diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-02-09 12:19:14 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-02-09 12:19:14 +0100 |
| commit | d8f31d1323998f33d07535f55c81be380d93ca45 (patch) | |
| tree | ef0e614878397974bb4040e146fb116bb4ee40c5 /R | |
| parent | 0fa8a770812775d697717ad723f7f61fb04b7fef (diff) | |
Adapt saemix interface to saemix 3.0 on CRAN
Diffstat (limited to 'R')
| -rw-r--r-- | R/intervals.R | 2 | ||||
| -rw-r--r-- | R/plot.mixed.mmkin.R | 5 | ||||
| -rw-r--r-- | R/saem.R | 9 |
3 files changed, 13 insertions, 3 deletions
diff --git a/R/intervals.R b/R/intervals.R index e2d342f0..8ab2b7ec 100644 --- a/R/intervals.R +++ b/R/intervals.R @@ -10,6 +10,7 @@ nlme::intervals #' @param backtransform In case the model was fitted with mkin transformations, #' should we backtransform the parameters where a one to one correlation #' between transformed and backtransformed parameters exists? +#' @param \dots For compatibility with the generic method #' @return An object with 'intervals.saem.mmkin' and 'intervals.lme' in the #' class attribute #' @export @@ -101,6 +102,7 @@ intervals.saem.mmkin <- function(object, level = 0.95, backtransform = TRUE, ... #' @param level The confidence level. #' @param backtransform Should we backtransform the parameters where a one to #' one correlation between transformed and backtransformed parameters exists? +#' @param \dots For compatibility with the generic method #' @importFrom nlme intervals #' @return An object with 'intervals.saem.mmkin' and 'intervals.lme' in the #' class attribute diff --git a/R/plot.mixed.mmkin.R b/R/plot.mixed.mmkin.R index 1ac62b07..2903a05c 100644 --- a/R/plot.mixed.mmkin.R +++ b/R/plot.mixed.mmkin.R @@ -104,8 +104,9 @@ plot.mixed.mmkin <- function(x, if (inherits(x, "saem.mmkin")) { if (x$transformations == "saemix") backtransform = FALSE - degparms_i <- saemix::psi(x$so) - rownames(degparms_i) <- ds_names + psi <- saemix::psi(x$so) + rownames(psi) <- x$saemix_ds_order + degparms_i <- psi[ds_names, ] degparms_i_names <- setdiff(x$so@results@name.fixed, names(fit_1$errparms)) colnames(degparms_i) <- degparms_i_names residual_type = ifelse(standardized, "standardized", "residual") @@ -158,9 +158,14 @@ saem.mmkin <- function(object, } return_data <- nlme_data(object) + saemix_data_ds <- f_saemix@data@data$ds + mkin_ds_order <- as.character(unique(return_data$ds)) + saemix_ds_order <- unique(saemix_data_ds) + psi <- saemix::psi(f_saemix) + rownames(psi) <- saemix_ds_order return_data$predicted <- f_saemix@model@model( - psi = saemix::psi(f_saemix), + psi = psi[mkin_ds_order, ], id = as.numeric(return_data$ds), xidep = return_data[c("time", "name")]) @@ -184,6 +189,8 @@ saem.mmkin <- function(object, bparms.optim = bparms_optim, bparms.fixed = object[[1]]$bparms.fixed, data = return_data, + mkin_ds_order = mkin_ds_order, + saemix_ds_order = saemix_ds_order, err_mod = object[[1]]$err_mod, date.fit = date(), saemixversion = as.character(utils::packageVersion("saemix")), |