[R-meta] Same command works on one machine but not another
James Pustejovsky
jepu@to @end|ng |rom gm@||@com
Tue Jun 8 03:19:17 CEST 2021
Hi Benoit,
I'm not sure what might be causing the issue you're encountering. I have
double-checked that all of the clubSandwich (v0.5.3) unit tests pass with
metafor 3.0-1. If you'd be willing to work up a reproducible example or
share your data with me (off-list), I can take a look and determine if
there's a bug in clubSandwich.
Kind Regards,
James
On Mon, Jun 7, 2021 at 7:33 AM Benoît Bediou <Benoit.Bediou using unige.ch> wrote:
> Dear Wolfgang
> Thank your for the quick reply
> Unfortunately specifying the clustering doesn’t work either
> However, updating metafor to 3.0-1 and downgrading club sandwich to
> version _0.5.0 did work
> Thanks so much!
> best
> ben
>
>
> > On 7 Jun 2021, at 08:23, Viechtbauer, Wolfgang (SP) <
> wolfgang.viechtbauer using maastrichtuniversity.nl> wrote:
> >
> > Dear Ben,
> >
> > I see various differences in package versions (most notably:
> clubSandwich_0.5.3 vs clubSandwich_0.5.0 and metafor_2.4-0 vs
> metafor_2.5-57).
> >
> > In any case, instead of relying on coef_test() to figure out the
> appropriate cluster variable for you, I would recommend to specify it
> manually to be on the safe side:
> >
> > CHE_model <- clubSandwich::coef_test(mlma_model, vcov = "CR2", cluster =
> es_data$Paper)
> >
> > Best,
> > Wolfgang
> >
> >> -----Original Message-----
> >> From: R-sig-meta-analysis [mailto:
> r-sig-meta-analysis-bounces using r-project.org] On
> >> Behalf Of Benoît Bediou
> >> Sent: Monday, 07 June, 2021 7:56
> >> To: r-sig-meta-analysis using r-project.org
> >> Subject: [R-meta] Same command works on one machine but not another
> >>
> >> Hi there
> >> I am facing a strange problem and would welcome some help
> >>
> >> My colleague is able to run a command that does not work on my machine
> and we
> >> haven’t been able to figure out why
> >>
> >> I am pasting below the command lines and then the sessionInfo from my
> machine and
> >> from my colleague’s
> >> Thank you so much for any help you can provide!
> >>
> >> best
> >> Ben
> >>
> >> The command is its simple as
> >>
> >> ## Multilevel model
> >> vcov_mat <- impute_covariance_matrix(es_data$g_var,
> >> cluster = es_data$Paper,
> >> r = 0.8)
> >> mlma_model<- metafor::rma.mv(g ~ 1, # Intercept only MLMA model
> >> V = vcov_mat,
> >> random = ~ 1 | Paper / ES_ID,# NOT WORKING WE COULD ADD
> >> COGNITIVE DOMAIN TOO!?
