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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| Package: beethoven | ||
| Title: Building an Extensible, rEproducible, Test-driven, Harmonized, Open-source, Versioned, ENsemble model for air quality | ||
| Version: 0.1.1 | ||
| Version: 0.3.0 | ||
| Authors@R: c( | ||
| person("Kyle", "Messier", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9508-9623")), | ||
| person("Insang", "Song", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-8732-3256")), | ||
|
|
@@ -15,14 +15,63 @@ Authors@R: c( | |
| ) | ||
| Description: Near Real Time air pollution model results and code produced by the SET group. It is fully tested, versioned, and open source and open access. | ||
| Depends: R (>= 4.1.0) | ||
| Imports: dplyr, sf, stats, terra, methods, BART, data.table, httr, rvest, spData, exactextractr, utils, stringr, testthat (>= 3.0.0), doParallel, parallelly, stars, foreach, future, ranger, xgboost, torch | ||
| Suggests: covr, withr, knitr, rmarkdown, sftime, lwgeom, FNN, ggplot2, scatterpie, doRNG | ||
| Imports: | ||
| dplyr, | ||
| sf, | ||
| stats, | ||
| terra, | ||
| methods, | ||
| BART, | ||
| data.table, | ||
| future, | ||
| targets, | ||
| tune (>= 1.2.1), | ||
| rlang, | ||
| rsample, | ||
| tidyr, | ||
| tidyselect, | ||
| yardstick, | ||
| workflows, | ||
| recipes, | ||
| missRanger, | ||
| parsnip, | ||
| future.apply, | ||
| future.batchtools, | ||
| anticlust, | ||
| qs, | ||
| stringi, | ||
| collapse, | ||
| tigris, | ||
| graphics | ||
| Suggests: | ||
| testthat (>= 3.0.0), | ||
| covr, | ||
| withr, | ||
| tarchetypes, | ||
| tidymodels, | ||
| xgboost, | ||
| torch, | ||
| brulee, | ||
| glmnet, | ||
| knitr, | ||
| rmarkdown, | ||
| stars, | ||
| sftime, | ||
| lwgeom, | ||
| FNN, | ||
| ggplot2, | ||
| doRNG, | ||
| DT, | ||
| scatterplot3d, | ||
| furrr, | ||
| quarto | ||
| Remotes: NIEHS/amadeus, NIEHS/chopin | ||
| Encoding: UTF-8 | ||
| VignetteBuilder: knitr, rmarkdown | ||
| Roxygen: list(markdown = TRUE) | ||
| RoxygenNote: 7.3.1 | ||
| Config/Needs/website: tidyverse/tidytemplate | ||
| Config/testhat/edition: 3 | ||
| License: MIT + file LICENSE | ||
| URL: https://github.com/Spatiotemporal-Exposures-and-Toxicology/beethoven, | ||
| https: //spatiotemporal-exposures-and-toxicology.github.io/beethoven/ | ||
| URL: https://github.com/NIEHS/beethoven, | ||
| https: //NIEHS.github.io/beethoven/ | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,94 +1,114 @@ | ||
| # Generated by roxygen2: do not edit by hand | ||
|
|
||
| export(build_pipeline) | ||
| export(calc_covariates) | ||
| export(calc_ecoregion) | ||
| export(calc_koppen_geiger) | ||
| export(calc_modis) | ||
| export(calc_nei) | ||
| export(calc_nlcd_ratio) | ||
| export(calc_temporal_dummies) | ||
| export(calc_tri) | ||
| export(check_crs_is_valid) | ||
| export(check_data_completeness) | ||
| export(check_input_raster_in_extent) | ||
| export(check_means_are_valid) | ||
| export(check_output_locs_are_valid) | ||
| export(check_variances_are_valid) | ||
| export(convert_stdt) | ||
| export(convert_stdt_sftime) | ||
| export(convert_stdt_spatrastdataset) | ||
| export(convert_stdt_spatvect) | ||
| export(convert_stobj_to_stdt) | ||
| export(generic_base_learner) | ||
| export(generic_meta_learner) | ||
| export(is_stdt) | ||
| export("%tin%") | ||
| export(add_time_col) | ||
| export(append_predecessors) | ||
| export(attach_xy) | ||
| export(calc_geos_strict) | ||
| export(calc_gmted_direct) | ||
| export(calc_narr2) | ||
| export(calculate) | ||
| export(convert_cv_index_rset) | ||
| export(df_params) | ||
| export(divisor) | ||
| export(fit_base_brulee) | ||
| export(fit_base_elnet) | ||
| export(fit_base_xgb) | ||
| export(generate_cv_index) | ||
| export(impute_all) | ||
| export(inject_calculate) | ||
| export(inject_geos) | ||
| export(inject_gmted) | ||
| export(inject_modis_par) | ||
| export(load_modis_files) | ||
| export(loadargs) | ||
| export(meta_learner_fit) | ||
| export(meta_learner_predict) | ||
| export(modis_aggregate_sds) | ||
| export(modis_get_vrt) | ||
| export(modis_mosaic_mod06) | ||
| export(modis_prefilter_sds) | ||
| export(modis_preprocess_vnp46) | ||
| export(modis_warp_stars) | ||
| export(modis_worker) | ||
| export(par_narr) | ||
| export(post_calc_autojoin) | ||
| export(post_calc_convert_time) | ||
| export(post_calc_df_year_expand) | ||
| export(post_calc_drop_cols) | ||
| export(post_calc_merge_all) | ||
| export(post_calc_merge_features) | ||
