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Update paper, meta data. Update test_gaea. Improve vignettes
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| Original file line number | Diff line number | Diff line change |
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| library(dplyr) | ||
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| # ------------------------------- | ||
| # Prepare example data | ||
| # ------------------------------- | ||
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| # output directory | ||
| output_dir_i <- file.path(getwd(), 'output') | ||
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| # download data | ||
| data_dir <- gaea::get_example_data( | ||
| download_url = 'https://zenodo.org/records/13179630/files/weighted_climate.zip?download=1', | ||
| data_dir = output_dir_i) | ||
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| # setup variables | ||
| climate_hist_dir_i <- file.path(data_dir, 'canesm5_hist') | ||
| climate_impact_dir_i <- file.path(data_dir, 'canesm5') | ||
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| climate_model_i <- 'canesm5' | ||
| climate_scenario_i <- 'gcam-ref' | ||
| member_i = 'r1i1p1f1' | ||
| bias_adj_i = 'w5e5' | ||
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| cfe_i = 'no-cfe' | ||
| gcam_version_i = 'gcam7' | ||
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| base_year_i = 2015 | ||
| start_year_i = 2015 | ||
| end_year_i = 2100 | ||
| smooth_window_i = 20 | ||
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| diagnostics_i <- T | ||
| use_default_coeff_i <- F | ||
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| # ------------------------------- | ||
| # Functions | ||
| # ------------------------------- | ||
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| # Step 1: weighted_climate | ||
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| # Step 2: crop_calendar | ||
| run_crop_calendars <- function(output_dir = output_dir_i){ | ||
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| output <- gaea::crop_calendars(output_dir = output_dir) | ||
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| return(output) | ||
| } | ||
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| # Step 3: data_aggregation | ||
| run_data_aggregation <- function(climate_hist_dir = climate_hist_dir_i, | ||
| climate_impact_dir = climate_impact_dir_i, | ||
| climate_model = climate_model_i, | ||
| climate_scenario = climate_scenario_i, | ||
| output_dir = output_dir_i){ | ||
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| output <- gaea::data_aggregation(climate_hist_dir = climate_hist_dir, | ||
| climate_impact_dir = climate_impact_dir, | ||
| climate_model = climate_model, | ||
| climate_scenario = climate_scenario, | ||
| output_dir = output_dir) | ||
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| return(output) | ||
| } | ||
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| # Step 4: yield_regression | ||
| run_yield_regression <- function(diagnostics = diagnostics_i, | ||
| output_dir = output_dir_i){ | ||
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| gaea::yield_regression(diagnostics = diagnostics, | ||
| output_dir = output_dir) | ||
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| } | ||
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| # Step 5: yield_projections | ||
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| run_yield_projections <- function(use_default_coeff = use_default_coeff_i, | ||
| climate_model = climate_model_i, | ||
| climate_scenario = climate_scenario_i, | ||
| base_year = base_year_i, | ||
| start_year = start_year_i, | ||
| end_year = end_year_i, | ||
| smooth_window = smooth_window_i, | ||
| diagnostics = diagnostics_i, | ||
| output_dir = output_dir_i){ | ||
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| output <- gaea::yield_projections(use_default_coeff = use_default_coeff, | ||
| climate_model = climate_model, | ||
| climate_scenario = climate_scenario, | ||
| base_year = base_year, | ||
| start_year = start_year, | ||
| end_year = end_year, | ||
