wip - rename Bowling 2003 methods.

lanl · Dec 28, 2024 · 581d0e3 · 581d0e3
1 parent c98d7a8
commit 581d0e3
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -23,7 +23,7 @@ URL: https://github.com/lanl/NEONiso,
     https://lanl.github.io/NEONiso/
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports:
     dplyr,
     zoo,

diff --git a/NEONiso.Rproj b/NEONiso.Rproj
@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 66dd6b57-a079-4675-8584-64aae38613ba
 
 RestoreWorkspace: No
 SaveWorkspace: No

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,13 @@
-# NEONiso 0.7.0.9000
+# NEONiso 0.7.1
+
+* Substantial upgrades to package documentation.
+* The name "Bowling_2003" in methods and functions has been deprecated in
+favor of "gainoffset." This change was made primarily to improve clarity of
+what the methods actually do. Code that uses the old "Bowling_2003" nomenclature
+will continue to work until at least version 0.8.0, but will issue a deprecation
+warning.
+
+# NEONiso 0.7.0
 
 * calibrate_carbon_bymonth and calibrate_water_bymonth have been removed. Use
 calibrate_carbon and calibrate_water instead.

diff --git a/R/calibrate_ambient_carbon_Bowling2003.R → R/calibrate_ambient_carbon_gainoffset.R b/R/calibrate_ambient_carbon_Bowling2003.R → R/calibrate_ambient_carbon_gainoffset.R
@@ -1,3 +1,9 @@
+calibrate_ambient_carbon_Bowling2003 <- function(...) {
+  lifecycle::deprecate_soft("0.7.1","calibrate_ambient_carbon_Bowling2003()",
+                            "calibrate_ambient_carbon_gainoffset()")
+  calibrate_ambient_carbon_gainoffset(...)
+}
+
 #' Calibrate ambient carbon isotope data using gain-and-offset method
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
@@ -14,8 +20,7 @@
 #'              12C and 13C isotopologues.
 #' @param site Four-letter NEON code corresponding to site being processed.
 #' @param filter_data Apply median absolute deviation filter from Brock 86 to
-#'             remove impulse spikes? Inherited from
-#'             `calibrate_ambient_carbon_Bowling2003()`
+#'             remove impulse spikes?
 #' @param force_to_end In given month, calibrate ambient data later than last
 #'             calibration, using the last calibration? (default true)
 #' @param force_to_beginning In given month, calibrate ambient data before than
@@ -38,7 +43,7 @@
 #' @importFrom magrittr %>%
 #' @importFrom lubridate %within%
 #'
-calibrate_ambient_carbon_Bowling2003 <- function(amb_data_list,
+calibrate_ambient_carbon_gainoffset <- function(amb_data_list,
                                                  caldf,
                                                  site,
                                                  filter_data = TRUE,

diff --git a/R/calibrate_carbon.R b/R/calibrate_carbon.R
@@ -147,6 +147,11 @@ calibrate_carbon         <- function(inname,
       inname <- inname[!grepl("2019-07", inname)]
     }
   }
+
+  if (method == "Bowling_2003") {
+    lifecycle::deprecate_warn("0.7.1","calibrate_carbon(method = 'Bowling_2003')",
+                              "calibrate_carbon(method = 'gainoffset')")
+  }
 
   #-----------------------------------------------------------
   # Extract reference data from input HDF5 file.
@@ -194,18 +199,18 @@ calibrate_carbon         <- function(inname,
 
   ciso_subset <- c(ciso$ambient, ciso$reference)
 
-  if (method == "Bowling_2003") {
+  if (method == "gainoffset" | method == "Bowling_2003") {
 
     ciso_subset_cal <-
       lapply(names(ciso_subset),
              function(x) {
-               calibrate_ambient_carbon_Bowling2003(amb_data_list = ciso_subset[[x]],
-                                                    caldf = cal_df,
-                                                    site = site,
-                                                    filter_data = filter_ambient,
-                                                    force_to_end = force_cal_to_end,
-                                                    force_to_beginning = force_cal_to_beginning,
-                                                    r2_thres = r2_thres)
+               calibrate_ambient_carbon_gainoffset(amb_data_list = ciso_subset[[x]],
+                                                   caldf = cal_df,
+                                                   site = site,
+                                                   filter_data = filter_ambient,
+                                                   force_to_end = force_cal_to_end,
+                                                   force_to_beginning = force_cal_to_beginning,
+                                                   r2_thres = r2_thres)
              })
 
   } else if (method == "linreg") {

diff --git a/R/reference_data_regression.R b/R/reference_data_regression.R
@@ -59,7 +59,7 @@ estimate_calibration_error <- function(formula, data) {
 #'                 to define a peak.
 #'
 #' @return Returns a data.frame of calibration parameters. If
-#'        `method == "Bowling_2003"`, then data.frame includes
+#'        `method == "gainoffset"`, then data.frame includes
 #'        gain and offset parameters for 12CO2 and 13CO2, and r^2
 #'        values for each regression. If `method == "linreg"`,
 #'        then data.frame includes slope, intercept, and r^2 values
@@ -87,7 +87,7 @@ fit_carbon_regression <- function(ref_data, method, calibration_half_width,
                                           analyte = "co2",
                                           min_nobs = min_nobs)
 
