R/parameter-values.R

In sebastianueckert/assemblerr: Assembly of Pharmacometric Models

#
#
# ParameterValues <- setClass("ParameterValues")
# #
# # ParameterValuesOnly <- setClass("ParameterValuesOnly", contains = "ParameterValues")
# #
# #
# # ParameterValuesMeanSd <- setClass("ParameterValuesMeanSd",
# #                                    contains = "ParameterValuesOnly",
# #                                    slots = c(mean = "numeric", sd = "numeric"))
# #
# # pv_mean_sd <- function(mean, sd) {
# #   ParameterValuesMeanSd(mean = mean, sd = sd)
# # }
# #
# # pv_mean_var <- function(mean, var) {
# #   ParameterValuesMeanSd(mean = mean, sd = sqrt(var))
# # }
# #
# #
# #
# #
# # ParameterValuesLogMeanLogSd <- setClass("ParameterValuesLogMeanLogSd",
# #                                   contains = "ParameterValuesOnly",
# #                                   slots = c(log_mean = "numeric", log_sd = "numeric"))
# #
# # pv_lmean_lsd <- function(log_mean, log_sd) {
# #   ParameterValuesLogMeanLogSd(log_mean = log_mean, log_sd = log_sd)
# # }
# #
# # ParameterValuesMedianLogSd <- setClass("ParameterValuesMedianLogSd",
# #                                         contains = "ParameterValuesOnly",
# #                                         slots = c(median = "numeric", log_sd = "numeric"))
# #
# # pv_median_lsd <- function(median, log_sd) {
# #   ParameterValuesMedianLogSd(median = median, log_sd = log_sd)
# # }
# #
# # add_pv_model <- function(pv, pv_model) {
# #   to_class <- paste0(class(pv_model),
# #                      gsub(
# #                        pattern = "^ParameterValues",
# #                        replacement = "",
# #                        x = class(pv)
# #                       )
# #                     )
# #   as(pv, to_class)
# # }
# #
# #
# # convert_pv <- function(from, to) {
# #   super_class <- selectSuperClasses(class(from))
# #   to_class <- paste0(super_class, snake_case_to_camel_case(to))
# #   as(from, to_class)
# # }
# #
# # ParameterValuesModel <- setClass("ParameterValuesModel", contains = "ParameterValues")
# #
# #
# # # normal distribution -----------------------------------------------------
# #
# #
# #
# ParameterValuesNormal <- setClass("ParameterValuesNormal",
#                                   contains = "ParameterValues",
#                                   slots = c(.mu = "numeric", .sigma2 = "numeric"))
# #
# # ParameterValuesNormalMeanVar <- setClass("ParameterValuesNormalMeanVar",
# #                                          contains = "ParameterValuesNormal",
# #                                          slots = c(mu = "numeric", sigma2 = "numeric"))
# # setMethod("initialize",
# #           signature = "ParameterValuesNormalMeanVar",
# #           function(.Object, mu, sigma2) {
# #             callNextMethod(.Object, .mu = mu, .sigma2 = sigma2, mu = mu, sigma2 = sigma2)
# #           })
# #
# # setAs("ParameterValuesNormal", "ParameterValuesNormalMeanVar",
# #       def = function(from) ParameterValuesNormalMeanVar(from@.mu, from@.sigma2)
# # )
# #
# # setAs("ParameterValuesMeanSd", "ParameterValuesNormalMeanVar",
# #       def = function(from) ParameterValuesNormalMeanVar(from@mean, from@sd^2)
# # )
# #
# # ParameterValuesNormalMeanSd <- setClass("ParameterValuesNormalMeanSd",
# #                                          contains = "ParameterValuesNormal",
# #                                          slots = c(mu = "numeric", sigma = "numeric"))
# #
# # setMethod("initialize",
# #           signature = "ParameterValuesNormalMeanSd",
# #           function(.Object, mu, sigma) {
# #             callNextMethod(.Object, .mu = mu, .sigma2 = sigma^2, mu = mu, sigma = sigma)
# #           })
# #
# # setAs("ParameterValuesNormal", "ParameterValuesNormalMeanSd",
# #       def = function(from) ParameterValuesNormalMeanSd(mu = from@.mu, sigma = sqrt(from@.sigma2))
# # )
# #
# # setAs("ParameterValuesMeanSd", "ParameterValuesNormalMeanSd",
# #       def = function(from) ParameterValuesNormalMeanSd(mu = from@mean, sigma = from@sd)
# # )
# #
# #
# # # log-normal distribution -------------------------------------------------
# #
# #
# #
# ParameterValuesLogNormal <- setClass("ParameterValuesLogNormal",
#                                   contains = "ParameterValuesModel",
#                                   slots = c(.log_mu = "numeric", .log_sigma = "numeric"))
# #
# # ParameterValuesLogNormalLogMeanLogSd <- setClass("ParameterValuesLogNormalLogMeanLogSd",
# #                                          contains = "ParameterValuesLogNormal",
# #                                          slots = c(log_mu = "numeric", log_sigma = "numeric"))
# # setMethod("initialize",
# #           signature = "ParameterValuesLogNormalLogMeanLogSd",
# #           function(.Object, log_mu, log_sigma) {
# #             callNextMethod(.Object, .log_mu = log_mu, .log_sigma = log_sigma, log_mu = log_mu, log_sigma = log_sigma)
# #           })
# #
# # setAs("ParameterValuesLogNormal", "ParameterValuesLogNormalLogMeanLogSd",
# #       def = function(from) ParameterValuesLogNormalLogMeanLogSd(from@.log_mu, from@.log_sigma)
# # )
# #
# # setAs("ParameterValuesLogMeanLogSd", "ParameterValuesLogNormalLogMeanLogSd",
# #       def = function(from) ParameterValuesLogNormalLogMeanLogSd(from@log_mean, from@log_sd)
# # )
# #
# #
# # ParameterValuesLogNormalMedianLogSd <- setClass("ParameterValuesLogNormalMedianLogSd",
# #                                                  contains = "ParameterValuesLogNormal",
# #                                                  slots = c(m = "numeric", log_sigma = "numeric"))
# # setMethod("initialize",
# #           signature = "ParameterValuesLogNormalMedianLogSd",
# #           function(.Object, m, log_sigma) {
# #             callNextMethod(.Object, .log_mu = log(m), .log_sigma = log_sigma, m = m, log_sigma = log_sigma)
# #           })
# #
# # setAs("ParameterValuesLogNormal", "ParameterValuesLogNormalMedianLogSd",
# #       def = function(from) ParameterValuesLogNormalMedianLogSd(m = exp(from@.log_mu), log_sigma = from@.log_sigma)
# # )
# #
# # setAs("ParameterValuesMedianLogSd", "ParameterValuesLogNormalMedianLogSd",
# #       def = function(from) ParameterValuesLogNormalMedianLogSd(from@median, from@log_sd)
# # )
# #
# # ParameterValuesLogNormalMeanSd <- setClass("ParameterValuesLogNormalMeanSd",
# #                                                 contains = "ParameterValuesLogNormal",
# #                                                 slots = c(mu = "numeric", sigma = "numeric"))
# # setMethod("initialize",
# #           signature = "ParameterValuesLogNormalMeanSd",
# #           function(.Object, mu, sigma) {
# #             callNextMethod(.Object, .log_mu = log(mu/sqrt(1 + sigma^2/mu^2)), .log_sigma = sqrt(log(sqrt(1 + sigma^2/mu^2))), mu = mu, sigma = sigma)
# #           })
# #
# # setAs("ParameterValuesLogNormal", "ParameterValuesLogNormalMeanSd",
# #       def = function(from) ParameterValuesLogNormalMeanSd(
# #         mu = exp(from@.log_mu + 0.5*from@.log_sigma^2),
# #         sigma = exp(from@.log_mu + 0.5*from@.log_sigma^2) * sqrt(exp(from@.log_sigma^2) - 1)
# #       )
# # )
# #
# # setAs("ParameterValuesMeanSd", "ParameterValuesLogNormalMeanSd",
# #       def = function(from) ParameterValuesLogNormalMeanSd(from@mean, from@sd)
# # )