Basic Call to RevBayes

Submits input to the RevBayes executable and returns output to R in string format. If coerce = TRUE, the function coerceRev() will attempt to coerce output to a similar R object.

callRev(
  ...,
  coerce = FALSE,
  path = Sys.getenv("rb"),
  viewCode = FALSE,
  use_wd = TRUE,
  knit = FALSE,
  timeout = 5
)

Arguments

...

character - input to send to RevBayes.

coerce

logical - If TRUE, attempts to coerce output to an R object. If FALSE, output will remain in String format. Default is FALSE.

path

character - Path to the RevBayes executable. Default is Sys.getEnv("RevBayesPath"), which is created with initRev().

viewCode

logical - If TRUE, the input and output in the temporary file used to interact with RevBayes will be displayed in the viewing pane. This option may be useful for diagnosing code errors.

use_wd

logical - If TRUE, sets the working directory in the temporary RevBayes session to the working directory of the active R session. Default is TRUE.

knit

logical - Argument used to manage output formatting for knitRev(). This argument should generally be ignored by the user.

timeout

integer - Determines how long the system2() call should wait before timing out (seconds). Default is 5.

Value

out: character - String formatted output from RevBayes coercedOut: type varies. R object formatted output from RevBayes. Object type varies according to Rev output (Ex: numeric vector or ape::Phylo object)

Details

##NOTE - This function provides very limited interaction with RevBayes, and is mostly intended to provide basic functionalities for other methods. For more effective RevBayes calls, use doRev().

Examples

if (FALSE) {
callRev("2^3")
callRev("2^3", coerce = FALSE, viewcode = TRUE)
}