The goal of setaria-predict is to train a model using simulation output from ED2 to create an ED2 “emulator” of sorts. Then, we can use this model to predict the growth of Setaria at new locations.
We will use runs from the sensitivity analysis as stand-ins for different Setaria genotypes and train models using site location and/or weather data as predictors, then predict aboveground biomass or NPP of Setaria at new sites.
This project uses
renv for package
management. When opening this repo as an RStudio Project for the first
time, renv should automatically install itself and prompt you to run
renv::restore() to install all package dependencies.
This project uses the targets
package for workflow management.
Run targets::tar_make() from the console to run the workflow and
reproduce all results.
Data for this project was originally on a server (named Welsch) in many
CSV files (one per simulation). These are not committed in this
repository, but the combined data is committed to data/ and the script
used to wrangle them is in data_welsch/.
Targets workflow:
graph LR
subgraph legend
direction LR
x7420bd9270f8d27d([""Up to date""]):::uptodate --- x0a52b03877696646([""Outdated""]):::outdated
x0a52b03877696646([""Outdated""]):::outdated --- xbf4603d6c2c2ad6b([""Stem""]):::none
xbf4603d6c2c2ad6b([""Stem""]):::none --- xf0bce276fe2b9d3e>""Function""]:::none
end
subgraph Graph
direction LR
x4b7f0494130845c9(["grid_data"]):::uptodate --> x1e2f629700cdf2b0(["grid_pred"]):::uptodate
x80f8daf00aa10777(["newdata"]):::uptodate --> x1e2f629700cdf2b0(["grid_pred"]):::uptodate
x251ec748a49d82a0(["rf_fit"]):::uptodate --> x1e2f629700cdf2b0(["grid_pred"]):::uptodate
xab1a71ecca0d9614(["grid_bioclim"]):::uptodate --> x80f8daf00aa10777(["newdata"]):::uptodate
xe79aca23d28071ab(["data_split"]):::uptodate --> xaa3dacfc0774d27e(["data_train"]):::uptodate
xaa3dacfc0774d27e(["data_train"]):::uptodate --> x251ec748a49d82a0(["rf_fit"]):::uptodate
x6f6ea77a33e65215(["rf_hyperparameters"]):::uptodate --> x251ec748a49d82a0(["rf_fit"]):::uptodate
x31fafe63f123d72c(["rf_workflow"]):::uptodate --> x251ec748a49d82a0(["rf_fit"]):::uptodate
x13288cb0758ce97d(["data_test"]):::uptodate --> x7ee10909b9e9ca92(["rf_pred_plot"]):::uptodate
x251ec748a49d82a0(["rf_fit"]):::uptodate --> x7ee10909b9e9ca92(["rf_pred_plot"]):::uptodate
x1e2f629700cdf2b0(["grid_pred"]):::uptodate --> x221c4544dec83bd3(["pred_map_diff"]):::uptodate
x29dca615c423dffb>"make_pred_map_diff"]:::uptodate --> x221c4544dec83bd3(["pred_map_diff"]):::uptodate
xae0bb90779bc5978(["seus"]):::uptodate --> x221c4544dec83bd3(["pred_map_diff"]):::uptodate
x8165fe9985c10a4a(["rf_model"]):::uptodate --> x31fafe63f123d72c(["rf_workflow"]):::uptodate
x2c6a769cc6041606(["rf_recipe"]):::uptodate --> x31fafe63f123d72c(["rf_workflow"]):::uptodate
xe79aca23d28071ab(["data_split"]):::uptodate --> xe0fba61fbc506510(["report"]):::uptodate
x4b7f0494130845c9(["grid_data"]):::uptodate --> xe0fba61fbc506510(["report"]):::uptodate
x0dd52ca5681d2dec(["lm_cv"]):::uptodate --> xe0fba61fbc506510(["report"]):::uptodate
x82c80750d3c3aa91(["lm_pred_plot"]):::uptodate --> xe0fba61fbc506510(["report"]):::uptodate
x40f6344f44be00c4(["pred_map"]):::uptodate --> xe0fba61fbc506510(["report"]):::uptodate
x221c4544dec83bd3(["pred_map_diff"]):::uptodate --> xe0fba61fbc506510(["report"]):::uptodate
