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LandWeb Manual: v. 3.0.0

12 LandWeb_summary Module

This documentation is work in progress. Please report any discrepancies or omissions at https://github.com/PredictiveEcology/LandWeb_summary/issues.

12.0.0.1 Authors:

Eliot J B McIntire [aut, cre], Alex M. Chubaty [aut]

12.1 Module Overview

12.1.1 Module summary

LandWeb simulation post-processing and summary creation.

12.1.2 Module inputs and parameters

Table 12.1 shows the full list of module inputs.

Table 12.1: List of LandWeb_summary input objects and their description.
objectName objectClass desc sourceURL
ml map map list object from LandWeb_preamble NA
speciesLayers RasterStack initial percent cover raster layers used for simulation. NA
sppColorVect character A named vector of colors to use for plotting. The names must be in sim$sppEquiv[[P(sim)$sppEquivCol]], and should also contain a color for ‘Mixed’ NA
sppEquiv data.table table of species equivalencies. See LandR::sppEquivalencies_CA. NA

Provide a summary of user-visible parameters (Table 12.2)

Table 12.2: List of LandWeb_summary parameters and their description.
paramName paramClass default min max paramDesc
ageClasses character Young, I…. NA NA descriptions/labels for age classes (seral stages)
ageClassCutOffs integer 0, 40, 8…. NA NA defines the age boundaries between age classes
ageClassMaxAge integer 400 NA NA maximum possible age
reps integer 1, 2, 3,…. 1 NA number of replicates/runs per study area.
simOutputPath character /tmp/Rtm…. NA NA Directory specifying the location of the simulation outputs.
sppEquivCol character EN_gener…. NA NA The column in sim$sppEquiv data.table to use as a naming convention
summaryInterval integer 100 NA NA simulation time interval at which to take ‘snapshots’ used for summary analyses
summaryPeriod integer 700, 1000 NA NA lower and upper end of the range of simulation times used for summary analyses
timeSeriesTimes integer 601, 602…. NA NA timesteps to use to build timeseries rasters showing leading cover change over time
upload logical FALSE NA NA if TRUE, uses the googledrive package to upload figures.
uploadTo character NA NA NA if upload = TRUE, a Google Drive folder id corresponding to .studyAreaName.
vegLeadingProportion numeric 0.8 0 1 a number that defines whether a species is leading for a given pixel
version integer 3 2 3 LandWeb model version (2 for runs using vegetation parameter forcings, else 3).
.clInit { NA NA Quoted expression to be evaluated on each node in a parallel cluster when running map analyses. Useful to set options or create non-serializable objects on each node.
.makeTiles logical FALSE NA NA If TRUE, will generate leaflet tiles during postprocessing.
.plots character screen NA NA Used by Plots function, which can be optionally used here
.plotInitialTime numeric 0 NA NA Describes the simulation time at which the first plot event should occur.
.plotInterval numeric NA NA NA Describes the simulation time interval between plot events.
.saveInitialTime numeric NA NA NA Describes the simulation time at which the first save event should occur.
.saveInterval numeric NA NA NA This describes the simulation time interval between save events.
.studyAreaName character NA NA NA Human-readable name for the study area used - e.g., a hash of the study area obtained using reproducible::studyAreaName()
.useCache character .inputOb…. NA NA Names of events to be cached.
.useParallel logical TRUE NA NA Logical. If TRUE, and there is more than one calculation to do at any stage, it will create and use a parallel cluster via makeOptimalCluster().

12.1.3 Module outputs

12.1.3.1 Large Patches Data for study region

  • Large Patches Data (.csv)
  • Large patches histograms (.png)

12.1.3.2 Leading Vegetation Cover Data for study region

  • Leading Vegetation Cover Data (.csv)
  • Leading Vegetation Cover histograms (.png)
  • Leading Vegetation Cover boxplots (.png)

Description of the module outputs (Table 12.3).

Table 12.3: List of LandWeb_summary outputs and their description.
objectName objectClass desc
ml map map list object