NEWS

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qtlsim 2025-05-05 (2025-05-05)

• Remove includes of R_ext/PrtUtil.h from C code

qtlsim 2017-05-22 (2017-05-22)

• Small changes to avoid note about "R_registerRoutines"

qtlsim 2015-07-23 (2015-07-23)

• Rename plot.res as plot_res.

• License to GPL-3

qtlsim 0.73-2

• Added NAMESPACE.

qtlsim 0.72-1

• Fixed links in help files.

• In anal.leaps, calls to summary.regsubsets() replaced with just summary().

qtlsim 0.71-7

• To get rid of a warning message in the latest version of R's package checks, changed the name of the functions convert.sim and convert.output to convertSim and convertOutput, respectively.

qtlsim 0.71-6

• Fixed some slight problems in the help files.

qtlsim 0.71-4

• Changed the name of the first argument in convert.sim and convert.output so that we don't get a warning message in R CMD check.

qtlsim 0.71-3

• In calls to C code (using the .C() function), now make use of the PACKAGE argument.

qtlsim 0.71-2

• The last column returned by which.correct() should be labelled "incor.unlinked" rather than "incor.total". This is now fixed.

• Changed a call to error() to stop() in anal.leaps(). (There is no function error().)

qtlsim 0.70-2

• Fixed a few minor problems in the help files.

qtlsim 0.70

• Added forward selection following by backward elimination (method="forwback") to the function anal.leaps().

qtlsim 0.69

• Edited the documentation files to make them more complete (and to remove a repeated typographical error that resulted in the descriptions of the arguments not appearing in the help files).

• Added a function convert.output() for converting the output of anal.leaps(), anal.mcmc() and perm() for use with which.correct().

• Fixed a bug in anal.leaps(): one line was hard-coded for exactly 100 markers!

qtlsim 0.68

• Revised anal.multi2() back, so that MCMC starts at the null model.

qtlsim 0.67

• Revised anal.multi2() so that MCMC starts at the model chosen by forward selection with BIC, for the first of the bic_mult given. Revised sim.mcmc() so that one may choose to do only forward selection and MCMC.

qtlsim 0.66

• The C function forw_perm() was clearly wrong. I totally re-did it (thanks to advice from/discussion with Saunak Sen!)

qtlsim 0.65

• There's a bug in anal.all() that causes a core dump. It turned out to be the simple problem of having the max.steps argument larger than the total number of markers.

qtlsim 0.64

• Added anal.multi2() to do everything anal.multi() does, plus run MCMC with BIC-delta.

qtlsim 0.63

• Added plot.cor() function for plotting the output of which.correct(). Revised which.correct() so that the last column is the number of unlinked (rather than total) extraneous loci.

qtlsim 0.62

• Added functions combine.sims() combine.mcmc() to combine the simulation results of multiple runs of anal.multi() or sim.mcmc(), respectively.

qtlsim 0.61

• Revised which.correct() to give both the total number of extraneous loci and the number of extraneous loci on the same chromosome as a QTL.

qtlsim 0.60

• Added function to call the "leaps" packages to use the branch-and-bound procedure, and ported my old MCMC code to do a simple MCMC model selection procedure

qtlsim 0.56

• Revised "anal.multi" to contain default LOD thresholds that I estimated via (extensive) computer simulations.

qtlsim 0.55

• Added "anal.multi" function to do repeated simulations + analysis by ANOVA, CIM, and forward selection with BIC and permutation tests.

qtlsim 0.54

• Completed addition of analysis programs, including the "bump finding" function necessary for turning LOD curves from ANOVA/IM and CIM into a selected model.

qtlsim 0.53

• Added analysis programs.

qtlsim 0.51

• Implemented an old (1996) simulation program. Why didn't I look for and reuse this code in the first place?

qtlsim 0.50

• A new package; the aim is to test different model selection approaches to identifying QTLs in backcrosses, in the case of an additive model.