R/distributions.R

In jmsigner/amt: Animal Movement Tools

valid_ta_distr <- function(...) {
  c("vonmises", "unif")
}

valid_sl_distr <- function(...) {
  c("exp", "gamma", "unif", "hnorm", "lnorm")
}

valid_distr <- function(...) {
  c(valid_ta_distr(), valid_sl_distr())
}


valid_distr_params <- function(dist_name, params) {
  if (dist_name == "vonmises") {
    return(all(c("kappa", "mu") %in% names(params)))
  } else if (dist_name == "unif") {
    return(all(c("min", "max") %in% names(params)))
  } else if (dist_name == "exp") {
    return(c("rate") %in% names(params))
  } else if (dist_name == "hnorm") {
    return(c("sd") %in% names(params))
  } else if (dist_name == "lnorm") {
    return(all(c("meanlog", "sdlog") %in% names(params)))
  } else if (dist_name == "gamma") {
    return(all(c("shape", "rate") %in% names(params)) |
      all(c("shape", "scale") %in% names(params)))
  }
  FALSE
}

#' Display available distributions for step lengths and turn angles.
#'
#' @param which_dist `[char(1)="all"]{"all", "ta", "sl"}` \cr Should `all`
#'   distributions be returned, or only distributions for turn angles (`ta`) or
#'   step lengths (`sl`).
#' @param names_only `[logical(1)=FALSE]` \cr Indicates if only the names of
#'   distributions should be returned.
#' @param ... none implemented.
#' @export
#' @return A `tibble` with the purpose of the distribution (turn angles \[ta\] or step length \[sl\]) and the distribution name.
#'
available_distr <- function(which_dist = "all", names_only = FALSE, ...) {

  checkmate::check_character(which_dist, len = 1)

  ta <- tibble::tibble(what = "ta", dist = valid_ta_distr())
  sl <- tibble::tibble(what = "sl", dist = valid_sl_distr())
  if (which_dist == "ta") {
    ret <- ta
  } else if (which_dist == "sl") {
    ret <- sl
  } else if (which_dist == "all") {
    ret <- dplyr::bind_rows(ta, sl)
  }
  if (names_only) {
    dplyr::pull(ret, 2)
  } else {
    ret
  }
}


#' Functions create statistical distributions
#'
#' `make_distributions` creates a distribution suitable for using it with integrated step selection functions
#'
#' @param name `[char(1)]` \cr Short name of distribution. See `available_distr()`
#'   for all currently implemented distributions.
#' @param params `[list]` \cr A named list with parameters of the distribution.
#' @param vcov `[matrix]` \cr A matrix with variance and covariances.
#' @param ... none implemented.
#' @export
#' @name distributions
#' @return A list of class `amt_distr` that contains the name (`name`) and parameters (`params`) of a distribution.

make_distribution <- function(name, params, vcov = NULL, ...) {
  checkmate::check_character(name, len = 1)
  checkmate::check_list(params)

  # check name
  if (!name %in% available_distr(names_only = TRUE)) {
    stop(paste(name, "is not implemented."))
  }

  # check params
  if (!valid_distr_params(name, params)) {
    stop(paste("Parameters for ", name, "are not valid."))
  }
  out <- list(name = name,
              params = params,
              vcov = vcov)

  class(out) <- c(paste0(name, "_distr"),
                  if (name %in% valid_ta_distr()) "ta_distr" else "sl_distr",
                  "amt_distr", "list")
  out
}

#' @export
#' @param rate `[double(1)>0]` \cr The rate of the exponential distribution.
#' @rdname distributions
make_exp_distr <- function(rate = 1) {
  checkmate::check_number(rate, lower = 0)
  make_distribution(name = "exp", params = list(rate = rate))
}

#' @export
#' @param sd `[double(1)>0]` \cr The standard deviation of the half-normal distribution.
#' @rdname distributions
make_hnorm_distr <- function(sd = 1) {
  checkmate::check_number(sd, lower = 0)
  make_distribution(name = "hnorm", params = list(sd = sd))
}

