Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

STRATA_SEQ error with assignment_ngs() #27

Open
lexymccarty opened this issue Jun 14, 2023 · 0 comments
Open

STRATA_SEQ error with assignment_ngs() #27

lexymccarty opened this issue Jun 14, 2023 · 0 comments

Comments

@lexymccarty
Copy link

lexymccarty commented Jun 14, 2023

Hello,

Describe the bug
I am having issues when running assignment_ngs() on a genlight object. I load my genlight file output from dartR and get the following error message (see below). I cannot find any reference to STRATA_SEQ in the package code, so I'm having trouble figuring out what my issue is. I get the same issue when using the simulated data from the package: data_assigner_sim_01

To Reproduce

Assign <- assignment_ngs(data=data_assigner_sim_01,
assignment.analysis = "gsi_sim",
marker.number = c(50,100,200,500,1000, "all"),
markers.sampling = "ranked",
thl = 0.2,
iteration.method = 5,
subsample = 15,
iteration.subsample= 3)

Error message:
################################################################################
########################## assigner::assignment_ngs ############################
################################################################################
Execution date/time: 20230614@1021
Assignment analysis with gsi_sim
Calibrating REF/ALT alleles...
Calibrating REF/ALT alleles...
Subsampling: selected
using subsample size of: 15
Error in purrr::map():
In index: 1.
Caused by error in dplyr::group_by():
! Must group by variables found in .data.
✖ Column STRATA_SEQ is not found.
Backtrace:

  1. assigner::assignment_ngs(...)
  2. dplyr:::group_by.data.frame(., STRATA_SEQ)

Computation time, overall: 2 sec
########################## assignment_ngs completed ############################

devtools::session_info()
─ Session info
setting value
version R version 4.3.0 (2023-04-21)
os macOS Monterey 12.5.1
system aarch64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2023-06-14
rstudio 2023.03.1+446 Cherry Blossom (desktop)
pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

