{ "_id": "6ae941f71e2c7b3a4f5328bd", "Package": "ham", "Title": "Healthcare Analysis Methods", "Version": "1.4.0.9000", "Authors@R": "person(\"Stephen\", \"Zuniga\", , \"rms.shiny@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-1458-3924\"))", "Description": "Conducts analyses for healthcare program evaluations or\nintervention studies. Calculates regression analyses for\nstandard ordinary least squares (OLS or linear) or logistic\nmodels. Performs regression models used for causal modeling\nsuch as differences-in-differences (DID) and interrupted time\nseries (ITS) models. Provides limited interpretations of model\nresults and a ranking of variable importance in models.\nPerforms propensity score models, top-coding of model outcome\nvariables, and can return new data with the newly formed\nvariables. Conducts Bayesian analysis summaries and graphs,\ndecision curve analysis, and produces some Shewhart control\ncharts. Also performs Cronbach's alpha for various scale items\n(e.g., survey questions). See Github URL for examples in the\nREADME file. For more details on the statistical methods, see\nAllen & Yen (1979, ISBN:0-8185-0283-5), Angrist & Pischke\n(2009, ISBN:9780691120355), Cohen (1988, ISBN:0-8058-0283-5),\nGebski (2012) , Gelman &\nGoodrich (2019) , Gelman &\nHill (2007, ISBN:978-0-521-68689-1), Harrell (2015,\nISBN:978-3-319-19424-0), Imbens & Rubin (2015,\nISBN:978-0-521-88588-1), Kline (1999, ISBN:9780415211581),\nKruschke (2014, ISBN:9780124058880), Linden (2015)\n, Merlo (2006)\n, Muthen & Satorra (1995)\n, Pitman (1993, ISBN:978-0-387-97974-8),\nRabe-Hesketh & Skrondal (2008, ISBN:978-1-59718-040-5),\nRosenbaum (2010, ISBN:978-1-4419-1212-1), Ryan (2011,\nISBN:978-0-470-59074-4), and Vickers & Elkin (2006)\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "LazyData": "true", "URL": "https://github.com/szuniga07/ham", "BugReports": "https://github.com/szuniga07/ham/issues", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Repository": "https://szuniga07.r-universe.dev", "Date/Publication": "2026-11-02 20:52:51 UTC", "RemoteUrl": "https://github.com/szuniga07/ham", "RemoteRef": "HEAD", "RemoteSha": "c11131fb949bca66fa3e52a402f15467494d80a5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-03 01:53:47 UTC", "User": "root" }, "Author": "Stephen Zuniga [aut, cre, cph] (ORCID:\n)", "Maintainer": "Stephen Zuniga ", "_user": "szuniga07", "_type": "src", "_file": "ham_1.4.0.9000.tar.gz", "_fileid": "https://r2.ropensci.org/679603d1114114fd82ea229c888f3601ea9fd30fe3dc67d640bb4fec51f13694", "_filesize": 5380593, "_sha256": "679603d1114114fd82ea229c888f3601ea9fd30fe3dc67d640bb4fec51f13694", "_expires": "2027-02-11T02:07:49.000Z", "_created": "2026-11-03T01:53:47.000Z", "_published": "2026-11-03T02:07:51.302Z", "_upstream": "https://github.com/szuniga07/ham", "_status": "success", "_maintainer": { "name": "Stephen Zuniga", "email": "rms.shiny@gmail.com", "orcid": "0000-0003-1458-3924" }, "_jobs": [ { "job": 125676855603, "time": 133, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13198096755" }, { "job": 125676855608, "time": 125, "config": "linux-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13198176550" }, { "job": 125676855587, "time": 96, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "13198108314" }, { "job": 125676855619, "time": 142, "config": "macos-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13198457083" }, { "job": 125675819397, "time": 184, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13198091370" }, { "job": 125676855708, "time": 82, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13197796553" }, { "job": 125676855644, "time": 101, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13197372443" }, { "job": 125676855631, "time": 96, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "13198560653" }, { "job": 125676855645, "time": 98, "config": "windows-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13198545663" } ], "_buildurl": "https://github.com/r-universe/szuniga07/actions/runs/41562373179", "_commit": { "id": "c11131fb949bca66fa3e52a402f15467494d80a5", "author": "szuniga07 ", "committer": "szuniga07 ", "message": "Bayes, interpret, switch risk ratio\n", "time": 1793652771 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "szuniga07", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-49", "n": 1 }, { "week": "2026-02", "n": 1 }, { "week": "2026-03", "n": 1 }, { "week": "2026-04", "n": 3 }, { "week": "2026-05", "n": 8 }, { "week": "2026-06", "n": 7 }, { "week": "2026-07", "n": 5 }, { "week": "2026-08", "n": 30 }, { "week": "2026-09", "n": 16 }, { "week": "2026-10", "n": 19 }, { "week": "2026-11", "n": 12 }, { "week": "2026-12", "n": 8 }, { "week": "2026-23", "n": 2 }, { "week": "2026-24", "n": 4 }, { "week": "2026-25", "n": 11 }, { "week": "2026-26", "n": 22 }, { "week": "2026-27", "n": 10 }, { "week": "2026-28", "n": 12 }, { "week": "2026-33", "n": 1 }, { "week": "2026-34", "n": 1 }, { "week": "2026-36", "n": 1 }, { "week": "2026-37", "n": 6 }, { "week": "2026-38", "n": 5 }, { "week": "2026-39", "n": 1 }, { "week": "2026-40", "n": 12 }, { "week": "2026-41", "n": 13 }, { "week": "2026-43", "n": 2 }, { "week": "2026-44", "n": 10 }, { "week": "2026-45", "n": 1 } ], "_tags": [ { "name": "v1.2.0", "date": "2026-03-19" }, { "name": "v1.3.0", "date": "2026-07-11" }, { "name": "v1.4.0", "date": "2026-10-09" } ], "_stars": 0, "_contributors": [ { "user": "szuniga07", "count": 343, "uuid": 9120301 } ], "_userbio": { "uuid": 9120301, "type": "user", "name": "szuniga07", "followers": 3 }, "_downloads": { "count": 371, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ham" }, "_devurl": "https://github.com/szuniga07/ham", "_searchresults": 17, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ham.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/szuniga07/ham", "_realowner": "szuniga07", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2025-08-28" }, { "version": "1.1.0", "date": "2025-10-28" }, { "version": "1.2.0", "date": "2026-03-20" }, { "version": "1.3.0", "date": "2026-07-11" }, { "version": "1.4.0", "date": "2026-10-10" } ], "_exports": [ "alpha", "assess", "Bayes", "control", "decide", "group", "importance", "interpret", "itsEffect", "review" ], "_datasets": [ { "name": "cas", "title": "Patient survey data", "object": "cas", "class": [ "data.frame" ], "fields": [ "i1", "i2", "i3", "i4", "i5" ], "rows": 100, "table": true, "tojson": true }, { "name": "co2mcmc", "title": "Markov Chain Monte Carlo linear regression estimates of plant's CO2 uptake regressed on ambient carbon dioxide concentrations", "object": "co2mcmc", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "co2multi", "title": "Bayes class object with summarized Markov Chain Monte Carlo estimates of plant's CO2 uptake as a binary variable that is above or below the median level", "object": "co2multi", "class": [ "Bayes", "ham", "list" ], "fields": [], "table": false, "tojson": true }, { "name": "compapt", "title": "VA's completed hospital appointments made in the reporting period ending in December, 2020.", "object": "compapt", "class": [ "data.frame" ], "fields": [ "ID", "State", "Name", "Comp07", "Comp814", "Comp1530", "Comp14", "Comp30", "Total", "aTotal", "Sites" ], "rows": 1245, "table": true, "tojson": true }, { "name": "covshort", "title": "The US Department of Health and Human Services data for state reported hospital's critical staff shortage or not for December 14, 2020.", "object": "covshort", "class": [ "data.frame" ], "fields": [ "state", "shortyes", "shortno", "total", "rate" ], "rows": 54, "table": true, "tojson": true }, { "name": "hosp1", "title": "Patient hospital program/intervention data, intervention group only", "object": "hosp1", "class": [ "data.frame" ], "fields": [ "survey", "los", "cost", "rdm30", "death30", "female", "age", "risk", "month", "program" ], "rows": 335, "table": true, "tojson": true }, { "name": "hosprog", "title": "Patient hospital program/intervention data", "object": "hosprog", "class": [ "data.frame" ], "fields": [ "survey", "los", "cost", "rdm30", "death30", "female", "age", "risk", "month", "program" ], "rows": 720, "table": true, "tojson": true }, { "name": "infections", "title": "Hospital acquired infections (HAI) during 41 months.", "object": "infections", "class": [ "data.frame" ], "fields": [ "Month", "HAI", "PatientDays" ], "rows": 41, "table": true, "tojson": true }, { "name": "losmcmc", "title": "Markov Chain Monte Carlo estimates of hospital length of stay from the hosprog data frame", "object": "losmcmc", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "losvary", "title": "Markov Chain Monte Carlo estimates of the differences-in-differences of mean and variation for the hospital length of stay from the hosprog data