R/lba.r

Defines functions rLBA qLBA inv_cdf_lba pLBA dLBA check_i_arguments

Documented in dLBA pLBA qLBA rLBA

#' The Linear Ballistic Accumulator (LBA)
#' 
#' Density, distribution function, quantile function, and random generation for
#' the LBA model with the following parameters: \code{A} (upper value of
#' starting point), \code{b} (response threshold), \code{t0} (non-decision
#' time), and driftrate (\code{v}). All functions are available with different
#' distributions underlying the drift rate: Normal (\code{norm}), Gamma
#' (\code{gamma}), Frechet (\code{frechet}), and log normal (\code{lnorm}). The
#' functions return their values conditional on the accumulator given in the
#' response argument winning.
#' 
#' @param rt vector of RTs. Or for convenience also a \code{data.frame} with
#'   columns \code{rt} and \code{response} (such as returned from \code{rLBA} or
#'   \code{\link{rdiffusion}}). See examples.
#' @param response integer vector of winning accumulators/responses
#'   corresponding to the vector of RTs/p (i.e., used for specifying the
#'   response for a given RT/probability). Will be recycled if necessary. Cannot
#'   contain values larger than the number of accumulators. First
#'   response/accumulator must receive value 1, second 2, and so forth. For
#'   conmvenience, \code{response} is converted via \code{as.numeric} thereby
#'   allowing factors to be passed as well (such as returned from
#'   \code{\link{rdiffusion}}). Ignored if \code{rt} or \code{p} is a
#'   \code{data.frame}.
#' @param p vector of probabilities. Or for convenience also a \code{data.frame}
#'   with columns \code{p} and \code{response}. See examples.
#' @param n desired number of observations (scalar integer).
#' @param A start point interval or evidence in accumulator before beginning of
#'   decision process. Start point varies from trial to trial in the interval
#'   [0, \code{A}] (uniform distribution). Average amount of evidence before
#'   evidence accumulation across trials is \code{A}/2.
#' @param b response threshold. (\code{b} - \code{A}/2) is a measure of
#'   "response caution".
#' @param t0 non-decision time or response time constant (in seconds). Lower
#'   bound for the duration of all non-decisional processes (encoding and
#'   response execution).
#' @param st0 variability of non-decision time, such that \code{t0} is uniformly
#'   distributed between \code{t0} and \code{t0} + \code{st0}. Default is 0. Can
#'   be trialwise, and will be recycled to length of \code{rt}.
#' @param ... two \emph{named} drift rate parameters depending on
#'   \code{distribution} (e.g., \code{mean_v} and \code{sd_v} for
#'   \code{distribution=="norm"}). The parameters can either be given as a
#'   numeric vector or a list. If a numeric vector is passed each element of the
#'   vector corresponds to one accumulator. If a list is passed each list
#'   element corresponds to one accumulator allowing again trialwise driftrates.
#'   The shorter parameter will be recycled as necessary (and also the elements
#'   of the list to match the length of \code{rt}). See details.
#' @param distribution character specifying the distribution of the drift rate.
#'   Possible values are \code{c("norm", "gamma", "frechet", "lnorm")}, default
#'   is \code{"norm"}.
#' @param args.dist list of optional further arguments to the distribution
#'   functions (i.e., \code{posdrift} or \code{robust} for
#'   \code{distribution=="norm"}, see \code{\link{single-LBA}}).
#' @param silent logical. Should the number of accumulators used be suppressed?
#'   Default is \code{FALSE} which prints the number of accumulators.
#' @param interval a vector containing the end-points of the interval to be
#'   searched for the desired quantiles (i.e., RTs) in \code{qLBA}. Default is
#'   \code{c(0, 10)}.
#' @param scale_p logical. Should entered probabilities automatically be scaled
#'   by maximally predicted probability? Default is \code{FALSE}. Convenience
#'   argument for obtaining predicted quantiles. Can be slow as the maximally
#'   predicted probability is calculated individually for each \code{p}.
#' @param scale_max numerical scalar. Value at which maximally predicted RT
#'   should be calculated if \code{scale_p} is \code{TRUE}.
#'   
#' @details
#' 
#' For convenience, all functions (with the exception of \code{rdiffusion})
#' allow that the first argument is a \code{data.frame} containing the
#' information of the first and second argument in two columns (i.e.,
#' \code{rt}/\code{p} and \code{response}). Other columns will be ignored. This
#' allows, for example, to pass the \code{data.frame} generated by \code{rLBA}
#' directly to \code{pLBA}. See examples.
#' 
#' \subsection{Parameters}{ The following arguments are allowed as \code{...}
#' drift rate parameters: \itemize{ \item \code{mean_v,sd_v} mean and standard
#' deviation of normal distribution for drift rate (\code{norm}). See
#' \code{\link{Normal}} \item \code{shape_v,rate_v,scale_v} shape, rate, and
#' scale of gamma (\code{gamma}) and scale and shape of Frechet (\code{frechet})
#' distributions for drift rate. See \code{\link{GammaDist}} or
#' \code{\link[evd]{frechet}}. For Gamma, scale = 1/shape and shape = 1/scale. 
#' \item \code{meanlog_v,sdlog_v} mean and standard deviation of lognormal
