In MalditoBarbudo/MedfateValidation: Medfate model validation

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In this vignette the sites/plots data structure needed for the automated calibration/validation of the medfate model is explained.

Data files format

Files must be in txt format, with headers, without rownames, separated by tabs ("\t") and with point (".") as decimal character. Also, names of the files must start with the site/plot code.

Needed files

Each site/plot data can be comprised of 9 files, some of them being optional:

• treeData
• shrubData (optional)
• seedData (optional)
• miscData
• meteoData
• soilData
• terrainData (optional)
• customParams (optional)
• measuredData

In the following sections each file will be described in detail using FOO as site code

treeData

Name: FOO_treeData.txt
Location: Sites_data/FOO/

This data file must have 6 columns and the same number of rows as tree species present in the site/plot:

Species | N | DBH | Height | Z50 | Z95 --------|---|-----|--------|-----|------ 54 | 168 | 37.55 | 800 | 750 | 3000 68 | 384 | 14.60 | 660 | 750 | 3000

Variables:

: Species A numeric code as found in the SpParams data from the medfate package : N Species density [trees/ha] : DBH Mean diameter at breast height for the species [cm] : Height Mean height for the species [cm] : Z50 Depth in mm enclosing the 50% of the roots : Z95 Depth in mm enclosing the 95% of the roots

shrubData

Name: FOO_shrubData.txt
Location: Sites_data/FOO/

This file is optional. If not supplied the shrub slot of the forest object will be emtpy.

File must have 4 columns and the same number of rows as shrub species present in the site/plot:

Species | Cover | Height | Z --------|-------|--------|---- 64 | 3.75 | 30 | 2000 78 | 30.00 | 100 | 1000

Variables:

: Species A numeric code as found in the SpParams data from the medfate package : Cover Percent cover of the species [%] : Height Mean height for the species [cm] : Z Depth in mm of the root system for the species

seedData

Name: FOO_seedData.txt
Location: Sites_data/FOO/

This file is optional. If not supplied the seedbank slot of the forest object will be empty.

File must have 2 columns and the same number of rows as species (tree + shrub) present in the site/plot:

Species | Abundance --------|---------- 54 | 100 65 | 100 68 | 100 78 | 100

Variables:

: Species A numeric code as found in the SpParams data from the medfate package : Abundance Abundance class

miscData

Name: FOO_miscData.txt
Location: Sites_data/FOO/

This file contains the single value elements of the forest object and must have 6 columns and one single row:

ID | patchsize | herbCover | herbHeight | Validation | Definitive ---|-----------|-----------|------------|------------|------------ FOO | 10000 | 10 | 20 | global | No

Variables:

: ID An identifier of the forest stand (a string) : patchsize The area of the forest stand in square meters : herbCover Percent cover of the herb layer : herbHeight Mean height in cm of the herb layer : Validation Validation to perform with this site, can be one of the following: "global", "global_transp" and "temperature" : Definitive Is this site in the definitive list of sites for Validation? 'Yes' or 'No'.

meteoData

Name: FOO_meteoData.txt
Location: Sites_data/FOO/

This file contains the metereological data series, with as many rows as days which must be modelled. It must have the following columns:

Variables:

: Date Day date in the ISO format YYYY-MM-DD : DOY Day of year (Julian day) : Precipitation Precipitation (in mm) : MeanTemperature Mean temperature (in degrees Celsius) : MinTemperature Minimum temperature (in degrees Celsius) : MaxTemperature Maximum temperature (in degrees Celsius) : MeanRelativeHumidity Mean relative humidity (in percent) : MinRelativeHumidity Minimum relative humidity (in percent) : MaxRelativeHumidity Maximum relative humidity (in percent) : Radiation Solar radiation (in MJ/m2/day) : WindSpeed Wind speed (in m/s). If not available, this column can be left with NA values : PET Potential evapotranspiration (in mm)

soilData

Name: FOO_soilData.txt
Location: Sites_data/FOO/

This file must have 8 columns and as many rows as soil layers present in the site/plot:

widths | clay | sand | macro | rfc | Gsoil | Ksoil | W | FC -------|------|------|-------|-----|-------|-------|---|----- 300 | 25 | 25 | 0.1 | 30 | 0.5 | 0.05 | 1 | NA 700 | 25 | 25 | 0.1 | 60 | 0.5 | 0.05 | 1 | NA

Variables:

: widths Width of soil layers in mm : clay Clay content percent for each soil layer : sand Sand content percent for each soil layer : macro Macroporosity for each layer : rcf Rock fragment content for each layer : Gsoil Gamma parameter for infiltration (same value for all layers) : Ksoil Kappa parameter for infiltration (same value for all layers) : W Initial water content of each soil layer in proportion (0-1) : FC Field capacity value in case of change from internal calculation

terrainData

Name: FOO_terrainData.txt
Location: Sites_data/FOO/

This file is optional if, and only if, complex mode will be not used. In any other situation is mandatory.

File must have 4 columns and one sigle row:

latitude | elevation | aspect | slope ---------|-----------|--------|------- 41.82592 | 100 | 0 | 0

Variables:

: latitude Site/plot latitude in degrees (decimal format) : elevation Site/plot elevation in meters : aspect Site/plot aspect in degrees from North : slope Site/plot slope in degrees

customParams

Name: FOO_customParams.txt
Location: Sites_data/FOO/

This file is optional if no custom/optimized/measured parameters are provided for the site.

It can contain any number of columns, and these must have the same names as in the SpParamsMED dataset from medfate package or the above and canopy slots of the swbInput object from the medfate package (see medfate::forest2swbInput help function). Also it must have two columns, SpIndex and Spcode. The first indicates the numeric code of the species as it appears in SpParamsMED dataset and the second indicates the species code as used internally in medfate (i.e. "T1_54"). As an example:

SpIndex | Spcode | xylem_kmax | Vmax298 --------|--------|------------|--------- 54 | T1_54 | 0.4082 | 121.4565 68 | T2_68 | 0.1089 | 160.9927

measuredData

Name: FOO_measuredData.txt
Location: Sites_data/FOO/

This file must have the same number of rows as the meteoData file, corresponding to the measured dates. After that the content depends on the kind of validation the file is for. For global and global_transp validations, it must have the measured values for SWC (SWC for the first layer, SWC_2 for the second layer, and so on...) and the values for transpiration (Eplanttot for total transpiration, and E_Tx_xx for the different cohorts, being "Tx_xx" or "Sx_xx" the internal sp code used in medfate). Also, there is an optional column "SWC_err" indicating the error value for SWC content measure. For example:

Date | SWC | SWC_err | SWC_2 | SWC_3 | Eplanttot | E_T1_54 | E_T2_64 -----|-----|---------|-------|-------|-----------|---------|--------- ... | ... | ... | ... | ... | ... | ... | ...

MalditoBarbudo/MedfateValidation documentation built on May 7, 2019, 1:22 p.m.