Halocarbon update and fix

DESCRIPTION

@@ -73,10 +73,11 @@ Collate:
     'hector.R'
     'messages.R'
     'units.R'
+    'zzz.R'
 VignetteBuilder: knitr
 Config/Needs/website: kableExtra, nleqslv
-RoxygenNote: 7.3.2
 SystemRequirements: GNU make
 URL: https://github.com/JGCRI/hector, https://jgcri.github.io/hector/
 BugReports: https://github.com/JGCRI/hector/issues
 Language: en-US
+Config/roxygen2/version: 8.1.0

NAMESPACE

@@ -3,6 +3,10 @@
 S3method(format,hcore)
 S3method(print,hcore)
 export(AERO_SCALE)
+export(ALL_HALOCARBON_CONCENTRATIONS)
+export(ALL_HALOCARBON_CONSTRAINTS)
+export(ALL_HALOCARBON_EMISSIONS)
+export(ALL_HALOCARBON_RF)
 export(ALL_VARS)
 export(ATMOSPHERIC_CO2)
 export(BETA)

R/RcppExports.R

@@ -174,14 +174,6 @@ RF_MISC <- function() {
     .Call('_hector_RF_MISC', PACKAGE = 'hector')
 }
 
-RFADJ_PREFIX <- function() {
-    .Call('_hector_RFADJ_PREFIX', PACKAGE = 'hector')
-}
-
-RF_PREFIX <- function() {
-    .Call('_hector_RF_PREFIX', PACKAGE = 'hector')
-}
-
 #' @describeIn haloforcings Radiative forcing due to CF4
 #' @export
 RF_CF4 <- function() {

R/aadoc.R

@@ -313,7 +313,3 @@ NULL
 #' }
 "fxntable"
 
-#' A vector containing all the hector output names.
-#'
-#' @format A vector of length 82.
-"all_vars"

R/fxns.R

@@ -9,15 +9,15 @@
 #' getfxn("beta")
 #' getfxn("q10_rh")
 getfxn <- function(str) {
-  rows <- match(str, hector::fxntable$string)
-  rslt <- hector::fxntable$fxn[rows]
-  if (any(is.na(rows))) {
-    warning(
-      "Functions for the following are not found: ",
-      paste(str[is.na(rslt)], collapse = ", ")
-    )
-  }
-  as.character(rslt)
+    rows <- match(str, hector::fxntable$string)
+    rslt <- hector::fxntable$fxn[rows]
+    if (any(is.na(rows))) {
+        warning(
+            "Functions for the following are not found: ",
+            paste(str[is.na(rslt)], collapse = ", ")
+        )
+    }
+    as.character(rslt)
 }
 
