Last updated: 2025-08-29
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Knit directory: muse/
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| Rmd | 2e7d525 | Dave Tang | 2025-08-29 | Information theory |
Install the dependencies required to render this document.
install.packages('mpmi')
packageVersion("mpmi")Example data.
set.seed(1984)
n <- 300
Org <- sample(c("Org1","Org2","Org3"), n, replace=TRUE, prob=c(0.3, 0.4, 0.3))
Cluster <- character(n)
for (i in 1:n) {
if (Org[i] == "Org1") {
Cluster[i] <- sample(c("C1","C2","C3","C4"), 1, prob=c(0.6,0.2,0.1,0.1))
} else if (Org[i] == "Org2") {
Cluster[i] <- sample(c("C1","C2","C3","C4"), 1, prob=c(0.2,0.5,0.2,0.1))
} else {
Cluster[i] <- sample(c("C1","C2","C3","C4"), 1, prob=c(0.1,0.1,0.3,0.5))
}
}
df <- data.frame(Cluster, Org)
table(df$Cluster, df$Org)
Org1 Org2 Org3
C1 58 30 5
C2 20 65 9
C3 8 21 22
C4 9 13 40This function calculates MI and BCMI between a set of discrete variables held as columns in a matrix. It also performs jackknife bias correction and provides a z-score for the hypothesis of no association. Also included are the .pw functions that calculate MI between two vectors only. The njk functions do not perform the jackknife and are therefore faster.
dmi(df)$mi
[,1] [,2]
[1,] 1.3537595 0.2110654
[2,] 0.2110654 1.0748830
$bcmi
[,1] [,2]
[1,] 1.3587896 0.2006073
[2,] 0.2006073 1.0782321
$zvalues
[,1] [,2]
[1,] 93.659447 5.547246
[2,] 5.547246 85.356796
sessionInfo()R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] mpmi_0.43.2.1 KernSmooth_2.23-26 lubridate_1.9.4 forcats_1.0.0
[5] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.4 readr_2.1.5
[9] tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.2 tidyverse_2.0.0
[13] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] sass_0.4.10 generics_0.1.4 stringi_1.8.7 hms_1.1.3
[5] digest_0.6.37 magrittr_2.0.3 timechange_0.3.0 evaluate_1.0.3
[9] grid_4.5.0 RColorBrewer_1.1-3 fastmap_1.2.0 rprojroot_2.0.4
[13] jsonlite_2.0.0 processx_3.8.6 whisker_0.4.1 ps_1.9.1
[17] promises_1.3.2 httr_1.4.7 scales_1.4.0 jquerylib_0.1.4
[21] cli_3.6.5 rlang_1.1.6 withr_3.0.2 cachem_1.1.0
[25] yaml_2.3.10 tools_4.5.0 tzdb_0.5.0 httpuv_1.6.16
[29] vctrs_0.6.5 R6_2.6.1 lifecycle_1.0.4 git2r_0.36.2
[33] fs_1.6.6 pkgconfig_2.0.3 callr_3.7.6 pillar_1.10.2
[37] bslib_0.9.0 later_1.4.2 gtable_0.3.6 glue_1.8.0
[41] Rcpp_1.0.14 xfun_0.52 tidyselect_1.2.1 rstudioapi_0.17.1
[45] knitr_1.50 farver_2.1.2 htmltools_0.5.8.1 rmarkdown_2.29
[49] compiler_4.5.0 getPass_0.2-4