Version log DEBtoxM flavour DEBtox

Version 1.01 (Date 15/06/2011)

- Removed possibility to have another TK stage. This option will be worked out further in a new flavour, if needed.
- Added different dose metrics, which is mainly used to give correct units for the parameters.
- Re-arranged files over the directories "engine" and "utils", for my own convenience. All files in "utils" are now the same for all flavours, which aids version control for me.
- For graded endpoints, the likelihood function was wrong when using means instead of individual data points.
- In calc_lik.m I provide an alternative (commented out) likelihood calculation for graded endpoints that requires a standard deviation for the error around the model estimate.
- Repaired a division-by-zero warning when there are zeros in the weight matrix for reproduction (when there are no animals alive anymore). 
- Repaired a division-by-zero warning when all replicate data points at one time and concentration are NaN. 
- Don't plot ranges for replicated survival data (because the individual obervations are not of interest).

Version 1.01b (Date 16/06/2011)

- In def_pars.m, I had set all parameters to be temporarily fitted on normal scale (which could lead to a more realistic sample from the slice sampler, when using TYPES.POSTswitch>0). Set them back to the default (some parameters estimated on log scale, such as ke).

Version 1.02 (Date 02/10/2011)

- I made more files common to all flavours, and included a new directory "common" to collect the engine files that are common. The pathdefine.m is adapted to include the new directory into the search path automatically.
- Corrected the PlotoverSwitch so that it works with more than one type of endpoints (all observations and model predictions for an endpoint are collected in one graph).
- Added the possibility to make confidence intervals on population growth rate with the Euler-Lotka equation(calc_popmod.m), using a previously saved sample from the slice sampler.
- Modified the plot_all.m routine: moved more code to subfunctions. This makes it easier to modify the plots for all endpoints in one go. Also improved legends.
- Added the possibility to include a hatching time for the population calculations (if not specified, Th=0).
- Added an oviparity switch for animals that hatch their eggs internally (as observed offspring are later than the production of the egg). This corrects the repro data for that (if not specified, Tovi=0).
- Added the possibility to use different assumptions for the scatter structure (for graded endpoints), including a fixed error variance per data set (as second argument of lam). If not specified, defaukt is optimising the error variance for each data set seperately.
- Fixed an error for plotting the iso-effect line for EC0 when body residues are given.

Version 1.03 (Date 19/05/2012)

- Added a simple ageing model as blanktype = 2. This is a one-state alternative to the DEB3 module.
- Changed the use of units. Instead of compound units such as mg/L and mg/kg, I now only use the single units for chemical mass, environment volume/weight, time, body length and body weight. Previous mydata files may give an error due to this change, so adapt the units to the new style.
- Added units in profile likelihoods and marginal posterior densities.
- For continuous data, there was an error in the implementation of the likelihood function in transfer.m, which affected the weighting of data when fitting on means of replicates.
- For reproduction data, the choice between different statistical ways to treat the data is now a choice in the mydata file (TYPES.reprotype). When fitting on cumulatives, the plotted datapoints are the MEAN of the cumulatives for each replicate. When fitting on intervals, the plotted points are the CUMULATED mean reproduction per interval! When fitting without zero repro events, these events are also removed from the plotting (and the means without zeros taken for replicated data).
- Also plot the relative population growth rate (relative to the control growth rate, for that study, in that scenario).

Version 1.04 (Date 17/04/2015)

- Corrected a silly error that prevented the calculation of standard errors to start when using multiple studies with a lot of common parameters.
- Added the possibility to plot error bars as range, s.d., s.e. or 1.96 x s.e. (conf. interval) with a switch in plot_all. This can produce counter-intuitive effects when scaling the data (s.d.,s.e., and conf. interval are calculated on transformed data). Also added the possibility to shift data slightly so error bars don't overlap.
- Adapted axis limits to suit error bars tightly.
- Corrected an error in the use of zero-variate data with multiple studies.
- Changed the calculation of fixed-tail CIs (quantiles) from the slice sample. Instead of using the sample, I now use the kernel-density estimate, which performs better for small samples.
- Also allow credible intervals on fitted external concentrations.