From e5d1df9a9b1f0951d7dfbaf24eee4294470b73e2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Nov 2022 14:54:20 +0100 Subject: Complete update of online docs for v1.2.0 --- docs/reference/plot.mixed.mmkin.html | 176 +++++++++++++++++++++++------------ 1 file changed, 117 insertions(+), 59 deletions(-) (limited to 'docs/reference/plot.mixed.mmkin.html') diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index 2af2328d..b1083204 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -17,7 +17,7 @@ mkin - 1.1.0 + 1.2.0 @@ -44,11 +44,14 @@ 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
    • @@ -56,7 +59,10 @@ Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
  • @@ -87,94 +93,146 @@
    - 
    # S3 method for mixed.mmkin
-plot(
-  x,
-  i = 1:ncol(x$mmkin),
-  obs_vars = names(x$mkinmod$map),
-  standardized = TRUE,
-  xlab = "Time",
-  xlim = range(x$data$time),
-  resplot = c("predicted", "time"),
-  pred_over = NULL,
-  test_log_parms = FALSE,
-  conf.level = 0.6,
-  default_log_parms = NA,
-  ymax = "auto",
-  maxabs = "auto",
-  ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
-  nrow.legend = ceiling((length(i) + 1)/ncol.legend),
-  rel.height.legend = 0.02 + 0.07 * nrow.legend,
-  rel.height.bottom = 1.1,
-  pch_ds = 1:length(i),
-  col_ds = pch_ds + 1,
-  lty_ds = col_ds,
-  frame = TRUE,
-  ...
-)
    + 
    # S3 method for mixed.mmkin
+plot(
+  x,
+  i = 1:ncol(x$mmkin),
+  obs_vars = names(x$mkinmod$map),
+  standardized = TRUE,
+  xlab = "Time",
+  xlim = range(x$data$time),
+  resplot = c("predicted", "time"),
+  pop_curve = "auto",
+  pred_over = NULL,
+  test_log_parms = FALSE,
+  conf.level = 0.6,
+  default_log_parms = NA,
+  ymax = "auto",
+  maxabs = "auto",
+  ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
+  nrow.legend = ceiling((length(i) + 1)/ncol.legend),
+  rel.height.legend = 0.02 + 0.07 * nrow.legend,
+  rel.height.bottom = 1.1,
+  pch_ds = 1:length(i),
+  col_ds = pch_ds + 1,
+  lty_ds = col_ds,
+  frame = TRUE,
+  ...
+)

    Arguments

    x

    An object of class mixed.mmkin, saem.mmkin or nlme.mmkin

    + +
    i

    A numeric index to select datasets for which to plot the individual predictions, in case plots get too large

    + +
    obs_vars

    A character vector of names of the observed variables for which the data and the model should be plotted. Defauls to all observed variables in the model.

    + +
    standardized

    Should the residuals be standardized? Only takes effect if resplot = "time".

    + +
    xlab

    Label for the x axis.

    + +
    xlim

    Plot range in x direction.

    + +
    resplot

    Should the residuals plotted against time or against predicted values?

    + + +
    pop_curve
    +

    Per default, a population curve is drawn in case +population parameters are fitted by the model, e.g. for saem objects. +In case there is a covariate model, no population curve is currently shown.

    + +
    pred_over

    Named list of alternative predictions as obtained from mkinpredict with a compatible mkinmod.

    + +
    test_log_parms

    Passed to mean_degparms in the case of an mixed.mmkin object

    + +
    conf.level

    Passed to mean_degparms in the case of an mixed.mmkin object

    + +
    default_log_parms

    Passed to mean_degparms in the case of an mixed.mmkin object

    + +
    ymax

    Vector of maximum y axis values

    + +
    maxabs

    Maximum absolute value of the residuals. This is used for the scaling of the y axis and defaults to "auto".

    + +
    ncol.legend

    Number of columns to use in the legend

    + +
    nrow.legend

    Number of rows to use in the legend

    + +
    rel.height.legend

    The relative height of the legend shown on top

    + +
    rel.height.bottom

    The relative height of the bottom plot row

    + +
    pch_ds

    Symbols to be used for plotting the data.

    + +
    col_ds

    Colors used for plotting the observed data and the corresponding model prediction lines for the different datasets.

    + +
    lty_ds

    Line types to be used for the model predictions.

    + +
    frame

    Should a frame be drawn around the plots?

    + +
    ...

    Further arguments passed to plot.

    +

    Value

    -

    The function is called for its side effect.

    + + +

    The function is called for its side effect.

    Author

    @@ -183,41 +241,41 @@ corresponding model prediction lines for the different datasets.

    Examples

    - 
    ds <- lapply(experimental_data_for_UBA_2019[6:10],
- function(x) x$data[c("name", "time", "value")])
-names(ds) <- paste0("ds ", 6:10)
-dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
-  A1 = mkinsub("SFO"), quiet = TRUE)
-# \dontrun{
-f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE)
-plot(f[, 3:4], standardized = TRUE)
+    
    ds <- lapply(experimental_data_for_UBA_2019[6:10],
+ function(x) x$data[c("name", "time", "value")])
+names(ds) <- paste0("ds ", 6:10)
+dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
+  A1 = mkinsub("SFO"), quiet = TRUE)
+# \dontrun{
+f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE)
+plot(f[, 3:4], standardized = TRUE)
 
-
-# For this fit we need to increase pnlsMaxiter, and we increase the
-# tolerance in order to speed up the fit for this example evaluation
-# It still takes 20 seconds to run
-f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3))
-plot(f_nlme)
+
+# For this fit we need to increase pnlsMaxiter, and we increase the
+# tolerance in order to speed up the fit for this example evaluation
+# It still takes 20 seconds to run
+f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3))
+plot(f_nlme)
 
-
-f_saem <- saem(f, transformations = "saemix")
-plot(f_saem)
+
+f_saem <- saem(f, transformations = "saemix")
+plot(f_saem)
 
-
-f_obs <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, error_model = "obs")
-f_nlmix <- nlmix(f_obs)
+
+f_obs <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, error_model = "obs")
+f_nlmix <- nlmix(f_obs)
 #> Error in nlmix(f_obs): could not find function "nlmix"
-plot(f_nlmix)
+plot(f_nlmix)
 #> Error in plot(f_nlmix): object 'f_nlmix' not found
-
-# We can overlay the two variants if we generate predictions
-pred_nlme <- mkinpredict(dfop_sfo,
-  f_nlme$bparms.optim[-1],
-  c(parent = f_nlme$bparms.optim[[1]], A1 = 0),
-  seq(0, 180, by = 0.2))
-plot(f_saem, pred_over = list(nlme = pred_nlme))
+
+# We can overlay the two variants if we generate predictions
+pred_nlme <- mkinpredict(dfop_sfo,
+  f_nlme$bparms.optim[-1],
+  c(parent = f_nlme$bparms.optim[[1]], A1 = 0),
+  seq(0, 180, by = 0.2))
+plot(f_saem, pred_over = list(nlme = pred_nlme))
 
-# }
+# }
    @@ -232,7 +290,7 @@ corresponding model prediction lines for the different datasets.

    -

    Site built with pkgdown 2.0.3.

    +

    Site built with pkgdown 2.0.6.

    -- cgit v1.2.1