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(nanhwe.pop <- seppop(nancycats) %>% lapply(hw.test, B = 0)) not working #38

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DrK-Lo opened this issue Sep 18, 2018 · 1 comment
Open

(nanhwe.pop <- seppop(nancycats) %>% lapply(hw.test, B = 0)) not working #38

DrK-Lo opened this issue Sep 18, 2018 · 1 comment

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@DrK-Lo
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DrK-Lo commented Sep 18, 2018

Hi guys,
This line of code is not working in your tutorial, but it worked for me last year (I use it in teaching)

(nanhwe.pop <- seppop(nancycats) %>% lapply(hw.test, B = 0))

I get the error message:

is.na() applied to non-(list or vector) of type 'NULL'The following loci were dropped (not the same ploidy for all individuals):
fca45longer argument not a multiple of length of shorterError in dimnames(ans) <- list(names(y), c("chi^2", "df", "Pr(chi^2 >)")) : 
  length of 'dimnames' [1] not equal to array extent

I traced the error to population 17:

for (i in 1:length(pops)){
  print(c("population", i))
  #in each population, calculate HWE
  (hw.test <- hw.test(pops[[i]], B=0))
  print(hw.test)
}

# the error message indicates that locus fca45 is having an issue
colSums(is.na(pops[[17]]@tab))
# check if this locus is missing data
# there is more missing data at this locus than other loci

rem.fca45 <- grep("fca45",colnames(nancycats@tab))
# columns in the data that contain information for the problem locus

hw.test(pops[[17]][, -rem.fca45], B=0)
# redo the test for population 17, but this time remove data for fca45

So, removing the locus for that one population works. But I know the code worked for me last year, so suggestions welcome!
@zkamvar
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zkamvar commented Sep 18, 2018

Hi @DrK-Lo,

This is a bug in pegas that will be fixed with the next release. You can see the issue here: emmanuelparadis/pegas#36

The output gives a more informative warning when run with the new version, but not an error.

remotes::install_github('emmanuelparadis/pegas/pegas')
#> Downloading GitHub repo emmanuelparadis/pegas@master
#> Installing 2 packages: digest, spData
#> Installing packages into '/home/zkamvar/Documents/RLibrary'
#> (as 'lib' is unspecified)
#> Installing package into '/home/zkamvar/Documents/RLibrary'
#> (as 'lib' is unspecified)
library('pegas')
#> Loading required package: ape
#> Loading required package: adegenet
#> Loading required package: ade4
#> 
#>    /// adegenet 2.1.1 is loaded ////////////
#> 
#>    > overview: '?adegenet'
#>    > tutorials/doc/questions: 'adegenetWeb()' 
#>    > bug reports/feature requests: adegenetIssues()
#> 
#> Attaching package: 'pegas'
#> The following object is masked from 'package:ade4':
#> 
#>     amova
#> The following object is masked from 'package:ape':
#> 
#>     mst
data(nancycats)
hw.test(nancycats[pop = 17], B=0)
#> Warning in hw.test.loci(x = x, B = B, ...): The following locus was ignored: fca45
#> (not the same ploidy for all individuals, or too many missing data)
#>           chi^2 df Pr(chi^2 >)
#> fca8  22.100000 15   0.1052085
#> fca23 10.631111 10   0.3869703
#> fca43 22.071111 10   0.0147464
#> fca45        NA NA          NA
#> fca77 24.180000 21   0.2844190
#> fca78  1.764543  3   0.6226810
#> fca90  6.686359  6   0.3508286
#> fca96  0.312500  1   0.5761501
#> fca37  5.097337  3   0.1648068

Created on 2018-09-18 by the reprex package (v0.2.0).

