Update package name from gaea to gaia

.github/CONTRIBUTING.md

@@ -1,14 +1,14 @@
 # How to contribute
 
-We welcome third-party patches, which are essential for advancing the science and architecture of gaea.
+We welcome third-party patches, which are essential for advancing the science and architecture of gaia.
 But there are a few guidelines that we ask contributors to follow, guidelines that ease the maintainers' organizational and logistical duties, while encouraging development by others. All contributors agree to abide by the code of conduct.
 
 ## Getting Started
 
 * Make sure you have a [GitHub account](https://github.com/signup/free).
 * **Open an issue** describing your proposed change or work (after making sure one does not already exist).
   * Clearly describe the issue including steps to reproduce when it is a bug.
-  * Discuss how your change will affect gaea, and thus whether it's MAJOR, MINOR, or a PATCH.
+  * Discuss how your change will affect gaia, and thus whether it's MAJOR, MINOR, or a PATCH.
   * Interact with the project maintainers to refine/change/prioritize your issue and identify what branch will be targeted (see below).
 * Trivial changes to comments or documentation do not require creating a new issue.
 
@@ -20,15 +20,15 @@ But there are a few guidelines that we ask contributors to follow, guidelines th
   * We will never accept pull requests to the `main` branch.
 * Check for unnecessary whitespace with `git diff --check` before committing.
 * Make sure your commit messages are descriptive but succinct, describing what was changed and why, and **reference the relevant issue number**. Make commits of logical units.
-* Make sure you have added the necessary tests for your changes. Tests should be included in the root `tests` directory and are facilitated using `pytest` which is installed with the development version of gaea.  See more info on using `pytest` here:  https://docs.pytest.org/en/7.4.x/contents.html
+* Make sure you have added the necessary tests for your changes. Tests should be included in the root `tests` directory and are facilitated using `pytest` which is installed with the development version of gaia.  See more info on using `pytest` here:  https://docs.pytest.org/en/7.4.x/contents.html
 * Run _all_ the tests to assure nothing else was accidentally broken.
 
 ## Submitting Changes
 
 * Submit a pull request.
 * **Your pull request should include one of the following two statements**:
-   * You own the copyright on the code being contributed, and you hereby grant PNNL unlimited license to use this code in this version or any future version of gaea. You reserve all other rights to the code.
-   * Somebody else owns the copyright on the code being contributed (e.g., your employer because you did it as part of your work for them); you are authorized by that owner to grant PNNL an unlimited license to use this code in this version or any future version of gaea, and you hereby do so. All other rights to the code are reserved by the copyright owner.
+   * You own the copyright on the code being contributed, and you hereby grant PNNL unlimited license to use this code in this version or any future version of gaia. You reserve all other rights to the code.
+   * Somebody else owns the copyright on the code being contributed (e.g., your employer because you did it as part of your work for them); you are authorized by that owner to grant PNNL an unlimited license to use this code in this version or any future version of gaia, and you hereby do so. All other rights to the code are reserved by the copyright owner.
 * The core team looks at Pull Requests on a regular basis, and will respond as soon as possible.
 
 

CITATION.cff

@@ -13,9 +13,9 @@ authors:
 - family-names: "Abigail"
   given-names: "Snyder"
   orcid: "https://orcid.org/0000-0002-9034-9948"
-title: "gaea: An R package to estimate crop yield responses to temperature and precipitation"
+title: "gaia: An R package to estimate crop yield responses to temperature and precipitation"
 version: 1.0.0
-url: "https://github.com/JGCRI/gaea"
+url: "https://github.com/JGCRI/gaia"
 preferred-citation:
     type: article
     authors:
@@ -33,7 +33,7 @@ preferred-citation:
       orcid: "https://orcid.org/0000-0002-9034-9948"
     doi: "10.xxxxx/joss.xxxxx"
     journal: "Journal of Open Source Software"
-    title: "gaea: An R package to estimate crop yield responses to temperature and precipitation"
+    title: "gaia: An R package to estimate crop yield responses to temperature and precipitation"
     issue: x
     volume: y
     year: 2024

DESCRIPTION

@@ -1,5 +1,5 @@
-Package: gaea
-Title: gaea: An R package to estimate crop yield responses to temperature
+Package: gaia
+Title: gaia: An R package to estimate crop yield responses to temperature
     and precipitation
 Version: 1.0.0
 Authors@R: c(
@@ -15,8 +15,8 @@ Authors@R: c(
 Description: An empirical model to estimate annual crop yield responses to
     temperature and precipitation.
 License: BSD_3_clause + file LICENSE
-URL: https://github.com/JGCRI/gaea
-BugReports: https://github.com/JGCRI/gaea/issues
+URL: https://github.com/JGCRI/gaia
+BugReports: https://github.com/JGCRI/gaia/issues
 Depends: 
     R (>= 4.1)
 Imports: 