#' @export
#' @param meanlog `[double(1)>0]` \cr The standard deviation of the half-normal distribution.
#' @param sdlog `[double(1)>0]` \cr The standard deviation of the half-normal distribution.
#' @rdname distributions
make_lnorm_distr <- function(meanlog = 0, sdlog = 1) {
  checkmate::check_number(meanlog)
  checkmate::check_number(sdlog, lower = 0)
  make_distribution(name = "lnorm", params = list(meanlog = meanlog, sdlog = sdlog))
}

#' @export
#' @rdname distributions
#' @param min `[double(1)]` \cr The minimum of the uniform distribution.
#' @param max `[double(1)]` \cr The minimum of the uniform distribution.
make_unif_distr <- function(min = -pi, max = pi) {
  checkmate::check_number(min)
  checkmate::check_number(max)
  make_distribution(name = "unif", params = list(min = min, max = max))
}

#' @export
#' @rdname distributions
#' @param kappa `[double(1)>=0]` \cr Concentration parameter of the von Mises distribution.
make_vonmises_distr <- function(kappa = 1, vcov = NULL) {
  checkmate::check_number(kappa, lower = 0)
  mu <- circular::circular(x = 0)
  make_distribution(name = "vonmises", params = list(kappa = kappa, mu = mu),
                    vcov = vcov)
}

#' @export
#' @rdname distributions
#' @param shape,scale `[double(1)>=0]` \cr Shape and scale of the Gamma distribution
make_gamma_distr <- function(shape = 1, scale = 1, vcov = NULL) {
  checkmate::check_number(shape)
  checkmate::check_number(scale)
  make_distribution(name = "gamma", params = list(shape = shape, scale = scale),
                    vcov = vcov)
}

#' Sample random numbers
#'
#' Sample radom numbers from a distribution created within the `amt` package.

#' @param x `[amt_distr]` \cr A distribution object.
#' @param n `[integer(1)=100]{>0}` \cr The number of random draws.
#' @param ... none implemented.
#' @return A numermic vector.
#' @export
random_numbers <- function(x, n = 100, ...) {
  UseMethod("random_numbers")
}

#' @export
random_numbers.vonmises_distr <- function(x, n = 100, ...) {

  suppressWarnings(
    x <- do.call(circular::rvonmises, c(list(n = n), x$params)))

  # turn angles for new steps
  x <- x %% (2 * pi)
  ifelse(x > base::pi, x - (2 * base::pi), x)
}

#' @export
random_numbers.hnorm_distr <- function(x, n = 100, ...) {
  base::abs(stats::rnorm(n, mean = 0, sd = x$params$sd))
}

#' @export
random_numbers.amt_distr <- function(x, n = 100, ...) {
  do.call(paste0("r", x$name), c(list(n = n), x$params))
}



# Fit distr ---------------------------------------------------------------

#' Fit distribution to data
#'
#' Wrapper to fit a distribution to data. Currently implemented distributions
#' are the exponential distribution (`exp`), the gamma distribution (`gamma`)
#' and the von Mises distribution (`vonmises`).
#'
#' @param x `[numeric(>1)]` \cr The observed data.
#' @param dist_name `[character(1)]{"exp", "gamma", "unif", "vonmises"}` \cr The name of the
#'   distribution.
#' @param na.rm `[logical(1)=TRUE]` \cr Indicating whether `NA` should be
#'   removed before fitting the distribution.
#'
#' @return An `amt_distr` object, which consists of a list with the `name` of
#'   the distribution and its parameters (saved in `params`).
#' @export
#'
#' @examples
#' set.seed(123)
#' dat <- rexp(1e3, 2)
#' fit_distr(dat, "exp")
fit_distr <- function(x, dist_name, na.rm = TRUE) {

