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add package to foreign Rd links
and regenerate documentation by inlinedocs and roxygen
1 parent ff6cb77 commit c61b3d1

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-634
lines changed

DESCRIPTION

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'logitnorm.R'
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'variableNames.R'
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'zzzDebugCode.R'
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RoxygenNote: 7.3.0
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RoxygenNote: 7.3.1

R/FileHandlingFormats.R

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

man/fKeepColumnAttributes.Rd

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\name{fKeepColumnAttributes}
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\alias{fKeepColumnAttributes}
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\title{fKeepColumnAttributes}
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\description{Copy column attributes after processing a data.frame}
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\usage{fKeepColumnAttributes(x, FUN, ...)}
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\arguments{
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\item{x}{data.frame to be processed}
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\item{FUN}{\code{function(x::data.frame, ...) -> data.frame} to be applied}
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\item{\dots}{additional arguments to FUN}
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}
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\details{The columns of the resulting data.frame that match a column name in x
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will get the same attributes as in x.}
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\value{result of \code{function(x, ...)} with column attributes preserved}
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\author{Department for Biogeochemical Integration at MPI-BGC, Jena, Germany <REddyProc-help@bgc-jena.mpg.de> [cph], Thomas Wutzler <twutz@bgc-jena.mpg.de> [aut, cre], Markus Reichstein <mreichstein@bgc-jena.mpg.de> [aut], Antje Maria Moffat <antje.moffat@bgc.mpg.de> [aut, trl], Olaf Menzer <omenzer@bgc-jena.mpg.de> [ctb], Mirco Migliavacca <mmiglia@bgc-jena.mpg.de> [aut], Kerstin Sickel <ksickel@bgc-jena.mpg.de> [ctb, trl], Ladislav <U+0160>igut <sigut.l@czechglobe.cz> [ctb]}
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\name{fKeepColumnAttributes}
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\alias{fKeepColumnAttributes}
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\title{fKeepColumnAttributes}
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\description{Copy column attributes after processing a data.frame}
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\usage{fKeepColumnAttributes(x, FUN, ...)}
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\arguments{
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\item{x}{data.frame to be processed}
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\item{FUN}{\code{function(x::data.frame, ...) -> data.frame} to be applied}
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\item{\dots}{additional arguments to FUN}
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}
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\details{The columns of the resulting data.frame that match a column name in x
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will get the same attributes as in x.}
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\value{result of \code{function(x, ...)} with column attributes preserved}
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\author{Department for Biogeochemical Integration at MPI-BGC, Jena, Germany <REddyProc-help@bgc-jena.mpg.de> [cph], Thomas Wutzler <twutz@bgc-jena.mpg.de> [aut, cre], Markus Reichstein <mreichstein@bgc-jena.mpg.de> [aut], Antje Maria Moffat <antje.moffat@bgc.mpg.de> [aut, trl], Olaf Menzer <omenzer@bgc-jena.mpg.de> [ctb], Mirco Migliavacca <mmiglia@bgc-jena.mpg.de> [aut], Kerstin Sickel <ksickel@bgc-jena.mpg.de> [ctb, trl], Ladislav <U+0160>igut <sigut.l@czechglobe.cz> [ctb]}
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man/fLoadAmeriflux22.Rd

