From fd205e13061de8abc595d266f3b0c7650773d442 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 16 Sep 2022 21:06:54 +0200 Subject: Improve multistart documentation, bugfix - Split out llhist and parhist documentation - Add example code for multistart - Create a multistart vignette, because the example code fails when run by pkgdown - Fix multistart for the case of mkin transformations in the saem fit --- docs/dev/reference/multistart.html | 64 ++++++++++++++++++++++++++------------ 1 file changed, 44 insertions(+), 20 deletions(-) (limited to 'docs/dev/reference/multistart.html') diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html index 9f2d297e..c85e6d1e 100644 --- a/docs/dev/reference/multistart.html +++ b/docs/dev/reference/multistart.html @@ -49,11 +49,14 @@ mixed-effects models by Duchesne et al (2021).">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models
  • - Example evaluation of FOCUS Example Dataset Z + Short demo of the multistart method
  • Performance benefit by using compiled model definitions in mkin
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Calculation of time weighted average concentrations with mkin
    • @@ -106,11 +109,7 @@ mixed-effects models by Duchesne et al (2021).

    print(x, ...) # S3 method for multistart -parms(object, ...) - -parhist(object, lpos = "topleft", main = "", ...) - -llhist(object, breaks = "Sturges", lpos = "topleft", main = "", ...) +parms(object, ...)
    @@ -129,25 +128,12 @@ used?

    ...
    -

    Passed to the update function, or to the basic plotting -function in the case of the graphical functions.

    +

    Passed to the update function.

    x

    The multistart object to print

    - -
    lpos
    -

    Positioning of the legend.

    - - -
    main
    -

    title of the plot

    - - -
    breaks
    -

    Passed to hist

    -

    Value

    @@ -160,6 +146,11 @@ function in the case of the graphical functions.

    Details

    Currently, parallel execution of the fits is only supported using parallel::mclapply, i.e. not available on Windows.

    +

    In case the online version of this help page contains error messages +in the example code and no plots, this is due to the multistart method +not working when called by pkgdown. Please refer to the +online vignette +in this case.

    References

    @@ -168,7 +159,40 @@ identifiability in the frame of nonlinear mixed effects models: the example of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. doi: 10.1186/s12859-021-04373-4.

    +
    +

    See also

    +

    parhist, llhist

    +
    +
    +

    Examples

    + 
    # \dontrun{
+library(mkin)
+dmta_ds <- lapply(1:7, function(i) {
+  ds_i <- dimethenamid_2018$ds[[i]]$data
+  ds_i[ds_i$name == "DMTAP", "name"] <-  "DMTA"
+  ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i]
+  ds_i
+})
+names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title)
+dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])
+dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL
+
+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)
+#> Warning: all scheduled cores encountered errors in user code
+parhist(f_saem_full_multi, lpos = "bottomright")
+#> Error in UseMethod("parms", object): no applicable method for 'parms' applied to an object of class "try-error"
+
+f_saem_reduced <- update(f_saem_full, covariance.model = diag(c(1, 1, 0, 1)))
+f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cores = 16)
+#> Warning: all scheduled cores encountered errors in user code
+parhist(f_saem_reduced_multi, lpos = "bottomright")
+#> Error in UseMethod("parms", object): no applicable method for 'parms' applied to an object of class "try-error"
+# }
+
    +