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I noticed a bug in gtypes2genind where the ids and strata columns are being incorporated as loci in the genind object:
library('strataG') library('magrittr') data(msats.g) msats.g %>% gtypes2genind() %>% locNames() ## [1] "ids" "strata" "D11t" "EV37" "EV94" "Ttr11" "Ttr34"
Here's my session info:
Session info ------------------------------------------------------------------------------- setting value version R version 3.3.0 (2016-05-03) system x86_64, darwin13.4.0 ui RStudio (0.99.1172) language (EN) collate en_US.UTF-8 tz America/Los_Angeles date 2016-05-06 Packages ----------------------------------------------------------------------------------- package * version date source abind 1.4-3 2015-03-13 CRAN (R 3.2.0) acepack 1.3-3.3 2014-11-24 CRAN (R 3.2.0) ade4 * 1.7-4 2016-03-01 CRAN (R 3.2.3) adegenet * 2.0.2 2016-04-29 Github (thibautjombart/adegenet@e61bc06) ADGofTest 0.3 2011-12-28 CRAN (R 3.2.0) ape * 3.4-0.3 2016-02-23 local apex * 1.0.2 2016-03-31 CRAN (R 3.2.4) assertthat 0.1 2013-12-06 CRAN (R 3.2.0) boot 1.3-18 2016-02-23 CRAN (R 3.2.3) chron 2.3-47 2015-06-24 CRAN (R 3.2.0) cluster 2.0.4 2016-04-18 CRAN (R 3.3.0) coda 0.18-1 2015-10-16 CRAN (R 3.2.0) colorspace 1.2-6 2015-03-11 CRAN (R 3.2.0) copula 0.999-14 2015-10-26 CRAN (R 3.2.0) data.table 1.9.6 2015-09-19 CRAN (R 3.2.0) DBI 0.4 2016-05-02 CRAN (R 3.2.5) deldir 0.1-12 2016-03-06 CRAN (R 3.2.4) devtools 1.11.1 2016-04-21 CRAN (R 3.3.0) digest 0.6.9 2016-01-08 CRAN (R 3.2.3) dplyr 0.4.3 2015-09-01 CRAN (R 3.2.0) fastmatch 1.0-4 2012-01-21 CRAN (R 3.2.0) foreign 0.8-66 2015-08-19 CRAN (R 3.2.0) Formula 1.2-1 2015-04-07 CRAN (R 3.2.0) gdata 2.17.0 2015-07-04 CRAN (R 3.2.0) ggplot2 2.1.0 2016-03-01 CRAN (R 3.2.3) gmodels 2.16.2 2015-07-22 CRAN (R 3.2.0) goftest 1.0-3 2015-07-03 CRAN (R 3.2.0) gridExtra 2.2.1 2016-02-29 CRAN (R 3.2.4) gsl 1.9-10.1 2015-12-02 CRAN (R 3.2.3) gtable 0.2.0 2016-02-26 CRAN (R 3.2.3) gtools 3.5.0 2015-05-29 CRAN (R 3.2.0) Hmisc 3.17-4 2016-05-02 CRAN (R 3.3.0) htmltools 0.3.5 2016-03-21 CRAN (R 3.2.4) httpuv 1.3.3 2015-08-04 CRAN (R 3.2.0) igraph 1.0.1 2015-06-26 CRAN (R 3.2.0) lattice 0.20-33 2015-07-14 CRAN (R 3.2.0) latticeExtra 0.6-28 2016-02-09 CRAN (R 3.2.3) LearnBayes 2.15 2014-05-29 CRAN (R 3.2.0) magrittr 1.5 2014-11-22 CRAN (R 3.2.0) mapdata 2.2-6 2016-01-14 CRAN (R 3.2.3) maps 3.1.0 2016-02-13 CRAN (R 3.2.3) MASS 7.3-45 2015-11-10 CRAN (R 3.2.2) Matrix 1.2-6 2016-05-02 CRAN (R 3.3.0) memoise 1.0.0 2016-01-29 CRAN (R 3.2.3) mgcv 1.8-12 2016-03-03 CRAN (R 3.2.4) mime 0.4 2015-09-03 CRAN (R 3.2.0) munsell 0.4.3 2016-02-13 CRAN (R 3.2.3) mvtnorm 1.0-5 2016-02-02 CRAN (R 3.2.3) nlme 3.1-127 2016-04-16 CRAN (R 3.3.0) nnet 7.3-12 2016-02-02 CRAN (R 3.2.3) nnls 1.4 2012-03-19 CRAN (R 3.2.0) pegas 0.9 2016-04-16 CRAN (R 3.2.5) permute 0.9-0 2016-01-24 CRAN (R 3.2.3) phangorn * 2.0.3 2016-05-01 CRAN (R 3.2.5) plyr 1.8.3 2015-06-12 CRAN (R 3.2.0) polyclip 1.5-6 2016-04-03 CRAN (R 3.2.4) poppr * 2.1.1.99-47 2016-05-05 local pspline 1.0-17 2015-06-29 CRAN (R 3.2.0) quadprog 1.5-5 2013-04-17 CRAN (R 3.2.0) R6 2.1.2 2016-01-26 CRAN (R 3.2.3) RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.2.0) Rcpp 0.12.4 2016-03-26 CRAN (R 3.2.4) reshape2 1.4.1 2014-12-06 CRAN (R 3.2.0) rpart 4.1-10 2015-06-29 CRAN (R 3.2.0) rsconnect 0.4.3 2016-05-02 CRAN (R 3.3.0) scales 0.4.0 2016-02-26 CRAN (R 3.2.3) seqinr 3.1-3 2014-12-17 CRAN (R 3.2.0) shiny 0.13.2 2016-03-28 CRAN (R 3.2.4) sp 1.2-3 2016-04-14 CRAN (R 3.3.0) spatstat 1.45-0 2016-03-10 CRAN (R 3.2.4) spdep 0.6-4 2016-04-12 CRAN (R 3.2.4) stabledist 0.7-0 2015-05-04 CRAN (R 3.2.0) strataG * 1.0.5 2016-05-06 Github (ericarcher/strataG@c29d1fc) stringi 1.0-1 2015-10-22 CRAN (R 3.2.0) stringr 1.0.0 2015-04-30 CRAN (R 3.2.0) survival 2.39-2 2016-04-16 CRAN (R 3.3.0) swfscMisc 1.1 2016-03-03 CRAN (R 3.2.4) tensor 1.5 2012-05-05 CRAN (R 3.2.0) vegan 2.3-5 2016-04-09 CRAN (R 3.2.4) withr 1.0.1 2016-02-04 CRAN (R 3.2.3) xtable 1.8-2 2016-02-05 CRAN (R 3.2.3)
The text was updated successfully, but these errors were encountered:
Good catch! Caused by a recent addition I made to as.matrix.gtypes. Should be fixed now.
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I noticed a bug in gtypes2genind where the ids and strata columns are being incorporated as loci in the genind object:
Here's my session info:
The text was updated successfully, but these errors were encountered: