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LandWeb_summary Manual |
v.0.0.1 |
Last updated: 2022-10-28 |
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citations/ecology-letters.csl |
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(ref:LandWeb-summary) LandWeb_summary
Eliot J B McIntire [email protected] [aut, cre], Alex M. Chubaty [email protected] [aut]
LandWeb simulation post-processing and summary creation.
Table @ref(tab:moduleInputs-LandWeb-summary) shows the full list of module inputs.
| objectName | objectClass | desc | sourceURL |
|---|---|---|---|
| ml | map | map list object from LandWeb_preamble | 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`.NANA | NA |
Provide a summary of user-visible parameters (Table @ref(tab:moduleParams-LandWeb-summary))
| 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 | outputPa.... | 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). |
| .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 | start(sim) | 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()`. |
- Large Patches Data (
.csv) - Large patches histograms (
.png)
- Leading Vegetation Cover Data (
.csv) - Leading Vegetation Cover histograms (
.png) - Leading Vegetation Cover boxplots (
.png)
Description of the module outputs (Table @ref(tab:moduleOutputs-LandWeb-summary)).
| objectName | objectClass | desc |
|---|---|---|
| ml | map | map list object |
Initially developed for use with the LandWeb model.