DISCLAIMER

@@ -1,4 +1,4 @@
-gaea
+gaia
 
 DISCLAIMER:
 

LICENSE

@@ -1,4 +1,4 @@
-gaea
+gaia
 
 BSD 3-Clause License
 

NEWS.md

@@ -1,3 +1,3 @@
-# gaea 1.0.0
+# gaia 1.0.0
 
 First release TBD

R/crop_calendars.R

@@ -18,8 +18,8 @@ crop_calendars <- function(output_dir = file.path(getwd(), 'output')){
   # format, subset data and replace location name
   d$Location <- ifelse( d$Location == "Georgia" & d$Source == "USDA UPHD", "Georgia_USA", d$Location )
   d <- subset( d, select = c( "Data.ID", "Location", "Crop", "Qualifier", "Plant.start", "Plant.end", "Harvest.start", "Harvest.end" ) )
-  d <- gaea::colname_replace( d, "Location", "country_name" )
-  d <- gaea::colname_replace( d, "Crop", "crop" )
+  d <- gaia::colname_replace( d, "Location", "country_name" )
+  d <- gaia::colname_replace( d, "Crop", "crop" )
   d$crop <- tolower( d$crop )
 
   # Average plant and harvest month
@@ -32,7 +32,7 @@ crop_calendars <- function(output_dir = file.path(getwd(), 'output')){
 
   # Country codes
   d <- merge( d, mapping_gcam_iso, by = "country_name", all.x = TRUE )
-  d <- gaea::iso_replace( d )
+  d <- gaia::iso_replace( d )
 
   # Indicators for crops
   crops <- tibble::tibble(

R/data.R

@@ -5,8 +5,8 @@
 #' @format R data frame
 #' @examples
 #' \dontrun{
-#'  library(gaea);
-#'  co2_historical <- gaea::co2_historical
+#'  library(gaia);
+#'  co2_historical <- gaia::co2_historical
 #' }
 "co2_historical"
 
@@ -17,8 +17,8 @@
 #' @format R data frame
 #' @examples
 #' \dontrun{
-#'  library(gaea);
-#'  co2_projection <- gaea::co2_projection
+#'  library(gaia);
+#'  co2_projection <- gaia::co2_projection
 #' }
 "co2_projection"
 
@@ -29,8 +29,8 @@
 #' @format R data frame
 #' @examples
 #' \dontrun{
-#'  library(gaea);
-#'  agprodchange_ni_gcam7 <- gaea::agprodchange_ni_gcam7
+#'  library(gaia);
+#'  agprodchange_ni_gcam7 <- gaia::agprodchange_ni_gcam7
 #' }
 "agprodchange_ni_gcam7"
 
@@ -40,8 +40,8 @@
 #' @format R data frame
 #' @examples
 #' \dontrun{
-#'  library(gaea);
-#'  agprodchange_ni_gcam6 <- gaea::agprodchange_ni_gcam6
+#'  library(gaia);
+#'  agprodchange_ni_gcam6 <- gaia::agprodchange_ni_gcam6
 #' }
 "agprodchange_ni_gcam6"
 
@@ -51,7 +51,7 @@
 #' @format R data frame
 #' @examples
 #' \dontrun{
-#'  library(gaea);
-#'  coef_default <- gaea::coef_default
+#'  library(gaia);
+#'  coef_default <- gaia::coef_default
 #' }
 "coef_default"

R/data_aggregation.R

@@ -24,13 +24,13 @@ data_aggregation <- function(climate_hist_dir = NULL,
   message('Starting Step: data_aggregation')
 
   # read crop calendar output from crop_calendars function
-  crop_cal <- gaea::input_data(
+  crop_cal <- gaia::input_data(
     folder_path = file.path(output_dir, 'data_processed'),
     input_file = 'crop_calendar.csv'
   )
 
   # merge fao yield and fao irrigation equip data
-  yield <- gaea::merge_data(fao_yield, fao_irr_equip, 'iso', 'year')
+  yield <- gaia::merge_data(fao_yield, fao_irr_equip, 'iso', 'year')
 
 
   # ----------------------------------------------------------------------------
@@ -46,7 +46,7 @@ data_aggregation <- function(climate_hist_dir = NULL,
 
