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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
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:
assigner::assignment_ngs(...)
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)
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:
Computation time, overall: 2 sec
########################## assignment_ngs completed ############################
─ 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
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