## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  warning = FALSE,
  message = FALSE,
  eval = FALSE
)


## ----setup, warning = FALSE, message = FALSE----------------------------------
# 
# library(PointedSDMs)
# library(terra)
# library(INLA)
# library(ggplot2)
# 

## ----safe, include = FALSE----------------------------------------------------
# 
# bru_options_set(inla.mode = "experimental")
# 

## ----load data----------------------------------------------------------------
# 
# data('SolitaryTinamou')
# projection <- "+proj=longlat +ellps=WGS84"
# 
# covariates <- terra::rast(system.file('extdata/SolitaryTinamouCovariates.tif',
#                                       package = "PointedSDMs"))
# 
# datasets <- SolitaryTinamou$datasets
# region <- st_as_sf(SolitaryTinamou$region)
# mesh <- SolitaryTinamou$mesh
# 

## ----look at data-------------------------------------------------------------
# 
# str(datasets)
# class(region)
# 

## ----covariates, fig.width=8, fig.height=5------------------------------------
# 
# covariates <- scale(covariates)
# crs(covariates) <- projection
# plot(covariates)
# 

## ----mesh, fig.width=8, fig.height=5------------------------------------------
# 
# ggplot() + gg(mesh)
# 

## ----set up base model, warning = FALSE, message = FALSE----------------------
# 
# base <- startISDM(datasets, spatialCovariates = covariates, Boundary = region,
#                  Projection = projection, responsePA = 'Present', Offset = 'area',
#                  Mesh = mesh, pointsSpatial = NULL)
# 

## ----data, fig.width=8, fig.height=5------------------------------------------
# 
# base$plot(Boundary = FALSE) +
#   geom_sf(data = st_boundary(region)) +
#   ggtitle('Plot of the species locations by dataset')
# 

## ----priorsFixed--------------------------------------------------------------
# 
# base$priorsFixed(Effect = 'Forest', mean.linear = 0.5, prec.linear = 0.01)
# 

## ----run base model, warning = FALSE, message = FALSE-------------------------
# 
# baseModel <- fitISDM(data = base)
# summary(baseModel)
# 

## ----set up model with fields, warning = FALSE, message = FALSE---------------
# 
# fields <- startISDM(datasets, spatialCovariates = covariates, Boundary = region,
#                    Projection = projection, Mesh = mesh, responsePA = 'Present')
# 
# fields$priorsFixed(Effect = 'Intercept', prec.linear = 1)
# 
# for (cov in names(covariates)) fields$priorsFixed(Effect = cov, prec.linear = 1)
# 

## ----specifySpatial-----------------------------------------------------------
# 
# fields$specifySpatial(sharedSpatial = TRUE,
#                       constr = TRUE,
#                       prior.range = c(3, 0.1),
#                       prior.sigma = c(1, 0.1))
# 

## ----run fields model, warning = FALSE, message = FALSE-----------------------
# 
# fieldsModel <- fitISDM(fields, options = list(control.inla =
#                                                 list(int.strategy = 'eb')))
# summary(fieldsModel)
# 

## ----correlate model----------------------------------------------------------
# 
# correlate <- startISDM(datasets, Boundary = region,
#                  Projection = projection, Mesh = mesh,
#                  spatialCovariates = covariates$Altitude,
#                  responsePA = 'Present',
#                  pointsSpatial = 'correlate')
# 
# correlate$priorsFixed(Effect = 'Intercept', prec.linear = 1)
# 
# correlate$priorsFixed(Effect = 'Altitude', prec.linear = 1)
# 
# correlate$specifySpatial(sharedSpatial = TRUE,
#                          prior.range = c(3, 0.1),
#                          prior.sigma = c(1, 0.1))
# 
# correlate$changeComponents()
# 

## ----addBias------------------------------------------------------------------
# 
# correlate$addBias('eBird')
# 
# correlate$specifySpatial(Bias = TRUE,
#                       prior.range = c(2, 0.1),
#                       prior.sigma = c(0.1, 0.1))
# 

## ----run correlate model------------------------------------------------------
# 
# correlateModel <- fitISDM(correlate,
#                           options = list(control.inla =
#                                            list(int.strategy = 'eb')))
# summary(correlateModel)
# 

## ----predict spatial, warning = FALSE, message = FALSE------------------------
# 
# spatial_predictions <- predict(correlateModel, mesh = mesh,
#                        mask = region,
#                        spatial = TRUE,
#                        fun = 'linear')
# 

## ----spatial, fig.width=8, fig.height=5---------------------------------------
# 
# plot(spatial_predictions, variable = c('mean', 'sd'))
# 

## ----predict bias, warning = FALSE, message = FALSE---------------------------
# 
# bias_predictions <- predict(correlateModel,
#                     mesh = mesh,
#                     mask = region,
#                     bias = TRUE,
#                     fun = 'linear')
# 

## ----bias, fig.width=8, fig.height=5------------------------------------------
# 
# plot(bias_predictions)
# 

## ----datasetOut, warning = FALSE, message = FALSE-----------------------------
# 
# eBird_out <- datasetOut(model = correlateModel, dataset = 'eBird')
# 

## ----print datasetOut---------------------------------------------------------
# 
# eBird_out
#