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man/fLoadFluxnet15.Rd

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man/fWriteFrench23.Rd

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\name{fWriteFrench23}
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\alias{fWriteFrench23}
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\title{fWriteFrench23}
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\description{Write data frame to ASCII comma-separated text file}
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\usage{fWriteFrench23(data, filename, isSplitDatetime = FALSE,
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digits = 5)}
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\arguments{
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\item{data}{Data frame to be exported, with unit attributes attached to columns}
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\item{filename}{(string) name (including path) of the output file}
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\item{isSplitDatetime}{set to TRUE to create columns Year, DoY and Hour}
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\item{digits}{(integer) number of digits, i.e. precision, for numeric values}
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}
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\details{Writes data.frame as comma-separated file after two header rows.
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The first header row contains the column names, and the second units.
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Spaces in column names are replaced by underscore and \% is replaced by
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the word percent.}
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\author{TW
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Department for Biogeochemical Integration at MPI-BGC, Jena, Germany <REddyProc-help@bgc-jena.mpg.de> [cph], Thomas Wutzler <twutz@bgc-jena.mpg.de> [aut, cre], Markus Reichstein <mreichstein@bgc-jena.mpg.de> [aut], Antje Maria Moffat <antje.moffat@bgc.mpg.de> [aut, trl], Olaf Menzer <omenzer@bgc-jena.mpg.de> [ctb], Mirco Migliavacca <mmiglia@bgc-jena.mpg.de> [aut], Kerstin Sickel <ksickel@bgc-jena.mpg.de> [ctb, trl], Ladislav <U+0160>igut <sigut.l@czechglobe.cz> [ctb]}
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\seealso{\code{\link{fWriteDataframeToFile}}}
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\name{fWriteFrench23}
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\alias{fWriteFrench23}
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\title{fWriteFrench23}
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\description{Write data frame to ASCII comma-separated text file}
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\usage{fWriteFrench23(data, filename, isSplitDatetime = FALSE,
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digits = 5)}
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\arguments{
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\item{data}{Data frame to be exported, with unit attributes attached to columns}
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\item{filename}{(string) name (including path) of the output file}
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\item{isSplitDatetime}{set to TRUE to create columns Year, DoY and Hour}
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\item{digits}{(integer) number of digits, i.e. precision, for numeric values}
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}
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\details{Writes data.frame as comma-separated file after two header rows.
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The first header row contains the column names, and the second units.
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Spaces in column names are replaced by underscore and \% is replaced by
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the word percent.}
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\author{TW
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Department for Biogeochemical Integration at MPI-BGC, Jena, Germany <REddyProc-help@bgc-jena.mpg.de> [cph], Thomas Wutzler <twutz@bgc-jena.mpg.de> [aut, cre], Markus Reichstein <mreichstein@bgc-jena.mpg.de> [aut], Antje Maria Moffat <antje.moffat@bgc.mpg.de> [aut, trl], Olaf Menzer <omenzer@bgc-jena.mpg.de> [ctb], Mirco Migliavacca <mmiglia@bgc-jena.mpg.de> [aut], Kerstin Sickel <ksickel@bgc-jena.mpg.de> [ctb, trl], Ladislav <U+0160>igut <sigut.l@czechglobe.cz> [ctb]}
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\seealso{\code{\link{fWriteDataframeToFile}}}
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man/filter_entire_days.Rd

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\name{filter_entire_days}
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\alias{filter_entire_days}
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\title{filter entire days}
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\description{Omit records before the start of the first full day and the end of the last full day}
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\usage{filter_entire_days(df, col_time = "DateTime")}
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\arguments{
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\item{df}{data.frame with column col_time of equidistant}
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\item{col_time}{Name of the column with the equidistant timesteps}
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}
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\details{Column attributes such as 'units' are kept.}
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\author{Department for Biogeochemical Integration at MPI-BGC, Jena, Germany <REddyProc-help@bgc-jena.mpg.de> [cph], Thomas Wutzler <twutz@bgc-jena.mpg.de> [aut, cre], Markus Reichstein <mreichstein@bgc-jena.mpg.de> [aut], Antje Maria Moffat <antje.moffat@bgc.mpg.de> [aut, trl], Olaf Menzer <omenzer@bgc-jena.mpg.de> [ctb], Mirco Migliavacca <mmiglia@bgc-jena.mpg.de> [aut], Kerstin Sickel <ksickel@bgc-jena.mpg.de> [ctb, trl], Ladislav <U+0160>igut <sigut.l@czechglobe.cz> [ctb]}
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\seealso{\code{\link{help_DateTimes}}, \code{\link{get_day_boundaries}}
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\code{\link{fKeepColumnAttributes}}}
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\name{filter_entire_days}
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\alias{filter_entire_days}
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\title{filter entire days}
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\description{Omit records before the start of the first full day and the end of the last full day}
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\usage{filter_entire_days(df, col_time = "DateTime")}
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\arguments{
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\item{df}{data.frame with column col_time of equidistant}
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\item{col_time}{Name of the column with the equidistant timesteps}
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}
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\details{Column attributes such as 'units' are kept.}
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\author{Department for Biogeochemical Integration at MPI-BGC, Jena, Germany <REddyProc-help@bgc-jena.mpg.de> [cph], Thomas Wutzler <twutz@bgc-jena.mpg.de> [aut, cre], Markus Reichstein <mreichstein@bgc-jena.mpg.de> [aut], Antje Maria Moffat <antje.moffat@bgc.mpg.de> [aut, trl], Olaf Menzer <omenzer@bgc-jena.mpg.de> [ctb], Mirco Migliavacca <mmiglia@bgc-jena.mpg.de> [aut], Kerstin Sickel <ksickel@bgc-jena.mpg.de> [ctb, trl], Ladislav <U+0160>igut <sigut.l@czechglobe.cz> [ctb]}
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\seealso{\code{\link{help_DateTimes}}, \code{\link{get_day_boundaries}}
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\code{\link{fKeepColumnAttributes}}}
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man/help_DateTimes.Rd

