poppr 1.0.4
===========
BUG FIX
* A previous error where bootstrap values greater than 100 were reported from `bruvo.boot` on UPGMA trees has been fixed. 
* Fixed correction of negative branch lenghts using Kuhner and Felsenstein (1994) normalization for NJ trees.

MISC
* github repository for poppr has changed from github.com/poppr/poppr to github.com/grunwaldlab/poppr

poppr 1.0.3
===========
IMPROVEMENTS
* Optimized internal sampling function to run up to 2x faster.
* Utilized rmultinom function to increase speed of bootstrap sampling methods for shufflepop and ia. 

NEW FEATURES
* Function `informloci` will remove phylogenetically uninformative loci.

NAMESPACE
* Now importing specific functions from igraph and ape due to dependency issues.
* Removed igraph, ape, ggplot2, and phangorn form "Dependencies", but keeping them in "Imports".

BUG FIXES
* `read.genalex` will no longer insert an "X" in front of loci with numeric names. 

poppr 1.0.2
===========
BUG FIXES
* Fixed bug in diss.dist function that would return an inflated distance for haploids.

DOCUMENTATION
* Added explanation for the index of association in poppr_manual.
* Expanded installation section to include installation instructions from github.

MISC
* internal permutation algorithm no longer lists permutations in reverse order

poppr 1.0.1
===========
IMPROVEMENTS
* Algorithm for the index of association was updated to increase speed.

BUG FIXES
* Removed unnecessary rounding factor for missing data in `bruvo.dist`.
* Corrected handling of duplicate entries for `read.genind`.
* Input values that are not multiples of the specified repeat length for Bruvo's distance are now rounded (as opposed to being forced as integers).

MISC
* Vignette updated for aesthetics and to reflect algorithmic changes.

poppr 1.0.0
===========
MISC
* Poppr has been confirmed to work on Linux, Mac, and Windows systems with R 3.0.0.
* Vignette `poppr_manual` now has cross-references to different sections.
* Vignette `poppr_manual` is quicker loading. 

BUG FIXES
* removed alpha channel from plot for resampled values of I_A and \bar{r}_d due to warnings.

poppr 0.4.1
===========
NEW FEATURES
* `getfile` has a new argument, "combine", which will automatically add the path to the list of files, so they can be read without switching working directory.
* information printed to screen from `missingno` and `mlg.crosspop` will now be wrapped to 80 characters.

BUG FIXES
* `poppr` will now be able to correctly recognize GenAlEx files with both geographic and regional data.
* calculation of the index of association on P/A data with missing values will no longer return an error. 

poppr 0.4
===========
BUG FIXES
* mistake in Bruvo's distance where it did not correctly check for ploidy level was fixed.
* `read.genalex` will be able to correctly distinguish between SNP and AFLP data.
* `read.genalex` can now correctly recognize regional formatting without an extra column.

NEW FEATURES
* `read.genalex` will now be able to take in a file that is formatted with both regional and geographic data.
* `genind2genalex` can now export xy coordinates into the GenAlEx format. 
* `poppr_manual` vignette now contains images of example GenAlEx files.

NEW FILES
* `rootrot2.csv` is an example of a GenAlEx file formatted with regional data.

OTHER UPDATES
* function for guessing repeat lengths for Bruvo's distance moved into internal file. 
* redundancy in `read.genalex` was removed.
* changed instructions in README

poppr 0.3.1
===========
BUG FIXES
* `read.genalex` will now give a warning whenever the input file is not comma delimited. 

poppr 0.3
===========
NEW FUNCTIONS
* `poppr.msn` will draw a minimum spanning network for any distance matrix derived from your data set.

NEW FEATURES
* vignette now has sections describing `poppr.msn`, `diss.dist`, `greycurve`, and a section discussing how to export graphics.

BUG FIXES
* The graphs output by `poppr` and `ia` will now display \bar{r}_d instead of \bar{r}_D.
* `bruvo.boot` now has a dedicated `quiet` argument.

poppr 0.2.2
===========
NEW FEATURES
* index of association distributions will now feature a rug plot at the bottom
  as a better way to visualize the distribution of the index of association from
  the shuffled data sets.

poppr 0.2.1
===========
NEW FUNCTIONS
* `diss.dist` will produce a distance matrix based on discreet distances.
* `greycurve` will produce a grey scale adjusted to user-supplied parameters. This
  will be useful for future minimum spanning network functions. 

NEW FEATURES
* `bruvo.msn` can now adjust the edge grey level to be weighted toward either
  closely or distantly weighted individuals.
* `bruvo.msn` will now return a list giving the user the graph with all of the
  color, label, and weight properties so that they can plot it themselves. The
  legend arguments are also returned.

BUG FIXES
* fixed shufflepop so that it will now shuffle PA markers with a specific method
* fixed warning message mistakes in clonecorrect function. 

poppr 0.2
=========
NEW FEATURES
* Added NEWS file and will now be incrementing version number (3/15/2013)


poppr 0.1
=========
* First development version of poppr (2012 - 3/2013)
