species_plan: Generate a drake plan for a species

In jscamac/edmaps: Estimate Likelihood of Pest Establishment

Generate a drake plan for a species

Description

Generate a drake plan that facilitates reproducible generation of species outputs.

Usage

species_plan(
  species,
  clum_classes,
  nvis_classes,
  host_path,
  pathways,
  include_abiotic_weight = TRUE,
  climate_suitability_path,
  exclude_bioclim_vars = NULL,
  include_ndvi = TRUE,
  aggregated_res = c(5000, 5000),
  make_interactive_maps = TRUE,
  processed_data_path,
  clum_path,
  nvis_path,
  ndvi_path,
  pop_density_path,
  airports_path,
  tourist_beds_path,
  airport_beta = log(0.5)/200,
  airport_tsi_beta = log(0.5)/10,
  port_data_path,
  port_weight_beta,
  fertiliser_data_path,
  nrm_path,
  containers_data_path,
  postcode_path,
  occurrence_path,
  infected_countries,
  cabi_path,
  use_gbif = FALSE,
  gbif_species,
  gbif_min_year = 1970,
  gbif_max_uncertainty = 20000,
  gbif_username,
  gbif_password,
  basemap_mode = c("osm", "boundaries"),
  minimum_probability_for_maps = 1e-05,
  manual_check_flagged_records = FALSE,
  wind_effect_width,
  leakage_tourists,
  establishment_tourists,
  leakage_returning,
  establishment_returning,
  leakage_torres,
  establishment_torres,
  leakage_mail,
  establishment_mail,
  leakage_vessels,
  establishment_vessels,
  leakage_fertiliser,
  establishment_fertiliser,
  leakage_machinery,
  establishment_machinery,
  leakage_containers,
  establishment_containers,
  leakage_nurserystock,
  establishment_nurserystock,
  leakage_food,
  establishment_food,
  leakage_goods,
  establishment_goods,
  leakage_northwind,
  establishment_northwind,
  leakage_pacificwind,
  establishment_pacificwind,
  leakage_nzwind,
  establishment_nzwind,
  overwrite = TRUE
)

