mkin/R, branch v0.9.50.1 Fitting kinetic models to chemical degradation data (also on github) https://cgit.jrwb.de/mkin/atom?h=v0.9.50.1 2020-05-11T13:20:53Z Add analytical solution for DFOP-SFO 2020-05-11T13:20:53Z Johannes Ranke jranke@uni-bremen.de 2020-05-11T13:00:25Z urn:sha1:6308e7d7898d4f064d321d97d162c6752c22b362 This is about twice as fast as deSolve compiled in the case of FOCUS D Analytical solutions for all SFO variants 2020-05-11T11:43:40Z Johannes Ranke jranke@uni-bremen.de 2020-05-11T11:43:40Z urn:sha1:b36ae3d710858ee3ff2907eb2d780e0dff48a4f3 Reduce precision of traced parameters, formatting 2020-05-11T07:05:25Z Johannes Ranke jranke@uni-bremen.de 2020-05-11T07:05:25Z urn:sha1:adb597eef6ef840ef28486dbe3d93dc62b097a6d Avoid merge() and data.frame() in cost function 2020-05-11T03:18:32Z Johannes Ranke jranke@uni-bremen.de 2020-05-11T03:15:19Z urn:sha1:234c9059a95e104917e488a6ddd2313234a96cdc also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette. Default to analytical for coupled models if available 2020-05-10T19:53:00Z Johannes Ranke jranke@uni-bremen.de 2020-05-10T19:53:00Z urn:sha1:d113cd79b178fdc91aecb894707ed356129dfb75 This revealed that transforming rates is necessary for fitting the analytical solution of the SFO-SFO model to the FOCUS D dataset. Benchmarks show that fitting coupled models with deSolve got a bit slower through the latest changes Avoid the call to merge for analytical solutions 2020-05-09T19:18:42Z Johannes Ranke jranke@uni-bremen.de 2020-05-09T19:18:42Z urn:sha1:efab37957381919c21d874906ce870f4941c760a This increases performance up to a factor of five! Make mkinpredict consistently return a dataframe 2020-05-09T09:30:52Z Johannes Ranke jranke@uni-bremen.de 2020-05-09T09:30:52Z urn:sha1:47ef00e3d0a961f8fbecf0bd5da0283bed21bb96 Profiling suggests the merge in mkinfit is the bottleneck 2020-05-08T15:36:04Z Johannes Ranke jranke@uni-bremen.de 2020-05-08T15:36:04Z urn:sha1:7b9f11562fa9ab8a023f47e6b99a2562b668e48c We do not need the n.outtimes argument for mkinfit 2020-05-08T14:25:34Z Johannes Ranke jranke@uni-bremen.de 2020-05-08T14:25:34Z urn:sha1:ea9b76c667620d75c5aeb4077117e722ed0bc3d6 As we set the tolerance for ode() appropriately Avoid duplicate merge in tc error model fit 2020-05-08T13:22:54Z Johannes Ranke jranke@uni-bremen.de 2020-05-08T13:22:54Z urn:sha1:636dade692b8eee012004a2740616385333efc48 This increases the performance in the complete test suite by about 20 secs from 120 to around 100 secs. I tried improving merge speed by using data.table on another branch, but this did not give a noticeable performance gain.