document arguments, fix typos and bump version

Author: bgctw

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: REddyProc
 Type: Package
-Version: 1.3.2
+Version: 1.3.3
 Title: Post Processing of (Half-)Hourly Eddy-Covariance Measurements
 Authors@R: c( person( "Department for Biogeochemical Integration at MPI-BGC, Jena, Germany", role=c("cph"), email="[email protected]" )
               ,person( "Thomas", "Wutzler", role=c("aut","cre"), email="[email protected]" )
@@ -39,9 +39,9 @@ VignetteBuilder: knitr
 LinkingTo: Rcpp
 Depends: R (>= 3.0.0), methods
 Imports: Rcpp, dplyr, purrr, rlang, readr, tibble, magrittr, solartime, 
-    bigleaf (>= 0.7)
+    bigleaf (>= 0.7), mlegp
 Suggests: testthat, minpack.lm, segmented, knitr, rmarkdown, lognorm, ggplot2, 
-    tidyr, markdown, mlegp
+    tidyr, markdown
 Collate: 
     'CheckVal.R'
     'DataFunctions.R'
@@ -67,4 +67,4 @@ Collate:
     'logitnorm.R'
     'variableNames.R'
     'zzzDebugCode.R'
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.0

NEWS.md

@@ -1,12 +1,13 @@
-# REddyProc 1.3.2_DEV
+# REddyProc 1.3.3
 - Fixed bug in plotting daily sums, where default scale (gC / day) was of by
   a factor nRecInDays.
 - Plotting daily sums: Uncertainty computation conservatively assumes fully
   correlated errors rather than fully independent errors
 - Provide argument isSplitDatetime to fWriteDataframeToFile to write files
   consistent with the REddyProc web tool.
-- Implement Vekuri23 lookup-table variant of gapfilling  
+- Implement experimental version of Vekuri23 lookup-table variant of gapfilling  
 - test breakpoint in Barr13 by more powerful pscore.test (Muggeo 2016)  
+- include mlegp dependency again - its on CRAN again
 
 # REddyProc 1.3.2
 - Avoid strong dependency on mlegp (https://github.com/bgctw/REddyProc/issues/58).

R/DataFunctions.R

@@ -15,7 +15,7 @@ help_DateTimes <- function(
   ##   \code{\link{fConvertTimeToPosix}}
   ## \item Convert JulianDate format used in Berkeley release to POSIXct:
   ##   \code{\link{BerkeleyJulianDateToPOSIXct}}
-  ## \item Return the first timestap at (end_of_first_record_in_day) and the
+  ## \item Return the first timestamp at (end_of_first_record_in_day) and the
   ## last at midnight:
   ##  \code{\link{get_day_boundaries}}
   ## \item Omit records before the start of the first full day and the end of
@@ -292,8 +292,8 @@ fCheckHHTimeSeries <- function(
   ## Check half-hourly time series data
   Time = Time.V.p              ##<< Time vector in POSIX format
   , DTS = DTS.n                ##<< Number of daily time steps (24 or 48)
-  , CallFunction = if (!missing(CallFunction.s)) CallFunction.s else ''    ##<<
-  ## Name of function called from
+  , CallFunction = if (!missing(CallFunction.s)) CallFunction.s else '' ##<< Name
+  ## of function called from
   , Time.V.p          ##<< deprecated
   , DTS.n             ##<< deprecated
   , CallFunction.s    ##<< deprecated
@@ -751,7 +751,7 @@ filterLongRuns <- function(
 