| export(post_calc_unify_timecols) | ||
| export(post_calc_year_expand) | ||
| export(process_counties) | ||
| export(process_geos_bulk) | ||
| export(process_narr2) | ||
| export(read_locs) | ||
| export(read_paths) | ||
| export(reduce_merge) | ||
| export(search_function) | ||
| export(set_slurm_resource) | ||
| export(vis_rset) | ||
| import(BART) | ||
| import(spData) | ||
| importClassesFrom(terra,SpatRaster) | ||
| importClassesFrom(terra,SpatRasterDataset) | ||
| importClassesFrom(terra,SpatVector) | ||
| importFrom(anticlust,balanced_clustering) | ||
| importFrom(collapse,fnth) | ||
| importFrom(collapse,fvar) | ||
| importFrom(collapse,join) | ||
| importFrom(collapse,replace_inf) | ||
| importFrom(collapse,replace_na) | ||
| importFrom(collapse,set_collapse) | ||
| importFrom(data.table,.SD) | ||
| importFrom(data.table,`:=`) | ||
| importFrom(data.table,as.data.table) | ||
| importFrom(data.table,fread) | ||
| importFrom(data.table,melt) | ||
| importFrom(data.table,copy) | ||
| importFrom(data.table,merge.data.table) | ||
| importFrom(data.table,month) | ||
| importFrom(data.table,rbindlist) | ||
| importFrom(data.table,year) | ||
| importFrom(doParallel,registerDoParallel) | ||
| importFrom(data.table,setDTthreads) | ||
| importFrom(data.table,setnafill) | ||
| importFrom(dplyr,`%>%`) | ||
| importFrom(dplyr,across) | ||
| importFrom(dplyr,all_of) | ||
| importFrom(dplyr,as_tibble) | ||
| importFrom(dplyr,bind_rows) | ||
| importFrom(dplyr,left_join) | ||
| importFrom(exactextractr,exact_extract) | ||
| importFrom(foreach,"%dopar%") | ||
| importFrom(foreach,foreach) | ||
| importFrom(future,cluster) | ||
| importFrom(dplyr,group_by) | ||
| importFrom(dplyr,summarize) | ||
| importFrom(dplyr,ungroup) | ||
| importFrom(future,multicore) | ||
| importFrom(future,multisession) | ||
| importFrom(future,plan) | ||
| importFrom(future,sequential) | ||
| importFrom(future,tweak) | ||
| importFrom(future.apply,future_lapply) | ||
| importFrom(future.batchtools,batchtools_slurm) | ||
| importFrom(methods,is) | ||
| importFrom(parallelly,availableWorkers) | ||
| importFrom(missRanger,missRanger) | ||
| importFrom(parsnip,boost_tree) | ||
| importFrom(parsnip,linear_reg) | ||
| importFrom(parsnip,mlp) | ||
| importFrom(parsnip,set_engine) | ||
| importFrom(parsnip,set_mode) | ||
| importFrom(qs,qread) | ||
| importFrom(qs,qsave) | ||
| importFrom(recipes,recipe) | ||
| importFrom(recipes,update_role) | ||
| importFrom(rlang,as_name) | ||
| importFrom(rlang,inject) | ||
| importFrom(rlang,sym) | ||
| importFrom(rsample,make_splits) | ||
| importFrom(rsample,manual_rset) | ||
| importFrom(rsample,vfold_cv) | ||
| importFrom(sf,st_as_sf) | ||
| importFrom(sf,st_as_sfc) | ||
| importFrom(sf,st_bbox) | ||
| importFrom(sf,st_buffer) | ||
| importFrom(sf,st_coordinates) | ||
| importFrom(sf,st_covered_by) | ||
| importFrom(sf,st_crs) | ||
| importFrom(sf,st_drop_geometry) | ||
| importFrom(sf,st_geometry) | ||
| importFrom(sf,st_sf) | ||
| importFrom(sf,st_transform) | ||
| importFrom(sf,st_union) | ||
| importFrom(sf,st_within) | ||
| importFrom(stars,read_stars) | ||
| importFrom(stars,st_warp) | ||
| importFrom(stats,predict) | ||
| importFrom(stats,reshape) | ||
| importFrom(terra,buffer) | ||
| importFrom(terra,coltab) | ||
| importFrom(terra,crop) | ||
| importFrom(stats,sd) | ||
| importFrom(stats,setNames) | ||
| importFrom(stringi,stri_replace_all_regex) | ||
| importFrom(targets,tar_resources) | ||
| importFrom(targets,tar_resources_future) | ||
| importFrom(terra,crs) | ||
| importFrom(terra,describe) | ||
| importFrom(terra,ext) | ||
| importFrom(terra,extract) | ||
| importFrom(terra,intersect) | ||
| importFrom(terra,merge) | ||
| importFrom(terra,mosaic) | ||
| importFrom(terra,nlyr) | ||
| importFrom(terra,project) | ||
| importFrom(terra,rast) | ||
| importFrom(terra,same.crs) | ||
| importFrom(terra,sds) | ||
| importFrom(terra,snap) | ||
| importFrom(terra,tapp) | ||
| importFrom(terra,vect) | ||
| importFrom(utils,data) | ||
| importFrom(utils,read.csv) | ||
| importFrom(terra,subset) | ||
| importFrom(terra,time) | ||
| importFrom(terra,varnames) | ||
| importFrom(tidyselect,all_of) | ||
| importFrom(tigris,counties) | ||
| importFrom(tune,tune_grid) | ||
| importFrom(workflows,add_model) | ||
| importFrom(workflows,add_recipe) | ||
| importFrom(workflows,workflow) | ||
| importFrom(yardstick,metric_set) | ||
| importFrom(yardstick,rmse) |
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