#' distribution on the log scale for drift rate (\code{lnorm}). See
#' \code{\link{Lognormal}}. }
#' 
#' As described above, the accumulator parameters can either be given as a
#' numeric vector or a list. If a numeric vector is passed each element of the
#' vector corresponds to one accumulator. If a list is passed each list element
#' corresponds to one accumulator allowing trialwise driftrates. The shorter
#' parameter will be recycled as necessary (and also the elements of the list to
#' match the length of \code{rt}).
#' 
#' The other LBA parameters (i.e., \code{A}, \code{b}, and \code{t0}, with the
#' exception of \code{st0}) can either be a single numeric vector (which will be
#' recycled to reach \code{length(rt)} or \code{length(n)} for trialwise
#' parameters) \emph{or} a \code{list} of such vectors in which each list
#' element corresponds to the parameters for this accumulator (i.e., the list
#' needs to be of the same length as there are accumulators). Each list will
#' also be recycled to reach \code{length(rt)} for trialwise parameters per
#' accumulator.
#' 
#' To make the difference between both paragraphs clear: Whereas for the
#' accumulators both a single vector or a list corresponds to different
#' accumulators, only the latter is true for the other parameters. For those
#' (i.e., \code{A}, \code{b}, and \code{t0}) a single vector always corresponds
#' to trialwise values and a list must be used for accumulator wise values.
#' 
#' \code{st0} can only vary trialwise (via a vector). And it should be noted
#' that \code{st0} not equal to zero will considerably slow done everything. }
#' 
#' \subsection{Quantile Function}{ Due to the bivariate nature of the LBA,
#' single accumulators only return defective CDFs that do not reach 1. Only the
#' sum of all accumulators reaches 1. Therefore, \code{qLBA} can only return
#' quantiles/RTs for any accumulator up to the maximal probability of that
#' accumulator's CDF. This can be obtained by evaluating the CDF at \code{Inf}.
#' 
#' As a conveniece for the user, if \code{scale_p = TRUE} in the call to
#' \code{qLBA} the desired probabilities are automatically scaled by the maximal
#' probability for the corresponding response. Note that this can be slow as the
#' maximal probability is calculated separately for each desired probability.
#' See examples.
#' 
#' Also note that quantiles (i.e., predicted RTs) are obtained by numerically
#' minimizing the absolute difference between desired probability and the value
#' returned from \code{pLBA} using \code{\link{optimize}}. If the difference
#' between the desired probability and probability corresponding to the returned
#' quantile is above a certain threshold (currently 0.0001) no quantile is
#' returned but \code{NA}. This can be either because the desired quantile is
#' above the maximal probability for this accumulator or because the limits for
#' the numerical integration are too small (default is \code{c(0, 10)}). }
#' 
#' \subsection{RNG}{ For random number generation at least one of the
#' distribution parameters (i.e., \code{mean_v}, \code{sd_v}, \code{shape_v},
#' \code{scale_v}, \code{rate_v}, \code{meanlog_v}, and \code{sdlog_v}) should
#' be of length > 1 to receive RTs from multiple responses. Shorter vectors are
#' recycled as necessary.\cr Note that for random number generation from a
#' normal distribution for the driftrate the number of returned samples may be
#' less than the number of requested samples if \code{posdrifts==FALSE}. }
#' 
#' 
#' @return \code{dLBA} returns the density (PDF), \code{pLBA} returns the
#'   distribution function (CDF), \code{qLBA} returns the quantile/RT,
#'   \code{rLBA} return random response times and responses (in a
#'   \code{data.frame}).
#'   
#'   The length of the result is determined by \code{n} for \code{rLBA}, equal
#'   to the length of \code{rt} for \code{dLBA} and \code{pLBA}, and equal to
#'   the length of \code{p} for \code{qLBA}.
#'   
#'   The distribution parameters (as well as \code{response}) are recycled to
#'   the length of the result. In other words, the functions are completely
#'   vectorized for all parameters and even the response.
#'   
#' @note These are the top-level functions intended for end-users. To obtain the
#'   density and cumulative density the race functions are called for each
#'   response time with the corresponding winning accumulator as first
#'   accumulator (see \code{\link{LBA-race}}).
#'   
#' @references
#' 
#' Brown, S. D., & Heathcote, A. (2008). The simplest complete model of choice
#' response time: Linear ballistic accumulation. \emph{Cognitive Psychology},
#' 57(3), 153-178. doi:10.1016/j.cogpsych.2007.12.002
#' 
#' Donkin, C., Averell, L., Brown, S., & Heathcote, A. (2009). Getting more from
#' accuracy and response time data: Methods for fitting the linear ballistic
#' accumulator. \emph{Behavior Research Methods}, 41(4), 1095-1110.
#' doi:10.3758/BRM.41.4.1095
#' 
#' Heathcote, A., & Love, J. (2012). Linear deterministic accumulator models of
#' simple choice. \emph{Frontiers in Psychology}, 3, 292.
#' doi:10.3389/fpsyg.2012.00292
#' 
#' @name LBA
#' @importFrom stats optimize uniroot
#'   
#' @example examples/examples.lba.R
#'   
NULL