 #' @export
 get_day_boundaries <- function(
-    ### Return the first timestap at (end_of_first_record_in_day) and the last at midnight
+    ### Return the first timestamp at (end_of_first_record_in_day) and the last at midnight
     dt ##<< vector of equidistant POSIXt timestamps with several records a day, usually 48
     ) {
   ##seealso<< \code{\link{help_DateTimes}}, \code{\link{filter_entire_days}}
@@ -769,7 +769,7 @@ get_day_boundaries <- function(
 #' @export
 filter_entire_days <- function(
   ### Omit records before the start of the first full day and the end of the last full day
-  df                       ##<< DataFrame with column col_time of equidistant
+  df                       ##<< data.frame with column col_time of equidistant
   , col_time = "DateTime"  ##<< Name of the column with the equidistant timesteps
 ) {
   ##seealso<< \code{\link{help_DateTimes}}, \code{\link{get_day_boundaries}}
@@ -785,7 +785,7 @@ filter_entire_days <- function(
 #' @export
 filter_years_eop <- function(
   ### Subset data.frame to given years respecting the end-of-period convention
-  df                       ##<< DataFrame with column col_time of equidistant
+  df                       ##<< data.frame with column col_time of equidistant
   , years                  ##<< integer vector of years of the form \code{c(1998, 1998)}
   , col_time = "DateTime"  ##<< Name of the column with the equidistant timesteps
 ) {

R/EddyGapfilling.R

@@ -443,10 +443,10 @@ sEddyProc$methods(sFillMDC = sEddyProc_sFillMDC)
 sEddyProc_sMDSGapFill <- function(
   ### MDS gap filling algorithm adapted after the PV-Wave code and paper by Markus Reichstein.
   Var = Var.s                 ##<< Variable to be filled
-  , QFVar = if (!missing(QFVar.s)) QFVar.s else 'none'       ##<<
-  ## Quality flag of variable to be filled
-  , QFValue = if (!missing(QFValue.n)) QFValue.n else NA_real_   ##<<
-  ## Value of quality flag for _good_ (original) data, other data is set to missing
+  , QFVar = if (!missing(QFVar.s)) QFVar.s else 'none'       ##<< Quality flag
+  ##  of variable to be filled
+  , QFValue = if (!missing(QFValue.n)) QFValue.n else NA_real_   ##<< Value of
+  ##  quality flag for _good_ (original) data, other data is set to missing
   , V1 = if (!missing(V1.s)) V1.s else 'Rg'            ##<< Condition variable 1
   ## (default: Global radiation 'Rg' in  W m-2)
   , T1 = if (!missing(T1.n)) T1.n else 50              ##<< Tolerance interval 1

R/EddyPartitioning.R

@@ -386,8 +386,8 @@ sEddyProc$methods(sMRFluxPartition = sEddyProc_sMRFluxPartition)
 #' @export
 sEddyProc_sCalcPotRadiation <- function(
   ### compute potential radiation from position and time
-  useSolartime = TRUE	##<<
-  ## by default corrects hour (given in local winter time)
+  useSolartime = TRUE	##<< by default
+  ## corrects hour (given in local winter time)
   ## for latitude to solar time(where noon is exactly at 12:00).
   ## Set this to FALSE to directly use local winter time
   , useSolartime.b 	##<< by default corrects hour (given in local winter time)

