faster and more stable

v.0.3.0

• Update that makes my coding life easier.
• Several internal functions to convert from a tidy dataframe to:
  vcf, plink, genind, genlight, gtypes, hierfstat, genepop, structure and betadiv
  are now separate modules available to users (look for write_... with the outputformat)
• New function genomic_converter: If you want the to convert from the supported
  input file formats to many output formats, at once, this is the function.
  With the new function genomic_converter, import and imputations are only
  done once, saving time if you were generating different output WITH imputations.
• Change: all the vcf2... functions (excep vcf2dadi) are now a shorcut of genomic_converter.
  This is particularly interesting and faster if you were generating different
  output WITH imputations. This makes the functions vcf2... and genomic_converter
  easier to debug for me and more stable for users.
• Deprecated: the haplo2... functions are all deprecated and replaced by
  genomic_converter, except haplo2colony that requires so many arguments that it
  would be too complicated, for now, to integrate with genomic_converter.
• New feature: when arguments pop.select, blacklist.id and imputation.method
  are used, the REF and ALT alleles are now re-computed to account for the filters
  and imputations.

v.0.2.9

v.0.2.9

• bug fix in tidy_genomic_data
• bug fix between stackr -> devtools -> github -> travis, this page helped

bug fix

v.0.2.8

• bug fix in tidy_genomic_data while using data.table::melt.data.table instead
  of tidyr::gather, and forgot to
  (i) add variable.factor = FALSE when melting the vcf and (ii) use as_data_frame
  at the end of the melting to be able to continue working with dplyr verbs.

dart2df_genind_plink

• dart2df_genind_plink: swiss army knife tool to prepare DArT output file (wide or binary format) for population genetics analysis. Import, filter and transform a DArT output file to different format: tidy data frame of genotypes, genind object and/or PLINK tped/tfam format. Map-independent imputation also available.

v.0.2.5: vcf2plink

• vcf2plink: to easily convert a VCF file created in STACKS to a PLINK input
  file (tped/tfam format). This function comes with the commonly used arguments
  in stackr: map-independent imputation, whitelist, blacklist, common marker filtering, etc.
• data_pruning: to prune your dataset with whitelist, blacklist of individuals,
  erase genotypes, use common markers and other filtering (see function argument
  while waiting for the upcomming documentation).

vcf2dadi for ALF ;)

v.0.2.3

• vcf2dadi: to easily convert a VCF file created in STACKS to a dadi input file.
  This function comes with the commonly used arguments in stackr:
  map-dependent imputation, whitelist, blacklist, common marker filtering, etc.

vcf2genepop for ALF :)

v.0.2.2

• vcf2genepop: to easily convert a VCF file created in STACKS to a genepop input file.
  This function comes with the commonly used arguments in stackr:
  map-dependent imputation, whitelist, blacklist, etc. For the haplotype version, see
  haplo2genepop.

v.0.2.1 SNP approach

You are no longer forced to use the haplotype approach to filter the markers. The functions: filter_maf, filter_fis and filter_het now works by SNP.

v.0.2.0 Introducing several vcf2 functions

Introducing several vcf2... functions.

Introducing haplo2gsi_sim function

Introducing haplo2gsi_sim function.
Conversion of STACKS haplotypes file into a gsi_sim data input file.
Map-independent imputations using Random Forest or the most frequent allele are options also available for this function.
gsi_sim is a tool developed by Eric C. Anderson for doing and simulating genetic stock identification.