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/mixed.html | 123 ++++++++++++++++++++++++++-------------------- 1 file changed, 70 insertions(+), 53 deletions(-) (limited to 'docs/reference/mixed.html') diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html index dfc7a731..5b250072 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.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
  • @@ -87,73 +93,84 @@
    - 
    mixed(object, ...)
-
-# S3 method for mmkin
-mixed(object, method = c("none"), ...)
-
-# S3 method for mixed.mmkin
-print(x, digits = max(3, getOption("digits") - 3), ...)
    + 
    mixed(object, ...)
+
+# S3 method for mmkin
+mixed(object, method = c("none"), ...)
+
+# S3 method for mixed.mmkin
+print(x, digits = max(3, getOption("digits") - 3), ...)

    Arguments

    object

    An mmkin row object

    + +
    ...

    Currently not used

    + +
    method

    The method to be used

    + +
    x

    A mixed.mmkin object to print

    + +
    digits

    Number of digits to use for printing.

    +

    Value

    -

    An object of class 'mixed.mmkin' which has the observed data in a + + +

    An object of class 'mixed.mmkin' which has the observed data in a single dataframe which is convenient for plotting

    Examples

    - 
    sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-n_biphasic <- 8
-err_1 = list(const = 1, prop = 0.07)
-
-DFOP_SFO <- mkinmod(
-  parent = mkinsub("DFOP", "m1"),
-  m1 = mkinsub("SFO"),
-  quiet = TRUE)
-
-set.seed(123456)
-log_sd <- 0.3
-syn_biphasic_parms <- as.matrix(data.frame(
-  k1 = rlnorm(n_biphasic, log(0.05), log_sd),
-  k2 = rlnorm(n_biphasic, log(0.01), log_sd),
-  g = plogis(rnorm(n_biphasic, 0, log_sd)),
-  f_parent_to_m1 = plogis(rnorm(n_biphasic, 0, log_sd)),
-  k_m1 = rlnorm(n_biphasic, log(0.002), log_sd)))
-
-ds_biphasic_mean <- lapply(1:n_biphasic,
-  function(i) {
-    mkinpredict(DFOP_SFO, syn_biphasic_parms[i, ],
-      c(parent = 100, m1 = 0), sampling_times)
-  }
-)
-
-set.seed(123456L)
-ds_biphasic <- lapply(ds_biphasic_mean, function(ds) {
-  add_err(ds,
-    sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2),
-    n = 1, secondary = "m1")[[1]]
-})
-
-# \dontrun{
-f_mmkin <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, error_model = "tc", quiet = TRUE)
-
-f_mixed <- mixed(f_mmkin)
-print(f_mixed)
+    
    sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+n_biphasic <- 8
+err_1 = list(const = 1, prop = 0.07)
+
+DFOP_SFO <- mkinmod(
+  parent = mkinsub("DFOP", "m1"),
+  m1 = mkinsub("SFO"),
+  quiet = TRUE)
+
+set.seed(123456)
+log_sd <- 0.3
+syn_biphasic_parms <- as.matrix(data.frame(
+  k1 = rlnorm(n_biphasic, log(0.05), log_sd),
+  k2 = rlnorm(n_biphasic, log(0.01), log_sd),
+  g = plogis(rnorm(n_biphasic, 0, log_sd)),
+  f_parent_to_m1 = plogis(rnorm(n_biphasic, 0, log_sd)),
+  k_m1 = rlnorm(n_biphasic, log(0.002), log_sd)))
+
+ds_biphasic_mean <- lapply(1:n_biphasic,
+  function(i) {
+    mkinpredict(DFOP_SFO, syn_biphasic_parms[i, ],
+      c(parent = 100, m1 = 0), sampling_times)
+  }
+)
+
+set.seed(123456L)
+ds_biphasic <- lapply(ds_biphasic_mean, function(ds) {
+  add_err(ds,
+    sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2),
+    n = 1, secondary = "m1")[[1]]
+})
+
+# \dontrun{
+f_mmkin <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, error_model = "tc", quiet = TRUE)
+
+f_mixed <- mixed(f_mmkin)
+print(f_mixed)
 #> Kinetic model fitted by nonlinear regression to each dataset
 #> Structural model:
 #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -177,12 +194,12 @@ single dataframe which is convenient for plotting
    
 #> 
 #> Mean fitted parameters:
 #>        parent_0        log_k_m1 f_parent_qlogis          log_k1          log_k2 
-#>      100.674757       -8.762456       -0.004347       -3.348812       -3.986853 
+#>      100.674757       -8.761916       -0.004347       -3.348812       -3.986853 
 #>        g_qlogis 
-#>       -0.087391 
-plot(f_mixed)
+#>       -0.087392 
+plot(f_mixed)
 
-# }
+# }
    @@ -197,7 +214,7 @@ single dataframe which is convenient for plotting

    -

    Site built with pkgdown 2.0.3.

    +

    Site built with pkgdown 2.0.6.

    -- cgit v1.2.1