R/EddyPlotting.R

@@ -137,10 +137,10 @@ sEddyProc$methods(.sxClosePlot = .sEddyProc_sxClosePlot)
 sEddyProc_sPlotFingerprintY <- function(
   ### Plot fingerprint for a single year scaled to all data.
   Var = Var.s               ##<< Variable to plot
-  , QFVar = 'none'     ##<<
-  ## Quality flag of variable to be filled
-  , QFValue = if (!missing(QFValue.n)) QFValue.n else NA_real_ ##<<
-  ## Value of quality flag for data to plot
+  , QFVar = 'none'          ##<< Quality
+  ##  flag of variable to be filled
+  , QFValue = if (!missing(QFValue.n)) QFValue.n else NA_real_ ##<< Value
+  ## of quality flag for data to plot
   , Year = Year.i             ##<< Year to plot
   , onlyLegend = if (!missing(Legend.b)) Legend.b else  F         ##<< Plot
   ## only legend
@@ -266,8 +266,8 @@ sEddyProc_sPlotFingerprint <- function(
   , QFVar = 'none'     ##<< Quality flag of variable to be filled
   , QFValue = if (!missing(QFValue.n)) QFValue.n else NA_real_ ##<< Value of
   ## quality flag for data to plot
-  , Format = if (!missing(Format.s)) Format.s else 'pdf'     ##<<
-  ## Graphics file format (e.g. 'pdf', 'png')
+  , Format = if (!missing(Format.s)) Format.s else 'pdf'     ##<< Graphics
+  ## file format (e.g. 'pdf', 'png')
   , Dir = if (!missing(Dir.s)) Dir.s else 'plots'      ##<< Directory
   ## for plotting
   , ...				##<< further arguments to \code{\link{sEddyProc_sPlotFingerprintY}}
@@ -490,10 +490,10 @@ sEddyProc$methods(sPlotDiurnalCycle = sEddyProc_sPlotDiurnalCycle)
 sEddyProc_sPlotHHFluxesY <- function(
   ### Plot half-hourly fluxes for a single year scaled to all data.
   Var = Var.s               ##<< Variable to plot
-  , QFVar = if (!missing(QFVar.s)) QFVar.s else 'none'     ##<<
-  ## Quality flag of variable to be filled
-  , QFValue = if (!missing(QFValue.n)) QFValue.n else NA_real_ ##<<
-  ## Value of quality flag for data to plot
+  , QFVar = if (!missing(QFVar.s)) QFVar.s else 'none'     ##<< Quality
+  ##  flag of variable to be filled
+  , QFValue = if (!missing(QFValue.n)) QFValue.n else NA_real_ ##<< Value
+  ##  of quality flag for data to plot
   , Year = Year.i             ##<< Year to plot
   , data = cbind(sDATA, sTEMP)   ##<< data.frame with variables to plot
   , dts = sINFO$DTS              ##<< numeric integer
@@ -844,7 +844,7 @@ sEddyProc_sPlotNEEVersusUStarForSeason <- function(
   , HInchSingle = 6 * 0.394	##<< height of a subplot in inches, defaults to 6cm
   , ...						##<< other arguments to \code{.plotNEEVersusUStarTempClass},
   ## such as xlab and ylab axis label strings
-  , data = cbind(sDATA, sTEMP, sUSTAR_DETAILS$bins[,c("uStarBin","tempBin")]) ##<<
+  , data = cbind(sDATA, sTEMP, sUSTAR_DETAILS$bins[,c("uStarBin","tempBin")]) ##<< a
   ## data.frame with variables to plot
 ) {
   ##author<< TW

R/EddyUStarFilterDP.R

@@ -20,8 +20,8 @@ sEddyProc_sEstUstarThold <- function(
   ## omitting night time data
   , ...						          ##<< further arguments to
   ## \code{\link{usEstUstarThreshold}}
-  , seasonFactor = usCreateSeasonFactorMonth(sDATA$sDateTime) ##<<
-  ## factor of seasons to split
+  , seasonFactor = usCreateSeasonFactorMonth(sDATA$sDateTime) ##<< factor of
+  ## seasons to split
 ) {
   ##author<< TW
   if (length(seasonFactor) )
@@ -1274,8 +1274,8 @@ sEddyProc_sEstimateUstarScenarios <- function(
   , RgColName = "Rg"			    ##<< column name for solar radiation for
   ## omitting night time data
   , ...		##<< further arguments to \code{\link{sEddyProc_sEstUstarThreshold}}
-  , seasonFactor = usCreateSeasonFactorMonth(sDATA$sDateTime) ##<<
-  ## factor of seasons to split (data is resampled only within the seasons)
+  , seasonFactor = usCreateSeasonFactorMonth(sDATA$sDateTime) ##<< factor of
+  ## seasons to split (data is resampled only within the seasons)
   , nSample = 200L				      ##<< the number of repetitions in the bootstrap
   , probs = c(0.05, 0.5, 0.95)	##<< the quantiles of the bootstrap sample
   ## to return. Default is the 5%, median and 95% of the bootstrap
@@ -1436,7 +1436,8 @@ sEddyProc_sApplyUStarScen <- function(
   ## entry in \code{uStarSuffixes}.
   , warnOnOtherErrors = FALSE ##<< Set to only display a warning on errors in
   ## uStarScenarios other than uStarScenKeep instead of stopping.
-  , uStarSuffixes = .self$sGetUstarSuffixes()
+  , uStarSuffixes = .self$sGetUstarSuffixes() ##<< Vector of suffixed
+  ##<< describing the uStar scenarios
 ) {
   ##details<<
   ## When repeating computations, some of the

