Bugfix: Whether an HMR fit was successful with difficult input datawas platform dependent. Fits are now reported as failed with errormessage “Dubious fit (extreme standard error)” if the p value of theflux is > (1 - .Machine$double.neg.eps), which ensures that fits withextreme standard error of the flux estimate (in particular SE = Inf) arenot reported anymore. This impacts the result of the recommendedsimulation to determinef.detect and thus the flux selection inselectfluxes on some platforms, especially on Windows systems.fdetect will be lower leading to successful HMR fits being morelikely to be selected but there will also be less successful but dubiousHMR fits.
Fixed for CRAN note (regarding a documentation link).
Fixed an embarrassing maths error in the documentation.
Following a suggestion by Thomas Gremmen, diagnostic plots are now ina single PDF file. The (potentially numerous) PNG files created byprevious versions caused issues on some network drives.
The old deprecated original HMR algorithm has been removed. Olddeprecated flux selection algorithms have been removed. Removeddependency on package AICcmodavg.
Warning handlers did not work correctly.
There was a scoping issue with the plot parameter ingasfluxes if one of the ID columns was called “plot”.
selectfluxes has now gained a tolerance parameter toenable fine-tuning the check introduced in the previousversion.
CRAN has asked for a package rebuild with the newest knitrversion due to encoding issues in the vignette.
Added Pearson’s correlation coefficient to output of linearfit.
Breaking change: Flux selection has now its own functionselectfluxes. This makes implementing new algorithms easier.Please consult help(“selectfluxes”) for usage examples.
Implemented Roman Hueppi’s flux selection algorithm.
New Vignette included.