R/workshop_test_functions.R

In roliveros-ramos/kali: Tools for habitat and niche modeling

# create color.themes environment
# addColorTheme() # names for the default color themes
# addDomain()
# setDefaultColorTheme()
# setDefaultDomain()


# Functions  --------------------------------------------------------------

# createGridAxes -> plots.R

# createTimeAxis -> plots.R

# #createCoordinatesAxis -> plots.R

# mapDetails -> plots.R

# .image.mapnl -> plots.R

# .checkLongitude -> plots.R

# image.map -> plots.R

# .plotSea -> plots.R

# .getDomain -> plots.R

# plot.map -> plots.R

# plot.domain -> plots.R

# map.axes2 -> plots.R

# .sub -> plots.R

# .rotate -> plots.R

# .rotate2 -> plots.R

# rotate -> plots.R

# .coord2text -> plots.R

# coord2text -> plots.R

# .axis.map -> plots.R

# rename -> remainder.R
  
# table2grid -> plots.R
  
# countMap -> plots.R

# table2array -> plots.R

# rotateMap -> plots.R

# .toPA -> remainder.R

# toPA -> remainder.R

# toPAm -> remainder.R

# map2data -> remainder.R

# .array2vector -> remainder.R

# map2 -> plots.R

# extractValidData -> remainder.R

# ncdf2data -> remainder.R

# .makeNameNcdfVar -> remainder.R

# extractData -> remainder.R

### extractEnvData = extractData -> remainder.R

# fill.map -> plots.R

# convexHull.map -> plots.R

# convexHull -> plots.R

# regridMap -> plots.R

# table2ncdf -> remainder.R

# trainingDatabase -> remainder.R

# writePredictionData -> remainder.R

# setDataBase -> remainder.R

# setFactors -> remainder.R

# makePredictions -> remainder.R

# fitModels -> remainder.R

# getPredictionMap -> remainder.R

# .getDistance -> remainder.R

# .getDistance.old -> remainder.R

# getDistance -> remainder.R

# getSignedDistance -> remainder.R

# read.Herve -> remainder.R

# DateStamp -> remainder.R

# getIsoline -> plots.R

# AUC -> niches_model.R

# kappa -> niches_model.R

# TSS -> niches_model.R

# PredictivePerformance -> niches_model.R

# plotROC -> niches_model.R

# plotThreshold -> niches_model.R

# calculateThresholds -> niches_model.R

# plotMAPt -> plots.R

# cleanBIOMOD -> niches_model.R

# is.inside -> remainder.R

# geq -> remainder.R

# leq -> remainder.R

# .insider -> remainder.R

# clearAbsences -> remainder.R

# cleanZeros -> remainder.R

# .getmfrow -> niches_model.R

# getmfrow -> niches_model.R

# table.summary -> niches_model.R

# balancePA -> niches_model.R

# splitDataSet -> niches_model.R

# .gam.fmla -> niches_model.R

# gam.fmla -> niches_model.R

# .fmla2txt -> niches_model.R

# .getObjectName -> niches_model.R

# fakeGAM -> niches_model.R

# fakeGAM2 -> niches_model.R

# fitGAMs -> niches_model.R

# getPredictions -> niches_model.R

# print.niche.models.formulas -> niches_model.R

# print.niche.models -> niches_model.R

# setPredictionFiles -> remainder.R

# .getModelVars2 -> niches_model.R

# .getModelVars -> niches_model.R

# predict.niche.models -> niches_model.R

# window.prediction.niche.models -> niches_model.R

# getModel -> niches_model.R

# getFormula -> niches_model.R   / coment: how to reference to data inside the object

# .getBestModel -> niches_model.R

# getBestModel -> niches_model.R

# getThreshold -> niches_model.R

# getMap -> niches_model.R

# getMap.prediction.niche.models -> niches_model.R

# .getPngFileName -> remainder.R

# plot.prediction.niche.models -> niches_model.R

# saveAnimation -> remainder.R

# saveAnimation.prediction.niche.models -> niches_model.R

# saveAnimation.default -> remainder.R

# climatology -> niches_model.R

# anova.niche.models -> niches_model.R

# printMaps -> plots.R

# plot.niche.models -> niches_model.R

# .plot.niche.models -> niches_model.R

# getCoordinates -> niches_model.R

# map2coord -> niches_model.R

# .getIndex -> niches_model.R

# fillSquare -> niches_model.R

# fillMap -> niches_model.R

# fillMap.matrix -> niches_model.R

# fillMap.data.frame -> niches_model.R

# fillMap.array -> niches_model.R

# fillMap.prediction.niche.models -> niches_model.R

# .interpolateMap -> niches_model.R

# interpolateMap -> niches_model.R

# addLHT -> remainder.R

# normalize -> remainder.R

# .inArea -> remainder.R

# .ponderate -> remainder.R

# ponderate -> remainder.R

# .na.sum -> remainder.R

# .getDensity -> remainder.R

# getDensity -> remainder.R

# getProfiles -> remainder.R

# .sevennum -> remainder.R

# getRleIndex -> remainder.R

# getValuesinRange -> remainder.R

# getYearMin -> remainder.R

# getYearMax -> remainder.R

# getSeasonalMap -> remainder.R

# year2month -> remainder.R

# .removeSector3 -> remainder.R

# .removeSector2 -> remainder.R

# removeSector -> remainder.R

# makeTransparent -> remainder.R

# barplot2 -> plots.R

# .removeVars -> remainder.R

# createPredictionFiles -> remainder.R

# createAuxPredictionFiles -> remainder.R

# plotDistributionMap -> niches_model.R