Merge pull request #69 from EarthyScience/v134

V134

Author: bgctw

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.3.4
+Date: 2025-07-30 07:50:37 UTC
+SHA: 060a53dcc0b87a3b860f15860fd28dcb37dff29a

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: REddyProc
 Type: Package
-Version: 1.3.3
+Version: 1.3.4
 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="REddyProc-help@bgc-jena.mpg.de" )
               ,person( "Thomas", "Wutzler", role=c("aut","cre"), email="twutz@bgc-jena.mpg.de" )
@@ -31,7 +31,7 @@ Description: Standard and extensible Eddy-Covariance data post-processing
   based and day-time based approaches
   (Lasslop et al. (2010) <doi:10.1111/j.1365-2486.2009.02041.x>).
 URL: https://www.bgc-jena.mpg.de/bgi/index.php/Services/REddyProcWeb, 
-  https://github.com/bgctw/REddyProc
+  https://github.com/EarthyScience/REddyProc
 License: GPL (>= 2)
 Encoding: UTF-8
 LazyData: true
@@ -67,4 +67,4 @@ Collate:
     'logitnorm.R'
     'variableNames.R'
     'zzzDebugCode.R'
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1

NEWS.md

@@ -1,3 +1,12 @@
+# REddyProc 1.3.4
+- Handles edge-case in daytime-partitioning where all temperature 
+  sensitivities are estimated the same numerical value
+- Updated documentation 
+  - references to new github home: EarthySciences
+  - identify package in foreign package links
+  - document plotting diurnal cycle (sPlotDiurnalCycleM)
+- Fixed unit of y-label in uStarThreshold plots
+
 # REddyProc 1.3.3
 - Fixed bug in plotting daily sums, where default scale (gC / day) was of by
   a factor nRecInDays.

R/FileHandlingFormats.R

@@ -55,9 +55,9 @@ fLoadEuroFlux16 <- function(
 #' @param file_path scalar string: the path to the csv file
 #' @param additional_columns character vector of columns to
 #'   read in addition of standard columns of \code{\link{read_from_fluxnet15}}.
-#'   Can be a character vector or a object return by \code{\link{cols}}
+#'   Can be a character vector or a object return by \code{\link[readr]{cols}}
 #' @param colname_NEE name (scalar string) of column that reports NEE observations
-#' @param ... further arguments to \code{\link{read_csv}}
+#' @param ... further arguments to \code{\link[readr]{read_csv}}
 #'
 #' @examples
 #'   ds_fn15 <- Example_DETha98 %>%
@@ -266,7 +266,7 @@ extract_FN15 <- function(EProc = .self, is_export_nonfilled = TRUE, keep_other_c
 #' it to \code{\link{read_from_ameriflux22}}.
 #'
 #' @param file_path scalar string: the path to the csv file
-#' @param ... further arguments to \code{\link{read_csv}}
+#' @param ... further arguments to \code{\link[readr]{read_csv}}
 #'
 #' @seealso \code{\link{read_from_ameriflux22}} \code{\link{help_export}}
 #'

cran-comments.md

@@ -1,26 +1,14 @@
 ## Notes
 Dear CRAN maintainers,
 
-following your email that noted empty documentation for some of the function 
-arguments, we submit a new version of the REddyProc package.
+following your email that required updating of foreign package links
+in documentation, we submit a new version of the REddyProc package.
 
-In addition to fixing the empty comments, we include a new features:
-- exporting the results in an additional format requested by a users
-- an experimental implementation of the gap-filling procedure by Vekuri et. al 2023
+In addition to fixing the links, some plotting and documetation was improved,
+and some edge-cases are dealt with in processing.
+Updated the URLs to the new github-organization home.
 
 ## Test environments
-* local Linux-Mint, R 4.3.2
+* local Linux-Mint, R 4.3.3
 * Github actions, current Ubuntu
-* (win_builder was not reachable by curl from devtools::check_win_devel())
-* r_hub: all default platforms
-
-## R CMD check results
-No warnings, nor errors.
-
-1 Note:
-"checking for detritus in the temp directory ... NOTE
-  Found the following files/directories:
-    ‘REddyProcExamples’"
-REddyProcExamples is there on purpose: It is created on a first call to
-getExamplePath(exampleId) and then reused by several tests.
-
+* r_hub2: linux, mac, windows