| smooth_window = smooth_window, | ||
| diagnostics = diagnostics, | ||
| output_dir = output_dir) | ||
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| return(output) | ||
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| } | ||
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| # Step 6: gcam_agprodchange | ||
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| run_gcam_agprodchange <- function(data = NULL, | ||
| climate_model = climate_model_i, | ||
| climate_scenario = climate_scenario_i, | ||
| member = member_i, | ||
| bias_adj = bias_adj_i, | ||
| cfe = cfe_i, | ||
| gcam_version = gcam_version_i, | ||
| diagnostics = diagnostics_i, | ||
| output_dir = output_dir_i){ | ||
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| output <- gaea::gcam_agprodchange(data = df_yield_projection, | ||
| climate_model = climate_model, | ||
| climate_scenario = climate_scenario, | ||
| member = member, | ||
| bias_adj = bias_adj, | ||
| cfe = cfe, | ||
| gcam_version = gcam_version, | ||
| diagnostics = diagnostics, | ||
| output_dir = output_dir) | ||
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| return(output) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,19 +1,71 @@ | ||
| library(gaea); library(testthat); | ||
| library(sf) | ||
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| timestep = 'monthly' | ||
| # climate_model = 'canesm5' | ||
| # climate_scenario = 'gcam-ref' | ||
| # time_periods = seq(2015, 2020, 1) | ||
| output_dir = file.path(getwd(), 'output') | ||
| testthat::skip_on_cran() | ||
| testthat::skip_on_travis() | ||
| testthat::skip_on_ci() | ||
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| # Run tests for each function | ||
| test_that("weighted_climate runs correctly", { | ||
| testthat::expect_error(gaea::weighted_climate(timestep = NULL)) | ||
| # ------------------------------------ | ||
| # Testing Outputs from Major Functions | ||
| # ------------------------------------ | ||
| # | ||
| # test_that("crop_calendars runs correctly", { | ||
| # | ||
| # out_crop_calendars <- run_crop_calendars() | ||
| # | ||
| # testthat::expect_snapshot_file( | ||
| # testthat::test_path('output', 'data_processed', 'crop_calendar.csv')) | ||
| # }) | ||
| # | ||
| # test_that("data_aggregation runs correctly", { | ||
| # | ||
| # out_data_aggregation <- run_data_aggregation() | ||
| # | ||
| # testthat::expect_snapshot_file( | ||
| # testthat::test_path('output', 'data_processed', 'weather_canesm5_gcam-ref_wheat.csv')) | ||
| # testthat::expect_snapshot_file( | ||
| # testthat::test_path('output', 'data_processed', 'historic_vars_wheat.csv')) | ||
| # }) | ||
| # | ||
| # | ||
| # test_that("yield_regression runs correctly", { | ||
| # | ||
| # out_yield_regression <- run_yield_regression() | ||
| # | ||
| # testthat::expect_snapshot_file( | ||
| # testthat::test_path('output', 'data_processed', 'reg_out_wheat_fit_lnyield_mmm_quad_noco2_nogdp.csv')) | ||
| # testthat::expect_snapshot_file( | ||
| # testthat::test_path('output', 'data_processed', 'weather_yield_wheat.csv')) | ||
| # testthat::expect_snapshot_file( | ||
| # testthat::test_path('output', 'figures', 'model_wheat_fit_lnyield_mmm_quad_noco2_nogdp.pdf')) | ||
| # }) | ||
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| test_that("yield_projections runs correctly", { | ||
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| out_yield_projections <- run_yield_projections() | ||
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| testthat::expect_snapshot_file( | ||
| testthat::test_path('output', 'yield_impacts_annual', 'yield_canesm5_gcam-ref_wheat.csv')) | ||
| testthat::expect_snapshot_file( | ||
| testthat::test_path('output', 'yield_impacts_smooth', 'yield_canesm5_gcam-ref_wheat.csv')) | ||
| testthat::expect_snapshot_file( | ||
| testthat::test_path('output', 'data_processed', 'format_yield_change_rel2015.csv')) | ||
| testthat::expect_snapshot_file( | ||
| testthat::test_path('output', 'figures', 'annual_projected_climate_impacts_canesm5_gcam-ref_wheat_fit_lnyield_mmm_quad_noco2_nogdp.pdf')) | ||
| testthat::expect_snapshot_file( | ||
