Version log GUTS package for BYOM
Version logging starts with 2.0 Beta 1 (earlier version have not been logged).
Version 2.0 Beta 1 (02/03/2017)
- The earlier GUTS1 and GUTS2 package have been merged in 2.0 beta 1. The files in the main folder are the ones to start with (reduced model, constant exposure, analytical solution, only pure SD and IT). The other folders contain the more fully featured 'reduced' and 'full' models.
- This version is made fully compatible with GUTS version 4.0 Beta 2, and the examples make use of several of the new features.
- The naming of the symbols and the model structure now closely follows the new definition as will be used in the GUTS e-book (to be released end of 2017). The model is still the same, and all analyses types that could be performed with the old version are still possible. The examples provided will cover the most common types.
- In the full model, there is an option to set damage repair to fast. This effectively implies that the actual internal concentration is used as dose metric.
- The derivatives.m for the full and reduced model contain the code to include time-varying concentrations. This is demonstrated in the diazinon case studies.
- For the GUTS e-book, we decided that the log-logistic distribution should be the standard for GUTS. This is therefore also the case in this package. In call_deri, you can still find the option for the log-normal.
- The options for the ODE solver have been moved to globals so they can be set in the script.
- For IT and the mixed model (IT and SD combined), a long time vector is needed for the calculations. This was earlier captured in prelim_checks, but is now placed in call_deri for the GUTS package.
- The starting values estimator has been updated and should work well for the simples cases (reduced model, no dynamic damage stage) and constant exposure.
Version 2.0 Beta 2 (2017)
- Several errors in startvals.m that led to errors for some data sets. Also added a short range for hb. Also corrected the call to startvals in all scripts apart from byom_guts_start.
- Corrected the legends for the dieldrin cases: should be ug/L and not uM.
- Forgot to change "clear all" to "clear, clear global" in several of the example scripts.
- Removed the use of the log-normal distribution in call_deri, as we will use the log-logistic as the GUTS default.
Version 2.0 (27 April 2017)
- No additional changes to the beta 2 version.
- Note: when using the likelihood-region method to make confidence intervals for the LC50, percentiles were taken. This should have been min-max, which leads to somewhat wider intervals on the LC50. This is now corrected in BYOM 4.1.
Version 2.1 (01 February 2018)
- Restructured the package into full and reduced, and included a still somewhat experimental part in a separate directory (see next point). Many small changes in comments and layout.
- Added a series of files that include a more extensive analytical solution for the TK+damage dynamics. This can be used with constant exposure, but also for pulsed exposure (as long as the total time vector can be divided into a limited number of episodes with a constant concentration). This latter option makes use of the new function make_te, which creates a global that carries the information on the forcing events (see example files in the 'experimental' directory).
- The full model now also makes use of the analytical solution for constant exposure.
- Increased the long time vector that needs to be calculated for IT and the mixed models from 100 to 200, which should be sufficient for almost all cases. This is now a parameter in call_deri, so when you model very long time periods (e.g., >20 days), this may need to be extended.
- Plot_guts now produces some warnings to let you know that some plots may need careful interpretation due to NaNs in the data, missing animals, or multiple data sets.
- Plot_guts now makes a predicted vs observed plot for the survival probability, and also calculates a significance test for the fit (when plotting expected vs. predicted deaths, and requires the statistics toolbox).
- Modified the calculation of LC50s and multiplication factors to work with the make_te version of an exposure profile (defining multiple episodes with constant concentration within an episode). Changes are made in the general BYOM engine, but only affect the GUTS calculations.