Build statistical models of vegetation cover

Given one or more sites and a model specification, builds a model of vegetation cover and report model assessment.

Usage

fit(
  site = NULL,
  datafile = "data",
  name = "",
  method = "rf",
  vars = "{*}",
  exclude = "",
  years = NULL,
  maxmissing = 0.05,
  top_importance = 20,
  holdout = 0.2,
  auc = TRUE,
  hyper = NULL,
  resources = NULL,
  local = FALSE,
  trap = TRUE,
  comment = NULL
)

Arguments

site: Three letter site code, or vector of site names if fitting multiple sites.
datafile: Name of data file. It must be an .RDS file, but exclude the extension. If fitting multiple sites, either use a single datafile name shared among sites, or a vector matching site.
name: Optional model name
method: One of rf for Random Forest, boost for AdaBoost. Default = rf.
vars: An optional vector of variables to restrict analysis to. Default = *, all variables. vars is processed by find_orthos, and may include file names, portable names, search names and regular expressions of file and portable names.
exclude: An optional vector of variables to exclude. As with vars, variables are processed by find_orthos.
years: An optional vector of years to restrict variables to.
maxmissing: Maximum proportion of missing training points allowed before a variable is dropped.
top_importance: Number of variables to keep for variable importance
holdout: Proportion of points to hold out. For Random Forest, this specifies the size of the single validation set, while for boosting, it is the size of each of the testing and validation sets.
auc: If TRUE, calculate class probabilities so we can calculate AUC.
hyper: Hyperparameters. To be defined.
resources: Slurm launch resources. See launch. These take priority over the function's defaults.
local: If TRUE, run locally; otherwise, spawn a batch run on Unity
trap: If TRUE, trap errors in local mode; if FALSE, use normal R error handling. Use this for debugging. If you get unrecovered errors, the job won't be added to the jobs database. Has no effect if local = FALSE.
comment: Optional launch / slurmcollie comment