poppr 1.0.5
===========
NOTABLE CHANGE
* The default shuffling algorithm for calculating the index of association has changed from multilocus-style sampling to permutation of alleles. All of the 4 methods are available, but new assignments are as follows: Method 1: permute alleles, Method 2: parametric bootstrap, Method 3: non-parametric bootstrap, Method 4: Multilocus-style sampling. Previously, Multilocus was 1 and the rest followed in the same order. There should be no compatability issues with this change. Functions affected: `ia`, `poppr` `shufflepop`

BUG FIX
* Bootstrapping algorithm for `bruvo.boot` function was not shuffling the repeat lengths for each locus resulting in potentially erroneous bootstrap support values. This has been fixed by implementing an internal S4 class that will allow direct bootstrapping of the data and repeat lengths together.
* An occasional error, "INTEGER() can only be applied to a 'integer', not a 'NULL'" in `bruvo.boot` or `bruvo.dist` fixed.

IMPROVEMENTS
* Changes to `bruvo.boot` allow for ever so slightly faster bootstrapping.

MISC
* Permutations for I_A and \bar{r}_d are now visualized as a progress bar as opposed to dots.

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)
