data.main {phenmod}

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)