shift.estimates()

[dylanHco]

Hello - I am trying to use shift.estimates() with the dolphin data and my own data. I am running it on my own Mac book - but it seems the analysis never finishes. How long does it usually take?

[dylanHco]

I guess to back up - the first thing was get.sampling.fractions() was not included in the RPANDA pull form github.

The same goes for get.comb.shift(). However when I ran that I got the following error.

  6 nodes produced errors; first error: unused argument (progressBar = base::quote(TRUE))

Since it said unused argument I just deleted that code, and proceeded.

Had to also upload shift.estiamtes() and div.models(). Altoghter this allowed me to run shift.estimates() - is there another function I am missing>?

Thanks!

[nmazet]

Hello @dylanHco,

Thank you for pointing out this issue. We just release a new updated version of this script on the branch clade.shift.model (cf Spplementary Material of the preprint). Have you tried to install this new branch on your Mac book? You can do it with devtools and the following command line in R: devtools::install_github("https://github.com/hmorlon/PANDA", ref = "clade.shift.model").

To be more specific, your problem seems to be related to on the package used to parallelize the analysis. If you just load the scripts from the R folder of RPANDA, these packages might be missing. In addition, some internal functions have been added to the script utils.R. Loading these functions might be necessary at some point if the proper installation of RPANDA does not work.

Let us know if it works with the new branch, I will try to reinstall this branch on a Mac book next week to test it.

Best regards,

Nathan

[dylanHco]

Hi @nmazet, thanks for the suggestion - I downloaded the newest version from the preprint and keep running into the same error- or lack there of it just doesnt seem like shift_estimates is working.

Thank you for looking into the issue - Would love to include this in my talks later this month and also in our publication if it can get sorted in time!

[dylanHco]

Also here is my session info:

R version 4.1.2 (2021-11-01) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.7

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] treebalance_1.1.0 phangorn_2.11.1 BAMMtools_2.1.10 ggtree_3.2.1
[5] phytools_1.5-1 maps_3.4.1 RPANDA_2.2 picante_1.8.2
[9] nlme_3.1-160 vegan_2.6-4 lattice_0.20-45 permute_0.9-7
[13] ape_5.7-1

loaded via a namespace (and not attached): [1] utf8_1.2.3 R.utils_2.12.2 tidyselect_1.2.0
[4] htmlwidgets_1.6.2 grid_4.1.2 combinat_0.0-8
[7] gmp_0.7-2 modeest_2.4.0 devtools_2.4.5
[10] SeqArray_1.34.0 munsell_0.5.0 codetools_0.2-18
[13] statmod_1.5.0 miniUI_0.1.1.1 withr_2.5.0
[16] gdsfmt_1.30.0 colorspace_2.1-0 pegas_1.2
[19] knitr_1.43 rstudioapi_0.14 pspline_1.0-19
[22] stats4_4.1.2 robustbase_0.95-1 pbmcapply_1.5.1
[25] poppr_2.9.4 GenomeInfoDbData_1.2.7 mnormt_2.1.1
[28] optimParallel_1.0-2 fBasics_4022.94 rprojroot_2.0.3
[31] treeio_1.18.1 coda_0.19-4 vctrs_0.6.3
[34] generics_0.1.3 clusterGeneration_1.3.7 xfun_0.39
[37] adegenet_2.1.10 diptest_0.76-0 R6_2.5.1
[40] doParallel_1.0.17 GenomeInfoDb_1.30.1 clue_0.3-64
[43] fields_14.1 flexmix_2.3-19 gridGraphics_0.5-1
[46] bitops_1.0-7 cachem_1.0.8 promises_1.2.0.1
[49] scales_1.2.1 nnet_7.3-18 gtable_0.3.3
[52] processx_3.8.2 spatial_7.3-15 spam_2.9-1
[55] timeDate_4022.108 rlang_1.1.1 scatterplot3d_0.3-44
[58] splines_4.1.2 lazyeval_0.2.2 GUniFrac_1.7
[61] BiocManager_1.30.19 yaml_2.3.7 reshape2_1.4.4
[64] httpuv_1.6.11 pvclust_2.2-0 tools_4.1.2
[67] usethis_2.1.6 ggplotify_0.1.0 statnet.common_4.9.0
[70] ggplot2_3.4.2 gplots_3.1.3 ellipsis_0.3.2
[73] raster_3.6-23 BiocGenerics_0.40.0 stabledist_0.7-1
[76] sessioninfo_1.2.2 Rcpp_1.0.11 plyr_1.8.8
[79] zlibbioc_1.40.0 purrr_1.0.1 RCurl_1.98-1.10
[82] ps_1.7.5 prettyunits_1.1.1 rpart_4.1.19
[85] viridis_0.6.3 statip_0.2.3 urlchecker_1.0.1
[88] S4Vectors_0.32.4 deSolve_1.35 ggrepel_0.9.3
[91] cluster_2.1.4 fs_1.6.2 magrittr_2.0.3
[94] timeSeries_4030.106 sna_2.7-1 mvtnorm_1.1-3
[97] matrixStats_1.0.0 pkgload_1.3.2 patchwork_1.1.2
[100] mime_0.12 evaluate_0.21 TESS_2.1.2
[103] xtable_1.8-4 mclust_6.0.0 IRanges_2.28.0
[106] gridExtra_2.3 compiler_4.1.2 tibble_3.2.1
[109] KernSmooth_2.23-20 crayon_1.5.2 R.oo_1.25.0
[112] htmltools_0.5.5 ggfun_0.0.7 mgcv_1.8-41
[115] corpcor_1.6.10 mvMORPH_1.1.7 later_1.3.1
[118] snow_0.4-4 tidyr_1.3.0 aplot_0.1.8
[121] expm_0.999-7 DBI_1.1.3 rmutil_1.1.10
[124] subplex_1.8 MASS_7.3-58.1 fpc_2.2-10
[127] boot_1.3-28 Matrix_1.5-1 ade4_1.7-22
[130] cli_3.6.1 R.methodsS3_1.8.2 quadprog_1.5-8
[133] dotCall64_1.0-2 igraph_1.4.2 GenomicRanges_1.46.1
[136] pkgconfig_2.0.3 numDeriv_2016.8-1.1 sp_2.0-0
[139] terra_1.7-39 foreach_1.5.2 SNPRelate_1.28.0
[142] XVector_0.34.0 yulab.utils_0.0.5 stringr_1.5.0
[145] callr_3.7.3 digest_0.6.32 pracma_2.4.2
[148] polysat_1.7-7 Biostrings_2.62.0 rmarkdown_2.22
[151] fastmatch_1.1-3 tidytree_0.4.1 glassoFast_1.0
[154] curl_4.3.3 kernlab_0.9-32 gtools_3.9.3
[157] shiny_1.7.4 modeltools_0.2-23 jsonlite_1.8.7
[160] lifecycle_1.0.3 network_1.18.1 seqinr_4.2-30
[163] viridisLite_0.4.2 fansi_1.0.4 pillar_1.9.0
[166] fastmap_1.1.1 plotrix_3.8-2 DEoptimR_1.0-14
[169] pkgbuild_1.3.1 glue_1.6.2 remotes_2.4.2
[172] prabclus_2.3-2 iterators_1.0.14 class_7.3-20
[175] stringi_1.7.12 profvis_0.3.7 stable_1.1.6
[178] caTools_1.18.2 bipartite_2.18 memoise_2.0.1
[181] Rmpfr_0.9-2 dplyr_1.1.2