_dummy_prediction_no_temp <- task_custom_prediction(diplodia_data_no_temp,908 ""diplodia"", ""diplo01"",909 dummy_features = c(""lithology"", ""soil""),910 dummy.factors = TRUE,911 remove.vars = TRUE912)913 914diplodia_task_dummy_prediction_no_precip <- task_custom_prediction(diplodia_data_no_precip,915 ""diplodia"", ""diplo01"",916 dummy_features = c(""lithology"", ""soil""),917 dummy.factors = TRUE,918 remove.vars = TRUE919)920 921diplodia_task_dummy_prediction_no_hail <- task_custom_prediction(diplodia_data_no_hail,922 ""diplodia"", ""diplo01"",923 dummy_features = c(""lithology"", ""soil""),924 dummy.factors = TRUE,925 remove.vars = TRUE926)927 928diplodia_task_dummy_prediction_no_soil <- task_custom_prediction(diplodia_data_no_soil,929 ""diplodia"", ""diplo01"",930 dummy_features = c(""lithology""),931 dummy.factors = TRUE,932 remove.vars = TRUE933)934 935diplodia_task_dummy_prediction_no_lithology <- task_custom_prediction(diplodia_data_no_lithology,936 ""diplodia"", ""diplo01"",937 dummy_features = c(""soil""),938 dummy.factors = TRUE,939 remove.vars = TRUE940)941 942diplodia_task_dummy_prediction_no_slope <- task_custom_prediction(diplodia_data_no_slope,943 ""diplodia"", ""diplo01"",944 dummy_features = c(""lithology"", ""soil""),945 dummy.factors = TRUE,946 remove.vars = TRUE947)948 949diplodia_task_dummy_prediction_no_pisr <- task_custom_prediction(diplodia_data_no_pisr,950 ""diplodia"", ""diplo01"",951 dummy_features = c(""lithology"", ""soil""),952 dummy.factors = TRUE,953 remove.vars = TRUE954)955 956# Combined tasks ---------------------------------------------------------957 958tasks <- list(959 armillaria_task_dummy,960 heterobasidion_task_dummy,961 diplodia_task_dummy,962 fusarium_task_dummy963)964 965tasks_pred <- list(966 armillaria_task_dummy,967 heterobasidion_task_dummy,968 diplodia_task_dummy_prediction,969 fusarium_task_dummy_prediction970)971 972tasks_pred_no_ph <- list(973 armillaria_task_dummy_no_ph,974 heterobasidion_task_dummy_no_ph,975 diplodia_task_dummy_prediction_no_ph,976 fusarium_task_dummy_prediction_no_ph977)978","R"
979"Pathogens","pat-s/pathogen-modeling","code/01-data/data.R",".R","18326","279","# data with ph -----------------------------------------------------------980 981armillaria_data = extract_variables(""https://zenodo.org/record/2621996/files/heterobasidion-armillaria.gpkg"",982 study_area = data_basque, drop_vars = ""heterobasi"",983 response = ""armillaria"",984 soil = soil, lithology = lithology, slope = slope,985 temperature = temperature_mean, ph = ph,986 hail = hail_raw, precipitation = precipitation_sum,987 pisr = pisr, elevation = elevation, age = FALSE)988heterobasidion_data = extract_variables(""https://zenodo.org/record/2621996/files/heterobasidion-armillaria.gpkg"",989 study_area = data_basque, drop_vars = ""armillaria"",990 response = ""heterobasi"",991 soil = soil, lithology = lithology, slope = slope,992 temperature = temperature_mean, ph = ph,993 hail = hail_raw, precipitation = precipitation_sum,994 pisr = pisr, elevation = elevation, age = FALSE)995fusarium_data = extract_variables(""https://zenodo.org/record/2621996/files/diplodia-fusarium.gpkg"",996 study_area = data_basque, drop_vars = ""diplo01"",997 response = ""fus01"",998 soil = soil, lithology = lithology, slope = slope,999 temperature = temperature_mean, ph = ph,1000 hail = hail_raw, precipitation = precipitation_sum,1001 pisr = pisr, elevation = elevation, age = TRUE)1002diplodia_data = extract_variables(""https://zenodo.org/record/2621996//files/diplodia-fusarium.gpkg"",1003 study_area = data_basque, drop_vars = ""fus01"",1004 response = ""diplo01"",1005 soil = soil, lithology = lithology, slope = slope,1006 temperature = temperature_mean, ph = ph,1007 hail = hail_raw, precipitation = precipitation_sum,1008 pisr = pisr, elevation = elevation, age = TRUE)1009 1010# data without ph ---------------------------------------------------------1011 1012armillaria_data_no_ph = extract_variables(""https://zenodo.org/record/2621996/files/heterobasidion-armillaria.gpkg"",1013 