# this functions takes the argument as entered by the user and always returns a
# list of length n_v in which each element is of length nn. This ensures that
# for each parameter we have a list of length equal to the number of
# accumulators with each element of length equal to the number of trials. This
# consistency will be exploited when passing to the n1functions.
check_i_arguments <- function(arg, nn, n_v, dots = FALSE) {
  mc <- match.call()
  varname <- sub("dots$", "", deparse(mc[["arg"]]), fixed = TRUE)
  if (!is.list(arg)) {
    if ((!is.vector(arg, "numeric")) || (length(arg) < 1)) 
      stop(paste(varname, "needs to be a numeric vector of length >= 1!"))
    if (dots) {
      arg <- as.list(arg)
      arg <- lapply(arg, rep, length.out=nn)
    } else arg <- lapply(seq_len(n_v), function(x) rep(arg, length.out=nn))
  } else {
    if (!dots && (length(arg) != n_v)) 
      stop(paste("if", varname, "is a list, its length needs to correspond to the number of accumulators."))
    for (i in seq_along(arg)) {
      if ((!is.vector(arg[[i]], "numeric")) || (length(arg[[i]]) < 1)) 
        stop(paste0(varname, "[[", i, "]] needs to be a numeric vector of length >= 1!"))
      arg[[i]] <- rep(arg[[i]], length.out=nn)
    }
  }
  #if (length(arg) != n_v) stop(paste("size of", varname, "does not correspond to number of accumulators."))
  return(arg)
}

#' @rdname LBA
#' @export 
dLBA <-  function(rt, response, A, b, t0, ..., st0=0, 
                  distribution = c("norm", "gamma", "frechet", "lnorm"), 
                  args.dist = list(), silent = FALSE) {
  dots <- list(...)
  if (is.null(names(dots))) stop("... arguments need to be named.")
  
