0.1 -> 0.2
Added function for power for F2 intercross
0.2 -> 0.3
Corrected function for discount factor for F2 intercross.
0.3 -> 0.31
Corrected F2 power function and detectable effects function.
It was not doing the right thing for non-zero marker intervals.
Analytical error.
0.31 -> 0.32
Changed the dominance coding to be consistent with Karl's R/qtl.
0.32 -> 0.80
Major changes; too many to document. Changed syntax of many
commands. Deleted the simulation commands. Made the whole
package more practical.
0.80 -> 0.81
More complete documentation. Corrected bug in powercalc
wrapper function.
0.81 -> 0.85
- Changed alpha to sel.frac in all arguments to minimize confusion
between alpha, the level of a test, and the selection fraction.
- Changed the name of the function "optalpha" to "optselection".
- The functions "powercalc", "samplesize", and "detectable"
now accept the arguments bio.var, gen.var, and bio.reps directly;
it is not necessary to call "error.var" any more.
- The functions "powercalc", "samplesize", and "detectable"
now output the percent variance explained also.
- New function called "prop.var" which calculates the proportion
of variance explained by a locus given the cross type, effect,
and error variance.
0.85 -> 0.90
- Added the functions to calculate genome-wide thresholds and
tail probabilities for genome scans using Poisson approximations.
- Changed search interval for detectable effect calculation.
- Renamed bio.var env.var in powercalc(), and error.var().
- Changed genome length argument to G from L in thresh() and tail.prob().
- Changed the units to centiMorgans from Morgans for genome length
and marker spacing arguments.
0.90 -> 0.91
- Partial argument matching no longer allowed in optimize, optim,
uniroot, nlm, and integrate. Changed functions to reflect that.
https://stat.ethz.ch/pipermail/r-devel/2007-May/045791.html
0.91 -> 0.92
- Add the ci.length function for calculating confidence interval
lengths
- Replaced optim by optimze in optspacing function for the 1-dim
optimization; works better
- Added functions for selective phenotyping (from Brian Yandell)
0.92 -> 0.93
- Added citation information.
- Fixed manpage formatting.
0.93 -> 0.94
- Changed license to generic GPL.
- Added citation information.
- Bug fix in optspacing().
0.94 -> 0.941
- Deleted duplicate CITATION file.
0.941 -> 0.95
- Added NAMESPACE file to be R 2.14 compliant.
0.95 -> 0.951
- Updated email address.
0.951 -> 0.952
Thanks for Karl Broman for help with these updates.
- Fixed DESCRIPTION file, suggests qtl package.
- Fixed CITATION file.
- In thresh.R, spell out all arguments to pchisq()
- In NAMESPACE, dd importFrom() for various stats functions
0.952 -> 0.953
Small changes to conform to CRAN regulations.