  checkmate::check_numeric(x)
  checkmate::check_character(dist_name, len = 1)
  if(!dist_name %in% valid_distr()) {
    stop("Distribution is currently not supported.")
  }

  if (na.rm) {
    x <- x[!is.na(x)]
  }


  # TODO: also save SE?
  switch(dist_name,
    gamma = {
      if (any(x == 0)) {
        sl_min <- min(x[x !=0])
        x[x == 0] <- sl_min
        base::message(paste0("Steps with length 0 are present. This will lead to an error when fitting a gamma distribution. 0 step lengths are replaced with the smallest non zero step length, which is: ", sl_min))
      }

      #  get closed form estimates as starting values for the optimation
      n <- length(x)
      t1 <- n * sum(x * log(x)) - sum(log(x)) * sum(x)
      shape_closed <- (n * sum(x)) / t1
      scale_closed <- 1/n^2 * t1

      fit <- fitdistrplus::fitdist(
        x, "gamma", keepdata = FALSE,
        start = list(scale = scale_closed, shape = shape_closed))

      make_gamma_distr(
        shape = unname(fit$estimate["shape"]),
        scale = unname(fit$estimate["scale"]),
        vcov = stats::vcov(fit)
      )
    },
    exp = {
      fit <- fitdistrplus::fitdist(x, "exp", keepdata = FALSE)
      make_exp_distr(rate = fit$estimate["rate"])
    },
    lnorm = {
      fit <- fitdistrplus::fitdist(x, "lnorm", keepdata = FALSE)
      make_lnorm_distr(meanlog = fit$estimate["meanlog"],
                       sdlog = fit$estimate["sdlog"])
    },
    hnorm = {
      # following: https://en.wikipedia.org/wiki/Half-normal_distribution#Parameter_estimation
      make_hnorm_distr(sd = sqrt(1/length(x) * sum(x^2)))
    },
    unif = {
      fit <- fitdistrplus::fitdist(x, "unif", keepdata = FALSE)
      make_unif_distr(min = min(x), max = max(x))
    },
    vonmises = {
      xx <- circular::as.circular(
        x, type = "angles", units = "radians", template = "none",
        modulo = "asis", zero = 0, rotation = "counter")
      fit <- circular::mle.vonmises(xx)
      make_vonmises_distr(kappa = fit$kappa, vcov = matrix(fit$se.kappa))
    }
  )
}

