SummaryPlotFunc: Summary plot
In PointProcess/SealPupProduction-JRSSC-code:

Produces several different summary plots showing the results from INLA approach

SummaryPlotFunc(
  meshplot = TRUE,
  boundariesplot = TRUE,
  covariatesplot = TRUE,
  summaryplot = TRUE,
  savingFolder,
  sealPhotoDataFile,
  sealTransectDataFile,
  dataList,
  orgPhotos,
  modPhotos,
  results.CI.level = 0.95,
  gridList,
  finalResList,
  mesh,
  covMesh,
  tilesList,
  weightAtMeshLoc,
  countingDomain,
  logicalGridPointsInsideCountingDomain,
  covNewGridval,
  pp.res,
  sealType,
  use.covariates,
  covariates.type,
  covariate.fitting,
  spatial,
  additional.iid.term,
  convHullVar.convex,
  convHullVar.concave,
  convHullVar.resolution,
  meshVar.max.edge,
  meshVar.offset,
  meshVar.cutoff,
  Matern.alpha,
  grid.pixelsize,
  INLA.theta.startval,
  parallelize.noSplits,
  parallelize.numCores,
  poisson.maxEvals,
  noSamp,
  time,
  testing,
  comment,
  leaveOutTransect,
  Data_2018 = F
)

`meshplot`	Logical, indicating whether a plot with the mesh should be produced
`boundariesplot`	Logical, indicating whether plots with the used boundaries and domains should be produced
`covariatesplot`	Logical, indicating whether various plots showing the covariates and their effects should be produced
`summaryplot`	Logical, indicating whether a plot showing the final posterior distribution and mean and pointwise sd of the latent field should be produced
`savingFolder`	String, indicating the complete path to where the plots are to be stored
`sealPhotoDataFile`	String, indicating the file where seal photo data are stored
`sealTransectDataFile`	String, indicating the file where seal transect data are stored
`dataList`	List with various data variables
`orgPhotos`	data frame with the coordinates of all original photos (both those used in the modelling and those not used)
`modPhotos`	data frame with the coordinates of the photos used in the modelling
`gridList`	List containing information about the grid, being the output of the function GridCreation
`finalResList`	List gathering all final results
`mesh`	Mesh object, being the output from inla.mesh.2d
`covMesh`	Mesh object representing the mesh for the covariate when applicable, being the output from inla.mesh.1d
`tilesList`	List containing all the voronoi tesselation tiles
`weightAtMeshLoc`	Numeric vector with the weight assigned to each tile in the tileList
`countingDomain`	data.frame containing x- and y-coordinates of the counting domain polygon
`logicalGridPointsInsideCountingDomain`	Logical vector, indicating which of the grid elements are within the counting domain
`covNewGridval`	Matrix with all covariate values at grid points
`pp.res`	Result object from INLA run
`sealType`	String, indicating which seal type to model "hooded" (default as it is quicker), or "harps"
`use.covariates`	Logical, indicating whether covariates are used or not (see description!)
`covariates.type`	String equal to "band1" or "band2" indicating which of the bands from the satellite data should be used.
`covariate.fitting`	String, indicating how to model covariates. "linear", quadratic (default) or "linAndLog", or FALSE for no covariates
`spatial`	Logical indicating whether this model includes a spatial term or not.
`additional.iid.term`	Logical, indicating whether to include an additional iid (Gaussian) term in the latent field specification. FALSE is default
`convHullVar.convex`	Numeric, corrresponding to the convex parameter of inla.nonvonvex.hull. See ?inla.nonconvex.hull for details
`convHullVar.concave`	Numeric, corrresponding to the concave parameter of inla.nonvonvex.hull. See ?inla.nonconvex.hull for details
`convHullVar.resolution`	Numeric vector of length 2, corrresponding to the resolution parameter of inla.nonvonvex.hull. See ?inla.nonconvex.hull for details
`meshVar.max.edge`	Numeric, corrresponding to the max.edge parameter of inla.mesh.2d. Smaller values gives smaller triangles outside triangles. See ?inla.mesh.2d for details
`meshVar.offset`	Numeric, corrresponding to the offset parameter of inla.mesh.2d. See ?inla.mesh.2d for details
`meshVar.cutoff`	Numeric, corrresponding to the cutoff parameter of inla.mesh.2d. See ?inla.mesh.2d for details
`Matern.alpha`	Numeric, corresponding to the alpha parameter in the Matern covariance function (2 is the default)
`grid.pixelsize`	Numeric, denoting the size (in km, in both x- and y-direction) of each pixel of the grid being used
`INLA.theta.startval`	List containing the start values for the theta parameter in the INLA run. (NULL indicates that automatic start values should be used, and is the default)
`parallelize.noSplits`	Numeric, deciding how many sublists samp should be splitted into. Should be a multiple of parallelize.numCores for the highest efficiency. The larger number the less memory is used (and longer time).
`parallelize.numCores`	Numeric, corresponding to the number of cores any parallelization should be run at
`poisson.maxEvals`	Numeric, corresponding to maximum number of points the Poisson distribution should be evaluated at (a much smaller number is typically used)
`noSamp`	Numeric, indicating the number of samples from posterior model to use when computing the posterior predictive distribution. 5000 (default) typically sufficient.
`time`	The number of seconds the function has been running
`testing`	Logical, indicating whether the testing parts of this function should be used
`comment`	String to add as a comment to the summary plot