From 234c9059a95e104917e488a6ddd2313234a96cdc Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 11 May 2020 05:15:19 +0200 Subject: Avoid merge() and data.frame() in cost function also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette. --- docs/reference/plot.mkinfit.html | 61 ++++++++++++++++++++-------------------- 1 file changed, 31 insertions(+), 30 deletions(-) (limited to 'docs/reference/plot.mkinfit.html') diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 33dc52b7..2ede2dec 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -39,7 +43,6 @@ - @@ -57,7 +60,7 @@ observed data together with the solution of the fitted model." /> - +

@@ -115,7 +118,12 @@ observed data together with the solution of the fitted model." />

@@ -130,7 +138,7 @@ observed data together with the solution of the fitted model." />

@@ -141,7 +149,7 @@ observed data together with the solution of the fitted model.

# S3 method for mkinfit
-plot(
+plot(
   x,
   fit = x,
   obs_vars = names(fit$mkinmod$map),
@@ -303,7 +311,7 @@ chi2 error percentage.
     
     
       ...
-      Further arguments passed to plot.
+      Further arguments passed to plot.
     
     
       standardized
@@ -327,29 +335,22 @@ latex is being used for the formatting of the chi2 error level, if
 # parent to sink included
 # \dontrun{
 SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
-                   m1 = mkinsub("SFO", full = "Metabolite M1" ))#> Successfully compiled differential equation model from auto-generated C code.
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc")
#> Warning: Observations with value of zero were removed from the data
plot(fit)
plot_res(fit)
plot_res(fit, standardized = FALSE)
plot_err(fit)

+                   m1 = mkinsub("SFO", full = "Metabolite M1" ))
#> Successfully compiled differential equation model from auto-generated C code.
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc")
#> Warning: Observations with value of zero were removed from the data
plot(fit)
plot_res(fit)
plot_res(fit, standardized = FALSE)
plot_err(fit)

 # Show the observed variables separately, with residuals
-plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"),
+plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"),
      show_errmin = TRUE)

 # The same can be obtained with less typing, using the convenience function plot_sep
 plot_sep(fit, lpos = c("topright", "bottomright"))

 # Show the observed variables separately, with the error model
-plot(fit, sep_obs = TRUE, show_errplot = TRUE, lpos = c("topright", "bottomright"),
+plot(fit, sep_obs = TRUE, show_errplot = TRUE, lpos = c("topright", "bottomright"),
      show_errmin = TRUE)
# }

- @@ -360,7 +361,7 @@ latex is being used for the formatting of the chi2 error level, if

Site built with pkgdown 1.4.1.

Site built with pkgdown 1.5.1.

-- cgit v1.2.1

Plot the observed data and the fitted model of an mkinfit object

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