R/utils.R

In ctsmTMB: Continuous Time Stochastic Modelling using Template Model Builder

#' Shortcut class constructor
#' @description
#' This is just a short-cut class constructor so that users can do
#' 
#' `model <- ctsm()` 
#' 
#' instead of 
#' 
#' `model <- ctsmTMB$new()`.
#' @examples
#' library(ctsmTMB)
#' model <- ctsm()
#' @export
ctsm <- function(){
  return(ctsmTMB$new())
}


#######################################################
# CHANGE FROM R POWER NOTATION TO C++
#######################################################

# Changes powers in expressions from R-style (e.g. x^2) to pow(x,2) which is interpretable by C++
# from https://stackoverflow.com/questions/40606723/substitute-the-power-symbol-with-cs-pow-syntax-in-mathematical-expression

hat2pow <- function(e) {
  #check if you are at the end of the tree's branch
  if (is.name(e) || is.atomic(e)) {
    #replace ^
    if (e == quote(`^`)) return(quote(pow))
    return(e)
  }
  #follow the tree with recursion
  for (i in seq_along(e)) e[[i]] <- hat2pow(e[[i]])
  return(e)
}

###########################################################
# TRY THAT SUPPRESSES AND RECOVERS ANSWER DESPITE WARNINGS
###########################################################

try_withWarningRecovery = function(expr, silent=TRUE){
  output = try(withCallingHandlers(
    {
      expr
    },
    warning = function(w) {
      invokeRestart("muffleWarning")
    }
  ), silent=silent)
  
  return(output)
}

###########################################################
# Upper-case first letter of string
###########################################################
capitalize_first <- function(s) {
  if (nchar(s) == 0) return(s)  # Handle empty string case
  paste0(toupper(substr(s, 1, 1)), substr(s, 2, nchar(s)))
}

#######################################################
# GGPLOT2 FUNCTIONS FOR USE IN PLOTS
#######################################################

getggplot2theme = function() {
  mytheme =
    ggplot2::theme_minimal() +
    ggplot2::theme(
      # text = ggplot2::element_text("Avenir Next Condensed",size=12),
      text = ggplot2::element_text(size=12),
      legend.text = ggplot2::element_text(size=12),
      axis.text = ggplot2::element_text(size=12),
      strip.text = ggplot2::element_text(face="bold",size=12),
      # panel.grid.major = element_blank(),
      # panel.grid.minor = element_blank(),
      legend.box = "horizontal",
      legend.direction = "horizontal",
      legend.position = "top",
      plot.title = ggplot2::element_text(hjust=0.5)
    )
  return(mytheme)
}

# getggplot2colors = function(n) {
#   hues = seq(15, 375, length = n + 1)
#   ggcolors = grDevices::hcl(h = hues, l = 65, c = 100)[1:n]
#   return(ggcolors)
# }