  # for convenience accept data.frame as first argument.
  if (is.data.frame(rt)) {
    response <- rt$response
    rt <- rt$rt
  }
  
  response <- as.numeric(response)
  nn <- length(rt)
  n_v <- max(vapply(dots, length, 0))  # Number of responses
  if(!silent) 
    message(paste("Results based on", n_v, "accumulators/drift rates."))
  if (!is.numeric(response) || max(response) > n_v) 
    stop("response needs to be a numeric vector of integers up to number of accumulators.")
  if (any(response < 1)) 
    stop("the first response/accumulator must have value 1.")
  if (n_v < 2) 
    stop("There need to be at least two accumulators/drift rates.")
  distribution <- match.arg(distribution)
  response <- rep(response, length.out = nn)
  A <- check_i_arguments(A, nn=nn, n_v=n_v)
  b <- check_i_arguments(b, nn=nn, n_v=n_v)
  t0 <- check_i_arguments(t0, nn=nn, n_v=n_v)
  switch(distribution, 
         norm = {
           if (any(!(c("mean_v","sd_v") %in% names(dots)))) 
             stop("mean_v and sd_v need to be passed for distribution = \"norm\"")
           dots$mean_v <- check_i_arguments(dots$mean_v, nn=nn, n_v=n_v, dots = TRUE)
           dots$sd_v <- check_i_arguments(dots$sd_v, nn=nn, n_v=n_v, dots = TRUE)
           dots <- dots[c("mean_v","sd_v")]
         },
         gamma = {
           if (!("shape_v" %in% names(dots))) 
             stop("shape_v needs to be passed for distribution = \"gamma\"")
           if ((!("rate_v" %in% names(dots))) & (!("scale_v" %in% names(dots)))) 
             stop("rate_v or scale_v need to be passed for distribution = \"gamma\"")
           dots$shape_v <- check_i_arguments(dots$shape_v, nn=nn, n_v=n_v, dots = TRUE)
           if ("scale_v" %in% names(dots)) {
             dots$scale_v <- check_i_arguments(dots$scale_v, nn=nn, n_v=n_v, dots = TRUE)
             if (is.list(dots$scale_v)) {
               dots$rate_v <- lapply(dots$scale_v, function(x) 1/x)
             } else dots$rate_v <- 1/dots$scale_v
           } else dots$rate_v <- check_i_arguments(dots$rate_v, nn=nn, n_v=n_v, dots = TRUE)
           dots <- dots[c("shape_v","rate_v")]
         },
         frechet = {
           if (any(!(c("shape_v","scale_v") %in% names(dots)))) 
             stop("shape_v and scale_v need to be passed for distribution = \"frechet\"")
           dots$shape_v <- check_i_arguments(dots$shape_v, nn=nn, n_v=n_v, dots = TRUE)
           dots$scale_v <- check_i_arguments(dots$scale_v, nn=nn, n_v=n_v, dots = TRUE)
           dots <- dots[c("shape_v","scale_v")]
         },
         lnorm = {
           if (any(!(c("meanlog_v","sdlog_v") %in% names(dots)))) 
             stop("meanlog_v and sdlog_v need to be passed for distribution = \"lnorm\"")
           dots$meanlog_v <- check_i_arguments(dots$meanlog_v, nn=nn, n_v=n_v, dots = TRUE)
           dots$sdlog_v <- check_i_arguments(dots$sdlog_v, nn=nn, n_v=n_v, dots = TRUE)
           dots <- dots[c("meanlog_v","sdlog_v")]
         }
  )
  #browser()
  for (i in seq_len(length(dots))) {
    if (length(dots[[i]]) < n_v) dots[[i]] <- rep(dots[[i]],length.out=n_v)
  }
  out <- vector("numeric", nn)
  for (i in unique(response)) {
    sel <- response == i
    out[sel] <- do.call(n1PDF, 
                        args = c(rt=list(rt[sel]), 
                                 A = list(lapply(A, "[", i = sel)[c(i, seq_len(n_v)[-i])]), 
                                 b = list(lapply(b, "[", i = sel)[c(i, seq_len(n_v)[-i])]),
                                 t0 = list(lapply(t0, "[", i = sel)[c(i, seq_len(n_v)[-i])]),
                                 lapply(dots, function(x) 
                                   lapply(x, "[", i = sel)[c(i, seq_len(n_v)[-i])]), 
                                 distribution=distribution, 
                                 args.dist=list(args.dist), 
                                 silent=TRUE, st0 = list(st0)))
  }
  return(out)
}