| testthat::test_path('output', 'figures', 'smooth_projected_climate_impacts_canesm5_gcam-ref_wheat_fit_lnyield_mmm_quad_noco2_nogdp.pdf')) | ||
| testthat::expect_snapshot_file( | ||
| testthat::test_path('output', 'maps', 'map_canesm5_gcam-ref_wheat_2090.pdf')) | ||
| }) | ||
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| # Run tests for each function | ||
| test_that("crop_calendars runs correctly", { | ||
| crop_cal <- gaea::crop_calendars(output_dir = output_dir) | ||
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| test_that("gcam_agprodchange runs correctly", { | ||
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| out_gcam_agprodchange <- run_gcam_agprodchange(data = out_yield_projections) | ||
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| testthat::expect_snapshot_file( | ||
| testthat::test_path('output', 'gcam7_agprodchange_no-cfe', 'agyield_impact_canesm5_r1i1p1f1_w5e5v2_gcam-ref.xml')) | ||
| testthat::expect_snapshot_file( | ||
| testthat::test_path('output', 'gcam7_agprodchange_no-cfe', 'figures_yield_impacts', 'Wheat.png')) | ||
| testthat::expect_snapshot_file( | ||
| testthat::test_path('output', 'data_processed', 'crop_calendar.csv')) | ||
| testthat::test_path('output', 'gcam7_agprodchange_no-cfe', 'figures_agprodchange', 'Wheat.png')) | ||
| }) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| ## ----eval=FALSE--------------------------------------------------------------- | ||
| # | ||
| # # load gaea | ||
| # library(gaea) | ||
| # | ||
| # # NOTE: please change `data_dir` to your desired location for downloaded data | ||
| # data_dir <- gaea::get_example_data( | ||
| # download_url = 'https://zenodo.org/records/13179630/files/gaea_example_climate.zip?download=1', | ||
| # data_dir = 'path/to/desired/location' | ||
| # ) | ||
| # | ||
| # # Path to the climate NetCDF files | ||
| # # NOTE: Each variable can have more than one file | ||
| # # historical climate data | ||
| # pr_historical_file <- file.path(data_dir, 'pr_monthly_canesm5_w5e5_rcp7_1950_2014.nc') | ||
| # tas_historical_file <- file.path(data_dir, 'tas_monthly_canesm5_w5e5_rcp7_1950_2014.nc') | ||
| # | ||
| # # projected climate data | ||
| # pr_projection_file <- file.path(data_dir, 'pr_monthly_canesm5_w5e5_rcp7_2015_2100.nc') | ||
| # tas_projection_file <- file.path(data_dir, 'tas_monthly_canesm5_w5e5_rcp7_2015_2100.nc') | ||
| # | ||
| # # Run gaea | ||
| # # The full run with raw climate data can take up to an hour | ||
| # gaea::yield_impact( | ||
| # pr_hist_ncdf = pr_historical_file, | ||
| # tas_hist_ncdf = tas_historical_file, | ||
| # pr_proj_ncdf = pr_projection_file, | ||
| # tas_proj_ncdf = tas_projection_file, | ||
| # timestep = 'monthly', # specify the time step of the NetCDF data (monthly or daily) | ||
| # historical_periods = c(1950:2014), # vector of historical years selected for fitting | ||
| # climate_model = 'canesm5', # label of climate model name | ||
| # climate_scenario = 'gcam-ref', # label of climate scenario name | ||
| # member = 'r1i1p1f1', # label of ensemble member name | ||
| # bias_adj = 'w5e5', # label of climate data for bias adjustment | ||
| # cfe = 'no-cfe', # label of CO2 fertilization effect in the formula (default is no CFE) | ||
| # gcam_version = 'gcam7', # output is different depending on the GCAM version (gcam6 or gcam7) | ||
| # use_default_coeff = FALSE, # set to TRUE when there is no historical climate data available | ||
| # base_year = 2015 # GCAM base year | ||
| # start_year = 2015, # start year of the projected climate data | ||
| # end_year = 2100, # end year of the projected climate data | ||
| # smooth_window = 20, # number of years as smoothing window | ||
| # co2_hist = NULL, # historical annual CO2 concentration. If NULL, will use default value | ||
| # co2_proj = NULL, # projected annual CO2 concentration. If NULL, will use default value | ||
| # diagnostics = TRUE, # set to TRUE to output diagnostic plots | ||
| # output_dir = 'path/to/output/folder' # path to the output folder | ||
| # ) | ||
| # | ||
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