Operator for concatenation.

Description

Rapid string parsing

Usage

a %+% b

Arguments

Details

Method for quicker pasting of Strings.

Value

character formatted concatenation of both input strings.

Basic Call to RevBayes

Description

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.

Usage

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

Arguments

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().

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)

Examples

## Not run: 
callRev("2^3")
callRev("2^3", coerce = FALSE, viewcode = TRUE)

## End(Not run)

Execute a .rev file in RevBayes Through an RStudio Terminal

Description

Accesses an RStudio terminal through the RStudio API and runs a .rev script.

Usage

callRevFromTerminal(revscript)

Arguments

Details

Many common RevBayes use-cases, such as generating mcmcs, take a long time to execute. Because of this fact, it is inefficient and inadvisable to run them in knitr documents or with RevBayes calls through repRev(). Instead, tutorial code or code that has been written interactively can be externally saved with saveRev(), and then executed in an RStudio terminal via callRevFromTerminal(). Output files can then be explored and visualized with the RevGadgets package.

Value

termID Unique identifier of the terminal used to call RevBayes

Examples

## Not run: 
saveRev("archertutorial.rev", use_quit=TRUE)
callRevFromTerminal("archertutorial.rev")

## End(Not run)

Clear Code from Revticulate History

Description

Removes code from .Revhistory file used for managing Revticulate history. Clears all code by default, or last 'n' lines of code specifed by the user.

Usage

clearRev(n = NULL, silent = FALSE)

Arguments

Value

pseudoError: NULL. Message warning user that they attempted to erase more items from the Rev history than exist. message() is used instead of stop() so that clearRev() functions in repRev().

undoRev(n): NULL. Removes n number of lines from .Revhistory and cats the remaining history to the screen.

Examples

## Not run: 
clearRev() #Clear all Revticulate history
clearRev(n = 3) #Remove the last 3 lines of Revticulate history

## End(Not run)

Convert RevBayes Output into R Objects

Description

Coerces a RevBayes output string into an equivalent R object. Automatically determines R object type based on the structure of the string, and returns the original string if R object equivalent cannot be determined.

Usage

coerceRev(revString)

Arguments

Value

rObject: Type varies depending on Rev object type. R object-formatted output coerced from a RevBayes output string.

Examples

## Not run: 
coerceRev("[1, 2, 3, 4]")

## End(Not run)

Call RevBayes with Continuous Session History

Description

The basic Revticulate function for interacting with RevBayes

Usage

doRev(input, coerce = TRUE, evaluate = TRUE, viewCode = FALSE, timeout = 5)

Arguments

Details

This function allows users to make multiple calls to RevBayes, while maintaining a persistent input history. This means that variables defined in one call can be referenced in another call, giving the feel of a continuous RevBayes session.

Because this function is the basis for repRev() and knitRev(), variables defined in RevBayes with any of these functions can be referenced by any of the others.

Value

now - RevBayes output, type varies. If coerce = TRUE, coerceRev() will attempt to convert RevBayes output into an equivalent R object. If else, the return type is character.

Examples

## Not run: 
doRev("simTree(16)", coerce=FALSE)
doRev("a <- 10")
doRev("a * 100")

## End(Not run)

Get Revticulate History

Description

Return the history of RevBayes code submitted with doRev() and similar functions

Usage

getRevHistory()

Value

lines - character. A vector of the line-by-line Revticulate history

Examples

## Not run: 
getRevHistory()

cat(getRevHistory(), sep="\n")

## End(Not run)

View RevBayes Variables

Description

Wrapper for RevBayes ls() function. Displays variables that have been defined in the working RevBayes session.

Usage

getRevVars()

Value

No return - wrapper for RevBayes ls() function to show variables in rb environment

Examples

## Not run: 

getRevVars()

## End(Not run)

Knitr Engine for RevBayes

Description

Creates a knitr engine for evaluating RevBayes code

Usage

knitRev()

Details

To use RevBayes in a knitr document, type 'library(Revticulate)' followed by 'knitRev()' on the next line in the initialization block. The language header for RevBayes chunks is 'rb'.

The RevBayes knitr engine is built around doRev(), allowing history to persist between chunks. If a variable 'x <- 10' is defined in one RevBayes chunk, 'x' can then be accessed in a later RevBayes chunk. Additionally, it could be accessed via doRev() in an R chunk, allowing for quick R analysis of RevBayes variables.

On top of the standard knitr chunk options, the rb engine provides two extras: rb_eval, and coerce.

If rb_eval = FALSE, the code in the chunk will be saved to the .Revhistory file, but will not be submitted to RevBayes. This option is useful for code chunks containing the final loop of an mcmc, which could be saved to an external file with saveRev() and ran in a terminal with callRevFromTerminal().

If coerce = TRUE, coerceRev() will attempt to convert RevBayes output into equivalent R formatted objects. The default value for both coerce and rb_eval is TRUE.

Value

No return. Initiates knitr engine for RevBayes.

Examples

## Not run: 
```{r setup, include=FALSE}
     knitr::opts_chunk$set(echo = TRUE)
     library(Revticulate)
     knitRev()
```

```{rb rb_eval=TRUE, coerce=FALSE}

x <- simTree(32)

```

```{r}

x <- doRev('x')
plot(x)

```

## End(Not run)

Load Revticulate History from a .Rev File

Description

Reads in the code from a .Rev file and writes it into the current Revticulate history.

Usage

loadRevHistory(filepath, overwrite = FALSE)

Arguments

Value

No return - reads in new code to the .Revhistory file

Examples

## Not run: 
     loadRevHistory("someCode.rev")

     loadRevHistory("someMoreCode.rev", overwrite=TRUE)

## End(Not run)

Interactive Session with RevBayes

Description

Simulates a continuous, interactive session with RevBayes. While this session is active, all code will be interpreted as Rev code, and attempting to run R code may result in error.

Usage

repRev(path = Sys.getenv("rb"), viewCode = FALSE, coerce = TRUE, use_wd = TRUE)

Arguments

Details

By default, the interactive session uses the present R working directory as the RevBayes working directory. This behavior can be turned off with use_wd = FALSE

The exit the session, type 'quit()', 'q()', or hit the 'esc' key. clearRev(), getRevVars(), and getRevHistory() can still be called from within the session for user convenience

Value

No return. RevBayes variables assigned within the session can be accessed externally via doRev() or viewed with getRevVars().

Examples

## Not run: 
repRev()

myNumber <- 4
myNumber

posteriorPredictiveProbability(v(2), 3)
getrRev()
clearRev()
quit()

## End(Not run)

Save Revticulate History

Description

Captures the current Revticulate history and saves it to an external file.

Usage

saveRev(filepath, use_wd = TRUE, use_quit = TRUE)

Arguments

Details

By providing a file path, the user can save the RevBayes code in their current Revticulate session to an external .Rev script. This script can then be executed in RevBayes via source(), or in an RStudio terminal via callRevFromTerminal(). Usage of this function can be combined with loadRev() to allow for the continual use of a Revticulate history instance between R sessions.

Examples

## Not run: 
      saveRev("mySavedCode.rev", use_quit=FALSE)
      saveRev("mySavedCode.rev", use_wd=FALSE, use_quit=TRUE)

## End(Not run)