study_area = data_basque, drop_vars = ""heterobasi"",1014 response = ""armillaria"",1015 soil = soil, lithology = lithology, slope = slope,1016 temperature = temperature_mean, ph = ph,1017 hail = hail_raw, precipitation = precipitation_sum,1018 pisr = pisr, elevation = elevation, age = FALSE,1019 remove_pred = ""ph"")1020diplodia_data_no_ph = extract_variables(""https://zenodo.org/record/2621996//files/diplodia-fusarium.gpkg"",1021 study_area = data_basque, drop_vars = ""fus01"",1022 response = ""diplo01"",1023 soil = soil, lithology = lithology, slope = slope,1024 temperature = temperature_mean, ph = ph,1025 hail = hail_raw, precipitation = precipitation_sum,1026 pisr = pisr, elevation = elevation, age = TRUE,1027 remove_pred = ""ph"")1028fusarium_data_no_ph = extract_variables(""https://zenodo.org/record/2621996//files/diplodia-fusarium.gpkg"",1029 study_area = data_basque, drop_vars = ""diplo01"",1030 response = ""fus01"",1031 soil = soil, lithology = lithology, slope = slope,1032 temperature = temperature_mean, ph = ph,1033 hail = hail_raw, precipitation = precipitation_sum,1034 pisr = pisr, elevation = elevation, age = TRUE,1035 remove_pred = ""ph"")1036heterobasidion_data_no_ph = extract_variables(""https://zenodo.org/record/2621996/files/heterobasidion-armillaria.gpkg"",1037 study_area = data_basque, drop_vars = ""armillaria"",1038 response = ""heterobasi"",1039 soil = soil, lithology = lithology, slope = slope,1040 temperature = temperature_mean, ph = ph,1041 hail = hail_raw, precipitation = precipitation_sum,1042 pisr = pisr, elevation = elevation, age = FALSE,1043 remove_pred = ""ph"")1044 1045 1046# debugging data ----------------------------------------------------------1047 1048 1049# data with extracted temp, precip and pisr1050diplodia_data_no_temp = extract_variables(""https://zenodo.org/record/2621996//files/diplodia-fusarium.gpkg"",1051 study_area = data_basque, drop_vars = ""fus01"",1052 response = ""diplo01"",1053 soil = soil, lithology = lithology, slope = slope,1054 temperature = temperature_mean, ph = ph,1055 hail = hail_raw, precipitation = precipitation_sum,1056 pisr = pisr, elevation = elevation, age = TRUE,1057 remove_pred = ""temp"")1058 1059# data with extracted temp, precip and pisr1060diplodia_data_no_precip = extract_variables(""https://zenodo.org/record/2621996//files/diplodia-fusarium.gpkg"",1061 study_area = data_basque, drop_vars = ""fus01"",1062 response = ""diplo01"",1063 soil = soil, lithology = lithology, slope = slope,1064 temperature = temperature_mean, ph = ph,1065 hail = hail_raw, precipitation = precipitation_sum,1066 pisr = pisr, elevation = elevation, age = TRUE,1067 remove_pred = ""precip"")1068 1069# data with extracted temp, precip and pisr1070diplodia_data_no_hail = extract_variables(""https://zenodo.org/record/2621996//files/diplodia-fusarium.gpkg"",1071 study_area = data_basque, drop_vars = ""fus01"",1072 response = ""diplo01"",1073 soil = soil, lithology = lithology, slope = slope,1074 temperature = temperature_mean, ph = ph,1075 hail = hail_raw, precipitation = precipitation_sum,1076 pisr = pisr, elevation = elevation, age = TRUE,1077 remove_pred = ""hail_probability"")1078 1079# data with extracted temp, precip and pisr1080diplodia_data_no_soil = extract_variables(""https://zenodo.org/record/2621996//files/diplodia-fusarium.gpkg"",1081 study_area = data_basque, drop_vars = ""fus01"",1082 response = ""diplo01"",1083 soil = soil, lithology = lithology, slope = slope,1084 temperature = temperature_mean, ph = ph,1085 hail = hail_raw, precipitation = precipitation_sum,1086 pisr = pisr, elevation = elevation, age = TRUE,1087 remove_pred = ""soil"")1088 1089# data with extracted temp, precip and pisr1090diplodia_data_no_lithology = extract_variables(""https://zenodo.org/record/2621996//files/diplodia-fusarium.gpkg"",1091 study_area = data_basque, drop_vars = ""fus01"",1092 response = ""diplo01"",1093 soil = soil, lithology = lithology, slope = slope,1094 temperature = temperature_mean, ph = ph,1095 hail = hail_raw, precipitation = precipitation_sum,1096 pisr = pisr, elevation = elevation, age = TRUE,1097 remove_pred = ""lithology"")1098 1099# data with extracted temp, precip and pisr1100diplodia_data_no_slope = extract_variables(""https://zenodo.org/record/2621996//files/diplodia-fusarium.gpkg"",1101 study_area = data_basque, drop_vars = ""fus01"",1102 response = ""diplo01"",1103 soil = soil, lithology = lithology, slope = slope,1104 temperature = temperature_mean, ph = ph,1105 hail = hail_raw, precipitation = precipitation_sum,1106 pisr = pisr, elevation = elevation, age = TRUE,1107 remove_pred = ""slope_degrees"")1108 1109# data with extracted temp, precip and pisr1110diplodia_data_no_pisr = extract_variables(""https://zenodo.org/record/2621996//files/diplodia-fusarium.gpkg"",1111 study_area = data_basque, drop_vars = ""fus01"",1112 response = ""diplo01"",1113 soil = soil, lithology = lithology, slope = slope,1114 temperature = temperature_mean, ph = ph,1115 hail = hail_raw, precipitation = precipitation_sum,1116 pisr = pisr, elevation = elevation, age = TRUE,1117 remove_pred = ""pisr"")1118 1119# Raw Data preprocessing ------------------------------------------------------------1120 1121data_basque = st_read(""https://zenodo.org/record/2621996/files/study-area.gpkg"",1122 quiet = TRUE)1123 1124dem_raw = dem_download(""https://zenodo.org/record/2621996/files/dem.zip"")1125slope = slope_processing(data = dem_raw)1126elevation = elevation_preprocessing(data = dem_raw)1127 1128temperature_mean = temperature_preprocessing(atlas_climatico = atlas_climatico)1129precipitation_sum = precipitation_preprocessing(atlas_climatico = atlas_climatico)1130pisr = pisr_preprocessing(atlas_climatico = atlas_climatico)1131 1132lithology_raw = lithology_download(url = ""https://zenodo.org/record/2621996/files/lithology.zip"")1133lithology = lithology_preprocessing(lithology_raw)1134 1135soil_raw = soil_download(""https://zenodo.org/record/2621996/files/soil.tif"")1136soil = soil_preprocessing(data = soil_raw,1137 study_area = data_basque)1138 1139# we cannot make ph public unfortunately so we load it locally from the repo1140ph = ph_preprocessing(data = ""data/ph/"", study_area = data_basque)1141 1142atlas_climatico_raw = atlas_climatico_download(""https://zenodo.org/record/2621996/files/atlas-climatico.zip"")1143atlas_climatico = atlas_climatico_preprocessing(data = atlas_climatico_raw,1144 study_area = data_basque)1145 1146hail_raw = hail_download(url = ""https://zenodo.org/record/2621996/files/hail-probability.tif"")1147 1148# Prediction data ---------------------------------------------------------1149 1150pred_data = create_prediction_data(temperature = temperature_mean,1151 precipitation = precipitation_sum,1152 pisr = pisr,1153 elevation = elevation,1154 soil = soil,1155 slope = slope,1156 lithology = lithology,1157 hail = hail_raw,1158 ph = ph,1159 dummy_features = c(""lithology"", ""soil"")1160 )1161 1162pred_data_no_temp = create_prediction_data(temperature = temperature_mean,1163 precipitation = precipitation_sum,1164 pisr = pisr,1165 elevation = elevation,1166 soil = soil,1167 slope = slope,1168 lithology = lithology,1169 hail = hail_raw,1170 ph = ph,1171 dummy_features = c(""lithology"", ""soil""),1172 drop_var = ""temp"")1173 1174pred_data_no_precip = create_prediction_data(temperature = temperature_mean,1175 precipitation = precipitation_sum,1176 pisr = pisr,1177 elevation = elevation,1178 soil = soil,1179 slope = slope,1180 lithology = lithology,1181 hail = hail_raw,1182 ph = ph,1183 dummy_features = c(""lithology"", ""soil""),1184 drop_var = ""precip"")1185 1186pred_data_no_soil = create_prediction_data(temperature = temperature_mean,1187 precipitation = precipitation_sum,1188 pisr = pisr,1189 elevation = elevation,1190 soil = soil,1191 slope = slope,1192 lithology = lithology,1193 hail = hail_raw,1194 ph = ph,1195 dummy_features = c(""lithology""),1196 drop_var = ""soil"")1197 1198pred_data_no_ph = create_prediction_data(temperature = temperature_mean,1199 precipitation = precipitation_sum,1200 pisr = pisr,