continue updating documentation

R/calibrate_ambient_carbon_Bowling2003.R

@@ -19,7 +19,7 @@
 #' @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
-#'              first calibration, using the first calibration? (default true)
+#'              first calibration, using the firs t calibration? (default true)
 #' @param r2_thres Minimum r2 value for calibration to be considered "good" and
 #'             applied to ambient data.
 #' @param gap_fill_parameters Should function attempt to 'gap-fill' across a

R/quality_control.R

@@ -100,7 +100,10 @@ validate_output_file <- function(inname, outname, site, analyte) {
 #--------------------------------------------------------------------
 # Diagnostic plots:::
 
-#' carbon_regression_plots
+#' Make plots of carbon calibration data for debugging
+#' 
+#' Makes plots of carbon calibration data regressions, primarily for
+#' debugging and validation purposes.
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
 #'

R/reference_data_extraction.R

@@ -1,4 +1,8 @@
-#' extract_carbon_calibration_data.R
+#' Extract only the data corresponding to validation/calibration time periods.
+#' 
+#' Extracts data matching a value of "co2Low," "co2Med," or "co2High" which
+#' correspond to the validation gases of known CO2, d13C that are fed to the 
+#' analyzer daily.
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
 #'
@@ -40,7 +44,11 @@ extract_carbon_cal_data <- function(data_list,
   return(data)
 }
 
-#' extract_water_calibration_data
+#' Extract only the data corresponding to validation/calibration time periods.
+#' 
+#' Extracts data matching a value of "h2oLow," "h2oMed," or "h2oHigh" which
+#' correspond to the validation gases of known d18O, d2H that are fed to the 
+#' analyzer daily.
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
 #'

R/reference_data_regression.R

@@ -1,4 +1,4 @@
-#' loocv
+#' Leave-one-out cross validation
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
 #'
@@ -12,7 +12,7 @@ loocv <- function(mod) {
   return(base::mean((stats::residuals(mod) / (1 - h)) ^ 2))
 }
 
-#' estimate_calibration_error
+#' Produce estimates of the calibration error.
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
 #'
@@ -38,7 +38,7 @@ estimate_calibration_error <- function(formula, data) {
 
 }
 
-#' fit_carbon_regression
+#' Estimate slope/intercept of carbon isotope calibration regression
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
 #'
@@ -419,7 +419,7 @@ fit_carbon_regression <- function(ref_data, method, calibration_half_width,
 
 }
 
-#' fit_water_regression
+#' Estimate slope/intercept of water isotope calibration regression
 #'
 #' @param ref_data Reference data.frame from which to estimate
 #'        calibration parameters.

R/reference_data_selection.R

@@ -1,7 +1,7 @@
 # process_calibration_data
 # functions to help select and filter validation data.
 
-#' select_daily_reference_data
+#' Select validation data corresponding to a particular day
 #'
 #' @param standard_df Input reference data.frame.
 #' @param analyte Are we calibrating CO2 and H2O?

R/restructure_data.R

@@ -1,5 +1,6 @@
-# restructure_data
-#' ingest_data
+# restructure_data script:
+#==============================
+#' Ingest and stack variables needed in calibration.
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
 #'
@@ -305,9 +306,10 @@ ingest_data <- function(inname,
 }
 
 #-----------------------------------------
-# restructure_variables
+# Restructure stacked data.frames to essential variables.
 #'
-#' Wrapper function around restructure_carbon_variables
+#' Restructures data.frames imported by ingest_data to shorten variable names
+#' and  Wrapper function around restructure_carbon_variables
 #' and restructure_water_variables.
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
@@ -347,7 +349,7 @@ restructure_variables <- function(dataframe,
 }
 
 #-----------------------------------------
-#' restructure_carbon_variables
+#' Restructure ingested variables for the carbon isotope system.
 #'
 #' @param varname Which variable are we applying this function to? There's
 #'                a list of ~10 common ones to write to the hdf5 file.
@@ -455,7 +457,7 @@ restructure_carbon_variables <- function(dataframe,
 }
 
 #-----------------------------------------
-#' restructure_water_variables
+#' Restructure ingested variables for the water isotope system.
 #'
 #' @param varname Which variable are we applying this function to? There's
 #'                a list of ~10 common ones to write to the hdf5 file.