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dysbiosisOBB error #5

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lxsteiner opened this issue Jul 2, 2024 · 1 comment
Open

dysbiosisOBB error #5

lxsteiner opened this issue Jul 2, 2024 · 1 comment

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@lxsteiner
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Hi,

Thank you for providing a nice summary of dysbiosis indexes in one package!

I was trying it out on the test data and then mine as well, unfortunately dysbiosisOBB gives me an error. I was able to calculate all other indexes with me own data.

> dysbiosis.oob <- dysbiosisOBB(fix.rarephi,
+                               group_col = "PhageCode",
+                               case_label = "PHI",
+                               seed_value = 1235,
+                               add_tuneRF_params = list(ntreeTry=100,
+                                                        stepFactor=1.5,
+                                                        improve=0.01,
+                                                        trace=TRUE,
+                                                        dobest=FALSE),
+                               ntree = 100,
+                               plot_roc = TRUE)
The random seed of your session for reproducibility is: 1235
mtry = 61  OOB error = 20% 
Searching left ...
mtry = 41 	OOB error = 20% 
0 0.01 
Searching right ...
mtry = 91 	OOB error = 20% 
0 0.01 
The mtry used is : 416191
Error in mtry < 1 || mtry > p : 'length = 3' in coercion to 'logical(1)'

Could you please tell if the error says anything to you? I'm not sure where the issue could be, I used a phyloseq object with absolute counts in all other calculations. Transformed it here to relative abundance summed to 1 or 100, made no difference (since in the tutorial you mention multiple times that the test data is relative abundance, summed to 100, so I wasn't sure if that was important).

The error seems rather to be coming from the logical evalution of "||" inside an if() statement (according to Google), so I guess it has to do with