-  if (method == "Bowling_2003") {
+  if (method == "gainoffset" | method == "Bowling_2003") {
 
     # calculate mole fraction (12CO2 / 13CO2) for ref gases and observed values
     ref_data$conc12CCO2_ref <- calculate_12CO2(ref_data$rtioMoleDryCo2Refe.mean,

diff --git a/man/calibrate_ambient_carbon_Bowling2003.Rd → man/calibrate_ambient_carbon_gainoffset.Rd b/man/calibrate_ambient_carbon_Bowling2003.Rd → man/calibrate_ambient_carbon_gainoffset.Rd
diff --git a/man/fit_carbon_regression.Rd b/man/fit_carbon_regression.Rd
diff --git a/tests/testthat/test-data_regression.R b/tests/testthat/test-data_regression.R
@@ -59,13 +59,13 @@ test_that("carbon calibration data frames correct even when no input data", {
 # work through ambient calibrations
 
 # test carbon - bowling ambient calibration
-temp <- calibrate_ambient_carbon_Bowling2003(co2test$ambient$`000_010_09m`,
-                                             caldf_b03,
-                                             site = "ONAQ")
-temp_gf <- calibrate_ambient_carbon_Bowling2003(co2test$ambient$`000_010_09m`,
-                                                caldf_b03,
-                                                site = "ONAQ",
-                                                gap_fill_parameters = TRUE)
+temp <- calibrate_ambient_carbon_gainoffset(co2test$ambient$`000_010_09m`,
+                                           caldf_b03,
+                                           site = "ONAQ")
+temp_gf <- calibrate_ambient_carbon_gainoffset(co2test$ambient$`000_010_09m`,
+                                               caldf_b03,
+                                               site = "ONAQ",
+                                               gap_fill_parameters = TRUE)
 
 test_that("calibrate_ambient_carbon_Bowling2003 returns a list",{
   skip_on_cran()

diff --git a/tests/testthat/test-high_level_functions.R b/tests/testthat/test-high_level_functions.R
@@ -20,16 +20,27 @@ test_that("calibrate_carbon returns no error", {
 
   skip_on_cran()
   # these tests could probably be made more useful!!
+  expect_warning(calibrate_carbon(fin, fout1, "ONAQ",
+                                  method = "Bowling_2003",
+                                  calibration_half_width = 0.5,
+                                  force_cal_to_beginning = TRUE,
+                                  force_cal_to_end = TRUE,
+                                  gap_fill_parameters = FALSE,
+                                  filter_ambient = TRUE,
+                                  r2_thres = 0.95,
+                                  correct_ref_data = TRUE,
+                                  write_to_file = TRUE))
+
   expect_no_error(calibrate_carbon(fin, fout1, "ONAQ",
-                                   method = "Bowling_2003",
-                                   calibration_half_width = 0.5,
-                                   force_cal_to_beginning = TRUE,
-                                   force_cal_to_end = TRUE,
-                                   gap_fill_parameters = FALSE,
-                                   filter_ambient = TRUE,
-                                   r2_thres = 0.95,
-                                   correct_ref_data = TRUE,
-                                   write_to_file = TRUE))
+                                  method = "gainoffset",
+                                  calibration_half_width = 0.5,
+                                  force_cal_to_beginning = TRUE,
+                                  force_cal_to_end = TRUE,
+                                  gap_fill_parameters = FALSE,
+                                  filter_ambient = TRUE,
+                                r2_thres = 0.95,
+                                  correct_ref_data = TRUE,
+                                  write_to_file = TRUE))
 
   expect_no_error(calibrate_carbon(fin, fout2, "ONAQ",
                                    method = "linreg",
@@ -44,7 +55,7 @@ test_that("calibrate_carbon returns no error", {
 
   # these tests could probably be made more useful!!
   expect_no_error(calibrate_carbon(fin, "/dev/null", "ONAQ",
-                                   method = "Bowling_2003",
+                                   method = "gainoffset",
                                    calibration_half_width = 0.5,
                                    force_cal_to_beginning = TRUE,
                                    force_cal_to_end = TRUE,

diff --git a/tests/testthat/test-output_values.R b/tests/testthat/test-output_values.R
@@ -24,13 +24,13 @@ ciso_subset <- co2test$ambient
 
 ciso_subset_cal <- lapply(names(ciso_subset),
                           function(x) {
-                            calibrate_ambient_carbon_Bowling2003(amb_data_list = ciso_subset[[x]],
-                                                                 caldf = caldf_b03,
-                                                                 site = "YELL",
-                                                                 filter_data = TRUE,
-                                                                 force_to_end = TRUE,
-                                                                 force_to_beginning = TRUE,
-                                                                 r2_thres = 0.9)
+                            calibrate_ambient_carbon_gainoffset(amb_data_list = ciso_subset[[x]],
+                                                                caldf = caldf_b03,
+                                                                site = "YELL",
+                                                                filter_data = TRUE,
+                                                                force_to_end = TRUE,
+                                                                force_to_beginning = TRUE,
+                                                                r2_thres = 0.9)
                           })
 
 names(ciso_subset_cal) <- names(ciso_subset)