Print method for mmkin objects

Subsetting method for mmkin objects.

Subsetting method for mmkin objects

# S3 method for mmkin
@@ -179,30 +179,46 @@ either a list of mkinfit objects or a single mkinfit object.
     Value
 
     An object of class mmkin.
+    Author
+
+    Johannes Ranke
 
     Examples
     
   # Only use one core, to pass R CMD check --as-cran
-  fits <- mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C),
-                cores = 1, quiet = TRUE)
-  fits["FOMC", ]
#>       dataset
-#> model  B       C      
-#>   FOMC List,39 List,39
-#> attr(,"class")
-#> [1] "mmkin"
  fits[, "B"]
#>       dataset
-#> model  B      
-#>   SFO  List,39
-#>   FOMC List,39
-#> attr(,"class")
-#> [1] "mmkin"
  fits["SFO", "B"]
#>      dataset
-#> model B      
-#>   SFO List,39
-#> attr(,"class")
-#> [1] "mmkin"

-  head(
+  fits <- mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C),
+                cores = 1, quiet = TRUE)
+  fits["FOMC", ]
+
#> <mmkin> object
+#> Status of individual fits:
+#> 
+#>       dataset
+#> model  B  C 
+#>   FOMC OK OK
+#> 
+#> OK: No warnings
  fits[, "B"]
+
#> <mmkin> object
+#> Status of individual fits:
+#> 
+#>       dataset
+#> model  B 
+#>   SFO  OK
+#>   FOMC OK
+#> 
+#> OK: No warnings
  fits["SFO", "B"]
+
#> <mmkin> object
+#> Status of individual fits:
+#> 
+#>      dataset
+#> model B 
+#>   SFO OK
+#> 
+#> OK: No warnings

+  head(
     # This extracts an mkinfit object with lots of components
-    fits[["FOMC", "B"]]
-  )
#> $par
+    fits[["FOMC", "B"]]
+  )
+
#> $par
 #>  parent_0 log_alpha  log_beta     sigma 
 #> 99.666193  2.549849  5.050586  1.890202 
 #> 
@@ -217,12 +233,11 @@ either a list of mkinfit objects or a single mkinfit object.
 #> 
 #> $evaluations
 #> function gradient 
-#>       25       72 
+#>       25       78 
 #> 
 #> $message
 #> [1] "both X-convergence and relative convergence (5)"
-#> 

-
+#>

# S3 method for nlme.mmkin -plot( - x, - i = 1:ncol(x$mmkin_orig), - main = "auto", - legends = 1, - resplot = c("time", "errmod"), - standardized = FALSE, - show_errmin = TRUE, - errmin_var = "All data", - errmin_digits = 3, - cex = 0.7, - rel.height.middle = 0.9, - ymax = "auto", - ... -)

Examples

ds <- lapply(experimental_data_for_UBA_2019[6:10], - function(x) subset(x$data[c("name", "time", "value")], name == "parent")) -f <- mmkin("SFO", ds, quiet = TRUE, cores = 1)

#> Warning: Shapiro-Wilk test for standardized residuals: p = 0.0195

#> Warning: Shapiro-Wilk test for standardized residuals: p = 0.011

#plot(f) # too many panels for pkgdown -plot(f[, 3:4])

library(nlme) -f_nlme <- nlme(f) - -#plot(f_nlme) # too many panels for pkgdown -plot(f_nlme, 3:4)

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) +f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, cores = 1) +plot(f[, 3:4], standardized = TRUE) +

library(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 +f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-4)) +plot(f_nlme) +

Site built with pkgdown 1.5.1.

Site built with pkgdown 1.6.1.

Print method for mmkin objects — print.mmkin • mkin

main	The main title placed on the outer margin of the plot.
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.
ylab	Label for the y axis.
xlim	Plot range in x direction.
legends	An index for the fits for which legends should be shown.
resplot	Should the residuals plotted against time, using -`mkinresplot`, or as squared residuals against predicted -values, with the error model, using `mkinerrplot`.	lpos	Position(s) of the legend(s). Passed to `legend` as +the first argument. If not length one, this should be of the same length +as the obs_var argument.
standardized	Should the residuals be standardized? This option -is passed to `mkinresplot`, it only takes effect if -`resplot = "time"`.	inset	Passed to `legend` if applicable.
show_errmin	Should the chi2 error level be shown on top of the plots -to the left?	resplot	Should the residuals plotted against time or against +predicted values?
errmin_var	The variable for which the FOCUS chi2 error value should -be shown.	ymax	Vector of maximum y axis values
errmin_digits	The number of significant digits for rounding the FOCUS -chi2 error percentage.	maxabs	Maximum absolute value of the residuals. This is used for the +scaling of the y axis and defaults to "auto".
cex
ymax	Maximum y axis value for `plot.mkinfit`.	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?
...

main

The main title placed on the outer margin of the plot.

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.

ylab

Label for the y axis.

xlim

Plot range in x direction.

legends

An index for the fits for which legends should be shown.

resplot

Should the residuals plotted against time, using -mkinresplot, or as squared residuals against predicted -values, with the error model, using mkinerrplot.

lpos

Position(s) of the legend(s). Passed to legend as +the first argument. If not length one, this should be of the same length +as the obs_var argument.

standardized

Should the residuals be standardized? This option -is passed to mkinresplot, it only takes effect if -resplot = "time".

inset

Passed to legend if applicable.

show_errmin

Should the chi2 error level be shown on top of the plots -to the left?

resplot

Should the residuals plotted against time or against +predicted values?

errmin_var

The variable for which the FOCUS chi2 error value should -be shown.

ymax

Vector of maximum y axis values

errmin_digits

The number of significant digits for rounding the FOCUS -chi2 error percentage.

maxabs

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

cex

ymax

Maximum y axis value for plot.mkinfit.

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?

...

x	An mmkin object.
...	Not used.

An mmkin object.

...

Not used.

Subsetting method for mmkin objects

Value

Author

Examples

Plot a fitted nonlinear mixed model obtained via an mmkin row object

Arguments

Value

Author

Examples

Arguments