 
@@ -37,5 +37,83 @@ getfxn <- function(str) {
 #' print(out)
 #' }
 ALL_VARS <- function() {
-  hector::all_vars
+    getFromNamespace("all_vars", "hector")
+}
+
+#' Get all of the possible Hector halocarbon concentrations
+#'
+#' This function returns a vector of the possible hector halocarbon concentrations
+#' that can be accessed with \code{\link{fetchvars}}.
+#' @return Character vector of variable names.
+#' @export
+#' @family outputs
+#' @examples
+#' \dontrun{
+#' ini <- system.file(package = "hector", "input/hector_ssp245.ini")
+#' hc <- newcore(ini)
+#' run(hc)
+#' out <- fetchvars(core = hc, dates = 1900:2100, vars = ALL_HALOCARBON_CONCENTRATIONS())
+#' print(out)
+#' }
+ALL_HALOCARBON_CONCENTRATIONS <- function() {
+    getFromNamespace("halo_conc", "hector")
+}
+
+
+#' Get all of the possible Hector halocarbon emissions
+#'
+#' This function returns a vector of the possible hector halocarbon emissions
+#' that can be accessed with \code{\link{fetchvars}} or set with \code{\link{setvar}}.
+#' @return Character vector of variable names.
+#' @export
+#' @family haloemiss
+#' @examples
+#' \dontrun{
+#' ini <- system.file(package = "hector", "input/hector_ssp245.ini")
+#' hc <- newcore(ini)
+#' run(hc)
+#' out <- fetchvars(core = hc, dates = 1900:2100, vars = ALL_HALOCARBON_EMISSIONS())
+#' print(out)
+#' }
+ALL_HALOCARBON_EMISSIONS <- function() {
+    getFromNamespace("halo_emiss", "hector")
+}
+
+
+#' Get all of the possible Hector halocarbon constraints
+#'
+#' This function returns a vector of the possible hector halocarbon constraints
+#' that can be accessed with \code{\link{fetchvars}} or set with \code{\link{setvar}}.
+#' @return Character vector of variable names.
+#' @export
+#' @family outputs, inputs
+#' @examples
+#' \dontrun{
+#' ini <- system.file(package = "hector", "input/hector_ssp245.ini")
+#' hc <- newcore(ini)
+#' run(hc)
+#' out <- fetchvars(core = hc, dates = 1900:2100, vars = ALL_HALOCARBON_CONSTRAINTS())
+#' print(out)
+#' }
+ALL_HALOCARBON_CONSTRAINTS <- function() {
+    getFromNamespace("halo_constraints", "hector")
+}
+
+#' Get all of the possible Hector halocarbon radiative forcings
+#'
+#' This function returns a vector of the possible hector halocarbon forcings
+#' that can be accessed with \code{\link{fetchvars}}.
+#' @return Character vector of variable names.
+#' @export
+#' @family outputs
+#' @examples
+#' \dontrun{
+#' ini <- system.file(package = "hector", "input/hector_ssp245.ini")
+#' hc <- newcore(ini)
+#' run(hc)
+#' out <- fetchvars(core = hc, dates = 1900:2100, vars = ALL_HALOCARBON_RF())
+#' print(out)
+#' }
+ALL_HALOCARBON_RF <- function() {
+    getFromNamespace("halo_rf", "hector")
 }

R/messages.R

@@ -78,9 +78,6 @@ fetchvars <- function(core, dates, vars = NULL, scenario = NULL) {
       sendmessage(core, GETDATA(), v, dates, NA, "")
     })
   )
-  ## Fix the variable name for the adjusted halocarbon forcings so that they are
-  ## consistent with other forcings.
-  rslt$variable <- sub(paste0("^", RFADJ_PREFIX()), RF_PREFIX(), rslt$variable)
   cols <- names(rslt)
   rslt$scenario <- scenario
   ## reorder the columns to put the scenario name first

R/zzz.R

@@ -0,0 +1,7 @@
+# Silence package checks
+utils::globalVariables(c(
+    "halo_conc",
+    "halo_constraints",
+    "halo_emiss",
+    "halo_rf"
+))

data-raw/internal_pkgdata.R

@@ -0,0 +1,32 @@
+# Generate the strings that are used in the ALL_OUTPUT function.
+# This script does require that an output stream has already been generated
+# from the command line.
+
+
+file <- list.files(path = "output", pattern = "outputstream_", full.names = TRUE)
+stopifnot("need to generate outputstream file" = length(file) > 0)
+
+dat <- read.csv(file = file[[1]], comment.char = "#")
+
+# Extract all of the halocarbon base names.
+componet_names <- unique(dat$component)
+halo_base_names <- gsub(x = componet_names[grepl(pattern = "halocarbon", x = componet_names)],
+                        pattern = "_halocarbon", replacement = "")
+
+# Format the halocarbon emissions, constraints, concentrations, and forcings
+# helper vectors.
+halo_emiss <- paste0(halo_base_names, "_emissions")
+halo_constraints <- paste0(halo_base_names, "_constrain")
+halo_conc <- paste0(halo_base_names, "_concentration")
+halo_rf <- paste0("RF_", halo_base_names)
+
+all_vars <- unique(c(dat$variable, halo_conc, halo_rf))
+all_vars <- all_vars[!all_vars %in% c(
+  "hc_concentration", "HL_downwelling", "HL_OmegaAr", "LL_OmegaAr",
+  "HL_OmegaCa", "LL_OmegaCa", "atmos_c_residual", "HL_Revelle", "HL_Revelle",
+  "LL_Revelle", "slr", "slr_no_ice", "sl_rc", "sl_rc_no_ice"
+)]
+
+
+usethis::use_data(halo_emiss, all_vars, halo_constraints, halo_conc, halo_rf, internal = TRUE, overwrite = TRUE)
+