#' @rdname LBA
#' @export 
pLBA <-  function(rt, response, A, b, t0, ..., st0=0, 
                  distribution = c("norm", "gamma", "frechet", "lnorm"), 
                  args.dist = list(), silent = FALSE) {
  dots <- list(...)
  if (is.null(names(dots))) 
    stop("... arguments need to be named.")
  
  # for convenience accept data.frame as first argument.
  if (is.data.frame(rt)) {
    response <- rt$response
    rt <- rt$rt
  }
  
  response <- as.numeric(response)
  nn <- length(rt)
  n_v <- max(vapply(dots, length, 0))  # Number of responses
  if(!silent) message(paste("Results based on", n_v, "accumulators/drift rates."))
  if (!is.numeric(response) || max(response) > n_v) 
    stop("response needs to be a numeric vector of integers up to number of accumulators.")
  if (n_v < 2) 
    stop("There need to be at least two accumulators/drift rates.")
  distribution <- match.arg(distribution)
  response <- rep(response, length.out = nn)
  A <- check_i_arguments(A, nn=nn, n_v=n_v)
  b <- check_i_arguments(b, nn=nn, n_v=n_v)
  t0 <- check_i_arguments(t0, nn=nn, n_v=n_v)
  switch(distribution, 
         norm = {
           if (any(!(c("mean_v","sd_v") %in% names(dots)))) 
             stop("mean_v and sd_v need to be passed for distribution = \"norm\"")
           dots$mean_v <- check_i_arguments(dots$mean_v, nn=nn, n_v=n_v, dots = TRUE)
           dots$sd_v <- check_i_arguments(dots$sd_v, nn=nn, n_v=n_v, dots = TRUE)
           dots <- dots[c("mean_v","sd_v")]
         },
         gamma = {
           if (!("shape_v" %in% names(dots))) 
             stop("shape_v needs to be passed for distribution = \"gamma\"")
           if ((!("rate_v" %in% names(dots))) & (!("scale_v" %in% names(dots)))) 
             stop("rate_v or scale_v need to be passed for distribution = \"gamma\"")
           dots$shape_v <- check_i_arguments(dots$shape_v, nn=nn, n_v=n_v, dots = TRUE)
           if ("scale_v" %in% names(dots)) {
             dots$scale_v <- check_i_arguments(dots$scale_v, nn=nn, n_v=n_v, dots = TRUE)
             if (is.list(dots$scale_v)) {
               dots$rate_v <- lapply(dots$scale_v, function(x) 1/x)
             } else dots$rate_v <- 1/dots$scale_v
           } else dots$rate_v <- check_i_arguments(dots$rate_v, nn=nn, n_v=n_v, dots = TRUE)
           dots <- dots[c("shape_v","rate_v")]
         },
         frechet = {
           if (any(!(c("shape_v","scale_v") %in% names(dots)))) 
             stop("shape_v and scale_v need to be passed for distribution = \"frechet\"")
           dots$shape_v <- check_i_arguments(dots$shape_v, nn=nn, n_v=n_v, dots = TRUE)
           dots$scale_v <- check_i_arguments(dots$scale_v, nn=nn, n_v=n_v, dots = TRUE)
           dots <- dots[c("shape_v","scale_v")]
         },
         lnorm = {
           if (any(!(c("meanlog_v","sdlog_v") %in% names(dots)))) 
             stop("meanlog_v and sdlog_v need to be passed for distribution = \"lnorm\"")
           dots$meanlog_v <- check_i_arguments(dots$meanlog_v, nn=nn, n_v=n_v, dots = TRUE)
           dots$sdlog_v <- check_i_arguments(dots$sdlog_v, nn=nn, n_v=n_v, dots = TRUE)
           dots <- dots[c("meanlog_v","sdlog_v")]
         }
  )
  #browser()
  for (i in seq_len(length(dots))) {
    if (length(dots[[i]]) < n_v) dots[[i]] <- rep(dots[[i]],length.out=n_v)
  }
  out <- vector("numeric", nn)
  for (i in unique(response)) {
    sel <- response == i
    #if(!all(rt[sel] == sort(rt[sel])))  stop("rt needs to be sorted (per response)")
    out[sel] <- do.call(n1CDF, 
                        args = c(rt=list(rt[sel]), 
                                 A = list(lapply(A, "[", i = sel)[c(i, seq_len(n_v)[-i])]), 
                                 b = list(lapply(b, "[", i = sel)[c(i, seq_len(n_v)[-i])]),
                                 t0 = list(lapply(t0, "[", i = sel)[c(i, seq_len(n_v)[-i])]),
                                 lapply(dots, function(x) 
                                   lapply(x, "[", i = sel)[c(i, seq_len(n_v)[-i])]), 
                                 distribution=distribution, 
                                 args.dist=list(args.dist), 
                                 silent=TRUE, st0 = list(st0)))
  }
  return(out)
}