R/FileHandling.R

@@ -167,8 +167,8 @@ fWriteDataframeToFile <- function(
   Data.F                ##<< Data frame
   , FileName = FileName.s           ##<< File base name as a string
   , Dir = if (!missing(Dir.s)) Dir.s else ''          ##<< Directory as a string
-  , Digits = if (!missing(Digits.n)) Digits.n else 5			##<<
-  ## (integer) number of digits, i.e. precision, for numeric values
+  , Digits = if (!missing(Digits.n)) Digits.n else 5			##<< (integer) number
+  ## of digits, i.e. precision, for numeric values
   , isSplitDatetime = FALSE ##<< set to TRUE to create columns Year, DoY and Hour
   , FileName.s         ##<< deprecated
   , Dir.s              ##<< deprecated
@@ -211,8 +211,8 @@ attr(fWriteDataframeToFile, 'ex') <- function() {
 
 #' @export
 fSplitDateTime <- function(
-  ### Replace Column DateTime by columns Year, DoY, and Hour in a DataFrame
-  df ##<< DataFrame with column DateTime
+  ### Replace Column DateTime by columns Year, DoY, and Hour in a data.frame
+  df ##<< data.frame with column DateTime
 ) {
   ##seealso<< \code{\link{fWriteDataframeToFile}}
   ##details<<

R/FileHandlingFormats.R

@@ -325,7 +325,7 @@ fWriteFrench23 <- function(
   ##author<< TW
   ##seealso<< \code{\link{fWriteDataframeToFile}}
   ##details<<
-  ## Writes data.frame as comma-seperated file after two header rows.
+  ## Writes data.frame as comma-separated file after two header rows.
   ##
   ## The first header row contains the column names, and the second units.
   ##

R/GeoFunctions.R

@@ -244,10 +244,10 @@ fLloydTaylor <- function(
   , E0 = E_0.n            ##<< Temperature sensitivity ("activation energy")
   ## in Kelvin (degK)
   , TSoil = Tsoil.n       ##<< Soil temperature in Kelvin (degK)
-  , TRef = if (missing(T_ref.n)) 273.15 + 10 else T_ref.n ##<<
-  ## Reference temperature of 10 degC in Kelvin (degK)
-  , T0 = if (missing(T_0.n)) 227.13 else T_0.n        ##<<
-  ## Regression temperature as fitted by LloydTaylor (1994) in Kelvin (degK)
+  , TRef = if (missing(T_ref.n)) 273.15 + 10 else T_ref.n ##<< Reference
+  ## temperature of 10 degC in Kelvin (degK)
+  , T0 = if (missing(T_0.n)) 227.13 else T_0.n        ##<< Regression
+  ## temperature as fitted by LloydTaylor (1994) in Kelvin (degK)
   , R_ref.n    ##<< deprecated way to specify RRef
   , E_0.n      ##<< deprecated way to specify E0
   , Tsoil.n    ##<< deprecated way to specify Tsoil
@@ -411,8 +411,8 @@ fCalcExtRadiation <- function(
   ##description<<
   ## Calculate the extraterrestrial solar radiation with the
   ## eccentricity correction
-  DoY = DoY.V.n
-  , DoY.V.n           ##<< Data vector with day of year (DoY)
+  DoY = DoY.V.n       ##<< Data vector with day of year (DoY)
+  , DoY.V.n           ##<< deprecated, use DoY
   ##author<<
   ## AMM
 ) {
@@ -450,8 +450,8 @@ fCalcPotRadiation <- function(
   , LatDeg = Lat_deg.n          ##<< Latitude in (decimal) degrees
   , LongDeg = Long_deg.n         ##<< Longitude in (decimal) degrees
   , TimeZone = TimeZone_h.n       ##<< Time zone (in hours)
-  , useSolartime = TRUE	##<<
-  ## by default corrects hour (given in local winter time) for latitude to solar time
+  , useSolartime = TRUE	##<< by default corrects hour (given in local winter time)
+  ##  for latitude to solar time
   ## (where noon is exactly at 12:00). Set this to FALSE to directly use local winter time
   , DoY.V.n            ##<< deprecated
   , Hour.V.n           ##<< deprecated