[R-meta] Same command works on one machine but not another
Benoît Bediou
Beno|t@Bed|ou @end|ng |rom un|ge@ch
Mon Jun 7 12:26:32 CEST 2021
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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