data.main: Main function for data conversion.

In phenmod: Auxiliary Functions for Phenological Data Processing, Modelling and Result Handling

Main function for data conversion.

Description

This function extracts data from tsv-Files, creates combined timeseries out of them if needed and adds temperature data.

Usage

data.main(extraction.done=TRUE, out2File=FALSE, 
			grid.related.to.temperaturefiles, 
			valid.years=1952:2009,
			combine.time.series=TRUE, range=10000, 
			alt.range=50, temperature.scale.factor=1,
			dataPath=getwd(),temperature.filenames,
			temperature.matrix, pathForTmpFiles=getwd(),
			pathToSave=getwd(), plant="beech")

Arguments

extraction.done	If data extraction was already done, turn this value to TRUE and the extracted values will be loaded from ‘pathForTmpFiles’.
out2File	A boolean value determining wether the output will be stored in log-files.
grid.related.to.temperaturefiles	A grid containing spatial informations for the temperature files.
valid.years	The years that should be included in extraction process (may be needed if some data in datasets are insufficient).
combine.time.series	A boolean value determining wether the extracted timeseries should be combined or not.
range	The maximum distance between two stations that should be connected in the station station-net needed for the timeserie-combination.
alt.range	The maximum altitude difference between two stations that should be connected in the station-net needed for the timeserie-combination.
temperature.scale.factor	The down-scaling factor for the temperature data (needed if the data is scaled).
dataPath	The path where the tsv-tables are stored. These tsv-tables should have the following name: ‘<PLANT>_budburst.tsv’ for budburst-data or ‘<PLANT>_leafcolouring.tsv’ for leafcolouring-data, where <PLANT> stands for the name of the plant, for example ‘beech’.
temperature.filenames	The full name of temperature files. The filenames have to contain the year (YYYY) of the temperature observation. The files should be stored as RData-Files and have to contain a matrix called ‘edk.one.year’ with 366 columns (one per day) and the number of rows equal to the number of rows in ‘grid.related.to.Temperatures’. Should have the value NULL if a temperature matrix should be used instead.
temperature.matrix	An array containing temperature data. The year of the observation should given as rowname, the columns should equal the julian day of the observation and the third dimension of the array should equal the location given in ‘grid.related.to.Temperatures’

. The matrix will be used instead of temperature files if ‘temperature.filenames’ is NULL.

pathForTmpFiles	The path where the extracted data should be temporarily stored as RData-files.
pathToSave	The path where the resulting dataframe should be stored as RData-file with the name ‘<PLANT>-dataset.RData’ for non-combined data or ‘<PLANT>-dataset-cts.RData’ for combined data.
plant	The name of the plant which should be processed.

Details

This function is the main method for data extraction. It exctracts budburst and leafcolouring data from tsv-Files, creates combined timeseries out of them if needed and adds temperature data from RData files containing daily mean temperatures.

Value

Returns nothing, but saves the resulting dataset in ‘pathToSave’.

Author(s)

Daniel Doktor, Maximilian Lange

See Also

data.extract,data.combine,data.addTemperatures

Examples

  ## load temperature data
  data(temperatures)
  ## load grid with spatial informations for temperature files
  data(relatedGrid)
  
  ## extract dataset from datafiles in working directory
  ## Not run: dataset <- data.main(extraction.done=FALSE, out2File=FALSE, 
			grid.related.to.temperaturefiles=relatedGrid,
			combine.timeseries=TRUE, range=5000, alt.range=50, 
			temperature.scale.factor=0.1, dataPath=getwd(), 
			temperature.filenames=NULL,
			temperature.matrix=temperatures,
			pathForTmpFiles=getwd(), pathToSave=getwd(),
			plant="beech")
## End(Not run)

phenmod documentation built on April 14, 2022, 5:08 p.m.