mkin - Fitting kinetic models to chemical degradation data (also on github)

Age	Commit message (Collapse)	Author	Files	Lines
2020-11-08	Improve saem method, add summary	Johannes Ranke	1	-6/+31
	Also make the endpoints function work for saem objects.
2020-11-07	Create saem generic for fitting saemix models	Johannes Ranke	1	-40/+45
	The reasons for this decision were - Creating an saemix generic in the saemix package caused problems with roxygen, because functions like saemix.plot.xy were documented in their help files as S3 methods, although explicitly exported with @export - Creating an saemix generic in this package is possible, but would make it necessary to load samix with exclude = "saemix" in order to avoid overwriting the generic when loading saemix. - The return object of such an saemix generic in this package cannot be an S3 class with class attribute c("saemix.mmkin", "SaemixObject") similar to nlme.mmkin, as saemix returns an S4 class. - Extending the S4 class SaemixObject using simple inheritance to a class SaemixMmkinObject with additional slots did not work as expected. When the initialize method was left untouched, it prevented creation of an SaemixMmkinObject even if it was based on an initialised SaemixObject, as the initialize method seems to always be called by new(). This could potentially be circumvented by a coerce method. If an alternative initialize method was used, an SaemixMmkinObject could be created. However, the methods written for SaemixObjects only worked in some instances, either because they checked for the class, and not for class inheritance (like compare.saemix), or because the initialize method was called for some reason. Therefore, the idea of creating a derived S4 class was abandoned. - A side effect of this decision is that the introduction of the saem generic opens the possibility to use the same generic also for other backends like nlmixr with the SAEM algorithm.
2020-11-07	Make deSolve predictions within saemix robust	Johannes Ranke	1	-13/+23
	Also, exclude the saemix function when loading saemix in the example code, to prevent overriding our generic
2020-11-06	Make saemix an S3 generic in this package	Johannes Ranke	1	-42/+72
	This commit also defined saemix.mmkin for mmkin row objects. This works fine, but if we set the class of the returned object to c("saemix.mmkin", "saemix"), it is not an S4 class any more which make it impossible to use saemix functions on it.
2020-11-06	Fast analytical solutions for saemix, update.mmkin	Johannes Ranke	1	-76/+137
	Also, use logit transformation for g and for solitary formation fractions, addressing #10.
2020-11-04	Update dynamic docs	Johannes Ranke	1	-5/+6

2020-11-04	Deprecate cores > 1 in saemix_model	Johannes Ranke	1	-3/+5

2020-10-15	More gentle example for saemix with combined error model	Johannes Ranke	1	-1/+2

2020-10-15	Don't run saemix examples on travis for now	Johannes Ranke	1	-1/+2

2020-10-15	Updating docs of current dev version	Johannes Ranke	1	-1/+41

2020-10-15	Reintroduce saemix helper functions	Johannes Ranke	1	-0/+134

2020-10-08	Avoid dep on dev version of saemix for release	Johannes Ranke	1	-134/+0

2020-05-26	Use all cores per default, confint tolerance	Johannes Ranke	1	-7/+24
	Also, use more intelligent starting values for the variance of the random effects for saemix. While this does not appear to speed up the convergence, it shows where this variance is greatly reduced by using mixed-effects models as opposed to the separate independent fits.
2020-05-25	Tell travis where to find the required saemix version	Johannes Ranke	1	-6/+5

2020-05-25	First working version of saemix helper functions	Johannes Ranke	1	-0/+118
	saemix_data depends on a development version of saemix, see pull request saemixdevelopment/saemixextension#2