R/simanalyse-derive.R

In audrey-b/simanalyse: Facilitate Model Comparisons and Simulation Studies

#' Apply R code to derive new variables.
#' 
#' @param object An object of class (or that can be coerced to) mcmcrs, mcmcr, nlists or nlist. 
#' @param code A string of R code to derive posterior samples for new parameters. E.g. "var = sigma^2".
#' @param monitor A character vector (or regular expression if a string) specifying the names of the variables in \code{object} and/or \code{code} to monitor. By default all variables are included.
#' @param values A named list of additional R objects to evaluate in the R expression.


#' @param progress A flag specifying whether to print a progress bar.
#' @param options The future specific options to use with the workers.

# @param append A flag indicating whether to return the derived parameters along with the original ones.
# @param parallel An integer specifying the number of CPU cores to use for generating the datasets in parallel. Defaul is 1 (not parallel).
# @param path A string specifying the path to the directory to save the data sets in. By default \code{path = NULL } the data sets are not saved but are returned as an nlists object.
# @param silent A flag specifying whether to suppress warnings.
# @param path.save A string specifying the path to the directory to save the derived results. By default path = NULL and the results are not saved but returned as a list of nlists objects.

#' @return An object of the same class as \code{object}
#' @export
#'
#' @examples
#' set.seed(10L)
#' code <- "for(i in 1:10){x[i] ~ dnorm(0,1/variance)}"
#' parameters = nlist(variance=4)
#' dat <- sims::sims_simulate(code, parameters = parameters, nsims=2)
#' res <- sma_analyse(dat, code, code.add = "variance ~ dunif(0,10)", 
#' mode=sma_set_mode("quick"), monitor="variance")
#' sma_derive(res, "sd=sqrt(variance)")
#' sma_derive(parameters, "sd=sqrt(variance)")
#' 
# set.seed(10L)
# code <- "for(i in 1:T){x[i] ~ dbinom(p[i],n[i])}"
# constants = list(T=10, n=rep(30, 10))
# parameters = list(p=rep(0.8, 10))
# dat  <- sims::sims_simulate(code, constants=constants, parameters = parameters, nsims=2)
# dat_outlier <- sma_derive(dat, "y = c(x[1:4], 1, x[6:10])", monitor=c("n","T","y"))
# res <- sma_analyse(dat_outlier, sub("x\\[", "y\\[", code), 
# code.add = "for(i in 1:T){p[i] = p.const}
#             p.const ~ dunif(0,1)", 
# mode=sma_set_mode("quick"), monitor="p.const")
# sma_derive(res, "odds=p.const/(1-p.const)", monitor="odds")
# sma_derive(parameters, "odds=p[1]/(1-p[1])", monitor="odds")

## No Files

sma_derive <- function(object=NULL, code, monitor=".*", 
                       values=list(),
                       
                       
                       progress = FALSE,
                       options = furrr::furrr_options())
{
  sma_derive_base(object=object, code = code, monitor=monitor, 
                  values= values,
                  path = NULL,
                  folder = NULL,
                  progress = progress,
                  options = options)
  
  
}

###### Files

#' Apply R code to derive new variables.
#' 

#' @param code A string of R code to derive posterior samples for new parameters. E.g. "var = sigma^2".
#' @param monitor A character vector (or regular expression if a string) specifying the names of the variables in \code{object} and/or \code{code} to monitor. By default all variables are included.
#' @param values A named list of additional R objects to evaluate in the R expression.
#' @param path A string. Analyses results are read from that path on disk.
#' @param folder A string for the name of the folder that contains the analysis.
#' @param progress A flag specifying whether to print a progress bar.
#' @param options The future specific options to use with the workers.

# @param append A flag indicating whether to return the derived parameters along with the original ones.
# @param parallel An integer specifying the number of CPU cores to use for generating the datasets in parallel. Defaul is 1 (not parallel).
# @param path A string specifying the path to the directory to save the data sets in. By default \code{path = NULL } the data sets are not saved but are returned as an nlists object.
# @param silent A flag specifying whether to suppress warnings.
# @param path.save A string specifying the path to the directory to save the derived results. By default path = NULL and the results are not saved but returned as a list of nlists objects.

#' @return An object of the same class as \code{object}
#' @export
#'

sma_derive_files <- function(code, monitor=".*", 
                             values=list(),
                             path = ".",
                             folder = "analysis0000001",
                             progress = FALSE,
                             options = furrr::furrr_options())
{
  sma_derive_base(object=NULL, code = code, monitor=monitor, 
                  values= values,
                  path = path,
                  folder = folder,
                  progress = progress,
                  options = options)
  
  
}