inst/doc/RedList.R

In intSDM: Reproducible Integrated Species Distribution Models Across Norway using 'INLA'

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>", 
  eval = FALSE,
  fig.width=8, 
  fig.height=5,
  warning = FALSE,
  message = FALSE)

## ----load packages------------------------------------------------------------
# 
# library(intSDM)
# library(INLA)
# 

## ----initialize workflow------------------------------------------------------
# 
# proj <- '+proj=tmerc +lat_0=0 +lon_0=15 +k=0.9996 +datum=WGS84 +units=km +x_0=500 +y_0=0 +no_defs'
# #proj <- '+proj=utm +zone=32 +datum=WGS84 +units=km +no_defs +type=crs'
# 
# workflow <- startWorkflow(
#         Projection = proj,
#         Species = c("Fraxinus_excelsior", "Ulmus_glabra", "Arnica_montana"),
#         saveOptions = list(projectName =  'Vascular'), Save = FALSE
#         )
# 

## ----addArea------------------------------------------------------------------
# 
# Norway <- fm_transform(giscoR::gisco_get_countries(country = 'Norway', resolution = 60),
#                        proj)
# Norway <- st_cast(st_as_sf(Norway), 'POLYGON')
# Norway <- Norway[which.max(st_area(Norway)),]
# Norway <- rmapshaper::ms_simplify(Norway, keep = 0.8)
# Norway <- st_as_sf(fm_extensions(Norway, convex = c(10, 20))[[1]])
# 
# workflow$addArea(Object = Norway)
# workflow$plot()
# 

## ----addGBIF------------------------------------------------------------------
# 
# workflow$addGBIF(datasetName = 'CZ',
#                  datasetType = 'PO',
#                  coordinateUncertaintyInMeters = '0,100',
#                  limit = 10000,
#                  datasetKey = 'b124e1e0-4755-430f-9eab-894f25a9b59c')
# 
# workflow$addGBIF(datasetName = 'UiO',
#                  datasetType = 'PA',
#                  limit = 10000,
#                  coordinateUncertaintyInMeters = '0,100',
#                  generateAbsences = TRUE,
#                  datasetKey = 'e45c7d91-81c6-4455-86e3-2965a5739b1f')
# 
# workflow$addGBIF(datasetName = 'NTNU',
#                  datasetType = 'PA',
#                  limit = 10000,
#                  coordinateUncertaintyInMeters = '0,100',
#                  generateAbsences = TRUE,
#                  datasetKey = 'd29d79fd-2dc4-4ef5-89b8-cdf66994de0d')
# 
# workflow$plot(Species = TRUE)
# 

## ----addCovariates, eval = FALSE----------------------------------------------
# 
# workflow$addCovariates(worldClim = 'tavg', res = 2.5, Function = scale)
# 
# workflow$addCovariates(landCover = 'grassland', Function = scale)
# 
# workflow$plot(Covariates = TRUE)
# 

## ----metadata-----------------------------------------------------------------
# 
# workflow$obtainMeta()
# 

## ----INLA---------------------------------------------------------------------
# 
# workflow$addMesh(cutoff = 20 * 0.5,
#                  max.edge = c(60, 180) * 0.5,
#                  offset= c(30, 250))
# 
# workflow$plot(Mesh = TRUE)
# 

## ----Priors-------------------------------------------------------------------
# 
# workflow$specifySpatial(prior.range = c(200, 0.2),
#                         prior.sigma = c(1, 0.01), constr = TRUE)
# 

## ----Fixed priors-------------------------------------------------------------
# 
# workflow$specifyPriors(effectNames = 'Intercept',
#                        Mean = 0, Precision = 1)
# 
# workflow$specifyPriors('tavg', Mean = 0, Precision = 1)
# 
# workflow$specifyPriors('grassland', Mean = 0, Precision = 1)
# 

## ----Bias---------------------------------------------------------------------
# 
# workflow$biasFields('CZ',
#                     prior.range = c(200, 0.2),
#                     prior.sigma = c(1, 0.01))
# 

## ----specPrior----------------------------------------------------------------
# 
# workflow$specifyPriors(copyModel = list(beta = list(fixed = TRUE)))
# 

## ----options------------------------------------------------------------------
# 
# workflow$workflowOutput(c('Maps', 'Model', 'Bias'))
# 

## ----Maps---------------------------------------------------------------------
# 
# Maps <- sdmWorkflow(workflow,inlaOptions = list(num.threads = 1,
#                                                 control.inla=list(int.strategy = 'ccd',
#                                                     h = 1e-4,
#                                                     cmin = 0,
#                                                     control.vb=list(enable = FALSE)),
#                                   safe = TRUE,
#                                   verbose = TRUE,
#                                   inla.mode = 'experimental'),
#               predictionDim = c(400, 400),
#               ipointsOptions = list(method = 'direct'))

## ----MapsOut------------------------------------------------------------------
# 
# Maps$Fraxinus_excelsior$Maps
# Maps$Ulmus_glabra$Maps
# Maps$Arnica_montana$Maps
# 

## ----model Summaries----------------------------------------------------------
# 
# lapply(Maps, function(x) x$Model)
#