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\name{help_DateTimes}
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\alias{help_DateTimes}
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\title{help DateTimes}
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\description{Overview of functions helping with Timestamps and Dates}
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\usage{help_DateTimes()}
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\details{Functions helping with preparing and subsetting timestamps:
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\itemize{
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\item Convert different time formats to POSIX:
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\code{\link{fConvertTimeToPosix}}
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\item Convert JulianDate format used in Berkeley release to POSIXct:
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\code{\link{BerkeleyJulianDateToPOSIXct}}
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\item Return the first timestamp at (end_of_first_record_in_day) and the
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last at midnight:
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\code{\link{get_day_boundaries}}
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\item Omit records before the start of the first full day and the end of
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the last full day:
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\code{\link{filter_entire_days}}
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\item Subset data.frame to given years respecting the end-of-period
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convention: \code{\link{filter_years_eop}}
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}
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Back to \link{REddyProc-package}.}
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\author{TW
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Department for Biogeochemical Integration at MPI-BGC, Jena, Germany <REddyProc-help@bgc-jena.mpg.de> [cph], Thomas Wutzler <twutz@bgc-jena.mpg.de> [aut, cre], Markus Reichstein <mreichstein@bgc-jena.mpg.de> [aut], Antje Maria Moffat <antje.moffat@bgc.mpg.de> [aut, trl], Olaf Menzer <omenzer@bgc-jena.mpg.de> [ctb], Mirco Migliavacca <mmiglia@bgc-jena.mpg.de> [aut], Kerstin Sickel <ksickel@bgc-jena.mpg.de> [ctb, trl], Ladislav <U+0160>igut <sigut.l@czechglobe.cz> [ctb]}
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\name{help_DateTimes}
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\alias{help_DateTimes}
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\title{help DateTimes}
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\description{Overview of functions helping with Timestamps and Dates}
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\usage{help_DateTimes()}
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\details{Functions helping with preparing and subsetting timestamps:
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\itemize{
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\item Convert different time formats to POSIX:
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\code{\link{fConvertTimeToPosix}}
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\item Convert JulianDate format used in Berkeley release to POSIXct:
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\code{\link{BerkeleyJulianDateToPOSIXct}}
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\item Return the first timestamp at (end_of_first_record_in_day) and the
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last at midnight:
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\code{\link{get_day_boundaries}}
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\item Omit records before the start of the first full day and the end of
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the last full day:
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\code{\link{filter_entire_days}}
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\item Subset data.frame to given years respecting the end-of-period
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convention: \code{\link{filter_years_eop}}
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}
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Back to \link{REddyProc-package}.}
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\author{TW
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Department for Biogeochemical Integration at MPI-BGC, Jena, Germany <REddyProc-help@bgc-jena.mpg.de> [cph], Thomas Wutzler <twutz@bgc-jena.mpg.de> [aut, cre], Markus Reichstein <mreichstein@bgc-jena.mpg.de> [aut], Antje Maria Moffat <antje.moffat@bgc.mpg.de> [aut, trl], Olaf Menzer <omenzer@bgc-jena.mpg.de> [ctb], Mirco Migliavacca <mmiglia@bgc-jena.mpg.de> [aut], Kerstin Sickel <ksickel@bgc-jena.mpg.de> [ctb, trl], Ladislav <U+0160>igut <sigut.l@czechglobe.cz> [ctb]}
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man/help_export.Rd

