Documentation updates.

DESCRIPTION

@@ -23,7 +23,7 @@ URL: https://github.com/lanl/NEONiso,
     https://lanl.github.io/NEONiso/
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Imports:
     dplyr,
     zoo,

R/calibrate_ambient_carbon_Bowling2003.R

@@ -1,4 +1,4 @@
-#' calibrate_ambient_carbon_Bowling2003
+#' Calibrate ambient carbon isotope data using gain-and-offset method
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
 #'

R/calibrate_ambient_carbon_linreg.R

@@ -1,4 +1,4 @@
-#' calibrate_ambient_carbon_linreg
+#' Calibrate ambient carbon isotope data using linear regression
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
 #'

R/calibrate_carbon.R

@@ -1,4 +1,4 @@
-#' calibrate_carbon
+#' Calibrate NEON carbon isotope data using validation data sets.
 #'
 #' `r lifecycle::badge("experimental")`
 #' This function drives a workflow that reads in NEON carbon isotope data

R/calibrate_water.R

@@ -1,4 +1,4 @@
-#' calibrate_water
+#' Calibrate NEON water isotope ratios using validation data sets.
 #'
 #' `r lifecycle::badge("experimental")`
 #' This function uses NEON validation data to apply drift corrections to

R/filtering_functions.R

@@ -1,9 +1,10 @@
 # filtering_functions.R
-# a file with a few optinos for filtering output data.
+# a file with a few option for filtering output data.
 #---------------------------------
-#' filter_median_Brock86
+#' Apply a median absolute deviation filter
 #'
-#' Median absolute deviation filter of Brock 1986.
+#' Median absolute deviation filter of Brock 1986, with user specified
+#' width and magnitude thresholds.
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
 #'

R/quality_control.R

@@ -1,7 +1,10 @@
 # quality control - functions to validate the output data file structure
 
-#' validate_analyte
-#'
+#' Standardize analyte names
+#' 
+#' Enforces standard capitalization and formatting of H2o and Co2 
+#' analyte names across calibration functions.
+#' 
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
 #' @param analyte Co2 or H2o?
 #'
@@ -10,7 +13,6 @@
 #'         are standardized across package functions.
 #'
 #'
-#'
 validate_analyte <- function(analyte) {
   # helper function to make sure the various output functions are consistent.
   # check to make sure first letter of analyte is capitalized,
@@ -25,7 +27,11 @@ validate_analyte <- function(analyte) {
 }
 
 
-#' validate_output_file
+#' Validate output file.
+#' 
+#' Function ensures that the output file has the correct
+#' groups in it, as a check to ensure proper file structure at the
+#' end of the calibration routines.
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
 #'

R/time_functions.R

@@ -1,8 +1,8 @@
 #--------------------------------------------------------------
-#' convert_POSIXct_to_NEONhdf5_time
+#' Convert a POSIXct object to the format used in NEON HDF5 files
 #'
 #' Converts a POSIXct object back to the character format used by NEON in their
-#' HDF eddy covariance files. Output format,  using strptime syntax,  is
+#' HDF eddy covariance files. Output format, using strptime syntax, is
 #' %Y-%m-%dT%H:%M:%OSZ.
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
@@ -45,7 +45,10 @@ convert_POSIXct_to_NEONhdf5_time <- function(intime) {
   return(outtime)
 }
 
-#' convert_NEONhdf5_to_POSIXct_time
+#' Convert NEON HDF5 file time to POSIXct
+#' 
+#' Converts the date time string in NEON HDF5 files to a POSIXct object
+#' for use in R. 
 #'
 #' @author Rich Fiorella \email{rfiorella@@lanl.gov}
 #'