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Course materials for STAMPS @ MBL
I'm running through the alphadiversitylab.R file in this tutorial. I have installed breakaway, and the tutorial works up to line 150
On line 150, when I run the function
shannon(frequency_count_list[[1]])
I get the error message
> Error in shannon(frequency_count_list[[1]]) :
> could not find function "shannon"
I looked through the github repository for the breakaway package and do not see a instance of the shannon function. I did find a function in shannon_chao_shen.R for a chao_shen estimator of shannon index.
chao_shen(frequency_count_list[[1]])
Works as expected:
> Estimate of shannon from method chao_shen:
> Estimate is 4.19
> with standard error 0.15
Is there another shannon()
method that I am somehow missing here, or does the language on the tutorial just need to be updated? Thanks for your consideration.
sessionInfo()
> R version 3.6.1 (2019-07-05)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 18.04.2 LTS
>
> Matrix products: default
> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
> [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] breakaway_4.6.11
>
> loaded via a namespace (and not attached):
> [1] tidyselect_0.2.5 reshape2_1.4.3 purrr_0.3.2 splines_3.6.1 lattice_0.20-38 rhdf5_2.28.0 colorspace_1.4-1
> [8] stats4_3.6.1 mgcv_1.8-28 survival_2.44-1.1 rlang_0.3.4 pillar_1.4.1 glue_1.3.1 BiocGenerics_0.30.0
> [15] foreach_1.4.4 plyr_1.8.4 stringr_1.4.0 zlibbioc_1.30.0 Biostrings_2.52.0 munsell_0.5.0 gtable_0.3.0
> [22] codetools_0.2-16 phyloseq_1.28.0 labeling_0.3 Biobase_2.44.0 permute_0.9-5 IRanges_2.18.1 biomformat_1.12.0
> [29] parallel_3.6.1 Rcpp_1.0.1 scales_1.0.0 vegan_2.5-5 S4Vectors_0.22.0 jsonlite_1.6 XVector_0.24.0
> [36] digest_0.6.19 ggplot2_3.1.1 packrat_0.5.0-8 stringi_1.4.3 dplyr_0.8.1 grid_3.6.1 ade4_1.7-13
> [43] tools_3.6.1 magrittr_1.5 lazyeval_0.2.2 tibble_2.1.3 cluster_2.0.9 crayon_1.3.4 ape_5.3
> [50] pkgconfig_2.0.2 MASS_7.3-51.4 Matrix_1.2-17 data.table_1.12.2 assertthat_0.2.1 rstudioapi_0.10 iterators_1.0.10
> [57] Rhdf5lib_1.6.0 R6_2.4.0 multtest_2.40.0 igraph_1.2.4.1 nlme_3.1-140 compiler_3.6.1
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