# Update distr ------------------------------------------------------------

#' Update movement distributions
#'
#' Update tentative step length or turning angle distribution from a fitted iSSF.
#'
#' @param object `[fit_clogit]` \cr A fitted iSSF model.
#' @param beta_sl `[character]` \cr The name of the coefficient of the step length.
#' @param beta_log_sl `[character]` \cr The name of the coefficient of the log of the step length.
#' @param beta_sl_sq `[character]` \cr The name of the coefficient of the square of the step length.
#' @param beta_log_sl_sq `[character]` \cr The name of the coefficient of the square of log of the step length.
#' @param beta_cos_ta `[character]` \cr The name of the coefficient of cosine of the turning angle.
#' @template dots_none
#'
#' @author Brian J. Smith and Johannes Signer
#'
#' @return An `amt_distr` object, which consists of a list with the `name` of
#'   the distribution and its parameters (saved in `params`).
#'
#' @seealso
#' Wrapper to fit a distribution to data \code{\link{fit_distr}()}
#'
#' @references
#' \insertRef{fieberg2020guide}{amt}
#'
#' @examples
#'
#' # Fit an SSF, then update movement parameters.
#' data(deer)
#' mini_deer <- deer[1:100, ]
#' sh_forest <- get_sh_forest()
#'
#' # Prepare data for SSF
#' ssf_data <- mini_deer |>
#'   steps_by_burst() |>
#'   random_steps(n = 15) |>
#'   extract_covariates(sh_forest) |>
#'   mutate(forest = factor(forest, levels = 1:0,
#'                     labels = c("forest", "non-forest")),
#'   cos_ta_ = cos(ta_),
#'   log_sl_ = log(sl_))
#'
#' # Check tentative distributions
#' # Step length
#' sl_distr_params(ssf_data)
#' attr(ssf_data, "sl_")
#' #    Turning angle
#' ta_distr_params(ssf_data)
#'
#' # Fit an iSSF
#' m1 <- ssf_data |>
#'   fit_issf(case_ ~ forest +
#'                sl_ + log_sl_ + cos_ta_ +
#'                strata(step_id_))
#'
#' # Update step length distribution
#' new_gamma <- update_sl_distr(m1)
#'
#' # Update turning angle distribution
#' new_vm <- update_ta_distr(m1)
#'
#' # It is also possible to use different step length distributions
#'
#' # exponential step-length distribution
#' s2 <- mini_deer |> steps_by_burst()
#' s2 <- random_steps(s2, sl_distr = fit_distr(s2$sl_, "exp"))
#' m2 <- s2 |>
#'   fit_clogit(case_ ~ sl_ + strata(step_id_))
#' update_sl_distr(m2)
#'
#' # half normal step-length distribution
#' s3 <- mini_deer |> steps_by_burst()
#' s3 <- random_steps(s3, sl_distr = fit_distr(s3$sl_, "hnorm"))
#' m3 <- s3 |>
#'   mutate(sl_sq_ = sl_^2) |>
#'   fit_clogit(case_ ~ sl_sq_ + strata(step_id_))
#' update_sl_distr(m3)
#'
#' # log normal step-length distribution
#' s4 <- mini_deer |> steps_by_burst()
#' s4 <- random_steps(s4, sl_distr = fit_distr(s4$sl_, "lnorm"))
#' m4 <- s4 |>
#'   mutate(log_sl_ = log(sl_), log_sl_sq_ = log(sl_)^2) |>
#'   fit_clogit(case_ ~ log_sl_ + log_sl_sq_ + strata(step_id_))
#' update_sl_distr(m4)
#'
#'
#'
#' @rdname update_distr
#' @export
update_sl_distr <- function(
  object, beta_sl = "sl_",
  beta_log_sl = "log_sl_",
  beta_sl_sq = "sl_sq_",
  beta_log_sl_sq = "log_sl_sq_", ...){
  #Check inputs
  if (!inherits(object, "fit_clogit")){
    stop("\'object\' must be of class \"fit_clogit\"")
  }

  # Get tentative distribution name
  tent_dist_name <- sl_distr_name(object)

  # Update distribution
  switch(
    tent_dist_name,
    unif = {
      stop("If you generate available steps with a uniform distribution,
            you cannot update the distribution. You may consider refitting
            your model using a different step length distribution.")
    },
    exp = {
      ## Update rate
      # Fitted coef
      beta_sl_ <- unname(object$model$coefficients[beta_sl])
      # Check
      if (is.na(beta_sl_)){
        warning(paste("The covariate \'sl_\' did not appear in your model,",
                      "and the rate parameter was not updated."))
        beta_sl_ <- 0
      }
      # Update distribution
      new_dist <- update_exp(object$sl_, beta_sl = beta_sl_)
    },
    gamma = {
      ## New shape
      # Fitted coef
      beta_log_sl_ <- unname(object$model$coefficients[beta_log_sl])
      # Check
      if (is.na(beta_log_sl_)){
        warning(paste("The covariate \'log_sl_\' did not appear in your model,",
                      "and the shape parameter was not updated."))
        beta_log_sl_ <- 0
      }

      ## New scale
      # Fitted coef
      beta_sl_ <- unname(object$model$coefficients[beta_sl])
      # Check
      if (is.na(beta_sl_)){
        warning(paste("The covariate \'sl_\' did not appear in your model,",
                      "and the scale parameter was not updated."))
        beta_sl_ <- 0
      }