# rt, response, A, b, t0, ..., st0=0, distribution = c("norm", "gamma", "frechet", "lnorm"), args.dist = list(), silent = FALSE
inv_cdf_lba <- function(x, response, A, b, t0, ..., st0, 
                        distribution, args.dist, value, abs = TRUE) {
  if (abs) abs(value - pLBA(rt=x, response=response, 
                            A=A, b = b, t0 = t0, ..., st0=st0, 
                            distribution=distribution, 
                            args.dist=args.dist, 
                            silent=TRUE))
  else (value - pLBA(rt=x, response=response, A=A, b = b, t0 = t0, ..., st0=st0, 
                     distribution=distribution, 
                     args.dist=args.dist, 
                     silent=TRUE))
}


#' @rdname LBA
#' @export 
qLBA <-  function(p, response, A, b, t0, ..., st0=0, 
                  distribution = c("norm", "gamma", "frechet", "lnorm"), 
                  args.dist = list(), silent = FALSE, interval = c(0, 10),
                  scale_p = FALSE, scale_max = Inf) {
  dots <- list(...)
  if (is.null(names(dots))) stop("... arguments need to be named.")
  
  # for convenience accept data.frame as first argument. 
  if (is.data.frame(p)) {
    response <- p$response
    p <- p$p
  }
  
  response <- as.numeric(response)
  nn <- length(p)
  n_v <- max(vapply(dots, length, 0))  # Number of responses
  if(!silent) 
    message(paste("Results based on", n_v, "accumulators/drift rates."))
  if (!is.numeric(response) || max(response) > n_v) 
    stop("response needs to be a numeric vector of integers up to number of accumulators.")
  if (any(response < 1)) 
    stop("the first response/accumulator must have value 1.")
  if (n_v < 2) 
    stop("There need to be at least two accumulators/drift rates.")
  distribution <- match.arg(distribution)
  response <- rep(response, length.out = nn)
  A <- check_i_arguments(A, nn=nn, n_v=n_v)
  b <- check_i_arguments(b, nn=nn, n_v=n_v)
  t0 <- check_i_arguments(t0, nn=nn, n_v=n_v)
  st0 <- rep(st0, length.out = nn)
  out <- vector("numeric", nn)
  p <- unname(p)
  
