Description Usage Arguments Value Author(s) Examples

Solves the differential equations with the optimised and fixed parameters
from a previous successful call to `mkinfit`

and plots
the observed data together with the solution of the fitted model.

If the current plot device is a `tikz`

device,
then latex is being used for the formatting of the chi2 error level,
if `show_errmin = TRUE`

.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
## S3 method for class 'mkinfit'
plot(x, fit = x,
obs_vars = names(fit$mkinmod$map),
xlab = "Time", ylab = "Observed",
xlim = range(fit$data$time),
ylim = "default",
col_obs = 1:length(obs_vars), pch_obs = col_obs,
lty_obs = rep(1, length(obs_vars)),
add = FALSE, legend = !add,
show_residuals = FALSE, maxabs = "auto",
sep_obs = FALSE, rel.height.middle = 0.9,
lpos = "topright", inset = c(0.05, 0.05),
show_errmin = FALSE, errmin_digits = 3, ...)
plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, ...)
``` |

`x` |
Alias for fit introduced for compatibility with the generic S3 method. |

`fit` |
An object of class |

`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. |

`xlab` |
Label for the x axis. |

`ylab` |
Label for the y axis. |

`xlim` |
Plot range in x direction. |

`ylim` |
Plot range in y direction. |

`col_obs` |
Colors used for plotting the observed data and the corresponding model prediction lines. |

`pch_obs` |
Symbols to be used for plotting the data. |

`lty_obs` |
Line types to be used for the model predictions. |

`add` |
Should the plot be added to an existing plot? |

`legend` |
Should a legend be added to the plot? |

`show_residuals` |
Should residuals be shown? If only one plot of the fits is shown, the residual plot is in the lower third of the plot? Otherwise, i.e. if "sep_obs" is given, the residual plots will be located to the right of the plots of the fitted curves. |

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

`sep_obs` |
Should the observed variables be shown in separate subplots? If yes, residual plots requested by "show_residuals" will be shown next to, not below the plot of the fits. |

`rel.height.middle` |
The relative height of the middle plot, if more than two rows of plots are shown. |

`lpos` |
Position(s) of the legend(s). Passed to |

`inset` |
Passed to |

`show_errmin` |
Should the FOCUS chi2 error value be shown in the upper margin of the plot? |

`errmin_digits` |
The number of significant digits for rounding the FOCUS chi2 error percentage. |

`...` |
Further arguments passed to |

The function is called for its side effect.

Johannes Ranke

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
# One parent compound, one metabolite, both single first order, path from
# parent to sink included, use Levenberg-Marquardt for speed
SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
m1 = mkinsub("SFO", full = "Metabolite M1" ))
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = "Marq")
plot(fit)
plot(fit, show_residuals = TRUE)
# Show the observed variables separately
plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))
# Show the observed variables separately, with residuals
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"))
``` |

mkin documentation built on May 19, 2017, 6:17 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.