R/is.R

In cvasi: Calibration, Validation, and Simulation of TKTD Models

# checks if all arguments are of type parameter_set
#' @importFrom methods is
is_parameter_set <- function(x) {
  if(is.list(x))
    return(sapply(x, is_parameter_set))
  is(x, "ParameterSet")
}

# checks if a parameter_set objects matches a certain scenario
is_param_match <- function(scenario, param, ignore_tags=FALSE) {
  if(is.vector(scenario))
    stop("scenario vectors not supported")
  if(!is_scenario(scenario))
    stop("scenario must be of type EffectScenario")
  if(is.vector(param))
    return(sapply(param, function(ps) is_param_match(scenario, ps)))
  if(!is_parameter_set(param))
    stop("param must be of type parameter_set")

  # if both tags are NA, then match by name only
  if(ignore_tags | all(is.na(get_tag(c(scenario, param)))))
    return(get_model(scenario) == get_model(param))
  # if one tag is NA, then no match possible
  if(any(is.na(get_tag(c(scenario, param)))))
    return(FALSE)
  # otherwise match by name and tag
  get_model(scenario) == get_model(param) & get_tag(scenario) == get_tag(param)
}

#' Test if argument is an effect scenario
#'
#' Supports vectorized arguments.
#'
#' @param x Some value or object
#' @return vector of `logical` values
#' @export
#' @examples
#' # returns `TRUE`
#' is_scenario(minnow_it)
#'
#' # returns `FALSE`
#' is_scenario(list())
#'
is_scenario <- function(x) {
  if(is.list(x)) {
    if(length(x) > 0)
      return(sapply(x, is_scenario))
  }
  is(x, "EffectScenario")
}

is_sequence <- function(x) {
  if(is.list(x)) {
    if(length(x) > 0)
      return(sapply(x, is_sequence))
  }

  is(x, "ScenarioSequence")
}

is_caliset <- function(x) {
  if(is.list(x))
    return(sapply(x, is_caliset))

  is(x, "CalibrationSet")
}

is_exp_series <- function(x) {
  if(is.list(x))
    return(sapply(x, is_exp_series))
  is(x, "ExposureSeries")
}

#' Test if argument is a GUTS scenario
#'
#' @param x vector of `EffectScenario` objects
#'
#' @return vector of `logical` values
#' @export
#' @examples
#' # returns `TRUE`
#' is_guts(minnow_it)
#' is_guts(GUTS_RED_IT())
#'
#' # returns `c(TRUE,TRUE,TRUE)`
#' is_guts(c(minnow_it, minnow_it, minnow_it))
#'
#' # returns `FALSE`
#' is_guts_sd(minnow_it)
is_guts <- function(x) {
  if(is.list(x)) {
    if(length(x) > 0)
      return(sapply(x, is_guts))
  }
  if(!is_scenario(x))
    return(FALSE)

  startsWith(get_model(x),"GUTS-")
}

#' @export
#' @describeIn is_guts Deprecated alias.
is_GUTS <- function(x) {
  is_guts(x)
}

#' @describeIn is_guts Test if argument is a GUTS-IT scenario
#' @export
is_guts_it <- function(x) {
  if(is.list(x)) {
    if(length(x) > 0)
      return(sapply(x, is_guts_it))
  }
  if(!is_scenario(x))
    return(FALSE)

  name <- get_model(x)
  startsWith(name,"GUTS-") & endsWith(name,"-IT")
}

#' @export
#' @describeIn is_guts Deprecated alias.
is_GUTS_IT <- function(x) {
  is_guts_it(x)
}

#' @describeIn is_guts Test if argument is a GUTS-SD scenario
#' @export
is_guts_sd <- function(x) {
  if(is.list(x)) {
    if(length(x) > 0)
      return(sapply(x, is_guts_sd))
  }
  if(!is_scenario(x))
    return(FALSE)

  name <- get_model(x)
  startsWith(name,"GUTS-") & endsWith(name,"-SD")
}

#' @export
#' @describeIn is_guts Deprecated alias.
is_GUTS_SD <- function(x) {
  is_guts_sd(x)
}

