Update testthat and vignette

JGCRI · Aug 4, 2024 · e227ff3 · e227ff3
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -39,7 +39,8 @@ Imports:
     stringr (>= 1.5.0),
     tibble (>= 3.2.1),
     tidyr (>= 1.3.0),
-    utils
+    utils,
+    xml2 (>= 1.3.6)
 Suggests: 
     knitr,
     rmarkdown (>= 2.16),

diff --git a/README.md b/README.md
@@ -19,7 +19,7 @@
 
 <p align="center">
 <a href="https://jgcri.github.io/gaea/" target="_blank"><img src="https://github.com/JGCRI/jgcricolors/blob/main/vignettes/button_user_guide.PNG?raw=true" 
-alt="https://jgcri.github.io/gaea/" height="60"/></a>
+alt="https://jgcri.github.io/gaea/articles/vignette.html" height="60"/></a>
 <img src="https://github.com/JGCRI/jgcricolors/blob/main/vignettes/button_divider.PNG?raw=true" height="40"/>
 </p>
 
@@ -50,11 +50,29 @@ alt="https://jgcri.github.io/gaea/" height="60"/></a>
 install.packages("devtools")
 devtools::install_github("JGCRI/gaea")
 ```
+
 or
+
 ```r
 install.packages("remotes")
 remotes::install_github("JGCRI/gaea")
 ```
+
+Additional steps for UBUNTU from a terminal
+
+```
+sudo add-apt-repository ppa:ubuntugis/ppa
+sudo apt-get update
+sudo apt-get install libudunits2-dev libgdal-dev libgeos-dev libproj-dev libmagick++-dev
+```
+
+Additional steps for MACOSX from a terminal
+
+```
+brew install pkg-config
+brew install gdal
+```
+
 <br/>
 
 

diff --git a/inst/extras/devTests.R b/inst/extras/devTests.R
@@ -26,8 +26,13 @@ gaea::weighted_climate(pr_ncdf = 'C:/WorkSpace/GCIMS/GCIMS_Yield/climate_process
 
 if(T){
 
-  pr_proj_ncdf = 'C:/WorkSpace/GCIMS/GCIMS_Yield/climate_process/data/climate/pr_mon_basd_CanESM5_W5E5v2_GCAM_ref_2015-2100.nc'
-  tas_proj_ncdf = 'C:/WorkSpace/GCIMS/GCIMS_Yield/climate_process/data/climate/tas_mon_basd_CanESM5_W5E5v2_GCAM_ref_2015-2100.nc'
+  # pr_proj_ncdf = 'C:/WorkSpace/GCIMS/GCIMS_Yield/climate_process/data/climate/pr_mon_basd_CanESM5_W5E5v2_GCAM_ref_2015-2100.nc'
+  # tas_proj_ncdf = 'C:/WorkSpace/GCIMS/GCIMS_Yield/climate_process/data/climate/tas_mon_basd_CanESM5_W5E5v2_GCAM_ref_2015-2100.nc'
+
+  pr_hist_ncdf = 'C:/WorkSpace/GCIMS/GCIMS_Yield/climate_process/data/climate/gaea_example_climate/pr_monthly_canesm5_w5e5_rcp7_1950_2014.nc'
+  tas_hist_ncdf = 'C:/WorkSpace/GCIMS/GCIMS_Yield/climate_process/data/climate/gaea_example_climate/tas_monthly_canesm5_w5e5_rcp7_1950_2014.nc'
+  pr_proj_ncdf = 'C:/WorkSpace/GCIMS/GCIMS_Yield/climate_process/data/climate/gaea_example_climate/pr_monthly_canesm5_w5e5_rcp7_2015_2100.nc'
+  tas_proj_ncdf = 'C:/WorkSpace/GCIMS/GCIMS_Yield/climate_process/data/climate/gaea_example_climate/tas_monthly_canesm5_w5e5_rcp7_2015_2100.nc'
   timestep = 'monthly'
   climate_model = 'canesm5'
   climate_scenario = 'gcam-ref'
@@ -46,7 +51,7 @@ if(T){
   co2_hist = NULL
   co2_proj = NULL
   diagnostics <- TRUE
-  output_dir = 'C:/WorkSpace/github/test_scripts/gaea/output_test'
+  output_dir = 'C:/WorkSpace/github/test_scripts/gaea/output_joss_test'
 
 }
 

diff --git a/paper/workflow.jpg b/paper/workflow.jpg
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
@@ -29,7 +29,7 @@ start_year_i = 2015
 end_year_i = 2100
 smooth_window_i = 20
 
-diagnostics_i <- T
+diagnostics_i <- F
 use_default_coeff_i <- F
 
 
@@ -112,7 +112,7 @@ run_gcam_agprodchange <- function(data = NULL,
                                   diagnostics = diagnostics_i,
                                   output_dir = output_dir_i){
 
-  output <- gaea::gcam_agprodchange(data = df_yield_projection,
+  output <- gaea::gcam_agprodchange(data = data,
                                     climate_model = climate_model,
                                     climate_scenario = climate_scenario,
                                     member = member,

diff --git a/tests/testthat/test-gaea.R b/tests/testthat/test-gaea.R
@@ -2,70 +2,84 @@ library(sf)
 
 testthat::skip_on_cran()
 testthat::skip_on_travis()
-testthat::skip_on_ci()
+
 
 # ------------------------------------
 # 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'))
-# })
+
+test_that("crop_calendars runs correctly", {
+
+  out_crop_calendars <- run_crop_calendars()
+
+  testthat::expect_snapshot(out_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(out_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(out_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'))
+})
 
 test_that("yield_projections runs correctly", {
 
   out_yield_projections <- run_yield_projections()
 
-  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'))
+  testthat::expect_snapshot(out_yield_projections)
+
+  # 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'))
 })
 
 
 test_that("gcam_agprodchange runs correctly", {
 
+  out_yield_projections <- run_yield_projections()
   out_gcam_agprodchange <- run_gcam_agprodchange(data = out_yield_projections)
 
-  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', 'gcam7_agprodchange_no-cfe', 'figures_agprodchange', 'Wheat.png'))
+  testthat::expect_snapshot(out_gcam_agprodchange)
+
+  # 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', 'gcam7_agprodchange_no-cfe', 'figures_agprodchange', 'Wheat.png'))
 })
diff --git a/vignettes/vignette.R b/vignettes/vignette.R
@@ -1,4 +1,4 @@
-## ----eval=FALSE---------------------------------------------------------------
+## ----eval=F-------------------------------------------------------------------
 #  
 #  # load gaea
 #  library(gaea)
@@ -19,6 +19,12 @@
 #  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')
 #  
+
+## ----eval=FALSE---------------------------------------------------------------
+#  
+#  # load gaea
+#  library(gaea)
+#  
 #  # Run gaea
 #  # The full run with raw climate data can take up to an hour
 #  gaea::yield_impact(
@@ -46,3 +52,51 @@
 #  )
 #  
 
+## ----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/weighted_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
+#  climate_hist_dir <- file.path(data_dir, 'canesm5_hist')
+#  
+#  # projected climate data
+#  climate_impact_dir <- file.path(data_dir, 'canesm5')
+#  
+
+## ----eval=FALSE---------------------------------------------------------------
+#  
+#  # load gaea
+#  library(gaea)
+#  
+#  # Run gaea
+#  gaea::yield_impact(
+#    climate_hist_dir = climate_hist_dir,
+#    climate_impact_dir = climate_impact_dir,
+#    timestep = 'monthly',                   # specify the time step of the NetCDF data (monthly or daily)
+#    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
+#  )
+#  
+