dysbiosisR/R/dysbiosisOBB.R

Line 86 in 292adc8

if(is.null(x) ||

though not really sure 😅

Session Info 
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.3 (2024-02-29 ucrt)
 os       Windows 10 x64 (build 19045)
 system   x86_64, mingw32
 ui       RStudio
 language en
 collate  German_Germany.utf8
 ctype    German_Germany.utf8
 tz       Europe/Budapest
 date     2024-07-03
 rstudio  2024.04.1+748 Chocolate Cosmos (desktop)
 pandoc   3.1.11 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 ! package          * version    date (UTC) lib source
   ade4               1.7-22     2023-02-06 [1] RSPM (R 4.3.0)
   ape                5.8        2024-04-11 [1] RSPM (R 4.3.0)
   backports          1.5.0      2024-05-23 [1] RSPM (R 4.3.0)
 P base64enc          0.1-3      2015-07-28 [?] RSPM (R 4.3.0)
   Biobase            2.62.0     2023-10-24 [1] Bioconductor
   BiocGenerics       0.48.1     2023-11-01 [1] Bioconductor
 P BiocManager      * 1.30.23    2024-05-04 [?] RSPM
   biomformat         1.30.0     2023-10-24 [1] Bioconductor
   Biostrings         2.70.3     2024-03-13 [1] Bioconductor 3.18 (R 4.3.3)
   bitops             1.0-7      2021-04-24 [1] RSPM (R 4.3.0)
 P cachem             1.1.0      2024-05-16 [?] RSPM
 P callr              3.7.6      2024-03-25 [?] RSPM
   checkmate          2.3.1      2023-12-04 [1] RSPM (R 4.3.0)
 P cli                3.6.3      2024-06-21 [?] RSPM
 P cluster            2.1.6      2023-12-01 [?] CRAN (R 4.3.3)
 P codetools          0.2-19     2023-02-01 [?] CRAN (R 4.3.3)
   colorspace         2.1-0      2023-01-23 [1] RSPM (R 4.3.0)
 P crayon             1.5.3      2024-06-20 [?] RSPM
 P curl               5.2.1      2024-03-01 [?] RSPM (R 4.3.0)
   data.table         1.15.4     2024-03-30 [1] RSPM (R 4.3.0)
 P desc               1.4.3      2023-12-10 [?] RSPM (R 4.3.0)
 P devtools           2.4.5      2022-10-11 [?] RSPM (R 4.3.0)
 P digest             0.6.36     2024-06-23 [?] RSPM
   distributional     0.4.0      2024-02-07 [1] RSPM (R 4.3.0)
   dplyr            * 1.1.4      2023-11-17 [1] RSPM (R 4.3.0)
   DT                 0.33       2024-04-04 [1] RSPM (R 4.3.0)
   dysbiosisR       * 1.0.4      2024-07-02 [1] Github (microsud/dysbiosisR@292adc8)
 P ellipsis           0.3.2      2021-04-29 [?] RSPM (R 4.3.0)
 P evaluate           0.24.0     2024-06-10 [?] RSPM
 P fansi              1.0.6      2023-12-08 [?] RSPM (R 4.3.0)
   farver             2.1.2      2024-05-13 [1] RSPM (R 4.3.0)
 P fastmap            1.2.0      2024-05-15 [?] RSPM
   foreach            1.5.2      2022-02-02 [1] RSPM (R 4.3.0)
 P foreign            0.8-86     2023-11-28 [?] CRAN (R 4.3.3)
   Formula            1.2-5      2023-02-24 [1] RSPM (R 4.3.0)
 P fs                 1.6.4      2024-04-25 [?] RSPM
   generics           0.1.3      2022-07-05 [1] RSPM (R 4.3.0)
   GenomeInfoDb       1.38.8     2024-03-15 [1] Bioconductor 3.18 (R 4.3.3)
   GenomeInfoDbData   1.2.11     2024-07-02 [1] Bioconductor
   ggdist             3.3.2      2024-03-05 [1] RSPM (R 4.3.0)
   ggplot2          * 3.5.1      2024-04-23 [1] RSPM (R 4.3.0)
 P glue               1.7.0      2024-01-09 [?] RSPM (R 4.3.0)
   gridExtra          2.3        2017-09-09 [1] RSPM (R 4.3.0)
   gtable             0.3.5      2024-04-22 [1] RSPM (R 4.3.0)
   Hmisc              5.1-3      2024-05-28 [1] RSPM (R 4.3.0)
   htmlTable          2.4.2      2023-10-29 [1] RSPM (R 4.3.0)
 P htmltools          0.5.8.1    2024-04-04 [?] RSPM (R 4.3.0)
 P htmlwidgets        1.6.4      2023-12-06 [?] RSPM (R 4.3.0)
 P httpuv             1.6.15     2024-03-26 [?] RSPM
   igraph             2.0.3      2024-03-13 [1] RSPM (R 4.3.0)
   IRanges            2.36.0     2023-10-24 [1] Bioconductor
   iterators          1.0.14     2022-02-05 [1] RSPM (R 4.3.0)
 P jsonlite           1.8.8      2023-12-04 [?] RSPM (R 4.3.0)
 P knitr              1.47       2024-05-29 [?] RSPM
   labeling           0.4.3      2023-08-29 [1] RSPM (R 4.3.0)
 P later              1.3.2      2023-12-06 [?] RSPM (R 4.3.0)
 P lattice            0.22-5     2023-10-24 [?] CRAN (R 4.3.3)
 P lifecycle          1.0.4      2023-11-07 [?] RSPM (R 4.3.0)
 P magrittr           2.0.3      2022-03-30 [?] RSPM (R 4.3.0)
 P MASS               7.3-60.0.1 2024-01-13 [?] CRAN (R 4.3.3)
 P Matrix             1.6-5      2024-01-11 [?] CRAN (R 4.3.3)
 P memoise            2.0.1      2021-11-26 [?] RSPM (R 4.3.0)
