Updating documentation

.github/workflows/test-coverage.yaml

@@ -44,7 +44,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,20 +1,26 @@
 Package: matilda
 Type: Package
 Title: A Probabilistic Framework for the Hector Simple Climate Model
-Version: 0.1.0
-Author: c(person("Joseph", "Brown",
-    email = "joseph.brown@pnnl.gov",
-    role = "aut",
-    comment = c(ORCID = "0000-0002-3828-4729")),
+Version: 1.0.0
+Authors@R: c(
+    person("Joseph", "Brown",
+        email = "joseph.brown@pnnl.gov",
+        role = c("aut", "cre"),
+        comment = c(ORCID = "0000-0002-3828-4729")),
     person("Ben", "Bond-Lamberty",
-    email = "bondlamberty@pnnl.gov",
-    role = "aut",
-    comment = c(ORCID = "0000-0001-9525-4633")),
-    person("Leeya", "Pressburger")
-    email = "leeya.pressburger@pnnl.gov",
-    role = "aut",
-    comment = c(ORCID = "0000-0002-6850-2504")))
-Maintainer: Joseph Brown <joseph.brown@pnnl.gov>
+        email = "bondlamberty@pnnl.gov",
+        role = "aut",
+        comment = c(ORCID = "0000-0001-9525-4633")),
+    person("Leeya", "Pressburger",
+        email = "leeya.pressburger@pnnl.gov",
+        role = "aut",
+        comment = c(ORCID = "0000-0002-6850-2504")),
+    person("Kalyn", "Dorheim",
+        email = "kalyn.dorheim@pnnl.gov",
+        role = "ctb",
+        comment = c(ORCID = "0000-0001-8093-8397")),
+    person("Melat", "Ghebreselassie",
+        role = "ctb"))
 Description: Provides a probabilistic framework for climate variable projections
     using the Hector simple climate model. Using this framework you can change 
     parameters, run the model, retrieve targeted model outputs, and quantify 

NAMESPACE

@@ -5,6 +5,7 @@ S3method(print,h_metric)
 export(RMSE_calc)
 export(criterion_co2_obs)
 export(criterion_gmst_obs)
+export(criterion_ocean_c_uptake_obs)
 export(generate_params)
 export(hector_matrix)
 export(is.criterion)

R/example_hector_result.R

@@ -4,7 +4,7 @@
 #' a single hector. The model results include the GMST() Hector variable for
 #' the years 1745:2300.
 #'
-#' @format \code{hector_result} {is a data frame with 556 rows and 5 columns:}
+#' @format hector_result is a data frame with 556 rows and 5 columns:
 #' \describe{
 #'   \item{scenario}{Scenario being used for the analysis}
 #'   \item{year}{Years}

R/example_matilda_result.R

@@ -7,7 +7,7 @@
 #' This ensures that data being saved from the core includes the data needed to
 #' score the Hector runs.
 #'
-#' @format \code{matilda_result} {is a data frame with 2820 rows and 6 columns:}
+#' @format matilda_result is a data frame with 2820 rows and 6 columns:
 #' \describe{
 #'   \item{scenario}{Scenario being used for the analysis}
 #'   \item{year}{Years}

R/new_criterion.R

@@ -84,9 +84,10 @@ is.criterion <- function(x) {
 #' @examples
 #' criterion_co2_obs()
 criterion_co2_obs <- function() {
+  get("observed_co2_data", envir = asNamespace("matilda"))
   new_criterion(CONCENTRATIONS_CO2(),
-    years = observed_data_co2$year,
-    obs_values = observed_data_co2$co2_ppm
+    years = observed_co2_data$year,
+    obs_values = observed_co2_data$co2_ppm
   )
 }
 
@@ -105,8 +106,30 @@ criterion_co2_obs <- function() {
 #' @examples
 #' criterion_gmst_obs()
 criterion_gmst_obs <- function() {
+  get("observed_gmst_data", envir = asNamespace("matilda"))
   new_criterion(GMST(),
-    years = adjusted_gmst_data$year,
-    obs_values = adjusted_gmst_data$anomaly_C
+    years = observed_gmst_data$year,
+    obs_values = observed_gmst_data$anomaly_C
+  )
+}
+
+
+#' Screening criterion using Global Carbon Project ocean carbon uptake
+#'
+#' @description This is a criterion identifier for screening Hector runs using
+#' observed ocean carbon uptake from the Global Carbon Project's 2023 Global Carbon Budget.
+#'
+#' @return A criterion identifier using GCP ocean carbon uptake
+#' @note This function uses ocean carbon uptake data from
+#' \href{ https://globalcarbonbudgetdata.org/latest-data.html}{ https://globalcarbonbudgetdata.org/latest-data.html}
+#' @export
+#'
+#' @examples
+#' criterion_ocean_c_uptake_obs()
+criterion_ocean_c_uptake_obs <- function() {
+  get("observed_ocean_c_uptake_data", envir = asNamespace("matilda"))
+  new_criterion(OCEAN_UPTAKE(),
+                years = observed_ocean_c_uptake_data$year,
+                obs_values = observed_ocean_c_uptake_data$ocean_uptake
   )
 }

R/score_runs.R

@@ -50,6 +50,9 @@ score_runs <- function(x, criterion, score_function, ...) {
     stop("criterion year and variable combination not represented in data")
   }
 
+  # retains run_number from x
+  run_numbers <- unique(x_subset$run_number)
+
   # converts x_subset to matrix - columns are vectors of values for each model iteration
   model_matrix <- hector_matrix(x_subset, columns = "value")
 
@@ -69,6 +72,6 @@ score_runs <- function(x, criterion, score_function, ...) {
 
   return(data.frame(
     weights = score_norm,
-    run_number = 1:length(scores)
+    run_number = run_numbers
   ))
 }