data-raw/lookup-data.R

@@ -21,7 +21,7 @@ lines <- readLines("./src/rcpp_constants.cpp")
 # Specific functions to exclude
 # TODO is there a way to make this not hard coded?
 lines <- lines[!grepl(
-  pattern = "GETDATA|SETDATA|BIOME_SPLIT_CHAR|RFADJ_PREFIX|RF_PREFIX",
+  pattern = "GETDATA|SETDATA|BIOME_SPLIT_CHAR|RF_PREFIX",
   x = lines
 )]
 

data-raw/units-data.R

@@ -53,32 +53,15 @@ temp_uni <- c(
 misc_emiss_vars <- c(EMISSIONS_BC(), EMISSIONS_OC(), EMISSIONS_NH3())
 misc_emiss_uni <- c("Tg", "Tg", "Tg")
 
-haloemis_vars <- c(
-  EMISSIONS_CF4(), EMISSIONS_C2F6(), EMISSIONS_HFC23(),
-  EMISSIONS_HFC32(), EMISSIONS_HFC4310(), EMISSIONS_HFC125(),
-  EMISSIONS_HFC134A(), EMISSIONS_HFC143A(), EMISSIONS_HFC227EA(),
-  EMISSIONS_HFC245FA(), EMISSIONS_SF6(), EMISSIONS_CFC11(),
-  EMISSIONS_CFC12(), EMISSIONS_CFC113(), EMISSIONS_CFC114(),
-  EMISSIONS_CFC115(), EMISSIONS_CCL4(), EMISSIONS_CH3CCL3(),
-  EMISSIONS_HCFC22(), EMISSIONS_HCFC141B(), EMISSIONS_HCFC142B(),
-  EMISSIONS_HALON1211(), EMISSIONS_HALON1301(),
-  EMISSIONS_HALON2402(), EMISSIONS_CH3CL(), EMISSIONS_CH3BR()
-)
+haloemis <- ALL_HALOCARBON_EMISSIONS()
 haloemis_uni <- "Gg"
 
-haloconstrain_vars <- c(
-  CF4_CONSTRAIN(), C2F6_CONSTRAIN(), HFC23_CONSTRAIN(),
-  HFC32_CONSTRAIN(), HFC4310_CONSTRAIN(), HFC125_CONSTRAIN(),
-  HFC134A_CONSTRAIN(), HFC143A_CONSTRAIN(), HFC227EA_CONSTRAIN(),
-  HFC245FA_CONSTRAIN(), SF6_CONSTRAIN(), CFC11_CONSTRAIN(),
-  CFC12_CONSTRAIN(), CFC113_CONSTRAIN(), CFC114_CONSTRAIN(),
-  CFC115_CONSTRAIN(), CCL4_CONSTRAIN(), CH3CCL3_CONSTRAIN(),
-  HCFC22_CONSTRAIN(), HCFC141B_CONSTRAIN(), HCFC142B_CONSTRAIN(),
-  HALON1211_CONSTRAIN(), HALON1301_CONSTRAIN(), HALON2402_CONSTRAIN(),
-  CH3CL_CONSTRAIN(), CH3BR_CONSTRAIN(), "HFC245_constrain"
-)
+haloconstrain_vars <- ALL_HALOCARBON_CONSTRAINTS()
 haloconstrain_uni <- "pptv"
 
+haloconc_vars <- ALL_HALOCARBON_CONCENTRATIONS()
+haloconc_uni <- haloconstrain_uni
+
 halodeltas_vars <- c(
   DELTA_CF4(), DELTA_C2F6(), DELTA_HFC23(), DELTA_HFC32(),
   DELTA_HFC4310(), DELTA_HFC125(), DELTA_HFC134A(), DELTA_HFC143A(),
@@ -104,8 +87,9 @@ unitstable <- rbind(
   data.frame(variable = forcing_vars, units = forcing_uni),
   data.frame(variable = temp_vars, units = temp_uni),
   data.frame(variable = misc_emiss_vars, units = misc_emiss_uni),
-  data.frame(variable = haloemis_vars, units = haloemis_uni),
+  data.frame(variable = haloemis, units = haloemis_uni),
   data.frame(variable = haloconstrain_vars, units = haloconstrain_uni),
+  data.frame(variable = haloconc_vars, units = haloconc_uni),
   data.frame(variable = halodeltas_vars, units = halodeltas_uni),
   data.frame(variable = misc_var, units = misc_uni)
 )

inst/include/component_data.hpp

@@ -69,6 +69,8 @@
 #define D_VOLCANIC_SCALE "vol_scalar"
 