 P mgcv               1.9-1      2023-12-21 [?] CRAN (R 4.3.3)
   microbiome       * 1.24.0     2023-10-24 [1] Bioconductor
 P microViz         * 0.12.4     2024-06-30 [?] https://d~
 P mime               0.12       2021-09-28 [?] RSPM (R 4.3.0)
 P miniUI             0.1.1.1    2018-05-18 [?] RSPM (R 4.3.0)
   multtest           2.58.0     2023-10-24 [1] Bioconductor
   munsell            0.5.1      2024-04-01 [1] RSPM (R 4.3.0)
   NADA               1.6-1.1    2020-03-22 [1] RSPM (R 4.3.0)
 P nlme               3.1-164    2023-11-27 [?] CRAN (R 4.3.3)
 P nnet               7.3-19     2023-05-03 [?] CRAN (R 4.3.3)
 P patchwork        * 1.2.0      2024-01-08 [?] RSPM (R 4.3.0)
   permute            0.9-7      2022-01-27 [1] RSPM (R 4.3.0)
   phyloseq         * 1.46.0     2023-10-24 [1] Bioconductor
 P pillar             1.9.0      2023-03-22 [?] RSPM (R 4.3.0)
 P pkgbuild           1.4.4      2024-03-17 [?] RSPM (R 4.3.0)
 P pkgconfig          2.0.3      2019-09-22 [?] RSPM (R 4.3.0)
 P pkgload            1.4.0      2024-06-28 [?] RSPM
   plyr               1.8.9      2023-10-02 [1] RSPM (R 4.3.0)
   pROC               1.18.5     2023-11-01 [1] RSPM (R 4.3.0)
 P processx           3.8.4      2024-03-16 [?] RSPM (R 4.3.0)
 P profvis            0.3.8      2023-05-02 [?] RSPM (R 4.3.0)
 P promises           1.3.0      2024-04-05 [?] RSPM
 P ps                 1.7.6      2024-01-18 [?] RSPM (R 4.3.0)
 P purrr              1.0.2      2023-08-10 [?] RSPM (R 4.3.0)
   qiime2R          * 0.99.6     2024-07-02 [1] Github (jbisanz/qiime2R@d0610e1)
 P R6                 2.5.1      2021-08-19 [?] RSPM (R 4.3.0)
   randomForest       4.7-1.1    2022-05-23 [1] RSPM (R 4.3.0)
   RColorBrewer       1.1-3      2022-04-03 [1] RSPM (R 4.3.0)
 P Rcpp               1.0.12     2024-01-09 [?] RSPM (R 4.3.0)
   RCurl              1.98-1.14  2024-01-09 [1] RSPM (R 4.3.0)
 P remotes            2.5.0      2024-03-17 [?] RSPM (R 4.3.0)
   renv               1.0.7      2024-04-11 [1] RSPM (R 4.3.0)
   reshape2           1.4.4      2020-04-09 [1] RSPM (R 4.3.0)
   rhdf5              2.46.1     2023-11-29 [1] Bioconductor
 D rhdf5filters       1.14.1     2023-11-06 [1] Bioconductor
   Rhdf5lib           1.24.2     2024-02-07 [1] Bioconductor 3.18 (R 4.3.2)
 P rlang              1.1.4      2024-06-04 [?] RSPM
 P rmarkdown          2.27       2024-05-17 [?] RSPM
 P rpart              4.1.23     2023-12-05 [?] CRAN (R 4.3.3)
 P rstudioapi         0.16.0     2024-03-24 [?] RSPM
   Rtsne              0.17       2023-12-07 [1] RSPM (R 4.3.0)
   S4Vectors          0.40.2     2023-11-23 [1] Bioconductor
   scales             1.3.0      2023-11-28 [1] RSPM (R 4.3.0)
 P sessioninfo        1.2.2      2021-12-06 [?] RSPM (R 4.3.0)
 P shiny              1.8.1.1    2024-04-02 [?] RSPM
 P stringi            1.8.4      2024-05-06 [?] RSPM
 P stringr            1.5.1      2023-11-14 [?] RSPM (R 4.3.0)
 P survival           3.5-8      2024-02-14 [?] CRAN (R 4.3.3)
 P tibble             3.2.1      2023-03-20 [?] RSPM (R 4.3.0)
   tidyr              1.3.1      2024-01-24 [1] RSPM (R 4.3.0)
   tidyselect         1.2.1      2024-03-11 [1] RSPM (R 4.3.0)
   truncnorm          1.0-9      2023-03-20 [1] RSPM (R 4.3.0)
 P urlchecker         1.0.1      2021-11-30 [?] RSPM (R 4.3.0)
   usedist            0.4.0      2020-03-01 [1] RSPM (R 4.3.0)
 P usethis            2.2.3      2024-02-19 [?] RSPM (R 4.3.0)
 P utf8               1.2.4      2023-10-22 [?] RSPM (R 4.3.0)
 P vctrs              0.6.5      2023-12-01 [?] RSPM (R 4.3.0)
   vegan              2.6-6.1    2024-05-21 [1] RSPM (R 4.3.0)
 P withr              3.0.0      2024-01-16 [?] RSPM (R 4.3.0)
 P xfun               0.45       2024-06-16 [?] RSPM
 P xtable             1.8-4      2019-04-21 [?] RSPM (R 4.3.0)
   XVector            0.42.0     2023-10-24 [1] Bioconductor
 P yaml               2.3.8      2023-12-11 [?] RSPM (R 4.3.0)
   zCompositions      1.5.0-4    2024-06-19 [1] RSPM (R 4.3.0)
   zlibbioc           1.48.2     2024-03-13 [1] Bioconductor 3.18 (R 4.3.3)

Thanks.
@gutmicrobe
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Thanks for using the R package and the query. My apologies for late response. I am unable to recreate the error. Is it possible that you have missing info or group column is not a 'factor'? in your sample_data?

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@lxsteiner @gutmicrobe