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\name{help_export}
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\alias{help_export}
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\title{help export}
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\description{Overview of functions helping with exporting Data and Results}
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\usage{help_export()}
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\details{Functions helping with exporting data
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\itemize{
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\item Export Input data from REddyProc class:
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\code{\link{sEddyProc_sExportData}}
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\item Export Computed results from REddyProc class:
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\code{\link{sEddyProc_sExportResults}}
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\item Write data frame to ASCII tab-separated text file:
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\code{\link{fWriteDataframeToFile}}
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\item Write data frame to ASCII comma-separated text file with units in header row:
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\code{\link{fWriteFrench23}}
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}
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Writing a file that can be supplied to the REddyProc webservice at
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MPI-BGC Jena can be done by exporting data from REddyProc class \code{EProc}.
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\preformatted{
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df <- EProc$sExportData()
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fWriteDataframeToFile(df, "myfilename.txt", isSplitDatetime = TRUE)
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}
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For preparing minimal working examples also consider
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\itemize{
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\item Omit records before the start of the first full day and the end of
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the last full day:
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\code{df <- \link{filter_entire_days}(df)}
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\item Subset data.frame to one or two years:
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\code{df <- \link{filter_years_eop}(df, c(1998))}
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}
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There are several functions that import from file of different formats.
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\itemize{
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\item Load text file with one header and one unit row into data frame:
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\code{\link{fLoadTXTIntoDataframe}}
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\item Reads sequence of annual files in the format of Europe-fluxdata 2016:
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\code{\link{fLoadEuroFlux16}}
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\item Read basic variables from Ameriflux standard (as of 2022) files:
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\code{\link{fLoadAmeriflux22}}
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\item Read NetCDF files -> moved to separate package REddyProcNCDF
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(https://github.com/bgctw/REddyProcNCDF)
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}
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Back to \link{REddyProc-package}.}
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\author{TW
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Department for Biogeochemical Integration at MPI-BGC, Jena, Germany <REddyProc-help@bgc-jena.mpg.de> [cph], Thomas Wutzler <twutz@bgc-jena.mpg.de> [aut, cre], Markus Reichstein <mreichstein@bgc-jena.mpg.de> [aut], Antje Maria Moffat <antje.moffat@bgc.mpg.de> [aut, trl], Olaf Menzer <omenzer@bgc-jena.mpg.de> [ctb], Mirco Migliavacca <mmiglia@bgc-jena.mpg.de> [aut], Kerstin Sickel <ksickel@bgc-jena.mpg.de> [ctb, trl], Ladislav <U+0160>igut <sigut.l@czechglobe.cz> [ctb]}
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\name{help_export}
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\alias{help_export}
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\title{help export}
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\description{Overview of functions helping with exporting Data and Results}
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\usage{help_export()}
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\details{Functions helping with exporting data
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\itemize{
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\item Export Input data from REddyProc class:
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\code{\link{sEddyProc_sExportData}}
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\item Export Computed results from REddyProc class:
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\code{\link{sEddyProc_sExportResults}}
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\item Write data frame to ASCII tab-separated text file:
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\code{\link{fWriteDataframeToFile}}
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\item Write data frame to ASCII comma-separated text file with units in header row:
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\code{\link{fWriteFrench23}}
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}
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Writing a file that can be supplied to the REddyProc webservice at
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MPI-BGC Jena can be done by exporting data from REddyProc class \code{EProc}.
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\preformatted{
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df <- EProc$sExportData()
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fWriteDataframeToFile(df, "myfilename.txt", isSplitDatetime = TRUE)
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}
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For preparing minimal working examples also consider
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\itemize{
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\item Omit records before the start of the first full day and the end of
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the last full day:
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\code{df <- \link{filter_entire_days}(df)}
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\item Subset data.frame to one or two years:
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\code{df <- \link{filter_years_eop}(df, c(1998))}
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}
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There are several functions that import from file of different formats.
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\itemize{
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\item Load text file with one header and one unit row into data frame:
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\code{\link{fLoadTXTIntoDataframe}}
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\item Reads sequence of annual files in the format of Europe-fluxdata 2016:
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\code{\link{fLoadEuroFlux16}}
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\item Read basic variables from Ameriflux standard (as of 2022) files:
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\code{\link{fLoadAmeriflux22}}
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\item Read NetCDF files -> moved to separate package REddyProcNCDF
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(https://github.com/EarthyScience/REddyProcNCDF)
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}
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Back to \link{REddyProc-package}.}
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\author{TW
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Department for Biogeochemical Integration at MPI-BGC, Jena, Germany <REddyProc-help@bgc-jena.mpg.de> [cph], Thomas Wutzler <twutz@bgc-jena.mpg.de> [aut, cre], Markus Reichstein <mreichstein@bgc-jena.mpg.de> [aut], Antje Maria Moffat <antje.moffat@bgc.mpg.de> [aut, trl], Olaf Menzer <omenzer@bgc-jena.mpg.de> [ctb], Mirco Migliavacca <mmiglia@bgc-jena.mpg.de> [aut], Kerstin Sickel <ksickel@bgc-jena.mpg.de> [ctb, trl], Ladislav <U+0160>igut <sigut.l@czechglobe.cz> [ctb]}
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