 // halocarbon components
+// These capabilities allow a caller to fetch the
+// adjusted values from the forcing component. 
 #define D_RF_CF4 D_RF_PREFIX CF4_COMPONENT_BASE
 #define D_RF_C2F6 D_RF_PREFIX C2F6_COMPONENT_BASE
 #define D_RF_HFC23 D_RF_PREFIX HFC23_COMPONENT_BASE
@@ -96,37 +98,36 @@
 #define D_RF_CH3Cl D_RF_PREFIX CH3Cl_COMPONENT_BASE
 #define D_RF_CH3Br D_RF_PREFIX CH3Br_COMPONENT_BASE
 
-// Adjusted (i.e., relative) halocarbon forcings
+// Unadjusted halocarbon forcings
 // Forcings are tracked relative to the base year forcings, but the
-// halocarbon components don't know that.  These capabilities allow
-// a caller to fetch the adjusted values from the forcing component.
-#define D_RFADJ_PREFIX "Fadj"
-#define D_RFADJ_CF4 D_RFADJ_PREFIX CF4_COMPONENT_BASE
-#define D_RFADJ_C2F6 D_RFADJ_PREFIX C2F6_COMPONENT_BASE
-#define D_RFADJ_HFC23 D_RFADJ_PREFIX HFC23_COMPONENT_BASE
-#define D_RFADJ_HFC32 D_RFADJ_PREFIX HFC32_COMPONENT_BASE
-#define D_RFADJ_HFC4310 D_RFADJ_PREFIX HFC4310_COMPONENT_BASE
-#define D_RFADJ_HFC125 D_RFADJ_PREFIX HFC125_COMPONENT_BASE
-#define D_RFADJ_HFC134a D_RFADJ_PREFIX HFC134a_COMPONENT_BASE
-#define D_RFADJ_HFC143a D_RFADJ_PREFIX HFC143a_COMPONENT_BASE
-#define D_RFADJ_HFC227ea D_RFADJ_PREFIX HFC227ea_COMPONENT_BASE
-#define D_RFADJ_HFC245fa D_RFADJ_PREFIX HFC245fa_COMPONENT_BASE
-#define D_RFADJ_SF6 D_RFADJ_PREFIX SF6_COMPONENT_BASE
-#define D_RFADJ_CFC11 D_RFADJ_PREFIX CFC11_COMPONENT_BASE
-#define D_RFADJ_CFC12 D_RFADJ_PREFIX CFC12_COMPONENT_BASE
-#define D_RFADJ_CFC113 D_RFADJ_PREFIX CFC113_COMPONENT_BASE
-#define D_RFADJ_CFC114 D_RFADJ_PREFIX CFC114_COMPONENT_BASE
-#define D_RFADJ_CFC115 D_RFADJ_PREFIX CFC115_COMPONENT_BASE
-#define D_RFADJ_CCl4 D_RFADJ_PREFIX CCl4_COMPONENT_BASE
-#define D_RFADJ_CH3CCl3 D_RFADJ_PREFIX CH3CCl3_COMPONENT_BASE
-#define D_RFADJ_HCFC22 D_RFADJ_PREFIX HCFC22_COMPONENT_BASE
-#define D_RFADJ_HCFC141b D_RFADJ_PREFIX HCFC141b_COMPONENT_BASE
-#define D_RFADJ_HCFC142b D_RFADJ_PREFIX HCFC142b_COMPONENT_BASE
-#define D_RFADJ_halon1211 D_RFADJ_PREFIX halon1211_COMPONENT_BASE
-#define D_RFADJ_halon1301 D_RFADJ_PREFIX halon1301_COMPONENT_BASE
-#define D_RFADJ_halon2402 D_RFADJ_PREFIX halon2402_COMPONENT_BASE
-#define D_RFADJ_CH3Cl D_RFADJ_PREFIX CH3Cl_COMPONENT_BASE
-#define D_RFADJ_CH3Br D_RFADJ_PREFIX CH3Br_COMPONENT_BASE
+// halocarbon components don't know that.
+#define D_RFUNADJ_PREFIX "RF_unadj"
+#define D_RFUNADJ_CF4 D_RFUNADJ_PREFIX CF4_COMPONENT_BASE
+#define D_RFUNADJ_C2F6 D_RFUNADJ_PREFIX C2F6_COMPONENT_BASE
