Michael Chirico MichaelChirico
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| # This script creates two dummy packages to prove that the binary search evaluation | |
| # correctly identifies packages that fail when digits.rank is set too low. | |
| # -- Create dummy3 -- | |
| # This package expects wilcox.test(c(1.11, 2.22), c(1.14, 2.25))$statistic to be exactly 1. | |
| # This assertion fails at digits.rank=1 and 2, but passes at digits.rank >= 3. | |
| dir.create("dummy3/R", recursive = TRUE, showWarnings = FALSE) | |
| dir.create("dummy3/tests/testthat", recursive = TRUE, showWarnings = FALSE) | |
| writeLines(c( |
MichaelChirico
/ cran_wilcox_rank.R
Last active
May 10, 2026 20:50
Search CRAN packages for senstivity to wilcox.test(digits.rank=X)
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| # Assume these are installed in a state to pass R CMD check, i.e., | |
| # with enough Suggests to pass with _R_CHECK_FORCE_SUGGESTS_=false | |
| packages <- c("cardx", "caTools", "clintools", "cogmapr", "CRMetrics", "EasyDescribe", | |
| "effectsize", "EnvStats", "eyetrackingR", "ggpubr", "ggpval", "ggsignif", | |
| "gtsummary", "iCellR", "iDOS", "jsmodule", "LGDtoolkit", "microeco", | |
| "mnda", "mt", "PairedData", "pairwiseCI", "papeR", "pctax", "pcutils", | |
| "PLEXI", "plotbb", "plotthis", "PopComm", "qPCRtools", "RadOnc", | |
| "rattle", "rbiom", "Rcmdr", "RcmdrPlugin.MPAStats", "rcompanion", | |
| "rempsyc", "ReporterScore", "SCpubr", "sigminer", "tinyarray", | |
| "TOSTER", "UCSCXenaShiny", "voiceR", "volcano3D") |
MichaelChirico
/ units_udunits_no_exceptions_crash.sh
Created
December 16, 2025 20:19
units crashes if udunits compiled with -fno-exceptions
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| #!/bin/bash | |
| set -e # Exit immediately if a command exits with a non-zero status. | |
| # --- 1. Environment Setup --- | |
| echo ">>> Installing System Dependencies..." | |
| sudo apt-get update -qq | |
| # Dependencies: | |
| # - flex/bison: for udunits parser compilation | |
| # - texinfo: for udunits documentation | |
| # - libexpat1-dev: for udunits XML parsing |
MichaelChirico
/ methods_load_unload.R
Last active
November 16, 2025 02:48
Check load/unload loop for methods downstreams
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| cran_repo = "https://cloud.r-project.org" | |
| bioc_repo = BiocManager::repositories()["BioCsoft"] | |
| cran_db <- data.frame(available.packages(repos = cran_repo)) | |
| bioc_db <- data.frame(available.packages(repos = bioc_repo)) | |
| methods_importers <- function(db, skip) db |> | |
| subset( | |
| grepl("(^|[^\\w.])methods($|[^\\w.])", Imports, perl=TRUE), | |
| "Package", |
MichaelChirico
/ methods_load_unload.R
Created
November 7, 2025 15:38
{methods} load+unload loop test
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| db <- data.frame(available.packages()) | |
| methods_imports <- db |> | |
| subset(grepl("(^|[^\\w.])methods($|[^\\w.])", Imports, perl=TRUE), "Package", drop=TRUE) | |
| test_lib = '/media/WesternDigital3839/tmpCRAN' | |
| # very slow, and requires some iteration to get SystemRequirements | |
| install.packages(methods_imports, lib=test_lib) |
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| library(rvest) | |
| library(xml2) | |
| PFR_URL = 'https://www.pro-football-reference.com' | |
| read_with_backoff = function(url, sleep = 0.1) { | |
| tryCatch(read_html(url), error = function(.) { | |
| Sys.sleep(sleep) | |
| sleep = 2 * sleep | |
| message(sprintf("Failed, retrying in %.2fs", sleep)) |
MichaelChirico
/ svn-range-finder.sh
Last active
September 30, 2025 20:36
Find range of SVN commits where a file matches a pattern
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| #!/bin/bash | |
| # GENERATED BY GEMINI | |
| # Configuration Variables | |
| # The path to the file in the SVN repository | |
| FILE_PATH="src/library/parallel/NAMESPACE" | |
| # The pattern you are searching for (case-sensitive) | |
| SEARCH_PATTERN="splitList" | |
| # --- Script Logic --- |
MichaelChirico
/ github_pr_file_metadata.R
Last active
July 2, 2025 16:44
Scrape GitHub PRs in a repo to see which files they touch
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| # INITIALLY GENERATED BY GEMINI | |
| # PR File Scraper | |
| # | |
| # Description: | |
| # This script inspects a local Git repository, identifies its GitHub remote, | |
| # and fetches all open pull requests. It then compiles a data.frame | |
| # where each row represents a file modified in a specific pull request, | |
| # along with metadata about that PR. | |
| # |
MichaelChirico
/ rcv_bootstrap.R
Created
June 6, 2025 14:19
Code for running bootstraps of ranked-choice voting elections
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| library(data.table) | |
| library(ggplot2) | |
| # Downloaded from https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/AMK8PJ | |
| dir="/media/michael/ab3f2700-872c-4b29-95f2-9a700166bc52/dataverse_files" | |
| run_rcv_election = function(ballots) { | |
| # TODO(michaelchirico): there should be a way to safely avoid a full copy, is it worth it? | |
| ballots = copy(ballots[, .(rank, candidate)]) | |
| # _don't_ rely on ballots$voterid from input -- in bootstrap, under resampling, we will have |
MichaelChirico
/ rbind.fill_vs_bind_rows.R
Last active
June 3, 2025 23:21
Comparing plyr::rbind.fill and dplyr::bind_rows()
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| # quick look sheet for comparing plyr::rbind.fill --> dplyr::bind_rows() | |
| # NB: I am only interested in migrating rbind.fill-->bind_rows(), so | |
| # features of bind_rows() absent from rbind.fill(), e.g. .id=, are not examined. | |
| rbind.fill = plyr::rbind.fill | |
| bind_rows = dplyr::bind_rows | |
| DF1 = data.frame(a = 1, b = 2) | |
| DF2 = data.frame(a = 1, b = 2) | |
| all.equal(rbind.fill(DF1, DF2), bind_rows(DF1, DF2)) |
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