Version 1.66

Version 1.66, 2023-11-27

Bug fixes

• Fixed problem in a call to Rprintf() in C++ code, identified by CRAN. (Issue #104.)

• Fixed additional compiler warnings on CRAN (Issue #105).

Version 1.62

Version 1.62, 2023-11-17

Bug fixes

• Fixed bug in summary.scanone() for the case format="onepheno" but threshold has length > 1. (Issue #102.)

• Fixed bug in read.cross() for format "csvs" when the phenotype file contains only the identifiers. (Issue #103.)

Version 1.60

Version 1.60, 2023-04-18

Minor changes

• In the CITATION file, change from citEntry() to bibentry().

Bug fixes

• Fixed bug in addint() and addcovarint(): when X chr QTL and missing phenotypes, would halt with error because cross wasn't getting subset. (Issue #101)

Version 1.58

Version 1.58, 2022-12-22

Minor changes

• In compiled code, replace calls to sprintf() with calls to snprintf(), to avoid warnings on CRAN.

Version 1.54

Version 1.54, 2022-12-01

Minor changes

• locateXO() and countXO() are now working for cross type BCsFt (by treating it as an F2 intercross).

Bug fixes

• Fixed a bug in summary.cross() re & vs &&.

• Fix bug in read.cross.bcsft() so that in read.cross() you can use crosstype="bcsft"

Version 1.52

Version 1.52, 2022-07-09

Minor changes

• checkAlleles() checks that the recombination fractions in the cross object are not only LOD scores (such as from markerlrt()); if they are, it re-runs est.rf().

• In sim.ril(), changed an instance of if(class(x)=="X") to if(inherits(x, "X"))

Version 1.50

Verison 1.50, 2021-10-06

New features

• cim() now includes an addcovar argument for including additional covariates in the model.

Minor changes

• Revised qtlversion() to handle a case like "1.50".

• Added #define USE_FC_LEN_T in C code that calls Fortran, because of a change in R 3.6.5 that's going to be required in R 4.2.0.

Version 1.48-1

Version 1.48, 2021-03-24

Bug fixes

• Fixed bug in addqtl() and addpair() in which the argument
  forceXcovar wasn't getting passed to scanqtl().

• Fixed bug in stepwiseqtl() regarding the way the null LOD score is
  calculated.

Version 1.47-9

Version 1.47, 2021-01-07

Minor changes

• Added function find_large_intervals() for finding inter-marker intervals in a map with length greater than some value.

• Fixed potential problem in documentation, since plot() has moved from the graphics package to base.

• Acknowledge R Core Team among contributors, as zeroin function (in C) had been taken from R version 2.15.1. Also add a Copyrights field to the DESCRIPTION file.

• Allow rescalemap(), shiftmap(), summaryMap(), and jittermap() to work with plain lists.

• Fixed Issue #91 where pull.rf() gives a cryptic error if marker names are not all distinct.

Bug fixes

• Fix a problem in inferredpartitions() that occurs in the devel version of R.

• Small change to read.cross() to avoid warning about length of alleles argument for crosstype="4way". (Fixes Issue #90.)

• Small change to read.cross() to avoid messing with X chromosome genotypes when crosstype=4way". (Fixes Issue #88.)

1.46-2 released to CRAN on 2020-03-11

Version 1.46, 2020-02-28

Minor changes

• In preparation for R 4.0, when the default for stringsAsFactors will become FALSE rather than TRUE in read.table() and data.frame(), we needed to add stringsAsFactors=TRUE to calls to read.table() and data.frame() in various places. Also there was some ugliness regarding addpair().

Bug fixes

• Fix bug in mqmpermutation() by removing the uses of batches and the batchsize argument.