Add new variables that translate updates to base SORTIE parameter file
treelistDfn.RdtreelistDfn() adds additional initial tree diameter size classes and prefixes
to VariableNames
Arguments
- initname
Naming convention
character()used to describe diameter size classes- numDigits
Number of decimal places required to match the base parameter file
- diamMin
Minimum diameter size
- diamMax
Maximum diameter size
- diamInc
Size (in cm) of diameter bins
Details
VariableNames is a table that translates the names of parameters found within behaviours
(variables) defined by a user in the newvals object to the names of these parameters (variables) found in
the base SORTIE parameter file. This file is essential to finding the right variable within the right
behaviour to update with new values during a makeFiles() call.
For details on how to write a new VariableNames file, see the Preparing inputs for rsortie vignette,
linked below
There is a default VariableNames loaded with the rsortie package, but a user may wish to add additional
variable translations.
Examples
samplebasexml[1:30]
#> [1] "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>"
#> [2] "<paramFile fileCode=\"07050101\">"
#> [3] " <plot>"
#> [4] " <timesteps>10</timesteps>"
#> [5] " <rt_timestep>0</rt_timestep>"
#> [6] " <randomSeed>0</randomSeed>"
#> [7] " <yearsPerTimestep>5.0</yearsPerTimestep>"
#> [8] " <plot_lenX>300.0</plot_lenX>"
#> [9] " <plot_lenY>300.0</plot_lenY>"
#> [10] " <plot_latitude>41.92</plot_latitude>"
#> [11] " <plot_precip_mm_yr>0.0</plot_precip_mm_yr>"
#> [12] " <plot_seasonal_precipitation>0.0</plot_seasonal_precipitation>"
#> [13] " <plot_water_deficit>0.0</plot_water_deficit>"
#> [14] " <plot_temp_C>0.0</plot_temp_C>"
#> [15] " <plot_n_dep>0.0</plot_n_dep>"
#> [16] " <plot_title>Default parameter file-use for testing only</plot_title>"
#> [17] " </plot>"
#> [18] " <trees>"
#> [19] " <tr_speciesList>"
#> [20] " <tr_species speciesName=\"ACRU\"/>"
#> [21] " <tr_species speciesName=\"ACSA\"/>"
#> [22] " <tr_species speciesName=\"BEAL\"/>"
#> [23] " <tr_species speciesName=\"FAGR\"/>"
#> [24] " <tr_species speciesName=\"TSCA\"/>"
#> [25] " <tr_species speciesName=\"FRAM\"/>"
#> [26] " <tr_species speciesName=\"PIST\"/>"
#> [27] " <tr_species speciesName=\"PRSE\"/>"
#> [28] " <tr_species speciesName=\"QURU\"/>"
#> [29] " </tr_speciesList>"
#> [30] " <tr_sizeClasses>"
VariableNames[1:30,]
#> InputFileParameterName Type code.name
#> 1 Timesteps 1 timesteps
#> 2 Randomseed 1 randomSeed
#> 3 YearsPerTimestep 1 yearsPerTimestep
#> 4 rt_timestep 1 rt_timestep
#> 5 randomSeed 1 randomSeed
#> 6 yearsPerTimestep 1 yearsPerTimestep
#> 7 plot_lenX 1 plot_lenX
#> 8 plot_lenY 1 plot_lenY
#> 9 plot_latitude 1 plot_latitude
#> 10 plot_precip_mm_yr 1 plot_precip_mm_yr
#> 11 plot_seasonal_precipitation 1 plot_seasonal_precipitation
#> 12 plot_water_deficit 1 plot_water_deficit
#> 13 plot_temp_C 1 plot_temp_C
#> 14 plot_n_dep 1 plot_n_dep
#> 15 plot_title 1 sph
#> 16 !nci
#> 17 nciWhichShadingEffect 3 nciWhichShadingEffect
#> 18 nciWhichCrowdingEffect 3 nciWhichCrowdingEffect
#> 19 nciWhichNCITerm 3 nciWhichNCITerm
#> 20 nciWhichSizeEffect 3 nciWhichSizeEffect
#> 21 nciWhichDamageEffect 3 nciWhichDamageEffect
#> 22 nciWhichPrecipitationEffect 3 nciWhichPrecipitationEffect
#> 23 nciWhichTemperatureEffect 3 nciWhichTemperatureEffect
#> 24 nciWhichNitrogenEffect 3 nciWhichNitrogenEffect
#> 25 nciWhichInfectionEffect 3 nciWhichInfectionEffect
#> 26 NCI.MaxGrowth 4 gr_nmpgVal species
#> 27 Std.Dev.Norm.Log.Adj 4 gr_sdVal species
#> 28 NCI.Shading.Coeff.m 4 nscVal species
#> 29 NCI.Shading.Exp.n 4 nseVal species
#> 30 NCI.Size.Sensit 4 ncgVal species
#> group.name
#> 1
#> 2
#> 3
#> 4
#> 5
#> 6
#> 7
#> 8
#> 9
#> 10
#> 11
#> 12
#> 13
#> 14
#> 15 plot_title
#> 16
#> 17
#> 18
#> 19
#> 20
#> 21
#> 22
#> 23
#> 24
#> 25
#> 26 gr_nciMaxPotentialGrowth
#> 27 gr_standardDeviation
#> 28 nciShadingCoefficient
#> 29 nciShadingExponent
#> 30 nciCrowdingGamma