poppr 1.1.5
===========
BUG FIX
* Fixed internal bug for fix_negative_branch when only one branch had a negative edge.
* Fixed bug in `diss.dist` where a single locus would return an error.
* Fixed bug in poppr.amova where a single locus would return an error due to `repool_haplotypes`.
* Fixed bug from the future! mlg.table will now return a matrix all the time (Fix #25).

poppr 1.1.4
===========
BUG FIX
* Fixed an internal bug that fails only on Windows OS.

poppr 1.1.3
===========
NEW FEATURES
* new arguments to `plot_poppr_msn` to allow for easier manipulation of node sizes and of labeling
* read.genalex can now take read text connections as input. Addresses issue #8
* users can now specify cutoff for missing values in `aboot`

BUG FIX
* Fixed issue where monomorphic loci would cause an error in `recode_polyploids`
* Fixed logical error that would cause The infinite alleles model of Bruvo's distance to inflate the distance. (Found by Michael Metzger. Addresses issue #5).
* AMOVA can now take subset genclone objects (Addresses issue #7).
* in `mlg.table`, the mlgsub argument will now subset by name instead of index (fixed in #7).
* Fixed issue for neighbor-joining trees where the internal function to fix negative branch lengths was accidentally shuffling the corrected branches. Addresses issue #11.
* `diss.dist` can now be used with `aboot`

MISC
* `info_table` will print a discrete scale as opposed to colorbar when type = "ploidy"
* attempted to make model choices for Bruvo's distance more clear in the documentation

poppr 1.1.2
===========
BUG FIX
* Fixed memory allocation bug (Further addresses issue #2).
* Memory allocated in C function bruvo_dist is now properly freed.

poppr 1.1.1
===========
BUG FIX
* Fixed bug where the loss and add options for Bruvo's distance were switched. 
* Fixed illegal memory access error by UBSAN. Made memory management of internal C functions more sane. (Addresses issue #2).
* Fixed directional quotes and em-dashes produced by Mavericks (Addresses issue #3).

poppr 1.1.0
===========
NEW FEATURES
* Polyploids with ambiguous genotypes are now supported in poppr. See documentation for `recode_polyploids` for details. 
* Calculations of Bruvo's distance now features correction for partial missing data utilizing genome addition and genome loss models as presented in Bruvo et al. 2004. 
* `diss.dist` now has options to return raw distances and a matrix instead of a dist object.
* `read.genalex` now has the option to import as a genclone object. This is the default action.
* `poppr.all` will be able to analyze lists of genind or genclone objects.
* `ia` now has the argument valuereturn which will return the sampled data.
* `[bruvo,poppr].msn` functions now give the user the choice to show the graph.
* `bruvo.boot` has a cleaner plot style. 

NEW DATA CLASSES
* The `genclone` object is a new extension of the `genind` object from adegenet. This object contains slots containing population hierarchies and multilocus genotype definitions and will work with all analyses in adegenet and poppr. 

NEW FUNCTIONS
* [get,set,name,split,add]hierarchy - functions that will manipulate the hierarchy slot in a `genclone` object utilizing hierarchical formulae as arguments for simplification.
* `setpop` will set the population of a `genclone` object utilizing model formulae regarding the hierarchy slot.
* `as.genclone` will automatically convert genind objects to genclone objects.
* `is.genclone` checks the validity of genclone objects.
* `poppr.amova` will run amova on any hierarchical level. This also includes the feature to run amova on clone censored data sets. It utilizes the ade4 version of amova. 
* `info_table` will calculate missing data per population per locus or ploidy per individual per locus and gives the user the option to visualize this as a heatmap.
* `locus_table` will calculate diversity and evenness statistics over all loci in a genind or genclone object.
* `*.dist` functions will calculate Nei's distance, Rogers' Distance, Edwards' Distance, Reynolds' Distance, and Provestis' Distance.
* `aboot` will allow the user to create bootstrapped dendrograms for ANY distance that can be calculated on genind or genpop objects.
* `plot_poppr_msn` will plot minimum spanning networks produced with poppr. 
* `private_alleles` will give information about the presence of private alleles within a genind or genclone object. 
* `recode_polyploids` will take in a polyploid genind/genclone object (with missing alleles coded as extra zero-value allele) and recode them to have frequencies relative to the observed number of alleles.
* `genotype_curve` will create a genotype accumulation curve for increasing number of loci.
* `mlg.id` will return a list indicating the samples belonging to a specific multilocus genotype.

NEW DATA SETS
* Pinf - a data set of 86 isolates from different populations of the late blight pathogen, Phytophthora infestans. Provided by Erica Goss
* monpop - a large data set of 694 Monilinia fructicola isolates from a single orchard over three years. Provided by Sydney E. Everhart

NEW CAR
* Not really.

NAMESPACE CHANGES
* poppr no longer depends on pegas.
* ade4 and reshape2 are now explicitly required.

IMPROVEMENTS
* default shuffling algorithm has been implemented in C to increase speed.
* output of the mlg functions are now represented as integers to decrease their size in memory.
* `mlg.matrix` is now calculated faster utilizing R's internal tabulating capabilities.
* The function `poppr` will no longer return rounded results, but rather is printed with three significant digits.

MISC
* Added unit tests.
* The poppr user manual has been shortened to only include instructions on data manipulation. 
* A new vignette, "Algorithms and Equations" gives algorithmic details for calculations performed in poppr. 

poppr 1.0.7
===========
UPDATE
* Updated README to include link to poppr google group.

BUG FIX UPDATE
* Made last bug fix more stable (corrected on ape side).

poppr 1.0.6
===========
BUG FIX
* Fixed bug for users who have downloaded ape version 3.1 or higher where bruvo.boot would throw an error. 

MISC
* Updated citation information.

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 compatibility 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 lengths 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)