> >> # random = list(~ 1 | Paper, ~ 1 | ES_ID),#
> >> # random = ~ 1 | ES_ID,# WORKING
> >> sparse = TRUE,
> >> data = es_data,
> >> test="t")
> >> ## Add RVE using clubSandwich
> >> CHE_model <- clubSandwich::coef_test(mlma_model, vcov = "CR2")
> >>
> >>> Error in if (!all(nested)) stop("Random effects are not nested within
> >> clustering") :
> >> missing value where TRUE/FALSE needed
> >>>
> >>
> >> ## SESSION INFO --- NOT WORKING
> >> R version 4.0.4 (2021-02-15)
> >> Platform: x86_64-apple-darwin17.0 (64-bit)
> >> Running under: macOS Big Sur 10.16
> >>
> >> Matrix products: default
> >> LAPACK:
> >>
> /Library/Frameworks/R.framework/Versions/4.0/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] matrixStats_0.57.0 doMC_1.3.7 iterators_1.0.13
> foreach_1.5.1
> >> partitions_1.10-2 DescTools_0.99.38 ggsci_2.9
> RColorBrewer_1.1-2
> >> plotly_4.9.2.1
> >> [10] ggthemes_4.2.0 scales_1.1.1 wesanderson_0.3.6
> ggExtra_0.9
> >> ggstatsplot_0.6.5 metafor_2.4-0 Matrix_1.3-2
> clubSandwich_0.5.3
> >> robumeta_2.0
> >> [19] zoo_1.8-9 kableExtra_1.3.1 knitr_1.30
> summarytools_0.9.6
> >> plyr_1.8.6 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.3
> >> purrr_0.3.4
> >> [28] readr_1.4.0 tidyr_1.1.2 tibble_3.1.0
> ggplot2_3.3.3
> >> tidyverse_1.3.0 lavaan_0.6-8 data.table_1.13.6 reshape2_1.4.4
> >> pacman_0.5.1
> >>
> >> loaded via a namespace (and not attached):
> >> [1] coda_0.19-4 multcomp_1.4-15 inline_0.3.16
> >> generics_0.1.0 callr_3.5.1 cowplot_1.1.0
> >> [7] TH.data_1.0-10 correlation_0.4.0 webshot_0.5.2
> >> xml2_1.3.2 lubridate_1.7.9.2 httpuv_1.5.4
> >> [13] StanHeaders_2.21.0-6 assertthat_0.2.1 WRS2_1.1-0
> >> xfun_0.20 hms_0.5.3 evaluate_0.14
> >> [19] promises_1.1.1 tidyBF_0.4.0 fansi_0.4.2
> >> dbplyr_2.0.0 readxl_1.3.1 DBI_1.1.0
> >> [25] tmvnsim_1.0-2 htmlwidgets_1.5.2 reshape_0.8.8
> >> kSamples_1.2-9 stats4_4.0.4 Rmpfr_0.8-2
> >> [31] paletteer_1.2.0 ellipsis_0.3.1
> crosstalk_1.1.0.1
> >> selectr_0.4-2 rcompanion_2.3.26 ggpubr_0.4.0
> >> [37] backports_1.2.1 V8_3.4.0 pbivnorm_0.6.0
> >> insight_0.10.0 ggcorrplot_0.1.3 rapportools_1.0
> >> [43] RcppParallel_5.0.2 libcoin_1.0-6 vctrs_0.3.6
> >> abind_1.4-5 withr_2.4.1 pryr_0.1.4
> >> [49] metaBMA_0.6.5 bdsmatrix_1.3-4 checkmate_2.0.0
> >> prettyunits_1.1.1 fastGHQuad_1.0 mnormt_2.0.2
> >> [55] lazyeval_0.2.2 crayon_1.4.1 labeling_0.4.2
> >> pkgconfig_2.0.3 SuppDists_1.1-9.5 nlme_3.1-152
> >> [61] statsExpressions_0.6.0 rematch_1.0.1 rlang_0.4.10
> >> lifecycle_1.0.0 miniUI_0.1.1.1 LaplacesDemon_16.1.4
> >> [67] MatrixModels_0.4-1 sandwich_3.0-1 mathjaxr_1.0-1