x03f8f197baa464a7(["rf_cv"]):::uptodate --> xe0fba61fbc506510(["report"]):::uptodate
x7ee10909b9e9ca92(["rf_pred_plot"]):::uptodate --> xe0fba61fbc506510(["report"]):::uptodate
x2c6a769cc6041606(["rf_recipe"]):::uptodate --> xe0fba61fbc506510(["report"]):::uptodate
xae0bb90779bc5978(["seus"]):::uptodate --> xe0fba61fbc506510(["report"]):::uptodate
x86547e801250e368>"get_daymet_monthly"]:::uptodate --> x4f1371d8a31ead17(["grid_daymet"]):::uptodate
x4b7f0494130845c9(["grid_data"]):::uptodate --> x4f1371d8a31ead17(["grid_daymet"]):::uptodate
x13288cb0758ce97d(["data_test"]):::uptodate --> x82c80750d3c3aa91(["lm_pred_plot"]):::uptodate
xfe69c4366ba0129f(["lm_fit"]):::uptodate --> x82c80750d3c3aa91(["lm_pred_plot"]):::uptodate
xaa3dacfc0774d27e(["data_train"]):::uptodate --> x2dc7e80e5e9b239f(["rf_grid_results"]):::uptodate
xb66df7ac83f87f08(["rf_grid"]):::uptodate --> x2dc7e80e5e9b239f(["rf_grid_results"]):::uptodate
x31fafe63f123d72c(["rf_workflow"]):::uptodate --> x2dc7e80e5e9b239f(["rf_grid_results"]):::uptodate
x2dc7e80e5e9b239f(["rf_grid_results"]):::uptodate --> x6f6ea77a33e65215(["rf_hyperparameters"]):::uptodate
x86547e801250e368>"get_daymet_monthly"]:::uptodate --> x001de431ee97eb4a(["daymet_monthly"]):::uptodate
x2032b88ecc3ceb3d(["site_data"]):::uptodate --> x001de431ee97eb4a(["daymet_monthly"]):::uptodate
xdf9ada886c9d78b8(["dens_plot"]):::uptodate --> xa7181699c76fad2b(["dens_plot_png"]):::uptodate
x4bb16a5c13f5da41(["lm_model"]):::uptodate --> x7d700859457f5791(["lm_workflow"]):::uptodate
x2c6a769cc6041606(["rf_recipe"]):::uptodate --> x7d700859457f5791(["lm_workflow"]):::uptodate
x88226e7f0f4662b1(["data_folds"]):::uptodate --> x03f8f197baa464a7(["rf_cv"]):::uptodate
x6f6ea77a33e65215(["rf_hyperparameters"]):::uptodate --> x03f8f197baa464a7(["rf_cv"]):::uptodate
x31fafe63f123d72c(["rf_workflow"]):::uptodate --> x03f8f197baa464a7(["rf_cv"]):::uptodate
xaa3dacfc0774d27e(["data_train"]):::uptodate --> xfe69c4366ba0129f(["lm_fit"]):::uptodate
x541d164e38df8517(["lm_hyperparameters"]):::uptodate --> xfe69c4366ba0129f(["lm_fit"]):::uptodate
x7d700859457f5791(["lm_workflow"]):::uptodate --> xfe69c4366ba0129f(["lm_fit"]):::uptodate
x8b4f1321e0983862(["sa_output_file"]):::uptodate --> xd19f10296bf4aecb(["sa_output"]):::uptodate
x691fe2667432a68c>"make_phenotype_data"]:::uptodate --> x84746b2e0f9f6b50(["setaria_data"]):::uptodate
xba8bb58288d54f0e(["setaria_raw"]):::uptodate --> x84746b2e0f9f6b50(["setaria_data"]):::uptodate
x9d9a71525b73affe>"make_grid_data"]:::uptodate --> x4b7f0494130845c9(["grid_data"]):::uptodate
xae0bb90779bc5978(["seus"]):::uptodate --> x4b7f0494130845c9(["grid_data"]):::uptodate
x40f6344f44be00c4(["pred_map"]):::uptodate --> xd1d5de95fb768940(["pred_map_png"]):::uptodate
xaa3dacfc0774d27e(["data_train"]):::uptodate --> x88226e7f0f4662b1(["data_folds"]):::uptodate
x1e2f629700cdf2b0(["grid_pred"]):::uptodate --> x40f6344f44be00c4(["pred_map"]):::uptodate
x446632179a854016>"make_pred_map"]:::uptodate --> x40f6344f44be00c4(["pred_map"]):::uptodate
xae0bb90779bc5978(["seus"]):::uptodate --> x40f6344f44be00c4(["pred_map"]):::uptodate
xc26e685f03c57771(["bioclim"]):::uptodate --> xa3f7d12cb273bbe2(["model_data"]):::uptodate
xb1bfd93c0984802a>"create_model_data"]:::uptodate --> xa3f7d12cb273bbe2(["model_data"]):::uptodate
x84746b2e0f9f6b50(["setaria_data"]):::uptodate --> xa3f7d12cb273bbe2(["model_data"]):::uptodate
