poppr version 2.0.0 released on CRAN

[poppr]

poppr version 2.0.0 has been released

Here's a link to the details of all the changes for this release.

Note: It might take a day or two for the windows and OSX versions to build. You can check the status by going to http://cran.r-project.org/package=poppr

This version implements all of the features described in our Frontiers paper that was released in June. It also implements changes that were a result of a Population Genetics in R hackathon at NESCent in March of 2015, where major changes happened to the adegenet package. Many of the changes helped improved the stability and efficiency of both poppr and adegenet. 

This version of poppr contains breaking changes. Please read this vignette for details on those changes. If you have questions after reading the vignette, please post to this forum so others can find the solutions. 

Major (breaking) Changes:

• The genind/genclone objects are now half their original size
• The "hierarchy" slot from genclone objects (poppr) have been moved to genind objects (adegenet) and renamed to "strata"
• The function splitcombine has been removed

New Features (highlights):

• Multilocus genotype definitions can be changed with the mlg.filter and mll.custom functions (read the vignette on MLGs)
• The new object snpclone allows you to perform multilocus genotype analysis on SNP data (inherited from genlight objects)
• Sliding window analysis of the index of association
• Add reticulations to minimum spanning networks with the option include.ties = TRUE in poppr.msn and bruvo.msn
• Interactive Minimum Spanning Network construction with the function imsn (view an example on github)

Cheers,

Zhian N. Kamvar

[Zhian Kamvar]

Bug report 2015-07-13:

A bug was discovered in read.genalex that prevented missing data from being

imported. A fix was written and will be uploaded soon. In the meantime, please use 

the source code at https://gist.github.com/zkamvar/b64078a0d04d2452c905

Below is an example of how to install the fix within R:

library("poppr")
data(nancycats)
outfile <- tempfile()
genind2genalex(nancycats, outfile)

## Extracting the table ... Writing the table to /var/folders/qd/dpdhfsz12wb3c7wz0xdm6dbm0000gn/T//RtmpGojara/file262234cd650e ... Done.

summary(read.genalex(outfile)) # no missing data!

##
##  # Total number of genotypes:  237
##
##  # Population sample sizes:  
## P01 P02 P03 P04 P05 P06 P07 P08 P09 P10 P11 P12 P13 P14 P15 P16 P17
##  10  22  12  23  15  11  14  10   9  11  20  14  13  17  11  12  13
##
##  # Number of alleles per locus:  
##  fca8 fca23 fca43 fca45 fca77 fca78 fca90 fca96 fca37
##    16    11    10     9    12     8    12    12    18
##
##  # Number of alleles per population:  
## P01 P02 P03 P04 P05 P06 P07 P08 P09 P10 P11 P12 P13 P14 P15 P16 P17
##  36  53  50  67  48  56  42  54  43  46  70  52  44  61  42  40  35
##
##  # Percentage of missing data:  
## [1] 2.344116
##
##  # Observed heterozygosity:  
##      fca8     fca23     fca43     fca45     fca77     fca78     fca90
## 0.6682028 0.6666667 0.6793249 0.7083333 0.6329114 0.5654008 0.6497890
##     fca96     fca37
## 0.6184211 0.4514768
##
##  # Expected heterozygosity:  
##      fca8     fca23     fca43     fca45     fca77     fca78     fca90
## 0.8657224 0.7928751 0.7953319 0.7603095 0.8702576 0.6884669 0.8157881
##     fca96     fca37
## 0.7603493 0.6062686

Installing the fix (should use devtools):

devtools::source_gist("https://gist.github.com/zkamvar/b64078a0d04d2452c905",
                      sha1 = "74ff482c9832237092ffb29a5955ee68b255005f")


## Sourcing https://gist.githubusercontent.com/zkamvar/b64078a0d04d2452c905/raw/62ba9500d8fdaa09b0b520a45d2b04ebb44d6940/poppr_patches.R
##
## fixing function 'read.genalex' ...
##
## Everything is up to date!

both_identical <- identical(summary(read.genalex(outfile), verbose = FALSE), summary(nancycats, verbose = FALSE))
both_identical

## [1] TRUE

I apologize any inconvenience this may have caused anyone

Cheers,

Zhian

[Zhian Kamvar]

UPDATE:

Use this command instead. The previous one has a typo:

devtools::source_gist("https://gist.github.com/zkamvar/b64078a0d04d2452c905",

                      sha1 = "9c0a9a0b20f02d0df6bf85a60f30fd9ff2a3d0c2")

Zhian