   } else {
 
-    gaea::path_check(climate_hist_dir)
+    gaia::path_check(climate_hist_dir)
 
     # get file list
     list_precip_rfc <- list.files(
@@ -70,17 +70,17 @@ data_aggregation <- function(climate_hist_dir = NULL,
       file_temp <-list_temp_rfc[grepl(crop_id, list_temp_rfc)]
 
       # aggregate weather data for crop_i
-      d_climate <- gaea::weather_agg(file_precip = file_precip,
+      d_climate <- gaia::weather_agg(file_precip = file_precip,
                                      file_temp = file_temp,
                                      crop_name = crop_i)
 
       # estimate growing season for each crop and country (SAGE db)
-      d_crop <- gaea::crop_month(climate_data = d_climate,
+      d_crop <- gaia::crop_month(climate_data = d_climate,
                                  crop_name = crop_i,
                                  crop_calendar = crop_cal)
 
       # merge data
-      d_crop <- gaea::data_merge(data = d_crop,
+      d_crop <- gaia::data_merge(data = d_crop,
                                  crop_name = crop_i,
                                  yield = yield,
                                  co2_hist = co2_hist,
@@ -99,7 +99,7 @@ data_aggregation <- function(climate_hist_dir = NULL,
   if(is.null(climate_impact_dir)){
     stop('Please provide folder path to the projected climate data.')
   } else {
-    gaea::path_check(climate_impact_dir)
+    gaia::path_check(climate_impact_dir)
   }
 
   # get file list
@@ -124,17 +124,17 @@ data_aggregation <- function(climate_hist_dir = NULL,
     file_temp <-list_temp_rfc[grepl(crop_id, list_temp_rfc)]
 
     # aggregate weather data for crop_i
-    d_climate <- gaea::weather_agg(file_precip = file_precip,
+    d_climate <- gaia::weather_agg(file_precip = file_precip,
                                    file_temp = file_temp,
                                    crop_name = crop_i)
 
     # estimate growing season for each crop and country (SAGE db)
-    d_crop <- gaea::crop_month(climate_data = d_climate,
+    d_crop <- gaia::crop_month(climate_data = d_climate,
                                crop_name = crop_i,
                                crop_calendar = crop_cal)
 
     # merge data
-    d_crop <- gaea::data_trans(data = d_crop,
+    d_crop <- gaia::data_trans(data = d_crop,
                                climate_model = climate_model,
                                climate_scenario = climate_scenario,
                                crop_name = crop_i,

R/pkg_utils.R

@@ -11,9 +11,9 @@
 pkg_example <- function(path = NULL) {
 
   if (is.null(path)) {
-    dir(system.file('extras', package = 'gaea'))
+    dir(system.file('extras', package = 'gaia'))
   } else {
-    system.file('extras', path, package = 'gaea', mustWork = TRUE)
+    system.file('extras', path, package = 'gaia', mustWork = TRUE)
   }
 
 }
@@ -222,8 +222,8 @@ merge_data <- function( d1, d2, x1, x2 )
   x2.y <- paste( x2, "y", sep = "." )
   d1[[x1.y]] <- NULL
   d1[[x2.y]] <- NULL
-  d1 <- gaea::colname_replace( d1, x1.x, x1 )
-  d1 <- gaea::colname_replace( d1, x2.x, x2 )
+  d1 <- gaia::colname_replace( d1, x1.x, x1 )
+  d1 <- gaia::colname_replace( d1, x2.x, x2 )
   d1$id <- NULL
   return( d1 )
 }
@@ -251,7 +251,7 @@ agprodchange_ref <- function(gcam_version = 'gcam7',
   if(!is.null(gcamdata_dir)){
 
     # If user provide their own gcamdata dirctory, then use user provided data
-    gaea::path_check(gcamdata_dir)
+    gaia::path_check(gcamdata_dir)
 
     if(grepl('ssp1|ssp5', climate_scenario)){
       agprodchange_ag <- data.table::fread(file.path(gcamdata_dir, 'outputs', 'L2052.AgProdChange_irr_high.csv'))
@@ -283,11 +283,11 @@ agprodchange_ref <- function(gcam_version = 'gcam7',
 
     # if user doesn't provide any gcamdata, then use default
     if(gcam_version == 'gcam6'){
-      agprodchange_ni <- gaea::agprodchange_ni_gcam6
+      agprodchange_ni <- gaia::agprodchange_ni_gcam6
     }
 
     if(gcam_version == 'gcam7'){
-      agprodchange_ni <- gaea::agprodchange_ni_gcam7
+      agprodchange_ni <- gaia::agprodchange_ni_gcam7
     }
 