Session info 
devtools::session_info()
#> Session info -------------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.5.1 (2018-07-02)
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language en_GB:en                    
#>  collate  en_GB.UTF-8                 
#>  tz       Europe/London               
#>  date     2018-09-18
#> Packages -----------------------------------------------------------------
#>  package    * version date       source                                
#>  ade4       * 1.7-13  2018-08-31 CRAN (R 3.5.1)                        
#>  adegenet   * 2.1.1   2018-02-02 CRAN (R 3.5.1)                        
#>  ape        * 5.1     2018-04-04 CRAN (R 3.5.1)                        
#>  assertthat   0.2.0   2017-04-11 CRAN (R 3.5.1)                        
#>  backports    1.1.2   2017-12-13 CRAN (R 3.5.1)                        
#>  base       * 3.5.1   2018-07-03 local                                 
#>  bindr        0.1.1   2018-03-13 CRAN (R 3.5.1)                        
#>  bindrcpp     0.2.2   2018-03-29 CRAN (R 3.5.1)                        
#>  boot         1.3-20  2017-07-30 CRAN (R 3.5.1)                        
#>  cluster      2.0.7-1 2018-04-09 CRAN (R 3.5.1)                        
#>  coda         0.19-1  2016-12-08 CRAN (R 3.5.1)                        
#>  colorspace   1.3-2   2016-12-14 CRAN (R 3.5.1)                        
#>  compiler     3.5.1   2018-07-03 local                                 
#>  crayon       1.3.4   2017-09-16 CRAN (R 3.5.1)                        
#>  datasets   * 3.5.1   2018-07-03 local                                 
#>  deldir       0.1-15  2018-04-01 CRAN (R 3.5.1)                        
#>  devtools     1.13.6  2018-06-27 CRAN (R 3.5.1)                        
#>  digest       0.6.17  2018-09-12 CRAN (R 3.5.1)                        
#>  dplyr        0.7.6   2018-06-29 CRAN (R 3.5.1)                        
#>  evaluate     0.11    2018-07-17 CRAN (R 3.5.1)                        
#>  expm         0.999-2 2017-03-29 CRAN (R 3.5.1)                        
#>  gdata        2.18.0  2017-06-06 CRAN (R 3.5.1)                        
#>  ggplot2      3.0.0   2018-07-03 CRAN (R 3.5.1)                        
#>  glue         1.3.0   2018-07-17 CRAN (R 3.5.1)                        
#>  gmodels      2.18.1  2018-06-25 CRAN (R 3.5.1)                        
#>  graphics   * 3.5.1   2018-07-03 local                                 
#>  grDevices  * 3.5.1   2018-07-03 local                                 
#>  grid         3.5.1   2018-07-03 local                                 
#>  gtable       0.2.0   2016-02-26 CRAN (R 3.5.1)                        
#>  gtools       3.8.1   2018-06-26 CRAN (R 3.5.1)                        
#>  htmltools    0.3.6   2017-04-28 CRAN (R 3.5.1)                        
#>  httpuv       1.4.5   2018-07-19 CRAN (R 3.5.1)                        
#>  igraph       1.2.2   2018-07-27 CRAN (R 3.5.1)                        
#>  knitr        1.20    2018-02-20 CRAN (R 3.5.1)                        
#>  later        0.7.4   2018-08-31 CRAN (R 3.5.1)                        
#>  lattice      0.20-35 2017-03-25 CRAN (R 3.5.1)                        
#>  lazyeval     0.2.1   2017-10-29 CRAN (R 3.5.1)                        
#>  LearnBayes   2.15.1  2018-03-18 CRAN (R 3.5.1)                        
#>  magrittr     1.5     2014-11-22 CRAN (R 3.5.1)                        
#>  MASS         7.3-50  2018-04-30 CRAN (R 3.5.1)                        
#>  Matrix       1.2-14  2018-04-09 CRAN (R 3.5.1)                        
#>  memoise      1.1.0   2017-04-21 CRAN (R 3.5.1)                        
#>  methods    * 3.5.1   2018-07-03 local                                 
#>  mgcv         1.8-24  2018-06-18 CRAN (R 3.5.1)                        
#>  mime         0.5     2016-07-07 CRAN (R 3.5.1)                        
#>  munsell      0.5.0   2018-06-12 CRAN (R 3.5.1)                        
#>  nlme         3.1-137 2018-04-07 CRAN (R 3.5.1)                        
#>  nvimcom    * 0.9-75  2018-08-22 local                                 
#>  parallel     3.5.1   2018-07-03 local                                 
#>  pegas      * 0.11-3  2018-09-18 Github (emmanuelparadis/pegas@a989da2)
#>  permute      0.9-4   2016-09-09 CRAN (R 3.5.1)                        
#>  pillar       1.3.0   2018-07-14 CRAN (R 3.5.1)                        
#>  pkgconfig    2.0.2   2018-08-16 CRAN (R 3.5.1)                        
#>  plyr         1.8.4   2016-06-08 CRAN (R 3.5.1)                        
#>  promises     1.0.1   2018-04-13 CRAN (R 3.5.1)                        
#>  purrr        0.2.5   2018-05-29 CRAN (R 3.5.1)                        
#>  R6           2.2.2   2017-06-17 CRAN (R 3.5.1)                        
#>  Rcpp         0.12.18 2018-07-23 CRAN (R 3.5.1)                        
#>  remotes      1.1.1   2017-12-20 CRAN (R 3.5.1)                        
#>  reshape2     1.4.3   2017-12-11 CRAN (R 3.5.1)                        
#>  rlang        0.2.2   2018-08-16 CRAN (R 3.5.1)                        
#>  rmarkdown    1.10    2018-06-11 CRAN (R 3.5.1)                        
#>  rprojroot    1.3-2   2018-01-03 CRAN (R 3.5.1)                        
#>  scales       1.0.0   2018-08-09 CRAN (R 3.5.1)                        
#>  seqinr       3.4-5   2017-08-01 CRAN (R 3.5.1)                        
#>  shiny        1.1.0   2018-05-17 CRAN (R 3.5.1)                        
#>  sp           1.3-1   2018-06-05 CRAN (R 3.5.1)                        
#>  spData       0.2.9.4 2018-09-15 CRAN (R 3.5.1)                        
#>  spdep        0.7-8   2018-08-15 CRAN (R 3.5.1)                        
#>  splines      3.5.1   2018-07-03 local                                 
#>  stats      * 3.5.1   2018-07-03 local                                 
#>  stringi      1.2.4   2018-07-20 CRAN (R 3.5.1)                        
#>  stringr      1.3.1   2018-05-10 CRAN (R 3.5.1)                        
#>  tibble       1.4.2   2018-01-22 CRAN (R 3.5.1)                        
#>  tidyselect   0.2.4   2018-02-26 CRAN (R 3.5.1)                        
#>  tools        3.5.1   2018-07-03 local                                 
#>  utils      * 3.5.1   2018-07-03 local                                 
#>  vegan        2.5-2   2018-05-17 CRAN (R 3.5.1)                        
#>  withr        2.1.2   2018-03-15 CRAN (R 3.5.1)                        
#>  xtable       1.8-3   2018-08-29 CRAN (R 3.5.1)                        
#>  yaml         2.2.0   2018-07-25 CRAN (R 3.5.1)

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@zkamvar @DrK-Lo