inst/WORDLIST

@@ -1,45 +1,52 @@
+1001L
+16cm
+6cm
+A1
 AMM
 AVP
 Ameriflux
 Aubinet
 BGC
 Baldocchi
+Barr13
 Bayley
 BerkeleyJulianDateToPOSIXct
 Berkley
 Biogeochemical
 Biogeosciences
 CARBODATA
 CMD
+CO2
 CPT
 ChangePointDetection
 DEGebExample
-DETha
+DETha98
 DJF
 DateTime
 DateTimes
 Dez
 DoY
+E0
+EarthyScience
 EddyData
 Esat
-Evapotranspiration
 ExtRad
 FC
 FLUXNET
-FP
-FW
+FW1
+FW2
 Falge
 FillAll
 FluxVar
 Fluxnet
-Fw
+Fluxnet15
+Fw2Binned
 GPP
 Gapfilling
 Gebesee
 GeoFunctions
-JA
+H20
 JJA
-Jena
 JulianDate
 Knauer
 LRC
@@ -68,6 +75,8 @@ Papale
 PotRad
 Provding
 QFFluxVar
+R4
+R5
 README
 REco
 REddyProcNCDF
@@ -81,45 +90,48 @@ Rg
 Rmd
 SVP
 Seasonfactor
-Sigmoid
+T0
 TRangeDay
 TRef
 TW
 Tair
 Tharandt
 TimeDate
 TminOftheDay
-ToAmerifluxVariableNameMapping
 Tsoil
+U05
+U95
 USTAR
 UStar
 Ust
 Ustar
 UstarScens
+UstarScens’
 VMF
 VPD
+VPD0
 VPDfromDew
 Vapour
-VariableNameMapping
-Vekuri
+Vekuri23
 VisRad
 YYYY
 YYYYMMDDHHMM
 YYYYMMddhhmm
 Zieba
 aggUncertainty
 aggregationMode
-al
 antje
+base10
+beta0
 bg
 bgc
-bgctw
 bigleaf
 bugfix
 calendaryear
 changepoint
 circ
 colour
+coloured
 computeCost
 computeGPPGradient
 computeLRCGradient
@@ -132,7 +144,6 @@ ctrlUstarEst
 cz
 czechglobe
 daymin
-de
 degC
 degK
 dewpoint
@@ -142,10 +153,8 @@ downweighs
 dplyr
 eSat
 eop
-et
 eu
 europe
-evapotranspiration
 fCalcAVPfromVMFandPress
 fCalcETfromLE
 fCalcExtRadiation
@@ -158,20 +167,21 @@ fConvertCtoK
 fConvertGlobalToVisible
 fConvertKtoC
 fConvertTimeToPosix
-fConvertVisibleWm
+fConvertVisibleWm2toPhotons
 fKeepColumnAttributes
-fLoadEuroFlux
+fLoadEuroFlux16
 fLoadFluxNCIntoDataframe
-fLoadFluxnet
+fLoadFluxnet15
 fSplitDateTime
 fWriteDataframeToFile
-fWriteFrench
+fWriteFrench23
 filterLongRuns
 filterLongRunsInVector
 fitLRC
 fixVPD
 fluxdata
 fluxnet
+fluxnet2015
 fmeth
 fnum
 formular
@@ -184,10 +194,10 @@ gC
 gapfilled
 gapfilling
 geo
-getAmerifluxToBGC
-getBGC
+getAmerifluxToBGC05VariableNameMapping
+getBGC05ToAmerifluxVariableNameMapping
 getExamplePath
-getFilledExampleDETha
+getFilledExampleDETha98Data
 getOptimizedParameterPositions
 getParameterInitials
 getParameterNames
@@ -204,7 +214,6 @@ https
 iOpt
 igut
 invlogit
-irradiance
 isFilterMeteoQualityFlag
 isParameterInBounds
 isSplitDatetime
@@ -215,6 +224,7 @@ jena
 kPa
 ksickel
 logitnorm
+m2
 maximise
 mbar
 md
@@ -227,7 +237,6 @@ mmiglia
 mmol
 modelled
 moffat
-mol
 mreichstein
 mumol
 nAggSeason
@@ -259,7 +268,6 @@ ppfd
 pre
 predictGPP
 predictLRC
-preprocessed
 pscore
 pvWave
 qc
@@ -272,6 +280,7 @@ renameVariablesInDataframe
 replaceMissingSdNEEParms
 rlang
 rstudio
+s41559
 sApplyUStarScen
 sCalcPotRadiation
 sDATA
@@ -305,6 +314,7 @@ sMRFluxPartitionUStarScens
 sPlotDailySums
 sPlotDailySumsY
 sPlotDiurnalCycle
+sPlotDiurnalCycleM
 sPlotFingerprint
 sPlotFingerprintY
 sPlotHHFluxes
@@ -318,25 +328,22 @@ sTKFluxPartition
 sTKFluxPartitionUStarScens
 sTemp
 sUSTAR
-sd
 sdBeta
 sdE
 sdNEE
 seasonFactor
 seasonYear
-sigmoid
 sigut
 sitename
 solartime
 stdDev
 strptime
-subclasses
 tempdir
 testthat
+theta0
 thetaPrior
 tidyverse
 tmp
-toPhotons
 twutz
 uStar
 uStarAggr
@@ -349,7 +356,7 @@ uStarSeasonEst
 uStarTh
 uStarThreshold
 umol
-umolCO
+umolCO2
 upscaling
 usControlUstarEst
 usControlUstarSubsetting
@@ -358,7 +365,8 @@ usCreateSeasonFactorMonthWithinYear
 usCreateSeasonFactorYday
 usCreateSeasonFactorYdayYear
 usEstUstarThreshold
-usEstUstarThresholdSingleFw
+usEstUstarThresholdSingleFw1Binned
+usEstUstarThresholdSingleFw2Binned
 usGetAnnualSeasonUStarMap
 usGetAnnualSeasonUStarMappingFromDistributionResult
 usGetSeasonalSeasonUStarMap
@@ -374,11 +382,11 @@ varnames
 webservice
 whichValueGreaterEqualC
 withUstar
-writeable
 www
 xlab
 yday
 yearDay
 yearday
 ylab
 Šigut
+μ