      #Create distribution
      new_dist <- update_gamma(object$sl_,
                               beta_sl = beta_sl_,
                               beta_log_sl = beta_log_sl_)
    },
    lnorm = {
      ## New shape
      # Fitted coef
      beta_log_sl_ <- unname(object$model$coefficients[beta_log_sl])
      beta_log_sl_sq_ <- unname(object$model$coefficients[beta_log_sl_sq])

      # Check
      if (is.na(beta_log_sl_)){
        warning("The covariate \'log_sl_\' did not appear in your model.")
        beta_log_sl_ <- 0
      }
      if (is.na(beta_log_sl_sq_)){
        warning("The covariate \'log_sl_sq_\' did not appear in your model.")
        beta_log_sl_sq_ <- 0
      }

      #Create distribution
      new_dist <- update_lnorm(object$sl_,
                               beta_log_sl = beta_log_sl_,
                               beta_log_sl_sq = beta_log_sl_sq_)
    },
    hnorm = {
      beta_sl_sq_ <- unname(object$model$coefficients[beta_sl_sq])
      # Check
      if (is.na(beta_sl_sq_)){
        warning("The covariate \'log_sl_sq_\' did not appear in your model.")
        beta_sl_sq_ <- 0
      }

      #Create distribution
      new_dist <- update_hnorm(object$sl_,
                               beta_sl_sq = beta_sl_sq_)
    })

  #Return
  return(new_dist)
}

#' @rdname update_distr
#' @export
update_ta_distr <- function(object, beta_cos_ta = "cos_ta_", ...){
  #Check inputs
  if (!inherits(object, "fit_clogit")){
    stop("\'object\' must be of class \"fit_clogit\"")
  }

  # Get tentative distribution name
  tent_dist_name <- ta_distr_name(object)

  # Update distribution
  switch(tent_dist_name,
         unif = {
           # Note: same as von Mises, but with kappa = 0
           ## Update kappa
           # Fitted coef
           beta_cos_ta_ <- unname(object$model$coefficients[beta_cos_ta])
           # Check
           if (is.na(beta_cos_ta_)){
             warning(
               paste(
                 "The covariate \'cos_ta_\' did not appear in your model,",
                 "and the concentration parameter (kappa) was not updated."))
             beta_cos_ta_ <- 0
           }
           # Create distribution
           new_dist <- update_vonmises(make_vonmises_distr(kappa = 0),
                                       beta_cos_ta = beta_cos_ta_)
         },
         vonmises = {
           ## Update kappa
           # Fitted coef
           beta_cos_ta_ <- unname(object$model$coefficients[beta_cos_ta])
           # Check
           if (is.na(beta_cos_ta_)){
             warning(paste(
               "The covariate \'cos_ta_' did not appear in your model,",
               "and the concentration parameter (kappa) was not updated."))
             beta_cos_ta_ <- 0
           }

           #Create distribution
           new_dist <- update_vonmises(object$ta_, beta_cos_ta = beta_cos_ta_)
         })

  #Return
  return(new_dist)
}

#' Manually update `amt_distr`
#'
#' Functions to update `amt_distr` from iSSF coefficients
#'
#' @param beta_sl `[numeric]` \cr The estimate of the coefficient of the step length.
#' @param beta_log_sl `[numeric]` \cr The estimate of the coefficient of the log of the step length.
#' @param beta_sl_sq `[character]` \cr The name of the coefficient of the square of the step length.
#' @param beta_log_sl_sq `[character]` \cr The name of the coefficient of the square of log of the step length.
#' @param beta_cos_ta `[numeric]` \cr The estimate of the coefficient of cosine of the turning angle.
#' @param dist `[amt_distr]` The tentative distribution to be updated
#' respective distributions.
#' @name update_distr_man
#' @return A distribution
#'
#' @details These functions are called internally by
#' \code{\link{update_sl_distr}()} and \code{\link{update_ta_distr}()}.
#' However, those simple functions assume that the selection-free step-length
#' and turn-angle distributions are constant (i.e., they do not depend on
#' covariates). In the case of interactions between movement parameters and
#' covariates, the user will want to manually access these functions to update
#' their selection-free movement distributions.
#'
#' @examples
#' #  sh_forest <- get_sh_forest()
#' #  # Fit an SSF, then update movement parameters.
#' #
#' #   #Prepare data for SSF
#' #  ssf_data <- deer |>
#' #    steps_by_burst() |>
#' #    random_steps(n = 15) |>
#' #    extract_covariates(sh_forest) |>
#' #    mutate(forest = factor(forest, levels = 1:0,
#' #                      labels = c("forest", "non-forest")),
#' #    cos_ta_ = cos(ta_),
#' #    log_sl_ = log(sl_))
#' #
#' #  # Check tentative distributions
#' #  #    Step length
#' #  attr(ssf_data, "sl_")
#' #  #    Turning angle
#' #  attr(ssf_data, "ta_")
#' #
#' #  # Fit an iSSF (note model = TRUE necessary for predict() to work)
#' #  m1 <- ssf_data |>
#' #    fit_issf(case_ ~ forest * (sl_ + log_sl_ + cos_ta_) +
#' #                 strata(step_id_), model = TRUE)
#' #
#' #  # Update forest step lengths (the reference level)
#' #  forest_sl <- update_gamma(m1$sl_,
#' #                            beta_sl = m1$model$coefficients["sl_"],
#' #                            beta_log_sl = m1$model$coefficients["log_sl_"])
#' #
#' #  # Update non-forest step lengths
#' #  nonforest_sl <- update_gamma(m1$sl_,
#' #                               beta_sl = m1$model$coefficients["sl_"] +
#' #                                 m1$model$coefficients["forestnon-forest:sl_"],
#' #                               beta_log_sl = m1$model$coefficients["log_sl_"] +
#' #                                 m1$model$coefficients["forestnon-forest:log_sl_"])
#' #
#' #  # Update forest turn angles (the reference level)
#' #  forest_ta <- update_vonmises(m1$ta_,
#' #                               beta_cos_ta = m1$model$coefficients["cos_ta_"])
#' #
#' #  # Update non-forest turn angles
#' #  nonforest_ta <- update_vonmises(m1$ta_,
#' #                                  beta_cos_ta = m1$model$coefficients["cos_ta_"] +
#' #                                    m1$model$coefficients["forestnon-forest:cos_ta_"])
#' #
#' @export
update_gamma <- function(dist, beta_sl, beta_log_sl){
  #Update shape
  new_shape <- unname(dist$params$shape + beta_log_sl)
  #Update scale
  new_scale <- unname(1/((1/dist$params$scale) - beta_sl))
  #Make new distribution
  new_dist <- make_gamma_distr(shape = new_shape, scale = new_scale)
  #Return
  return(new_dist)
}

#' @rdname update_distr_man
#' @export
update_exp <- function(dist, beta_sl){
  #Update rate
  new_rate <- unname(dist$params$rate - beta_sl)
  #Make new distribution
  new_dist <- make_exp_distr(rate = new_rate)
  #Return
  return(new_dist)
}

#' @rdname update_distr_man
#' @export
update_hnorm <- function(dist, beta_sl_sq){
  #Update rate
  new_sd <- unname(dist$params$sd / sqrt(1 - 2 * dist$params$sd^2 * beta_sl_sq))
  #Make new distribution
  new_dist <- make_hnorm_distr(sd = new_sd)
  #Return
  return(new_dist)
}

#' @rdname update_distr_man
#' @export
update_lnorm <- function(dist, beta_log_sl, beta_log_sl_sq){
  #Update rate
  new_meanlog <- unname(
    (dist$params$meanlog - dist$params$sdlog * beta_log_sl) /
      (1 - 2 * dist$params$sdlog^2 * beta_log_sl_sq))
  new_sdlog <- unname(dist$params$sdlog / sqrt(1 - 2 * dist$params$sd^2 * beta_log_sl_sq))

