diff options
| -rw-r--r-- | R/saem.R | 48 |
1 files changed, 27 insertions, 21 deletions
@@ -15,41 +15,46 @@ utils::globalVariables(c("predicted", "std")) #' #' @importFrom utils packageVersion #' @param object An [mmkin] row object containing several fits of the same -#' [mkinmod] model to different datasets +#' [mkinmod] model to different datasets #' @param verbose Should we print information about created objects of -#' type [saemix::SaemixModel] and [saemix::SaemixData]? +#' type [saemix::SaemixModel] and [saemix::SaemixData]? #' @param transformations Per default, all parameter transformations are done -#' in mkin. If this argument is set to 'saemix', parameter transformations -#' are done in 'saemix' for the supported cases, i.e. (as of version 1.1.2) -#' SFO, FOMC, DFOP and HS without fixing `parent_0`, and SFO or DFOP with -#' one SFO metabolite. +#' in mkin. If this argument is set to 'saemix', parameter transformations +#' are done in 'saemix' for the supported cases, i.e. (as of version 1.1.2) +#' SFO, FOMC, DFOP and HS without fixing `parent_0`, and SFO or DFOP with +#' one SFO metabolite. #' @param degparms_start Parameter values given as a named numeric vector will -#' be used to override the starting values obtained from the 'mmkin' object. +#' be used to override the starting values obtained from the 'mmkin' object. #' @param test_log_parms If TRUE, an attempt is made to use more robust starting -#' values for population parameters fitted as log parameters in mkin (like -#' rate constants) by only considering rate constants that pass the t-test -#' when calculating mean degradation parameters using [mean_degparms]. +#' values for population parameters fitted as log parameters in mkin (like +#' rate constants) by only considering rate constants that pass the t-test +#' when calculating mean degradation parameters using [mean_degparms]. #' @param conf.level Possibility to adjust the required confidence level -#' for parameter that are tested if requested by 'test_log_parms'. +#' for parameter that are tested if requested by 'test_log_parms'. #' @param solution_type Possibility to specify the solution type in case the -#' automatic choice is not desired +#' automatic choice is not desired #' @param no_random_effect Character vector of degradation parameters for -#' which there should be no variability over the groups. Only used -#' if the covariance model is not explicitly specified. +#' which there should be no variability over the groups. Only used +#' if the covariance model is not explicitly specified. #' @param covariance.model Will be passed to [saemix::SaemixModel()]. Per -#' default, uncorrelated random effects are specified for all degradation -#' parameters. +#' default, uncorrelated random effects are specified for all degradation +#' parameters. +#' @param covariates A data frame with covariate data for use in +#' 'covariate_models', with dataset names as row names. +#' @param covariate_models A list containing linear model formulas with one explanatory +#' variable, i.e. of the type 'parameter ~ covariate'. Covariates must be available +#' in the 'covariates' data frame. #' @param fail_with_errors Should a failure to compute standard errors -#' from the inverse of the Fisher Information Matrix be a failure? +#' from the inverse of the Fisher Information Matrix be a failure? #' @param quiet Should we suppress the messages saemix prints at the beginning -#' and the end of the optimisation process? +#' and the end of the optimisation process? #' @param nbiter.saemix Convenience option to increase the number of -#' iterations +#' iterations #' @param control Passed to [saemix::saemix]. #' @param \dots Further parameters passed to [saemix::saemixModel]. #' @return An S3 object of class 'saem.mmkin', containing the fitted -#' [saemix::SaemixObject] as a list component named 'so'. The -#' object also inherits from 'mixed.mmkin'. +#' [saemix::SaemixObject] as a list component named 'so'. The +#' object also inherits from 'mixed.mmkin'. #' @seealso [summary.saem.mmkin] [plot.mixed.mmkin] #' @examples #' \dontrun{ @@ -717,6 +722,7 @@ saemix_data <- function(object, covariates = NULL, verbose = FALSE, ...) { #' logLik method for saem.mmkin objects #' +#' @param object The fitted [saem.mmkin] object #' @param method Passed to [saemix::logLik.SaemixObject] #' @export logLik.saem.mmkin <- function(object, ..., method = c("lin", "is", "gq")) { |