  for (i in seq_len(nn)) {
    if (scale_p)
      max_p <- do.call(
        pLBA,
        args = c(
          rt = list(scale_max),
          response = list(response[i]),
          A = ret_arg(A, i),
          b = ret_arg(b, i),
          t0 = ret_arg(t0, i),
          sapply(dots, function(z, i)
            sapply(z, ret_arg2, which = i,
                   simplify = FALSE), i =
              i,
            simplify = FALSE),
          args.dist = list(args.dist),
          distribution = distribution,
          st0 = list(st0[i]),
          silent = TRUE
        )
      )
    else
      max_p <- 1
    tmp <- do.call(
      optimize,
      args = c(
        f = inv_cdf_lba,
        interval = list(interval),
        response = list(response[i]),
        A = ret_arg(A, i),
        b = ret_arg(b, i),
        t0 = ret_arg(t0, i),
        sapply(dots, function(z, i) 
          sapply(z, ret_arg2, which = i, simplify = FALSE), 
          i = i, simplify = FALSE),
        args.dist = list(args.dist),
        distribution = distribution,
        st0 = list(st0[i]),
        value = p[i] * max_p,
        tol = .Machine$double.eps ^ 0.5
      )
    )
    if (tmp$objective > 0.0001) {
      tmp <-
        do.call(
          optimize,
          args = c(
            f = inv_cdf_lba,
            interval = list(c(min(interval), max(interval) / 2)),
            response = list(response[i]),
            A = ret_arg(A, i),
            b = ret_arg(b, i),
            t0 = ret_arg(t0, i),
            sapply(dots, function(z, i)
              sapply(z, ret_arg2, which = i, simplify = FALSE), 
              i = i, simplify = FALSE),
            args.dist = list(args.dist),
            distribution = distribution,
            st0 = list(st0[i]),
            value = p[i] * max_p,
            tol = .Machine$double.eps ^ 0.5
          )
        )
    }
    if (tmp$objective > 0.0001) {
      try({
        uni_tmp <-
          do.call(
            uniroot,
            args = c(
              f = inv_cdf_lba,
              interval = list(c(min(interval), max(interval) / 2)),
              response = list(response[i]),
              A = ret_arg(A, i),
              b = ret_arg(b, i),
              t0 = ret_arg(t0, i),
              sapply(dots, function(z, i)
                sapply(z, ret_arg2, which = i, simplify = FALSE), 
                i = i, simplify = FALSE),
              args.dist = list(args.dist),
              distribution = distribution,
              st0 = list(st0[i]),
              value = p[i] * max_p,
              tol = .Machine$double.eps ^ 0.5,
              abs = FALSE
            )
          )
        tmp$objective <- uni_tmp$f.root
        tmp$minimum <- uni_tmp$root
      }, silent = TRUE)
    }
    if (tmp$objective > 0.0001) {
      tmp[["minimum"]] <- NA
      warning(
        "Cannot obtain RT that is less than 0.0001 away from desired p = ",
        p[i],
        ".\nIncrease/decrease interval or obtain for different boundary.",
        call. = FALSE
      )
    }
    out[i] <- tmp[["minimum"]]
  }
  return(out
  )
}



