Last updated: 2025-10-08
Checks: 7 0
Knit directory: muse/
This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20200712)
was run prior to running
the code in the R Markdown file. Setting a seed ensures that any results
that rely on randomness, e.g. subsampling or permutations, are
reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 466f85f. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
(you can use wflow_publish
or
wflow_git_commit
). workflowr only checks the R Markdown
file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
Ignored files:
Ignored: .Rproj.user/
Ignored: data/1M_neurons_filtered_gene_bc_matrices_h5.h5
Ignored: data/293t/
Ignored: data/293t_3t3_filtered_gene_bc_matrices.tar.gz
Ignored: data/293t_filtered_gene_bc_matrices.tar.gz
Ignored: data/5k_Human_Donor1_PBMC_3p_gem-x_5k_Human_Donor1_PBMC_3p_gem-x_count_sample_filtered_feature_bc_matrix.h5
Ignored: data/5k_Human_Donor2_PBMC_3p_gem-x_5k_Human_Donor2_PBMC_3p_gem-x_count_sample_filtered_feature_bc_matrix.h5
Ignored: data/5k_Human_Donor3_PBMC_3p_gem-x_5k_Human_Donor3_PBMC_3p_gem-x_count_sample_filtered_feature_bc_matrix.h5
Ignored: data/5k_Human_Donor4_PBMC_3p_gem-x_5k_Human_Donor4_PBMC_3p_gem-x_count_sample_filtered_feature_bc_matrix.h5
Ignored: data/97516b79-8d08-46a6-b329-5d0a25b0be98.h5ad
Ignored: data/Parent_SC3v3_Human_Glioblastoma_filtered_feature_bc_matrix.tar.gz
Ignored: data/brain_counts/
Ignored: data/cl.obo
Ignored: data/cl.owl
Ignored: data/jurkat/
Ignored: data/jurkat:293t_50:50_filtered_gene_bc_matrices.tar.gz
Ignored: data/jurkat_293t/
Ignored: data/jurkat_filtered_gene_bc_matrices.tar.gz
Ignored: data/pbmc20k/
Ignored: data/pbmc20k_seurat/
Ignored: data/pbmc3k.h5ad
Ignored: data/pbmc3k/
Ignored: data/pbmc3k_bpcells_mat/
Ignored: data/pbmc3k_export.mtx
Ignored: data/pbmc3k_matrix.mtx
Ignored: data/pbmc3k_seurat.rds
Ignored: data/pbmc4k_filtered_gene_bc_matrices.tar.gz
Ignored: data/pbmc_1k_v3_filtered_feature_bc_matrix.h5
Ignored: data/pbmc_1k_v3_raw_feature_bc_matrix.h5
Ignored: data/refdata-gex-GRCh38-2020-A.tar.gz
Ignored: data/seurat_1m_neuron.rds
Ignored: data/t_3k_filtered_gene_bc_matrices.tar.gz
Ignored: r_packages_4.4.1/
Ignored: r_packages_4.5.0/
Untracked files:
Untracked: analysis/bioc_scrnaseq.Rmd
Untracked: bpcells_matrix/
Untracked: data/Caenorhabditis_elegans.WBcel235.113.gtf.gz
Untracked: data/GCF_043380555.1-RS_2024_12_gene_ontology.gaf.gz
Untracked: data/arab.rds
Untracked: data/astronomicalunit.csv
Untracked: data/femaleMiceWeights.csv
Untracked: m3/
Unstaged changes:
Modified: analysis/isoform_switch_analyzer.Rmd
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were
made to the R Markdown (analysis/rater.Rmd
) and HTML
(docs/rater.html
) files. If you’ve configured a remote Git
repository (see ?wflow_git_remote
), click on the hyperlinks
in the table below to view the files as they were in that past version.
File | Version | Author | Date | Message |
---|---|---|---|---|
Rmd | 466f85f | Dave Tang | 2025-10-08 | Cohen’s Kappa with random results |
html | 9a6ead6 | Dave Tang | 2025-10-06 | Build site. |
Rmd | 47f2160 | Dave Tang | 2025-10-06 | Manually calculate Fleiss’ Kappa |
html | a8d6f16 | Dave Tang | 2025-10-06 | Build site. |
Rmd | 59c9392 | Dave Tang | 2025-10-06 | Inter-rater reliability |
Measures of inter-rater reliability (IRR) provide an index indicating how much agreement there is between raters/observers, correcting for agreement that would happen just by chance.