> >> EMT_1.1 modelr_0.1.8 cellranger_1.1.0
> >> [73] tcltk_4.0.4 broomExtra_4.1.0 lmtest_0.9-38
> >> loo_2.3.1 mc2d_0.1-18 carData_3.0-4
> >> [79] boot_1.3-26 reprex_0.3.0 base64enc_0.1-3
> >> processx_3.4.5 viridisLite_0.3.0 PMCMRplus_1.7.0
> >> [85] parameters_0.9.0 rootSolve_1.8.2.1 debugme_1.1.0
> >> pander_0.6.3 multcompView_0.1-8 coin_1.3-1
> >> [91] rstatix_0.6.0 ggsignif_0.6.0 memoise_1.1.0
> >> magrittr_2.0.1 compiler_4.0.4 rstantools_2.1.1
> >> [97] bbmle_1.0.23.1 lme4_1.1-25 cli_2.3.1
> >> pbapply_1.4-3 ps_1.5.0 TMB_1.7.18
> >> [103] Brobdingnag_1.2-6 MASS_7.3-53 mgcv_1.8-33
> >> tidyselect_1.1.0 stringi_1.5.3 highr_0.8
> >> [109] yaml_2.2.1 ggrepel_0.8.2
> bridgesampling_1.0-0
> >> grid_4.0.4 polynom_1.4-0 tools_4.0.4
> >> [115] lmom_2.8 rio_0.5.16
> rstudioapi_0.13
> >> foreign_0.8-81 gridExtra_2.3 ipmisc_4.1.0
> >> [121] gld_2.6.2 pairwiseComparisons_3.1.0 farver_2.1.0
> >> RcppZiggurat_0.1.6 digest_0.6.27 shiny_1.5.0
> >> [127] nortest_1.0-4 BWStest_0.2.2 Rcpp_1.0.6
> >> car_3.0-10 broom_0.7.3.9000 ez_4.4-0
> >> [133] BayesFactor_0.9.12-4.2 performance_0.5.1
> metaplus_0.7-11
> >> later_1.1.0.1 httr_1.4.2 rsconnect_0.8.16
> >> [139] effectsize_0.4.0 colorspace_2.0-0 rvest_0.3.6
> >> fs_1.5.0 splines_4.0.4 statmod_1.4.35
> >> [145] rematch2_2.1.2 expm_0.999-5 Exact_2.1
> >> xtable_1.8-4 gmp_0.6-1 jsonlite_1.7.2
> >> [151] nloptr_1.2.2.2 rstan_2.21.2 Rfast_2.0.1
> >> zeallot_0.1.0 modeltools_0.2-23 R6_2.5.0
> >> [157] broom.mixed_0.2.6 pillar_1.5.1
> htmltools_0.5.1
> >> mime_0.9 DT_0.16 glue_1.4.2
> >> [163] fastmap_1.0.1 minqa_1.2.4 class_7.3-18
> >> codetools_0.2-18 pkgbuild_1.2.0 mvtnorm_1.1-1
> >> [169] utf8_1.2.1 lattice_0.20-41
> numDeriv_2016.8-1.1
> >> curl_4.3 gtools_3.8.2 magick_2.5.2
> >> [175] logspline_2.1.16 zip_2.1.1 openxlsx_4.2.3
> >> survival_3.2-7 rmarkdown_2.6 munsell_0.5.0
> >> [181] e1071_1.7-4 haven_2.3.1 gtable_0.3.0
> >> bayestestR_0.7.5
> >>
> >> ## SESSION INFO — WORKING MACHINE
> >> R version 4.0.2 (2020-06-22)
> >> Platform: x86_64-w64-mingw32/x64 (64-bit)
> >> Running under: Windows >= 8 x64 (build 9200)
> >>
> >> Matrix products: default
> >>
> >> locale:
> >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252
> >> LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> >> [5] LC_TIME=English_United States.1252
> >>
> >> attached base packages:
> >> [1] stats graphics grDevices utils datasets methods base
> >>
> >> other attached packages:
> >> [1] DescTools_0.99.37 ggsci_2.9 RColorBrewer_1.1-2
> plotly_4.9.3
> >> ggthemes_4.2.0 scales_1.1.1 wesanderson_0.3.6 ggExtra_0.9
