kbroman (Karl W Broman)

Build OSX: Remove STATUS on OSX - which sends to GUI

MQMtut: xQTL

MQMtut: racing to the end (textually)

MQMtut: effects section

MQM: a few more fixes for the rename

Renamed mqmall to mqmscanall

MQMtut: incremental improvements

MQMtut: fixed macro

MQM: fixed mqm reference to mqmscan

MQMtut: added 'info' header for code sections

MQM: Improving documentation

R: Disabled mqm() in favour of mqmscan()

Merge branch 'MQM' of git://github.com/kbroman/qtl into karl-MQM

Minor edits

Merge branch 'master' into MQM

Add functions convert2risib and convert2riself for converting crosses.

Remove a TODO item (regarding stepwiseqtl) that seems to have already been fixed.

Fix bug in scanone permutations for case of multiple phenotypes with missing data.

Add map.function and error.prob arguments to read.cross, for use with est.map.

Fix bug in summary.scanone for case of format="allpeaks".

Revise scanone/two so that X chr in RIL treated like an autosome.

Removed some odd code from the plot.qtl function.

Make lodint and bayesint stop with error if chr or qtl.index have length > 1.

Close cluster connections in scanone and scantwo if functions stopped early.

Fix bug in summary.scanone for case of format="allpeaks".

Working on the introduction

Sweave: problem got fixed after build version was fixed

Clean up tar ball after testing

Skipping 64-bits tests

Skip T32 on 64-bit

Fix: Query R executable for include and lib paths

Build system: improving locating R and libs

run_all_tests: Allow passing in --library options

R CMD check R/QTL script

test_qtl.R: improved test somewhat

Listeria test shows real markers in output

Minor printout information

Testing for version information

Man page update

Tutorial

R mqm function should be mqmscan

Removed unused test

mqmscan: The (inaptly named) analyseF2 now returns logL, so it can be tested

Test script should clean up object files

Some extra output in test script

Regression test changed outcome

Some lines got lost creating the headers

Standardized headers for MQM tests (standalone)

Normalized MQM .[ch] headers using contrib/scripts/update_header.rb script

Modified first header

Removed on R CMD check warning (transf)

Testing script

A script for running all tests

Fixed regression tests - should show same on Unix and Windows

Merge branch 'pjotr' of git@github.com:pjotrp/rqtl-mqm into pjotr

MQM regression tests fully working on Linux. Note that we have a problem

Standalone: do not always fail on cofactor file missing

Path error failed silently for cofactor file

Spelling of likelihood

TODO

Updated all MQM R files with a new header.

Update R headers

Script updates headers dynamically

Adding header rewrite

mqmcircleplot: rename my test function from plot.circle to plot_c

mqmscan: MAYOR bug, the model parameter could NOT be set to dominance. Now it can again

mqm-todo: -1 (example circle plot, in tutorial and man pages)

mqmutil:estmarkerlod: some text to explain what it does + a check to only estimate on the same chromosome

mqmutil:estmarkerlod: Put in some checks

Merge branch 'MQM' of git://github.com/kbroman/qtl into karl

mqmscan.R: Checking on Inf phenotype, (which occurs after logtransforming a 0.00)

circleplots: better output

tutorial: more info about the circleplots

plotcircle: A small bug in a hidden function

mqmplotcircle: Color updates, now using rainbow for multitrait

mqmscanall.R: random cleanup action, spacing and verbose statement

mqmscanall.R: random cleanup action, spacing and verbose statement

Merge branch 'pjotr' of git://github.com/pjotrp/rqtl-mqm into pjotr

tutorial: forgot \begin figure labels at the circle plots

Tutorial: 3 circle plots added

circleplot minor + pull from pjotr

Merge branch 'pjotr' of git://github.com/pjotrp/rqtl-mqm into pjotr

circleplot: minor updates

Close cluster connections in scanone and scantwo if functions stopped early.

Remove [qtl] from links in .Rd files; add nortest package as "Suggests:"

Merge branch 'master' into MQM

Revise INDEX file.

Add items to TODO list.

Add a bug report to the TODO list.

Add item to TODO list.

Add items to TODO list.

Fixed an apparent bug in read.cross for format="qtlcart".

Add items to TODO list.

Add items to TODO list.

Removed always printed (meaningless output)

Removed 2 CHECKS and 1 FIXME, (because we dont plot information content anymore

SWEAVE WORKS AGAIN !!!

Updates CisTransPLot

Sweave

Update man

Renamed functions

Testupdates removing attr()

mqmscan & util changed (wrapped the attr function and changed a variablename aa into something meaningfull

Latex fixings (untill page 20)

Remved scaling using INFO from mqm

Removed info*qtl line from the plots

Tutorial

Tutorial

tutorial

More editing of tutorial

editing the tutorial

Updates van Pjotr

Latex

tutorial to inst/docs

Merge branch 'danny' of git://github.com/DannyArends/rqtl-mqm into danny

Updates

Merge branch 'master' of git@github.com:pjotrp/rqtl-mqm

Reverted on 'Enhances' - as per Karl's request

Sweave updates (some more images)

Updates to sweave documentation

Way 2 many permutations in the pdf so ~10 min compile now should be 2

Dumb mistakes

Augmentation -1 parameter (which was nonsense) and now with augment_above + sweave update

Sweave update + Rignore (so i dont load all the eps/pdf in git by accident)

Sweave update + 2 R bugfixes based on walking throug an analysis

Working Sweave =)

First stab at sweave

Some updates

Start of tutorial and a additional function to set cofactors more easily

Use 'suggests', rather than 'enhances'. Favoured by Karl.

Test added

New test output for t21