Changes in version 1.0                         

README

    o   Version 1.0-x of the ASMap package celebrates the Journal of
	Statistical Software publication, Taylor and Butler (2017). The
	paper succinctly summarizes the important contents of the
	package vignette and provides a useful quick reference for the
	functionality of the package. If you use ASMap in your
	publication please reference it using the bibliographic
	reference obtainable using citation("ASMap") and given below.

    o   Taylor, J., Butler, D. (2017) R Package ASMap: Efficient
	Genetic Linkage Map Construction and Diagnosis. Journal of
	Statistical Software, *79*(6), 1-29.

NEW FEATURES

    o   There is now a p-value function to emulate Figure 1.1 in the
	vignette. The function allows users to specify their own set of
	threshold distances and population sizes, making it easier to
	determine the correct choice of p.value to use in mstmap.cross
	and mstmap.data.frame.

    o   The function combineMap has been updated to include merging of
	linkage maps by "marker" or "genotype". Merging by "genotype"
	is identical to the previous version of the function. Merging
	by "marker" provides the ability to combine linkage maps with
	different sets of genotypes through common markers.

BUG FIXES

    o   fixClones muddled linkage groups when an inputted map had more
	than one linkage group. This has now been amended.

    o   The fixClones function crashed when consensus = FALSE was set.
	This has now been amended.

    o   The cross.scheme of the object was lost when pushing back
	markers using pushCross. This has now been amended.

    o   The function quickEst crashed when there were linkage groups
	with one marker. This has now been amended.

    o   The function alignCross crashed with a non-descript error when
	there were no matching markers in supplied reference maps. This
	has now been amended to provide a more descript error.

                  Changes in version 0.4 (2015-04-13)                   

README

    o   This is the first documented NEWS release of ASMap. For this
	reason it contains information about features of the package as
	well as recent bug fixes.

NEW FEATURES

    o   The package now contains a function to assist in identifying
	and orienting linkage groups (see ?alignCross).

    o   The heat map in the package now uses a diverging colour palette
	chosen from the default palettes available in RColorBrewer.

    o   The package now includes a PDF vignette. This can be found on
	any operating system using the command
	
	> vignette("ASMap")
	
	The vignette includes extensive descriptions of the package
	functions as well as fully worked example that showcases the
	package functions throuh pre-diagnosis, construction and post
	diagnosis of a linkage map. It also describes how the package
	can be used efficiently for techniques such as fine mapping or
	combining maps.

    o   The package now includes three fully documented marker data
	sets for users to explore. See the vignette for more details.

BUG FIXES

    o   Fixed a nasty bug in combineMap() that switched genotype names
	for certain linkage maps

    o   Fixed bug that returned inflated distances for "ARIL"
	populations when using mstmap.data.frame().

    o   If the constructed map contained linkage groups with one marker
	profileMark() graphically displaced the interval statistics.
	This has now been amended.

    o   pushCross() can now push large volumes of co-located markers
	back into the constructed map very efficiently.

    o   profileMark() was not outputting crti.val column when crit.val
	= "bonf" argument was chosen. This has now been amended.

    o   quickEst() has been improved and now provides an even more
	accurate and efficient distance calculations for linkage maps.