Install {irr}.
install.packages("irr")
Measures agreement between two raters who classify items into categories.
\[ \kappa = \frac{P_o - P_e}{1 - P_e} \]
where
cohen_kappa <- function(x, y) {
stopifnot(length(x) == length(y))
confusion_matrix <- table(x, y)
n <- sum(confusion_matrix)
P_o <- sum(diag(confusion_matrix)) / n
row_marginals <- rowSums(confusion_matrix) / n
col_marginals <- colSums(confusion_matrix) / n
P_e <- sum(row_marginals * col_marginals)
kappa <- (P_o - P_e) / (1 - P_e)
return(list(
kappa = kappa,
observed = P_o,
expected = P_e,
confusion_matrix = confusion_matrix
))
}
Agreement between two doctors on 50 patients.
Doctor 2: Disease | Doctor 2: No Disease | Row Total | |
---|---|---|---|
Doctor 1: Disease | 15 | 5 | 20 |
Doctor 1: No Disease | 10 | 20 | 30 |
Column Total | 25 | 25 | 50 |
Total agreement = 15 + 20 = 35.
\[ P_o = \frac{35}{50} = 0.70 \quad \text{(70% agreement observed)} \]
How much agreement would we expect just by chance, given how often each doctor says “Disease” versus “No Disease”?
Now multiply matching probabilities:
Expected agreement = 0.20 + 0.30 = 0.50 (50%)
Now calculate Cohen’s Kappa manually:
\[ \kappa = \frac{Po - Pe}{1 - Pe} = \frac{0.70 - 0.50}{1 - 0.50} = \frac{0.20}{0.50} = 0.40 \]
Using our function and irr::kappa2()
.
doc1 <- c(rep('D', 15), rep('N', 20), rep('N', 10), rep('D', 5))
doc2 <- c(rep('D', 15), rep('N', 20), rep('D', 10), rep('N', 5))
cohen_kappa(doc1, doc2)$kappa
[1] 0.4
irr::kappa2(data.frame(x = doc1, y = doc2))
Cohen's Kappa for 2 Raters (Weights: unweighted)
Subjects = 50
Raters = 2
Kappa = 0.4
z = 2.89
p-value = 0.00389
Generalises Cohen’s Kappa to more than two raters. Each item is rated by k raters (not necessarily the same raters for every item). Compute the agreement per item, then average across items, correcting for chance.
\[ \kappa = \frac{\bar{P} - \bar{P_e}}{1 - \bar{P_e}} \]
where
Data:
Psychiatric diagnoses of n=30 patients provided by different sets of m=6 raters. Data were used by Fleiss (1971) to illustrate the computation of Kappa for m raters.
data(diagnoses)
dim(diagnoses)
[1] 30 6
Fleiss’ Kappa.
kappam.fleiss(diagnoses)
Fleiss' Kappa for m Raters
Subjects = 30
Raters = 6
Kappa = 0.43
z = 17.7
p-value = 0
Manually calculate.
lapply(diagnoses, \(x) as.integer(sub("\\. .*", "", x))) |>
as.data.frame() |>
as.matrix() -> ratings
# patients
N <- nrow(ratings)
# doctors
n <- ncol(ratings)
cats <- sort(unique(as.numeric(ratings)))
# build item × category counts
counts <- t(apply(ratings, 1, function(row) {
tab <- table(factor(row, levels = cats))
as.integer(tab)
}))
colnames(counts) <- cats
# category proportions across all items
p_j <- colSums(counts) / (N * n)
# agreement per item
P_i <- (rowSums(counts^2) - n) / (n * (n - 1))
# observed and expected agreement
P_bar <- mean(P_i)
P_e <- sum(p_j^2)
fkappa <- (P_bar - P_e) / (1 - P_e)
fkappa
[1] 0.4302445
Since the expected number of agreements is taken into consideration, random guesses should result in a Kappa close to zero.
set.seed(1984)
replicate(
100,
{
a <- rbinom(n = 100, size = 1, prob = 0.5)
b <- rbinom(n = 100, size = 1, prob = 0.5)
irr::kappa2(data.frame(a, b))$value
}
) |>
mean()
[1] 0.003047436
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] irr_0.84.1 lpSolve_5.6.23 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