+#define D_RFUNADJ_HFC23 D_RFUNADJ_PREFIX HFC23_COMPONENT_BASE
+#define D_RFUNADJ_HFC32 D_RFUNADJ_PREFIX HFC32_COMPONENT_BASE
+#define D_RFUNADJ_HFC4310 D_RFUNADJ_PREFIX HFC4310_COMPONENT_BASE
+#define D_RFUNADJ_HFC125 D_RFUNADJ_PREFIX HFC125_COMPONENT_BASE
+#define D_RFUNADJ_HFC134a D_RFUNADJ_PREFIX HFC134a_COMPONENT_BASE
+#define D_RFUNADJ_HFC143a D_RFUNADJ_PREFIX HFC143a_COMPONENT_BASE
+#define D_RFUNADJ_HFC227ea D_RFUNADJ_PREFIX HFC227ea_COMPONENT_BASE
+#define D_RFUNADJ_HFC245fa D_RFUNADJ_PREFIX HFC245fa_COMPONENT_BASE
+#define D_RFUNADJ_SF6 D_RFUNADJ_PREFIX SF6_COMPONENT_BASE
+#define D_RFUNADJ_CFC11 D_RFUNADJ_PREFIX CFC11_COMPONENT_BASE
+#define D_RFUNADJ_CFC12 D_RFUNADJ_PREFIX CFC12_COMPONENT_BASE
+#define D_RFUNADJ_CFC113 D_RFUNADJ_PREFIX CFC113_COMPONENT_BASE
+#define D_RFUNADJ_CFC114 D_RFUNADJ_PREFIX CFC114_COMPONENT_BASE
+#define D_RFUNADJ_CFC115 D_RFUNADJ_PREFIX CFC115_COMPONENT_BASE
+#define D_RFUNADJ_CCl4 D_RFUNADJ_PREFIX CCl4_COMPONENT_BASE
+#define D_RFUNADJ_CH3CCl3 D_RFUNADJ_PREFIX CH3CCl3_COMPONENT_BASE
+#define D_RFUNADJ_HCFC22 D_RFUNADJ_PREFIX HCFC22_COMPONENT_BASE
+#define D_RFUNADJ_HCFC141b D_RFUNADJ_PREFIX HCFC141b_COMPONENT_BASE
+#define D_RFUNADJ_HCFC142b D_RFUNADJ_PREFIX HCFC142b_COMPONENT_BASE
+#define D_RFUNADJ_halon1211 D_RFUNADJ_PREFIX halon1211_COMPONENT_BASE
+#define D_RFUNADJ_halon1301 D_RFUNADJ_PREFIX halon1301_COMPONENT_BASE
+#define D_RFUNADJ_halon2402 D_RFUNADJ_PREFIX halon2402_COMPONENT_BASE
+#define D_RFUNADJ_CH3Cl D_RFUNADJ_PREFIX CH3Cl_COMPONENT_BASE
+#define D_RFUNADJ_CH3Br D_RFUNADJ_PREFIX CH3Br_COMPONENT_BASE
 #define N_HALO_FORCINGS 26
 
 // halocarbon emissions

inst/include/core.hpp

@@ -36,7 +36,7 @@ class IModelComponent;
  */
 class Core : public IVisitable {
 public:
-  Core(Logger::LogLevel loglvl = Logger::DEBUG, bool echotoscreen = true,
+    Core(Logger::LogLevel loglvl = Logger::DEBUG, bool echotoscreen = true,
        bool echotofile = true);
   ~Core();
 

inst/include/forcing_component.hpp

@@ -134,9 +134,9 @@ class ForcingComponent : public IModelComponent {
   Logger logger; //! Logger
 
   static const char
-      *adjusted_halo_forcings[]; //! Capability strings for halocarbon forcings
+      *unadjusted_halo_forcings[]; //! Capability strings for unadjusted halocarbon forcings
   static const char
-      *halo_forcing_names[]; //! Internal names of halocarbon forcings
+      *halo_forcing_names[]; //! Names of adjusted (relative) halocarbon forcings
   static std::map<std::string, std::string> forcing_name_map;
 };