     # filter based on the scenario

R/weighted_climate.R

@@ -118,13 +118,13 @@ weighted_climate <- function(pr_ncdf = NULL,
     for(pr_file in pr_ncdf) {
 
       # check if pr file is valid
-      gaea::path_check(path = pr_file, file_type = 'nc')
+      gaia::path_check(path = pr_file, file_type = 'nc')
 
       # precipitation
       message(paste0('Processing: ', pr_file))
 
       # get time periods of the nc file
-      nc_time <- gaea::get_nc_time(pr_file)
+      nc_time <- gaia::get_nc_time(pr_file)
 
       # check if the data periods is within the selected periods
       if (!is.null(time_periods)){
@@ -175,13 +175,13 @@ weighted_climate <- function(pr_ncdf = NULL,
     for(tas_file in tas_ncdf) {
 
       # check if pr file is valid
-      gaea::path_check(path = tas_file, file_type = 'nc')
+      gaia::path_check(path = tas_file, file_type = 'nc')
 
       # precipitation
       message(paste0('Processing: ', tas_file))
 
       # get time periods of the nc file
-      nc_time <- gaea::get_nc_time(tas_file)
+      nc_time <- gaia::get_nc_time(tas_file)
 
       # check if the data periods is within the selected periods
       if (!is.null(time_periods)){
@@ -265,7 +265,7 @@ weighted_climate <- function(pr_ncdf = NULL,
     }
 
 
-  } # end of for(crop in names(gaea::mirca_harvest_area))
+  } # end of for(crop in names(gaia::mirca_harvest_area))
 
   message('The function weighted_climate is complete.')
 

R/yield_impact.R

@@ -56,7 +56,7 @@ yield_impact <- function(pr_hist_ncdf = NULL,
   # Step 1b: Process standard NetCDF files from ISIMIP to country level historical climate
   if(any(!is.null(pr_hist_ncdf), !is.null(tas_hist_ncdf))){
 
-    gaea::weighted_climate(pr_ncdf = pr_hist_ncdf,
+    gaia::weighted_climate(pr_ncdf = pr_hist_ncdf,
                            tas_ncdf = tas_hist_ncdf,
                            timestep = timestep,
                            climate_model = climate_model,
@@ -70,7 +70,7 @@ yield_impact <- function(pr_hist_ncdf = NULL,
   # Step 1b: Process standard NetCDF files from ISIMIP to country level projected climate
   if(any(!is.null(pr_proj_ncdf), !is.null(tas_proj_ncdf))){
 
-    gaea::weighted_climate(pr_ncdf = pr_proj_ncdf,
+    gaia::weighted_climate(pr_ncdf = pr_proj_ncdf,
                            tas_ncdf = tas_proj_ncdf,
                            timestep = timestep,
                            climate_model = climate_model,
@@ -83,7 +83,7 @@ yield_impact <- function(pr_hist_ncdf = NULL,
 
 
   # Step 2: Generate planting months for each country
-  gaea::crop_calendars(output_dir = output_dir)
+  gaia::crop_calendars(output_dir = output_dir)
 
   # Step 3: Process multiple models to analyze historical weather variables and crop yields
   if(all(is.null(climate_hist_dir),
@@ -99,21 +99,21 @@ yield_impact <- function(pr_hist_ncdf = NULL,
   }
 
 
-  gaea::data_aggregation(climate_hist_dir = climate_hist_dir,
+  gaia::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)
 
   # Step 4: Yield regressions and create figures
   if(!use_default_coeff){
-    gaea::yield_regression(diagnostics = diagnostics,
+    gaia::yield_regression(diagnostics = diagnostics,
                            output_dir = output_dir)
   }
 
 
   # Step 5: Project yields for future climate scenarios using regression analysis
-  df_yield_projection <- gaea::yield_shock_projection(use_default_coeff = use_default_coeff,
+  df_yield_projection <- gaia::yield_shock_projection(use_default_coeff = use_default_coeff,
                                                       climate_model = climate_model,
                                                       climate_scenario = climate_scenario,
                                                       base_year = base_year,
@@ -125,7 +125,7 @@ yield_impact <- function(pr_hist_ncdf = NULL,
   )
 
   # Step 6:
-  df_yield_impact_gcam <- gaea::gcam_agprodchange(data = df_yield_projection,
+  df_yield_impact_gcam <- gaia::gcam_agprodchange(data = df_yield_projection,
                                                   climate_model = climate_model,
                                                   climate_scenario = climate_scenario,
                                                   member = member,