  #Make new distribution
  new_dist <- make_lnorm_distr(meanlog = new_meanlog, sdlog = new_sdlog)
  #Return
  return(new_dist)
}


#' @rdname update_distr_man
#' @export
update_vonmises <- function(dist, beta_cos_ta){
  #Update rate
  new_conc <- unname(dist$params$kappa + beta_cos_ta)
  #Make new distribution
  new_dist <- make_vonmises_distr(kappa = new_conc)
  #Return
  return(new_dist)
}


# Utility functions -------------------------------------------------------

#' Obtain the step length and/or turn angle distributions from random steps or a fitted model.
#'
#' @param x Random steps or fitted model
#' @param ... None implemented.
#' @returns An amt distribution
#'
#' @export
#' @name get_distr
sl_distr <- function(x, ...) {
  UseMethod("sl_distr")
}


#' @export
#' @rdname get_distr
sl_distr.random_steps <- function(x, ...) {
  attr(x, "sl_")
}

#' @export
#' @rdname get_distr
sl_distr.fit_clogit <- function(x, ...) {
  x$sl_
}


#' @export
#' @rdname get_distr
ta_distr <- function(x, ...) {
  UseMethod("ta_distr")
}

#' @export
#' @rdname get_distr
ta_distr.random_steps <- function(x, ...) {
  attr(x, "ta_")
}

#' @export
#' @rdname get_distr
ta_distr.fit_clogit <- function(x, ...) {
  x$ta_
}


#' Name of step-length distribution and turn-angle distribution
#'
#' @param x Random steps or fitted model
#' @param ... None implemented.
#'
#' @export
#' @return Character vector of length 1.
#' @name distr_name
sl_distr_name <- function(x, ...) {
  UseMethod("sl_distr_name")
}


#' @export
#' @rdname distr_name
sl_distr_name.random_steps <- function(x, ...) {
  attr(x, "sl_")$name
}

#' @export
#' @rdname distr_name
sl_distr_name.fit_clogit <- function(x, ...) {
  x$sl_$name
}

#' @export
#' @rdname distr_name
ta_distr_name <- function(x, ...) {
  UseMethod("ta_distr_name")
}

#' @export
#' @rdname distr_name
ta_distr_name <- function(x, ...) {
  UseMethod("ta_distr_name")
}

#' @export
#' @rdname distr_name
ta_distr_name.random_steps <- function(x, ...) {
  attr(x, "ta_")$name
}

#' @export
#' @rdname distr_name
ta_distr_name.fit_clogit <- function(x, ...) {
  x$ta_$name
}

#' Get parameters from a (fitted) distribution
#'
#' @param x `[amt_distr]`\cr A (fitted) distribution
#' @param ... None
#' @return A list with the parameters of the distribution.
#'
#' @name params
#' @export
#' @examples
#' data(deer)
#' d <- deer |> steps() |> random_steps()
#' sl_distr_params(d)
#' ta_distr_params(d)
#'
#'
sl_distr_params <- function(x, ...) {
  UseMethod("sl_distr_params")
}

#' @rdname params
#' @export
sl_distr_params.random_steps <- function(x, ...) {
  attr(x, "sl_")$params
}

#' @rdname params
#' @export
sl_distr_params.fit_clogit <- function(x, ...) {
  x$sl_$params
}

#' @rdname params
#' @export
ta_distr_params <- function(x, ...) {
  UseMethod("ta_distr_params")
}

#' @rdname params
#' @export
ta_distr_params.random_steps <- function(x, ...) {
  attr(x, "ta_")$params
}

#' @rdname params
#' @export
ta_distr_params.fit_clogit <- function(x, ...) {
  x$ta_$params
}