#' Test if argument is a DEB scenario
#'
#' @param x vector of `EffectScenario` objects
#' @return vector of `logical` values
#' @export
is_deb <- function(x) {
  if(is.list(x)) {
    if(length(x) > 0)
      return(sapply(x, is_deb))
  }
  if(!is_scenario(x))
    return(FALSE)

  startsWith(get_model(x), "DEB")
}

#' @export
#' @describeIn is_deb Deprecated alias.
is_DEB <- function(x) {
  is_deb(x)
}

#' Test if argument is a Lemna scenario
#'
#' @param x vector of [scenario] objects
#' @return vector of logical values
#' @export
is_lemna <- function(x) {
  if(is.list(x)) {
    if(length(x) > 0)
      return(sapply(x, is_lemna))
  }
  if(!is_scenario(x))
    return(FALSE)

  is(x, "Lemna")
}

#' @export
#' @describeIn is_lemna Deprecated alias.
is_Lemna <- function(x) {
  is_lemna(x)
}

#' Test if argument is a LemnaThreshold scenario
#'
#' `r lifecycle::badge("deprecated")`
#'
#' @param x vector of [scenarios] objects
#' @return vector of `logical` values
#' @seealso [is_lemna()]
#' @export
is_LemnaThreshold <- function(x) {
  lifecycle::deprecate_warn("1.5.0", "is_LemnaThreshold()")

  if(is.list(x)) {
    if(length(x) > 0)
      return(sapply(x, is_LemnaThreshold))
  }
  if(!is_scenario(x))
    return(FALSE)

  get_model(x) == "Lemna_SchmittThold"
}

# Check if an exposure series is complete, i.e. regular
#
is_regular_series <- function(x) {
  if(is(x,"ExposureSeries")) {
    if("regular.series" %in% names(x@meta))
      return(x@meta$regular.series)
    return(FALSE)
  }
  else if(is.vector(x) & is.numeric(x) & length(x) > 0) {
    x_diff <- unique(diff(x))
    if(length(x_diff) <= 1)
      return(TRUE)

    # disregard numerical issuesm i.e. very small deviations from a single value
    x_min <- min(x_diff[which(x_diff > 0)])
    return(all(1 - abs(x_diff/x_min) < 1e-10))
  }
  stop("type not supported")
}

# Check if scenarios requires a control for effect calculation
#
is_control_required <- function(x) {
  if(is.vector(x) & length(x) > 1)
    return(sapply(x, is_control_required))
  if(is_sequence(x))
    return(is_control_required(x[[1]]))
  if(!is_scenario(x))
    stop("Argument `x` must be a scenario")

  x@control.req
}

# Check if an R package is locally available
#
# The check is case-sensitive
# @param name `character`, name of an R package, e.g. 'dplyr'
# @return `logical`, `TRUE` if package is installed, else `FALSE`
#' @importFrom utils installed.packages
is_pckg_avail <- function(name) {
  require(package=name, quietly=TRUE, character.only=TRUE)
}

# Check if an exposure series represents zero/no exposure
#
# @param x `EffectScenario` or `ExposureSeries` object
# @return `logical`, `TRUE` if no/zero exposure
is_no_exposure <- function(x) {
  if(is.list(x))
    return(sapply(x, is_no_exposure))
  if(all(is_sequence(x))) # ordering of these checks is important! due to length(sequence) > 1 in most cases
    return(all(sapply(x@scenarios, is_no_exposure)))
  if(length(x) > 1)
    return(sapply(x, is_no_exposure))

  if(is.vector(x))
    x <- x[[1]] # unbox
  if(is(x, "EffectScenario"))
    x <- x@exposure
  if(!is(x, "ExposureSeries"))
    return(FALSE)
  if(nrow(x@series) == 0) {
    return(TRUE)
  } else if(nrow(x@series) == 1) {
    if(x@series[[1,2]] == 0)
      return(TRUE)
  } else {
    if(all(x@series[,2] == 0))
      return(TRUE)
  }
  return(FALSE)
}