Modelling Tools for Reproduction and Survival Data in
Tools for ecotoxicologists and regulators dedicated to the
mathematical and statistical modelling of toxicity test data. They use advanced and
innovative methods for a valuable quantitative environmental risk assessment.
Companion R package for MOSAIC website
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cd to source directory
- Build from sources (creates vignette and archive)
R CMD build .
- Build and install
R CMD INSTALL --build .
- Check the package
R CMD check --as-cran morse_X.X.X.tar.gz
- Update package description/NAMESPACE
- under the R interpreter:
- Generate documentation
- reference manual:
R CMD Rd2pdf .
- vignettes (using the R interpreter):
devtools::document(roclets=c('rd', 'collate', 'namespace', 'vignette'))
- Run unit tests
- under the R interpreter:
Compilation (with RStudio)
ROxygen2 v5.0.1 or higgher
- RStudio builder configuration:
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: all enable exeptVignettes
andSource and binary package build`
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Document or Ctrl + Shift + D
- check if the two folder inst and build were created.
- build the source file :
More : Build Source Package
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R: remove.packages("morse", lib="~/Documents/R/R-X.X.X/library")
R: install.packages("~/Documents/morse_X.X.X.tar.gz", repos = NULL, type = "source")
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=== morse : MOdelling tools for Reproduction and Survival data in Ecotoxicology ===
- add survival dataset for pulse exposure: 'propiconazole_pulse_exposure'.
- add S3 'survFit' method for TKTD modeling with model SD or IT for both 'time constant exposure' or 'time varying exposure'.
- add 'LCx' function to plot Lethal Concentration for x percent of the population for survFit model (TKTD SD or IT with constant or varying exposure).
- add option 'main' to add title in plot for PPC.
- add section for 'survFit' TKTD IT and SD (cst and var exposure) in the tutorial vignette.
- change the require dataset for survData and reproData: replicates are unique for each time-serie all over concentration profiles
- change the struture of all datasets included to satisfy that all replicates are unique for each time-serie all over concentration profiles.
- add the 'survFitTKTD' function to analyse 'survData' object with a time-exposure-
- add the S3 'plot', 'print', 'summary' and 'ppc' methods for the 'survFitTKTD'
- add two survival datasets : dichromate and propiconazole.
- the method plotDoseResponse replaces the plot.survData and plot.reproData
when the argument target.time was set. Now the response is expressed in
survival rate or in number of offspring per individual-days.
- the calcul of the mean fitted curve of 'plot.reproFitTT' and 'plot.survFitTT'
is the same of the 95 % Credible limits.
- the ci arg in 'plot.reproFitTT' and 'plot.survFitTT' was suppressed and the
credible limites was allways plotted.
- added a new argument 'adddata' in 'plot.reproFitTT' and 'plot.survFitTT'
to draw the datas with theyre confidence interval.
- add a new argument 'spaghetti' in 'plot.reproFitTT' and 'plot.survFitTT'
to draw the credible interval as multiple curves.
- update the cross-references link to ggplot2 package
- JAGS version 4.0.0 or higher is required
- rjags version 4.4 or higher is required
- the dataset cadmium2 now reports the number of eggs instead of the number of
- add S3 method ppc to plot the posterior predictive check on reproFitTT and
- added a new argument 'remove.someLabels' to plot.reproData and plot.survData
functions to avoid the overlap of labels of the X-axis in ggplot style.
- the check on replicate's label has been removed in the survDatacheck
- minor changes in the tutorial vignette.
- remove titles in legend of plot.reproFitTT and plot.survFitTT in
- remove observed value points in plot.reproFitTT.
- survDataCheck and reproDataCheck would fail on datasets with integer-only
- the summary functions for survData and reproData now don't show the
number of datapoints per concentration and the number of datapoints
per time. This was considered misleading in the case where some
replicates have a different initial number of individuals.
- plot.survData (and plot.reproData) don't display a legend anymore with
unconstrained time and concentration. They used to display a misleading
"replicate" legend, which would not correspond to a real replication unit
- in plot.survData all ggplot style graphique start at 0,0.
- the DIC is not calculated in survFiTT anymore. Since we don't
perform model selection, this was not really useful and we thus
obtain a significant speed-up.
- the column ID was removed in survData and reproData objects.
- new package structure and function names.
- the repro.data function is now called reproData and creates an object of class
reproData without specific target time.
- the repro.check.data function is now called reproDataCheck.
- the repro.fullsurvplot and repro.cumulplot functions are replaced by the generic
plot S3 method for the class reproData.
- the repro.survplot function now depends on the plot S3 metod for the new class
- the repro.fit function is now called reproFitTT with the associated class
reproFitTT, with the argument target.time.
- add of new arguments for the reproFitTT function:
- "stoc.part" to choose the stochastic part of the model.
- "ecx" to choose the value of ECx estimated by the function.
- the deterministic part name are now in the legend of the plot function.
- when stoc.part = "bestfit" is choosen, the model "gammapoisson" is chosen if
the DIC of gamma-poisson model is smaller than DIC of poisson model of 10
(1 in the previous version).
- upgrade the informations in the summary of the reproData class.
- upgrade the informations in the summary of the reproFitTT function, and values
of parameters are expressed in untransformed values.
- the credible interval in plot.reproFitTT are now a ribbon.
- add a new group of functions to analyze survival data:
- the survDataCheck function checks the integrity of the dataset.
- the survData function with associated S3 method creates survData object.
- the survFitTT function run the bayesian estimation to fit an exposure-response
model for survival data with the associated specific S3 method: print, plot
- the lattice graphics was suppressed.
- the repro.convergence function was suppressed.
- new selection rules for the "bestfit" method in the function reproFitTT.
- in log scale the points at concentration = 0 are not drawn (ggplot).
- correction of points color in the legend for the plot.repro.fit function (ggplot).
- change the ylim range for the plot.repro.fit function (generic).
- correction of the log.scale option for the repro.survplot function.