Version log DEBtoxM flavour Surv
Version 1.01 (Date 15/06/2011)
- 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 (i.e., body residues), 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 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 1.02 (Date 02/10/2011)
- Modified the units structure to match the other flavours. Note that in all your mydata files, units must be specified as: TYPES.units = {'mg/L' 'd' 'cm' 'mg/kg'}. The body size unit is needed for consistency with the other flavours.
- 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).
- 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 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)
- 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.
- Added the possibility to use the log-logistic instead of the lognormal for IT (in call_deri.m there is now a switch). The lognormal requires the statistics toolbox while the log-logistic does not (the CDF can be written in closed form).
- 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.
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.
- Corrected small error in the output to the screen (number of data sets was not shown when working with multiple studies).
- For continuous data only: 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.
Version 1.04b (Date 06/05/2015)
- The mydata files state that the log-normal distribution is the standard for IT and mixed GUTS models, but the switch was set to log-logistic in call_deri. Note that the log-normal requires the statistics toolbox, so if you do not have that one, use the log-logistic instead.