x25a132700f092ff0(["prop_agb_plot"]):::uptodate --> x562ba761c4660183(["prop_agb_plot_png"]):::uptodate
xaa3dacfc0774d27e(["data_train"]):::uptodate --> x69c7dddc4e8cfd76(["lm_grid_results"]):::uptodate
x7c34938a17ec8f51(["lm_grid"]):::uptodate --> x69c7dddc4e8cfd76(["lm_grid_results"]):::uptodate
x7d700859457f5791(["lm_workflow"]):::uptodate --> x69c7dddc4e8cfd76(["lm_grid_results"]):::uptodate
x203b51acacd25f0d(["site_plot"]):::uptodate --> x771e078224a9c200(["site_plot_png"]):::uptodate
xe79aca23d28071ab(["data_split"]):::uptodate --> x13288cb0758ce97d(["data_test"]):::uptodate
x5cc0a89ed2100046>"calc_bioclim"]:::uptodate --> xc26e685f03c57771(["bioclim"]):::uptodate
x001de431ee97eb4a(["daymet_monthly"]):::uptodate --> xc26e685f03c57771(["bioclim"]):::uptodate
xaa3dacfc0774d27e(["data_train"]):::uptodate --> x2c6a769cc6041606(["rf_recipe"]):::uptodate
xb8f889fdd5ebdfca>"define_recipe"]:::uptodate --> x2c6a769cc6041606(["rf_recipe"]):::uptodate
x88226e7f0f4662b1(["data_folds"]):::uptodate --> x0dd52ca5681d2dec(["lm_cv"]):::uptodate
x541d164e38df8517(["lm_hyperparameters"]):::uptodate --> x0dd52ca5681d2dec(["lm_cv"]):::uptodate
x7d700859457f5791(["lm_workflow"]):::uptodate --> x0dd52ca5681d2dec(["lm_cv"]):::uptodate
x221c4544dec83bd3(["pred_map_diff"]):::uptodate --> xd64eb7c952356186(["pred_map_diff_png"]):::uptodate
x27f4571812c133e6>"make_site_data"]:::uptodate --> x2032b88ecc3ceb3d(["site_data"]):::uptodate
x84746b2e0f9f6b50(["setaria_data"]):::uptodate --> x2032b88ecc3ceb3d(["site_data"]):::uptodate
x5cc0a89ed2100046>"calc_bioclim"]:::uptodate --> xab1a71ecca0d9614(["grid_bioclim"]):::uptodate
x4f1371d8a31ead17(["grid_daymet"]):::uptodate --> xab1a71ecca0d9614(["grid_bioclim"]):::uptodate
x69c7dddc4e8cfd76(["lm_grid_results"]):::uptodate --> x541d164e38df8517(["lm_hyperparameters"]):::uptodate
xbea1d239f1152dfe>"get_seus_shape"]:::uptodate --> xae0bb90779bc5978(["seus"]):::uptodate
xc226421a0b14850a>"plot_prop_agb"]:::uptodate --> x25a132700f092ff0(["prop_agb_plot"]):::uptodate
x84746b2e0f9f6b50(["setaria_data"]):::uptodate --> x25a132700f092ff0(["prop_agb_plot"]):::uptodate
xc54ef022d789b870>"plot_dens"]:::uptodate --> xdf9ada886c9d78b8(["dens_plot"]):::uptodate
x84746b2e0f9f6b50(["setaria_data"]):::uptodate --> xdf9ada886c9d78b8(["dens_plot"]):::uptodate
xa3f7d12cb273bbe2(["model_data"]):::uptodate --> xe79aca23d28071ab(["data_split"]):::uptodate
xe9b1fcaedc0f4938>"plot_sites"]:::uptodate --> x203b51acacd25f0d(["site_plot"]):::uptodate
xae0bb90779bc5978(["seus"]):::uptodate --> x203b51acacd25f0d(["site_plot"]):::uptodate
x2032b88ecc3ceb3d(["site_data"]):::uptodate --> x203b51acacd25f0d(["site_plot"]):::uptodate
x2869030bf0e5bc40(["setaria_file"]):::uptodate --> xba8bb58288d54f0e(["setaria_raw"]):::uptodate
x5514f561fe72dbd6(["sa_summary_plot"]):::uptodate --> x88c7f5ba567d879e(["sa_summary_png"]):::uptodate
x81e8c613fe6d8848>"plot_sa_summary"]:::uptodate --> x5514f561fe72dbd6(["sa_summary_plot"]):::uptodate
xd19f10296bf4aecb(["sa_output"]):::uptodate --> x5514f561fe72dbd6(["sa_summary_plot"]):::uptodate
x6e52cb0f1668cc22(["readme"]):::outdated --> x6e52cb0f1668cc22(["readme"]):::outdated
x81273780ea74b537>"get_data_paths"]:::uptodate --> x81273780ea74b537>"get_data_paths"]:::uptodate
xb0435bc32be38d36>"combine_wrangle"]:::uptodate --> xb0435bc32be38d36>"combine_wrangle"]:::uptodate
end
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