fullSimulationApp: Run full simulation, accepting all defaults
In natedemaagd/LandCover: Model the Spread of Landcovers and Effect on Water Yield

Description Usage Arguments Value Examples

This function runs the entire simulation by wrapping all other functions into a single function, accepting all default customization options

fullSimulationApp(
  data,
  shp_reg = NULL,
  shp_app = NULL,
  convertFromUTM = FALSE,
  dat_sample = NULL,
  landcover_varname,
  reg_formula,
  landcover_invasive,
  landcover_susceptible,
  x_coords_varname,
  y_coords_varname,
  spread_rate,
  birdcell,
  simlength,
  simulation_count = 100,
  dep_var_modifier = NA,
  unit_converter = 1,
  covar_adjustment = 1,
  zero_break = FALSE,
  outlier_value = NA,
  dep_var_plot_label = "mm/yr",
  dep_var_plot_label_cumulative = "mm",
  line_plot_labels = c("Water yield", "Recharge"),
  line_plot_positive_vals_only = TRUE,
  line_plot_axis_label = "mm/yr",
  landcover_label_invasive = "Invasive",
  landcover_label_susceptible = "Susceptible",
  preview_plot_scalebar_position = "bottomright",
  preview_plot_scalebar_unit = "km",
  preview_plot_scalebar_dist = 10,
  priority_plot_scalebar_position = "bottomright",
  priority_plot_scalebar_unit = "km",
  priority_plot_scalebar_dist = 1,
  num_cores = parallel::detectCores() - 1
)

`data`	`data.frame` if data is in environement, or character string specifying location of xlsx data with directory if `data_as_directories = TRUE`
`shp_reg`	character string specifying layer (.shp) filename corresponding to `shp_reg_directory`, or spatial polygon object if `data_as_directories = FALSE`
`shp_app`	character string specifying layer (.shp) filename corresponding to `shp_app_directory`, or spatial polygon object if `data_as_directories = FALSE`
`convertFromUTM`	logical. Set to `TRUE` if you are subsetting your data with shapefile(s) and your shapefile(s) are in UTM coordinates instead of lon/lat.
`dat_sample`	numerical. If specified, will take a sample of `n` observations for the regression (suggested if `shp_reg` has lots of observations)
`landcover_varname`	character string specifying the landcover variable from `data`
`reg_formula`	regression formula to be used, as in `lm()`, with columns from `data` (e.g. `c ~ a + b`)
`landcover_invasive`	value. Numerical or character value of the invasive landcover.
`landcover_susceptible`	value. Numerical or character value(s) of the susceptible landcover(s). If more than one susceptible landcover, provide a vector `c()`.
`x_coords_varname`	character string. Name of the x-coordinate variable in `data`.
`y_coords_varname`	character string. Name of the y-coordinate variable in `data`.
`spread_rate`	numerical. Value between 0 and 1 indicating the annual spread rate of the invading landcover.
`birdcell`	numerical. Value between 0 and 1 indicating the probability a random cell can be invaded, regardless of adjacency to existing invaded pixels.
`simlength`	integer. Number of years the simulation should run.
`simulation_count`	integer. Length of simulation bootstrap.
`dep_var_modifier`	numerical. A scalar to optionally return a list of rasters with modified dep_var rasters (e.g. multiply water yield rasters to obtain recharge rasters)
`unit_converter`	numerical. A scalar to optionally modify the values of the resulting dependent variable (and modified dependent variable, if present) to convert units (e.g. mm/yr to gal/acre/day). Default value is `1`.
`covar_adjustment`	list. List specifying change in covariate values. See ?gls_spatial_predict.
`zero_break`	numerical. Should the priority plots have a breakpoint at 0 if values are both negative and positive?
`outlier_value`	numerical. Cutoff value for outliers in the priority plots.
`dep_var_plot_label`	character. Label for the dependent variable used in plots.
`dep_var_plot_label_cumulative`	character. Legend title for the cumulative change priority plot (also applied to modified values, if `dep_var_modifier` provided).
`line_plot_labels`	character vector of length 1 or 2, for dependent variable and modified dependent variable if provided, for the line graph. e.g. `c('Water yield', 'Recharge')`
`line_plot_positive_vals_only`	logical. When plotting the line graph, should the negative values be removed when aggregating by year?
`num_cores`	numerical. Number of cores for parallel processing, max 5
`data_as_directories`	logical. `TRUE` if data and shapefiles must be loaded from files. `FALSE` if data and shapefiles are `R` objects already loaded in the environment.
`shp_reg_directory`	character string specifying directory of shapefile outlining the area of `data` to be used for the regression. `NULL` if `data_as_directories = FALSE`
`shp_app_directory`	character string specifying directory of shapefile outlining the area of `data` to which the final simulation will be applied, if different from `shp_reg`. `NULL` if `data_as_directories = FALSE`