#' @rdname LBA
#' @export
rLBA <- function(n,A,b,t0, ..., st0=0, distribution = c("norm", "gamma", "frechet", "lnorm"), args.dist = list(), silent = FALSE) {
  dots <- list(...)
  if (is.null(names(dots))) stop("... arguments need to be named.")
  if (any(names(dots) == "")) stop("all ... arguments need to be named.")
  n_v <- max(vapply(dots, length, 0))  # Number of responses
  if(!silent) message(paste("Results based on", n_v, "accumulators/drift rates."))
  #if (n_v < 2) stop("There need to be at least two accumulators/drift rates.")
  nn <- n
  distribution <- match.arg(distribution)
  A <- check_i_arguments(A, nn=nn, n_v=n_v)
  b <- check_i_arguments(b, nn=nn, n_v=n_v)
  t0 <- check_i_arguments(t0, nn=nn, n_v=n_v)
  st0 <- rep(unname(st0), length.out = nn)
  switch(distribution, 
         norm = {
           rng <- rlba_norm
           if (any(!(c("mean_v","sd_v") %in% names(dots)))) 
             stop("mean_v and sd_v need to be passed for distribution = \"norm\"")
           dots$mean_v <- check_i_arguments(dots$mean_v, nn=nn, n_v=n_v, dots = TRUE)
           dots$sd_v <- check_i_arguments(dots$sd_v, nn=nn, n_v=n_v, dots = TRUE)
           dots <- dots[c("mean_v","sd_v")]
         },
         gamma = {
           rng <- rlba_gamma
           if (!("shape_v" %in% names(dots))) 
             stop("shape_v needs to be passed for distribution = \"gamma\"")
           if ((!("rate_v" %in% names(dots))) & (!("scale_v" %in% names(dots)))) 
             stop("rate_v or scale_v need to be passed for distribution = \"gamma\"")
           dots$shape_v <- check_i_arguments(dots$shape_v, nn=nn, n_v=n_v, dots = TRUE)
           if ("scale_v" %in% names(dots)) {
             dots$scale_v <- check_i_arguments(dots$scale_v, nn=nn, n_v=n_v, dots = TRUE)
             if (is.list(dots$scale_v)) {
               dots$rate_v <- lapply(dots$scale_v, function(x) 1/x)
             } else dots$rate_v <- 1/dots$scale_v
           } else dots$rate_v <- check_i_arguments(dots$rate_v, nn=nn, n_v=n_v, dots = TRUE)
           dots <- dots[c("shape_v","rate_v")]
         },
         frechet = {
           rng <- rlba_frechet
           if (any(!(c("shape_v","scale_v") %in% names(dots)))) 
             stop("shape_v and scale_v need to be passed for distribution = \"frechet\"")
           dots$shape_v <- check_i_arguments(dots$shape_v, nn=nn, n_v=n_v, dots = TRUE)
           dots$scale_v <- check_i_arguments(dots$scale_v, nn=nn, n_v=n_v, dots = TRUE)
           dots <- dots[c("shape_v","scale_v")]
         },
         lnorm = {
           rng <- rlba_lnorm
           if (any(!(c("meanlog_v","sdlog_v") %in% names(dots)))) 
             stop("meanlog_v and sdlog_v need to be passed for distribution = \"lnorm\"")
           dots$meanlog_v <- check_i_arguments(dots$meanlog_v, nn=nn, n_v=n_v, dots = TRUE)
           dots$sdlog_v <- check_i_arguments(dots$sdlog_v, nn=nn, n_v=n_v, dots = TRUE)
           dots <- dots[c("meanlog_v","sdlog_v")]
         }
  )
  for (i in seq_len(length(dots))) {
    if (length(dots[[i]]) < n_v) dots[[i]] <- rep(dots[[i]],length.out=n_v)
  }
  
  tmp_acc <- as.data.frame(dots, optional = TRUE)
  colnames(tmp_acc) <- sub("\\.c\\(.+", "", colnames(tmp_acc))
  
  parameter_char <- apply(tmp_acc, 1, paste0, collapse = "\t")
  parameter_factor <- factor(parameter_char, levels = unique(parameter_char))
  parameter_indices <- split(seq_len(nn), f = parameter_factor)
  
  out <- vector("list", length(parameter_indices))
  for (i in seq_len(length(parameter_indices))) {
    ok_rows <- parameter_indices[[i]]
    tmp_dots <- lapply(dots, function(x) sapply(x, "[[", i = ok_rows[1]))
    out[[i]] <- do.call(rng, 
                        args = c(n=list(length(ok_rows)), 
                                 A = list(sapply(A, "[", i = ok_rows)), 
                                 b = list(sapply(b, "[", i = ok_rows)), 
                                 t0 = list(sapply(t0, "[", i = ok_rows)), 
                                 st0 = list(st0[ok_rows]), 
                                 tmp_dots, args.dist))
  }
  out <- do.call("rbind", out)
  as.data.frame(out)
}

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rtdists documentation built on Jan. 7, 2022, 5:16 p.m.