Arguments

species	The name of the species. This will be used for naming output files and folders.
clum_classes	An integer vector indicating which ACLUM classes are considered host plants for species. Either clum_classes or nvis_classes (or both) must be provided. If user_host_path is also provided, the union of the two datasets will be used to define host distribution.
nvis_classes	An integer vector indicating which NVIS classes are considered host plants for species. Either clum_classes or nvis_classes (or both) must be provided.
host_path	Character. Optional file path to a raster dataset that describes the distribution of host material for the species. The file must be readable by GDAL. All cell values other than zero or NA will be considered to be host material. Dataset will be projected and resampled as necessary to match the spatial extent and resolution of analysis. If clum_classes is also provided, the union of the two datasets will be used to define host distribution. A valid coordinate reference system must be associated with the spatial dataset.
pathways	A character vector of invasion pathways that should be included. Can be one or more of: 'containers', 'fertiliser', 'food', 'goods', 'machinery', 'mail', 'nurserystock', 'residents', 'torres', 'tourists', 'vessels', 'northwind', 'pacificwind', 'nzwind'.
include_abiotic_weight	Logical. Should suitability be dependent on climate? Considered TRUE if climate_suitability_path is provided, or if use_gbif is TRUE.
climate_suitability_path	Optional file path to a raster describing climatic suitability across the landscape. If provided, the raster must be have the Australian Albers coordinate system (EPSG:3577), spatial resolution of 1000 m, and must have xmin = -1888000, xmax = 2122000, ymin =-4847000, ymax = -1010000. If not provided and include_abiotic_weight is TRUE, a range bag model will be fit to estimate climatic suitability.
exclude_bioclim_vars	Character vector of bioclim variables that should not be used when fitting a range bag model (see range_bag()) of climatic suitability. Variables should be specified as, e.g., c("bio01", "bio12"). Ignored if climate_suitability_path is provided.
include_ndvi	Logical. Should biotic suitability be dependent on NDVI?
aggregated_res	A numeric vector of 2 elements, indicating the desired resolution of aggregated establishment likelihood rasters, in metres.
make_interactive_maps	Logical. Should interactive html maps be generated?
processed_data_path	Path to a directory that will be used to store processed datasets. This will be created, recursively, if it does not exist.
clum_path	Path to the ACLUM raster.
nvis_path	Path to the NVIS raster.
ndvi_path	Path to the NDVI raster.
pop_density_path	Path to the population density raster.
airports_path	Path to the major airports vector dataset.
tourist_beds_path	Path to the tourist beds vector dataset.
airport_beta	Numeric. Parameter controlling the distribution of international tourists passengers around international airport. Default is log(0.5)/200 (i.e. 50% of passengers within 200km of airport).
airport_tsi_beta	Numeric. Parameter controlling the distribution of Torres Strait passengers around Cairns airport. Default is log(0.5)/10 (i.e., 50% of passengers within 10km of Cairns airport).
port_data_path	File path to the marine ports .csv file.
port_weight_beta	Numeric. Defines the decay rate of an exponential model. In the context of pests entering via the vessel pathway, this reflects the decrease in the relative likelihood of pest arrival at locations distant from marine ports. For example, prob_weight_beta=log(0.5)/10 would lead to distance-decay that leads to 50% (i.e. 0.5) of establishment likelihood (prior to considering other relevant pathways) within a distance of 10 map units (i.e., 10 kilometres when res is 1000).
fertiliser_data_path	File path to a csv file containing information about fertiliser usage by NRM.
nrm_path	File path to a polygon shapefile of NRMs (natural resource management areas).
containers_data_path	File path to the dataset giving the distribution of containers by postcode.
postcode_path	File path to postal areas shapefile.
occurrence_path	Path to a .csv file containing occurrence data. Must include columns Longitude and Latitude. Coordinates are expected to be in decimal degrees (WGS84).
infected_countries	A character vector of countries within which the species occurs. Ignored if climate_suitability_path is provided.Only one of infected_countries or cabi_path should be provided.
cabi_path	Path to a .csv file downloaded from CABI, indicating the countries within which the species occurs. Download links to these files can be found at the bottom of CABI species datasheet webpages, e.g. https://www.cabi.org/isc/datasheet/17685. Ignored if climate_suitability_path is provided. Only one of infected_countries or cabi_path should be provided.
use_gbif	Logical. Should species occurrence records be sourced from GBIF? Ignored if climate_suitability_path is provided.
gbif_species	Character vector. Taxon names to use when querying GBIF. Ignored if climate_suitability_path is provided.
gbif_min_year	Integer. The minimum year (yyyy) to be included when downloading GBIF data. Ignored if climate_suitability_path is provided.
gbif_max_uncertainty	Numeric. The maximum permissable coordinate uncertainty for GBIF records. Ignored if climate_suitability_path is provided.
gbif_username	GBIF username to use for querying GBIF's occurrence download API endpoint. If missing, the less efficient "search" endpoint is used. Register at http://gbif.org.
gbif_password	GBIF password to use for querying GBIF's occurrence download API endpoint. If missing, the less efficient "search" endpoint is used. Register at http://gbif.org.
basemap_mode	Type of basemap for static maps. Either 'osm' (default), or 'boundaries' (polygons delineating borders of states/territories).
minimum_probability_for_maps	Numeric. A value between 0 and 1, defining the minimum establishment probability to be displayed on plotted maps. Values below this threshold will be excluded. Default is 1E-5.
manual_check_flagged_records	Logical. Should an interactive map be used for manually checking flagged occurrence records? If TRUE, the user will have the opportunity to select dubious points (i.e. occurrences in countries for which CABI has no record of the species' establishment), to be retained. If FALSE (the default), all such dubious points will be excluded. Ignored if climate_suitability_path is provided. Note that manual checking is not possible when using excel_to_plan() since the required interactivity will interrupt plan processing.
wind_effect_width	Numeric. For wind pathways, the distance (in metres) inland from the coastline, over which wind-based arrival applies. E.g. if pests are expected to be carried by wind up to 50 km inland from the coast, use 50000. Ignored if pathways does not include one or more of northwind, pacificwind, or nzwind.
leakage_tourists, leakage_returning, leakage_torres, leakage_mail, leakage_vessels, leakage_fertiliser, leakage_machinery, leakage_containers, leakage_nurserystock, leakage_food, leakage_goods, leakage_northwind, leakage_pacificwind, leakage_nzwind	Numeric vector with length = 2, giving the range (bounds of 95% CI) of the number of leakage events per year for the pathway.
establishment_tourists, establishment_returning, establishment_torres, establishment_mail, establishment_vessels, establishment_fertiliser, establishment_machinery, establishment_containers, establishment_nurserystock, establishment_food, establishment_goods, establishment_northwind, establishment_pacificwind, establishment_nzwind	Numeric vector with length = 2, giving the bounds of the 95% CI of the rate of survival & establishment to end of pathway, for leakage events on the pathway.
overwrite	Logical. Should the code executed by the resulting plan be allowed to overwrite existing raster files? Default is TRUE.

Details

To simplify reproducibility, edmaps provides an Excel interface for specifying species parameters relevant to estimating establishment likelihood. An example spreadsheet is bundled with the package, available at the path given by system.file('extdata/parameters.xlsx', package='edmaps'). The spreadsheet has two sheets, the first specifying "global" parameters that will apply to all species (e.g. file paths to rasters that will), be used regardless of species identity and the second specifying parameters that can vary by species. In the second sheet, each row corresponds to a separate species. Tooltips and data validation guide the user with respect to expected/allowable data.

See Also

excel_to_plan()

jscamac/edmaps documentation built on June 11, 2022, 1:26 a.m.