Example "Inspecting Paired Samples: Taxa Analysis" results in GUniFrac error

[SciLiciumTheo]

Hello,

Thanks to the team for this package, the help/wiki is very straightforward, easy to follow and clear.

I ran into an error trying to reproduce the tutorial "Paired Samples Analysis", specifically the part "Inspecting Paired Samples: Taxa Analysis". The generate_taxa_change_test_pair code

generate_taxa_change_test_pair(
  data.obj = peerj32.obj,
  subject.var = "subject",
  time.var = "time",
  group.var = "group",
  adj.vars = c("sex"),
  change.base = "1",
  change.func = "lfc",
  feature.level = "original",
  prev.filter = 0.01,
  abund.filter = 0.01,
  feature.dat.type = "count"
)

resulted in the following error:

Error in GUniFrac::ZicoSeq(meta.dat = sorted_unique_meta_tab, feature.dat = na.omit(value_diff_matrix),  :
  unused argument (change.func = "lfc")

Not sure where this comes from, here is my session info:

R version 4.3.1 (2023-06-16)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS/LAPACK: /home/sciliciumtheo/miniconda3/envs/r_microbiomestats/lib/libopenblasp-r0.3.23.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Paris
tzcode source: system (glibc)

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

other attached packages:
[1] vegan_2.6-4          lattice_0.21-8       permute_0.9-7
[4] MicrobiomeStat_1.1.1 tibble_3.2.1         rlang_1.1.1

loaded via a namespace (and not attached):
  [1] remotes_2.4.2.1     magrittr_2.0.3      clue_0.3-64
  [4] matrixStats_1.0.0   compiler_4.3.1      mgcv_1.9-0
  [7] systemfonts_1.0.4   callr_3.7.3         vctrs_0.6.3
 [10] rmutil_1.1.10       stringr_1.5.0       profvis_0.3.8
 [13] pkgconfig_2.0.3     crayon_1.5.2        fastmap_1.1.1
 [16] backports_1.4.1     ellipsis_0.3.2      labeling_0.4.3
 [19] pander_0.6.5        utf8_1.2.3          modeest_2.4.0
 [22] promises_1.2.1      rmarkdown_2.24      sessioninfo_1.2.2
 [25] ps_1.7.5            nloptr_2.0.3        ragg_1.2.5
 [28] purrr_1.0.2         xfun_0.40           cachem_1.0.8
 [31] highr_0.10          later_1.3.1         broom_1.0.5
 [34] parallel_4.3.1      prettyunits_1.1.1   cluster_2.1.4
 [37] R6_2.5.1            RColorBrewer_1.1-3  stringi_1.7.12
 [40] boot_1.3-28.1       pkgload_1.3.2.1     rpart_4.1.19
 [43] numDeriv_2016.8-1.1 Rcpp_1.0.11         iterators_1.0.14
 [46] knitr_1.43          usethis_2.2.2       httpuv_1.6.11
 [49] Matrix_1.6-1        splines_4.3.1       tidyselect_1.2.0
 [52] yaml_2.3.7          timeDate_4022.108   codetools_0.2-19
 [55] miniUI_0.1.1.1      curl_5.0.2          processx_3.8.2
 [58] pkgbuild_1.4.2      lmerTest_3.1-3      shiny_1.7.5
 [61] withr_2.5.0         evaluate_0.21       stable_1.1.6
 [64] desc_1.4.2          urlchecker_1.0.1    pillar_1.9.0
 [67] foreach_1.5.2       generics_0.1.3      rprojroot_2.0.3
 [70] ggplot2_3.4.3       munsell_0.5.0       scales_1.2.1
 [73] minqa_1.2.5         timeSeries_4031.107 xtable_1.8-4
 [76] glue_1.6.2          statip_0.2.3        pheatmap_1.0.12
 [79] tools_4.3.1         lme4_1.1-34         spatial_7.3-17
 [82] fBasics_4022.94     fs_1.6.3            grid_4.3.1
 [85] ape_5.7-1           tidyr_1.3.0         devtools_2.4.5
 [88] colorspace_2.1-0    nlme_3.1-163        cli_3.6.1
 [91] textshaping_0.3.6   fansi_1.0.4         dplyr_1.1.2
 [94] gtable_0.3.4        ggh4x_0.2.6         stabledist_0.7-1
 [97] digest_0.6.33       ggrepel_0.9.3       htmlwidgets_1.6.2
[100] farver_2.1.1        memoise_2.0.1       htmltools_0.5.6
[103] lifecycle_1.0.3     statmod_1.5.0       mime_0.12
[106] GUniFrac_1.7        MASS_7.3-60