diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/llhist.R | 3 | ||||
| -rw-r--r-- | R/multistart.R | 6 | ||||
| -rw-r--r-- | R/parplot.R (renamed from R/parhist.R) | 12 | ||||
| -rw-r--r-- | R/saem.R | 2 |
4 files changed, 15 insertions, 8 deletions
@@ -25,6 +25,7 @@ llhist <- function(object, breaks = "Sturges", lpos = "topleft", main = "", stop("llhist is only implemented for multistart.saem.mmkin objects") } + ll_orig <- logLik(attr(object, "orig")) ll <- stats::na.omit(sapply(object, llfunc)) par(las = 1) @@ -34,7 +35,7 @@ llhist <- function(object, breaks = "Sturges", lpos = "topleft", main = "", freq_factor <- h$counts[1] / h$density[1] - abline(v = logLik(attr(object, "orig")), col = 2) + abline(v = ll_orig, col = 2) legend(lpos, inset = c(0.05, 0.05), bty = "n", lty = 1, col = c(2), diff --git a/R/multistart.R b/R/multistart.R index 29ccdc44..14683c11 100644 --- a/R/multistart.R +++ b/R/multistart.R @@ -17,7 +17,7 @@ #' @param x The multistart object to print #' @return A list of [saem.mmkin] objects, with class attributes #' 'multistart.saem.mmkin' and 'multistart'. -#' @seealso [parhist], [llhist] +#' @seealso [parplot], [llhist] #' #' @references Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical #' identifiability in the frame of nonlinear mixed effects models: the example @@ -40,7 +40,7 @@ #' f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE) #' f_saem_full <- saem(f_mmkin) #' f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16) -#' parhist(f_saem_full_multi, lpos = "bottomleft") +#' parplot(f_saem_full_multi, lpos = "bottomleft") #' illparms(f_saem_full) #' #' f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2") @@ -52,7 +52,7 @@ #' cl <- makePSOCKcluster(12) #' clusterExport(cl, "f_mmkin") #' f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cluster = cl) -#' parhist(f_saem_reduced_multi, lpos = "topright") +#' parplot(f_saem_reduced_multi, lpos = "topright") #' } multistart <- function(object, n = 50, cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), diff --git a/R/parhist.R b/R/parplot.R index 0f9c9964..627a4eb8 100644 --- a/R/parhist.R +++ b/R/parplot.R @@ -1,4 +1,4 @@ -#' Plot parameter distributions from multistart objects +#' Plot parameter variability of multistart objects #' #' Produces a boxplot with all parameters from the multiple runs, scaled #' either by the parameters of the run with the highest likelihood, @@ -18,7 +18,13 @@ #' @seealso [multistart] #' @importFrom stats median #' @export -parhist <- function(object, llmin = -Inf, scale = c("best", "median"), +parplot <- function(object, ...) { + UseMethod("parplot") +} + +#' @rdname parplot +#' @export +parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, scale = c("best", "median"), lpos = "bottomleft", main = "", ...) { oldpar <- par(no.readonly = TRUE) @@ -35,7 +41,7 @@ parhist <- function(object, llmin = -Inf, scale = c("best", "median"), else return(logLik(object$so)) } } else { - stop("parhist is only implemented for multistart.saem.mmkin objects") + stop("parplot is only implemented for multistart.saem.mmkin objects") } ll <- sapply(object, llfunc) selected <- which(ll > llmin) @@ -726,7 +726,7 @@ saemix_data <- function(object, covariates = NULL, verbose = FALSE, ...) { #' @param \dots Passed to [saemix::logLik.SaemixObject] #' @param method Passed to [saemix::logLik.SaemixObject] #' @export -logLik.saem.mmkin <- function(object, ..., method = c("lin", "is", "gq")) { +logLik.saem.mmkin <- function(object, ..., method = c("is", "lin", "gq")) { method <- match.arg(method) return(logLik(object$so, method = method)) } |