─ Packages
package * version date (UTC) lib source
ade4 * 1.7-22 2023-02-06 [1] CRAN (R 4.3.0)
adegenet * 2.1.10 2023-01-26 [1] CRAN (R 4.3.0)
ape 5.7-1 2023-03-13 [1] CRAN (R 4.3.0)
assigner * 0.5.8 2023-06-13 [1] Github (d39a692)
bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0)
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
calibrate 1.7.7 2020-06-19 [1] CRAN (R 4.3.0)
callr 3.7.3 2022-11-02 [1] CRAN (R 4.3.0)
cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
cluster 2.1.4 2022-08-22 [1] CRAN (R 4.3.0)
codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.0)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
combinat 0.0-8 2012-10-29 [1] CRAN (R 4.3.0)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
dartR * 2.9.7 2023-06-07 [1] CRAN (R 4.3.0)
dartR.data * 1.0.2 2022-11-16 [1] CRAN (R 4.3.0)
data.table * 1.14.8 2023-02-17 [1] CRAN (R 4.3.0)
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.0)
digest 0.6.31 2022-12-11 [1] CRAN (R 4.3.0)
dismo 1.3-14 2023-05-21 [1] CRAN (R 4.3.0)
doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.3.0)
dotCall64 1.0-2 2022-10-03 [1] CRAN (R 4.3.0)
dplyr * 1.1.2 2023-04-20 [1] CRAN (R 4.3.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
evaluate 0.21 2023-05-05 [1] CRAN (R 4.3.0)
fansi 1.0.4 2023-01-22 [1] CRAN (R 4.3.0)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
fields 14.1 2022-08-12 [1] CRAN (R 4.3.0)
foreach 1.5.2 2022-02-02 [1] CRAN (R 4.3.0)
fs 1.6.2 2023-04-25 [1] CRAN (R 4.3.0)
gap 1.5-1 2023-01-22 [1] CRAN (R 4.3.0)
gap.datasets 0.0.5 2022-05-09 [1] CRAN (R 4.3.0)
gdata 2.19.0 2023-05-05 [1] CRAN (R 4.3.0)
gdistance 1.6.2 2023-04-20 [1] CRAN (R 4.3.0)
gdsfmt 1.36.0 2023-05-08 [1] Bioconductor
generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
genetics 1.3.8.1.3 2021-03-01 [1] CRAN (R 4.3.0)
GGally 2.1.2 2021-06-21 [1] CRAN (R 4.3.0)
ggplot2 * 3.4.2 2023-04-03 [1] CRAN (R 4.3.0)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.3.0)
gtable 0.3.3 2023-03-21 [1] CRAN (R 4.3.0)
gtools 3.9.4 2022-11-27 [1] CRAN (R 4.3.0)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0)
htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.3.0)
htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.3.0)
httpuv 1.6.11 2023-05-11 [1] CRAN (R 4.3.0)
igraph 1.4.3 2023-05-22 [1] CRAN (R 4.3.0)
iterators 1.0.14 2022-02-05 [1] CRAN (R 4.3.0)
knitr 1.43 2023-05-25 [1] CRAN (R 4.3.0)
later 1.3.1 2023-05-02 [1] CRAN (R 4.3.0)
lattice 0.21-8 2023-04-05 [1] CRAN (R 4.3.0)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
maps 3.4.1 2022-10-30 [1] CRAN (R 4.3.0)
MASS 7.3-60 2023-05-04 [1] CRAN (R 4.3.0)
Matrix 1.5-4.1 2023-05-18 [1] CRAN (R 4.3.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
mgcv 1.8-42 2023-03-02 [1] CRAN (R 4.3.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
mmod 1.3.3 2017-04-06 [1] CRAN (R 4.3.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0)
mvtnorm 1.2-2 2023-06-08 [1] CRAN (R 4.3.0)
nlme 3.1-162 2023-01-31 [1] CRAN (R 4.3.0)
patchwork 1.1.2 2022-08-19 [1] CRAN (R 4.3.0)
pegas 1.2 2023-02-23 [1] CRAN (R 4.3.0)
permute 0.9-7 2022-01-27 [1] CRAN (R 4.3.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.3.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.3.0)
plyr 1.8.8 2022-11-11 [1] CRAN (R 4.3.0)
png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0)
PopGenReport 3.0.7 2022-05-27 [1] CRAN (R 4.3.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.3.0)
processx 3.8.1 2023-04-18 [1] CRAN (R 4.3.0)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.3.0)
ps 1.7.5 2023-04-18 [1] CRAN (R 4.3.0)
purrr * 1.0.1 2023-01-10 [1] CRAN (R 4.3.0)
R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.3.0)
R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.3.0)
R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.3.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
radiator 1.2.8 2023-06-06 [1] Github (thierrygosselin/radiator@d2442e5)
raster 3.6-20 2023-03-06 [1] CRAN (R 4.3.0)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.3.0)
Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.3.0)
readr 2.1.4 2023-02-10 [1] CRAN (R 4.3.0)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.3.0)
reshape 0.8.9 2022-04-12 [1] CRAN (R 4.3.0)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.3.0)
rgdal 1.6-7 2023-05-31 [1] CRAN (R 4.3.0)
RgoogleMaps 1.4.5.3 2020-02-12 [1] CRAN (R 4.3.0)
rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.0)
rmarkdown 2.22 2023-06-01 [1] CRAN (R 4.3.0)
rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.3.0)
scales 1.2.1 2022-08-20 [1] CRAN (R 4.3.0)
seqinr 4.2-30 2023-04-05 [1] CRAN (R 4.3.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
shiny 1.7.4 2022-12-15 [1] CRAN (R 4.3.0)
SNPRelate 1.34.1 2023-05-08 [1] Bioconductor
sp 1.6-1 2023-05-31 [1] CRAN (R 4.3.0)
spam 2.9-1 2022-08-07 [1] CRAN (R 4.3.0)
StAMPP 1.6.3 2021-08-08 [1] CRAN (R 4.3.0)
stringi 1.7.12 2023-01-11 [1] CRAN (R 4.3.0)
stringr 1.5.0 2022-12-02 [1] CRAN (R 4.3.0)
terra 1.7-29 2023-04-22 [1] CRAN (R 4.3.0)
tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
tidyr 1.3.0 2023-01-24 [1] CRAN (R 4.3.0)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0)
tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.3.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0)
usethis 2.2.0 2023-06-06 [1] CRAN (R 4.3.0)
utf8 1.2.3 2023-01-31 [1] CRAN (R 4.3.0)
vctrs 0.6.2 2023-04-19 [1] CRAN (R 4.3.0)
vegan 2.6-4 2022-10-11 [1] CRAN (R 4.3.0)
viridis 0.6.3 2023-05-03 [1] CRAN (R 4.3.0)
viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0)
vroom 1.6.3 2023-04-28 [1] CRAN (R 4.3.0)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.3.0)
xfun 0.39 2023-04-20 [1] CRAN (R 4.3.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)
yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0)

[1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant