Error during gl.LDNe
Elspeth McLennan
replacement has 15 rows, data has 18
Calls: gl.LDNe -> $<- -> $<-.data.frame
In addition: Warning messages:
1: In rbind(freq, as.numeric(harmonic_mean[[i]]), as.numeric(comparisons[[i]]), :
number of columns of result is not a multiple of vector length (arg 3)
2: In rbind(freq, as.numeric(harmonic_mean[[i]]), as.numeric(comparisons[[i]]), :
number of columns of result is not a multiple of vector length (arg 3)
3: In rbind(freq, as.numeric(harmonic_mean[[i]]), as.numeric(comparisons[[i]]), :
number of columns of result is not a multiple of vector length (arg 3)
subset <- sample(size = 50000, replace = F, x = c(1:nrow(vcf)))
vcf_subset <- vcf[subset, ]
vcf_subset
### by cluster
gen_cluster <- vcfR2genind(vcf_subset, sep = "/", return.alleles = F)
pops_cluster <- read.table("wild_413_populations_faststructure.txt", header = T)
gen_cluster@pop <- as.factor(pops_cluster$cluster)
gen_cluster
# convert to genlight for NeEstimator
gl_cluster <- gi2gl(gen_cluster)
gl_cluster
nes <- gl.LDNe(gl_cluster, outpath = "/mnt/sdd/filteredvcf_analysis", neest.path = "/mnt/sdd/filteredvcf_analysis", critical = c(0,0.05), singleton.rm = T, mating = "random")
nes
Bernd.Gruber
Hi Elspeth,
Looks most likely something with the plot at the end goes wrong. Not sure why. Can you check you have no spaces in your indNames and popNames and lociNames
And or run the gl.LDNe with the option plot.out=FALSE (this might work), but still would be good to know what is going wrong here.
Also not sure why you go via genind there is a function
vcfR2genlight which should work as well, but maybe you tried that.
Another test would be to run
gl.compliance.check(gl_cluster) to try to make sure it is a complete genlight/dartR object.
Cheers, Bernd
==============================================================================
Dr Bernd Gruber )/_
_.--..---"-,--c_
Professor Ecological Modelling \|..' ._O__)_
Tel: (02) 6206 3804 ,=. _.+ _ \..--( /
Fax: (02) 6201 2328 \\.-''_.-' \ ( \_
Institute for Applied Ecology `''' `\__ /\
Faculty of Science and Technology ')
University of Canberra ACT 2601 AUSTRALIA
Email: bernd....@canberra.edu.au
WWW: bernd-gruber
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Jose Luis Mijangos
gl.install.vanilla.dartR(flavour = "dev")
Elspeth McLennan
Error in strt[y]:stp[y] : NA/NaN argument
Do you think it is still struggling to output the results?
Thanks again for your help!
Elle
Hi Luis,Thank you so much!!Have a lovely weekend,All my best,Elle
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Elspeth McLennan
checking for file 'C:\Users\emcl2913\AppData\Local\Temp\Rtmp044LTI\remotes6e0c315e9a6\green-striped-gecko-dartR-2d623f2/DESCRIPTION' ...
─ preparing 'dartR': (1.2s)
checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts (1.7s)
─ checking for empty or unneeded directories
─ building 'dartR_2.9.4.tar.gz'
Installing package into ‘C:/Users/emcl2913/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
* installing *source* package 'dartR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dartR)
Installing package ggtern from provisional GitHub Repository
Downloading GitHub repo mijangos81/ggtern@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
checking for file 'C:\Users\emcl2913\AppData\Local\Temp\Rtmp044LTI\remotes6e0c9ca4daa\mijangos81-ggtern-8bfb500/DESCRIPTION' (394ms)
─ preparing 'ggtern': (983ms)
checking DESCRIPTION meta-information ...
─ installing the package to process help pages (669ms)
-----------------------------------
─ installing *source* package 'ggtern' ...
files 'build/partial.rdb', 'man/approved_layers.Rd', 'man/geom_smooth_tern.Rd', 'man/ggtern_package.Rd', 'man/mahalanobis_distance.Rd', 'man/position_jitter_tern.Rd', 'man/position_nudge_tern.Rd', 'man/theme_gridsontop.Rd', 'man/theme_ticklength.Rd' are missing
file 'R/gg-internal.R' has the wrong MD5 checksum
** using staged installation
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
Registered S3 methods overwritten by 'ggtern':
method from
grid.draw.ggplot ggplot2
plot.ggplot ggplot2
print.ggplot ggplot2
Error : theme_elements.Rd:21: the condition has length > 1
ERROR: installing Rd objects failed for package 'ggtern'
─ removing 'C:/Users/emcl2913/AppData/Local/Temp/RtmpQRMbNw/Rinst74d44c9b270e/ggtern'
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'ggtern' from GitHub:
! System command 'Rcmd.exe' failedJose Luis Mijangos
Elspeth McLennan
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Elspeth McLennan
Jose Luis Mijangos
> gl_cluster_3 <- gl.subsample.loci(gl_cluster_2,n=5,method = "random")
Bernd.Gruber
Hi,
Not sure if helpful. We found in one of our student a “quirk” in the Neestimator. If there is a loci that is 100% heterozygous for all individuals (all ones) then the interval estimates become INF. Therefore we filtered for that loci “manually” before running it. This kind of loci do not get filtered by the monomorph filter and in your case it could be that by subsampling you might get such cases.
The way to filter is for example:
gl <- possums.gl
drop <- locNames(gl)[apply(as.matrix(gl), 2, function(x) all(as.numeric(x)==1, na.rm=T))]
if (length(drop)>0) gl <- gl.drop.loc(gl,loc.list = drop)
should work I think (but not tested)
==============================================================================
Dr Bernd Gruber )/_
_.--..---"-,--c_
Professor Ecological Modelling \|..' ._O__)_
Tel: (02) 6206 3804 ,=. _.+ _ \..--( /
Fax: (02) 6201 2328 \\.-''_.-' \ ( \_
Institute for Applied Ecology `''' `\__ /\
Faculty of Science and Technology ')
University of Canberra ACT 2601 AUSTRALIA
Email: bernd....@canberra.edu.au
WWW: bernd-gruber
Australian Government Higher Education Provider Number CRICOS #00212K
NOTICE & DISCLAIMER: This email and any files transmitted with it may contain
confidential or copyright material and are for the attention of the addressee
only. If you have received this email in error please notify us by email
reply and delete it from your system. The University of Canberra accepts
no liability for any damage caused by any virus transmitted by this email.
==============================================================================
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Elspeth McLennan
graphics.off()
setwd("C:/Users/emcl2913/OneDrive - The University of Sydney (Staff)/Documents - AWGG/KOALAS/GenomeSurvey/Population Genomics/Analysis/Effective Population Size")
### read in genlight object created via Ronin
load("gl_cluster_wild_413_100cr_1mac_0.005maf_15-60depth_unlinked_50000.Rdata")
gl_cluster
library(dartR)
set.seed(32)
gl_cluster_subset <- gl.subsample.loci(gl_cluster,n=15000,method = "random")
gl_cluster_subset
nes <- gl.LDNe(gl_cluster_subset, outpath = "./", neest.path = "./", critical = c(0,0.05), singleton.rm = T, mating = "random")
nes <- nes
R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.utf8 LC_CTYPE=English_Australia.utf8 LC_MONETARY=English_Australia.utf8
[4] LC_NUMERIC=C LC_TIME=English_Australia.utf8
attached base packages:
[1] tcltk stats graphics grDevices utils datasets methods base
other attached packages:
[1] sf_1.0-12 maps_3.4.1 maptools_1.1-6 plotrix_3.8-2 plotfunctions_1.4
[6] scales_1.2.1 shapefiles_0.7.2 foreign_0.8-84 gstat_2.1-1 fields_14.1
[11] viridis_0.6.3 viridisLite_0.4.2 spam_2.9-1 patchwork_1.1.2 ggrepel_0.9.3
[16] BiodiversityR_2.15-1 vegan_2.6-4 lattice_0.21-8 permute_0.9-7 ggmap_3.0.2
[21] rgdal_1.6-6 geodata_0.5-8 terra_1.7-29 ggpubfigs_0.0.1 lubridate_1.9.2
[26] forcats_1.0.0 stringr_1.5.0 purrr_1.0.1 readr_2.1.4 tidyr_1.3.0
[31] tibble_3.2.1 tidyverse_2.0.0 stringi_1.7.12 AlleleShift_1.1 raster_3.6-20
[36] sp_1.6-0 dartR_2.9.5 dartR.data_1.0.2 dplyr_1.1.2 ggplot2_3.4.2
[41] adegenet_2.1.10 ade4_1.7-22
loaded via a namespace (and not attached):
[1] utf8_1.2.3 R.utils_2.12.2 tidyselect_1.2.0 lme4_1.1-33 htmlwidgets_1.6.2
[6] grid_4.2.3 combinat_0.0-8 StAMPP_1.6.3 munsell_0.5.0 units_0.8-1
[11] codetools_0.2-19 withr_2.5.0 gdsfmt_1.34.1 colorspace_2.1-0 pegas_1.2
[16] knitr_1.42 rstudioapi_0.14 stats4_4.2.3 labeling_0.4.2 RgoogleMaps_1.4.5.3
[21] farver_2.1.1 gap.datasets_0.0.5 vctrs_0.6.2 generics_0.1.3 xfun_0.39
[26] timechange_0.2.0 R6_2.5.1 doParallel_1.0.17 bitops_1.0-7 reshape_0.8.9
[31] promises_1.2.0.1 nnet_7.3-18 gtable_0.3.3 sandwich_3.0-2 rlang_1.1.1
[36] calibrate_1.7.7 splines_4.2.3 checkmate_2.1.0 yaml_2.3.7 reshape2_1.4.4
[41] abind_1.4-5 backports_1.4.1 httpuv_1.6.11 Hmisc_5.0-1 tools_4.2.3
[46] Rcmdr_2.8-0 ellipsis_0.3.2 RColorBrewer_1.1-3 proxy_0.4-27 Rcpp_1.0.10
[51] plyr_1.8.8 base64enc_0.1-3 classInt_0.4-9 rpart_4.1.19 zoo_1.8-12
[56] haven_2.5.2 cluster_2.1.4 survey_4.1-1 magrittr_2.0.3 data.table_1.14.8
[61] visreg_2.7.0 spacetime_1.3-0 genetics_1.3.8.1.3 effects_4.2-2 mvtnorm_1.1-3
[66] hms_1.1.3 RcmdrMisc_2.7-2 mime_0.12 evaluate_0.21 xtable_1.8-4
[71] jpeg_0.1-10 readxl_1.4.2 gridExtra_2.3 MuMIn_1.47.5 compiler_4.2.3
[76] KernSmooth_2.23-20 crayon_1.5.2 minqa_1.2.5 gdistance_1.6.2 R.oo_1.25.0
[81] htmltools_0.5.5 mgcv_1.8-42 later_1.3.1 tzdb_0.3.0 Formula_1.2-5
[86] DBI_1.1.3 PopGenReport_3.0.7 MASS_7.3-59 boot_1.3-28.1 relimp_1.0-5
[91] Matrix_1.5-4 car_3.1-2 cli_3.6.1 mitools_2.4 R.methodsS3_1.8.2
[96] gdata_2.19.0 parallel_4.2.3 insight_0.19.1 dotCall64_1.0-2 igraph_1.4.2
[101] pkgconfig_2.0.3 foreach_1.5.2 SNPRelate_1.32.2 digest_0.6.31 rmarkdown_2.21
[106] cellranger_1.1.0 intervals_0.15.3 htmlTable_2.4.1 nortest_1.0-4 gap_1.5-1
[111] shiny_1.7.4 gtools_3.9.4 nloptr_2.0.3 lifecycle_1.0.3 nlme_3.1-162
[116] dismo_1.3-9 carData_3.0-5 seqinr_4.2-30 fansi_1.0.4 pillar_1.9.0
[121] GGally_2.1.2 fastmap_1.1.1 httr_1.4.6 survival_3.5-5 glue_1.6.2
[126] xts_0.13.1 FNN_1.1.3.2 mmod_1.3.3 png_0.1-8 iterators_1.0.14
[131] tcltk2_1.2-11 class_7.3-21 e1071_1.7-13 ape_5.7-1You received this message because you are subscribed to a topic in the Google Groups "dartR" group.
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Bernd.Gruber
Hi Elsbeth,
Can you try to run it locally and not from your onedrive with the “funny” characters and spaces in the path.
I know that R and oneDrive can have issues and that might be the case here.
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Dylan Westaway
I'm having a similar issue with Ne estimates falling outside of CIs. I'm wondering if you found a solution to this?
Jose Luis Mijangos
Dylan Westaway
Bernd.Gruber
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