> >> [9] ggstatsplot_0.7.1 metafor_2.5-57 Matrix_1.2-18
> clubSandwich_0.5.0
> >> robumeta_2.0 zoo_1.8-8 kableExtra_1.1.0 knitr_1.29
> >> [17] summarytools_0.9.6 plyr_1.8.6 forcats_0.5.0
> stringr_1.4.0
> >> dplyr_1.0.0 purrr_0.3.4 readr_1.3.1 tidyr_1.1.0
> >> [25] tibble_3.0.3 ggplot2_3.3.3 tidyverse_1.3.0
> lavaan_0.6-8
> >> data.table_1.13.0 reshape2_1.4.4 pacman_0.5.1
> >>
> >> loaded via a namespace (and not attached):
> >> [1] readxl_1.3.1 pairwiseComparisons_3.1.3 backports_1.1.8
> >> selectr_0.4-2 lazyeval_0.2.2 splines_4.0.2
> >> [7] gmp_0.6-2 kSamples_1.2-9 ipmisc_6.0.0
> >> pryr_0.1.4 digest_0.6.25 SuppDists_1.1-9.5
> >> [13] htmltools_0.5.0 magick_2.5.0 fansi_0.4.1
> >> magrittr_1.5 checkmate_2.0.0 memoise_2.0.0
> >> [19] paletteer_1.3.0 modelr_0.1.8
> matrixStats_0.57.0
> >> sandwich_2.5-1 colorspace_1.4-1 blob_1.2.1
> >> [25] rvest_0.3.6 ggrepel_0.8.2 haven_2.3.1
> >> xfun_0.16 tcltk_4.0.2 crayon_1.3.4
> >> [31] jsonlite_1.7.0 Exact_2.0 zeallot_0.1.0
> >> glue_1.4.1 gtable_0.3.0 webshot_0.5.2
> >> [37] MatrixModels_0.4-1 statsExpressions_1.0.0 Rmpfr_0.8-3
> >> rapportools_1.0 mvtnorm_1.1-1 DBI_1.1.0
> >> [43] PMCMRplus_1.9.0 miniUI_0.1.1.1 Rcpp_1.0.5
> >> viridisLite_0.3.0 xtable_1.8-4 performance_0.4.8
> >> [49] tmvnsim_1.0-2 stats4_4.0.2
> htmlwidgets_1.5.3
> >> httr_1.4.2 ellipsis_0.3.1 farver_2.0.3
> >> [55] pkgconfig_2.0.3 reshape_0.8.8
> multcompView_0.1-8
> >> dbplyr_1.4.4 labeling_0.3 tidyselect_1.1.0
> >> [61] rlang_0.4.7 later_1.1.0.1
> ggcorrplot_0.1.3
> >> effectsize_0.4.4 munsell_0.5.0 cellranger_1.1.0
> >> [67] tools_4.0.2 cachem_1.0.4 cli_2.0.2
> >> generics_0.0.2 broom_0.7.5 mathjaxr_1.0-1
> >> [73] evaluate_0.14 fastmap_1.0.1 BWStest_0.2.2
> >> yaml_2.2.1 rematch2_2.1.2 fs_1.4.2
> >> [79] pander_0.6.3 WRS2_1.1-1 pbapply_1.4-3
> >> nlme_3.1-148 mime_0.9 xml2_1.3.2
> >> [85] correlation_0.6.0 compiler_4.0.2 rstudioapi_0.11
> >> ggsignif_0.6.1 reprex_0.3.0 pbivnorm_0.6.0
> >> [91] stringi_1.4.6 highr_0.8
> parameters_0.12.0
> >> lattice_0.20-41 vctrs_0.3.2 pillar_1.4.6
> >> [97] lifecycle_0.2.0 mc2d_0.1-18 insight_0.13.2
> >> httpuv_1.5.4 patchwork_1.1.1 R6_2.4.1
> >> [103] promises_1.1.1 BayesFactor_0.9.12-4.2
> codetools_0.2-16
> >> boot_1.3-25 MASS_7.3-51.6 gtools_3.8.2
> >> [109] assertthat_0.2.1 withr_2.2.0 mnormt_2.0.1
> >> expm_0.999-5 mgcv_1.8-31 bayestestR_0.8.2
> >> [115] parallel_4.0.2 hms_0.5.3 grid_4.0.2
> >> coda_0.19-3 rmarkdown_2.3 shiny_1.5.0
> >> [121] lubridate_1.7.9 base64enc_0.1-3
>
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