Man pages for akeyel/behlpr
Functions to run my biodiversity analysis

check.loadingsQuick check to make sure I understand PC loadings
check.plausibilityCheck plausibility of model
check.sdm.qualityCheck SDM quality
check.thresholdsCheck Thresholds
check.var.namesCheck variable names for spatialdemography compliance
classify.plotsClassify Plots
compute.fragCreate fragmentation data set for use
convert.sp.dataConvert my.data to a format more easily used by the code
convert.sp.data.oldConvert my.data to a format more easily used by the code
do.basic.sdmBasic SDM approach
do.descriptivesDo descriptives
do.sdmA main function to run the Species Distribution Model
do.sdm.prefitSDM Evaluate the fit of an externally defined relationship
do.spatial.demographyMain function for generating the spatial demography outputs
drop.rare.spDrop rare species
evaluate.spatialdemographyEvaluate results of spatialdemography model runs
evaluate.spatialdemography.v2Evaluate results of spatialdemography model runs using list...
extract.actualExtract actual results
extract.cell.valuesExtract the value of a single cell from the SpeciesData.csv
extrapolation.testExtrapolation test
fix.plotidFix plot ID
frag.analysisFunction to process fragmentation data
frag.pcaReduce number of variables for highly-correlated multiscale...
frag.pca.oldExamine fragmentation data and consider variable reduction
get.indexGet Index
get.occ.plotsGet number of plots occupied by each species
get.scale.lstSet up scale.cells.lst for the biodiveristy exploratories
get.srGet species richness
get.survivalRead in survival data
get.thresholdsGet thresholds
get.thresholds.oldGet thresholds
hb.splitSplit aggregated trait file into separate files
make.fragRead in fragmentation data
merge.dataMerge data
metacom.analysisUse metacom package to assess the biotic filter for...
my.junkJunk - alternative approach that I may come back to
output.results.to.tableOutput Results to Table
plant.data.comparisonCompare plant data between exploratories and Eva's data
predictor.descriptive.analysisPredictor descriptive analysis
prepare.spfilePrepare species file
prepare.sp.locationsCreate species locations file
prepare.sp.locations.oldCreate species locations file
prep.dataprepare data for validation
prossesing.notesNotes on insectscales processing
read.8plot.dataRead in Data from Eva, Helge, & Ute
read.climateRead in (yearly) climate data
read.ludataRead in land use data
read.sp.dataRead in be_data file
read.traitsRead traits
reformat.sb.plant.dataReformat steffen's plant data
ReimagineFunction to fix problems with Imagine function in metacom...
sdm.visualize.mainSDM Visualize Main
set.up.biotic.predictorsmain function for biotic predictors
setup.env.lyrsHelper function to set data up for biomod
setup.locsSet up species locations
setup.predictorsMain function for reading in x variables
spdem.extractExtract data for a species distribution model from...
spdem.prepprepare data set for spatialdemography model
species.descriptive.analysisdescriptive analysis for species
subset.by.traitsSubset by traits
summarize.validationCreate a summary from multiple simulations
test.biomod2Test biomod
try.biomodTest biomod2 with Biodiversity Exploratories data
unfinished.functionI switched to processing in ArcGIS, but there are already...
validate.sdmValidate SDM
visualize.sdmCreate a visual of the SDM predictions
why.not.include.biotic.interactionsBiotic interactions note
year.subsetYear subset
akeyel/behlpr documentation built on May 12, 2019, 4:41 a.m.