frame", "object": "losvary", "class": [ "mcmc.list" ], "fields": [], "table": true, "tojson": false }, { "name": "NHSN", "title": "NHSN standardized incidence ratios for 4 incidents, 2016-2024.", "object": "NHSN", "class": [ "data.frame" ], "fields": [ "Observed", "Predicted", "Incident", "State", "Year", "Yr", "SIR", "Lower", "Upper", "logPredicted" ], "rows": 1800, "table": true, "tojson": true }, { "name": "unemployment", "title": "USA's unemployment rate between 1929 and 2024", "object": "unemployment", "class": [ "data.frame" ], "fields": [ "Year", "rate", "event", "year", "usa" ], "rows": 96, "table": true, "tojson": true } ], "_help": [ { "page": "alpha", "title": "Calculates Cronbach's alpha on scale items", "topics": [ "alpha" ] }, { "page": "assess", "title": "Assess models with regression", "topics": [ "assess" ] }, { "page": "Bayes", "title": "Summarize Bayesian Markov Chain Monte Carlo (MCMC) object", "topics": [ "Bayes" ] }, { "page": "cas", "title": "Patient survey data", "topics": [ "cas" ] }, { "page": "co2mcmc", "title": "Markov Chain Monte Carlo linear regression estimates of plant's CO2 uptake regressed on ambient carbon dioxide concentrations", "topics": [ "co2mcmc" ] }, { "page": "co2multi", "title": "Bayes class object with summarized Markov Chain Monte Carlo estimates of plant's CO2 uptake as a binary variable that is above or below the median level", "topics": [ "co2multi" ] }, { "page": "compapt", "title": "VA's completed hospital appointments made in the reporting period ending in December, 2020.", "topics": [ "compapt" ] }, { "page": "control", "title": "Statistics for Shewhart control charts", "topics": [ "control" ] }, { "page": "covshort", "title": "The US Department of Health and Human Services data for state reported hospital's critical staff shortage or not for December 14, 2020.", "topics": [ "covshort" ] }, { "page": "decide", "title": "Statistics for Decision Curve Analysis and logistic regression model classification", "topics": [ "decide" ] }, { "page": "group", "title": "Group level confidence intervals and between-group variation", "topics": [ "group" ] }, { "page": "hosp1", "title": "Patient hospital program/intervention data, intervention group only", "topics": [ "hosp1" ] }, { "page": "hosprog", "title": "Patient hospital program/intervention data", "topics": [ "hosprog" ] }, { "page": "importance", "title": "Importance of variables based on partial chi-square statistic", "topics": [ "importance" ] }, { "page": "infections", "title": "Hospital acquired infections (HAI) during 41 months.", "topics": [ "infections" ] }, { "page": "interpret", "title": "Interpret model output", "topics": [ "interpret" ] }, { "page": "itsEffect", "title": "Interrupted time series analysis effects", "topics": [ "itsEffect" ] }, { "page": "losmcmc", "title": "Markov Chain Monte Carlo estimates of hospital length of stay from the hosprog data frame", "topics": [ "losmcmc" ] }, { "page": "losvary", "title": "Markov Chain Monte Carlo estimates of the differences-in-differences of mean and variation for the hospital length of stay from the hosprog data frame", "topics": [ "losvary" ] }, { "page": "NHSN", "title": "NHSN standardized incidence ratios for 4 incidents, 2016-2024.", "topics": [ "NHSN" ] }, { "page": "plot.assess", "title": "Prediction plot of treatment and control groups for DID and ITS models and OLS, logistic, Poisson, and Cox models", "topics": [ "plot.assess" ] }, { "page": "plot.Bayes", "title": "Bayesian plots for various analyses", "topics": [ "plot.Bayes" ] }, { "page": "plot.control", "title": "Shewhart control charts", "topics": [ "plot.control" ] }, { "page": "plot.decide", "title": "Decision Curve Analysis plots and regression model classification graphs on sensitivity and specificity", "topics": [ "plot.decide" ] }, { "page": "plot.group", "title": "Confidence interval graphs for group class objects", "topics": [ "plot.group" ] }, { "page": "plot.importance", "title": "Plot of variable importance ranked by partial chi-square statistic", "topics": [ "plot.importance" ] }, { "page": "plot.review", "title": "Plot of a regression model's coefficient review", "topics": [ "plot.review" ] }, { "page": "print.alpha", "title": "Print alpha results", "topics": [ "print.alpha" ] }, { "page": "print.interpret", "title": "Print interpret object", "topics": [ "print.interpret" ] }, { "page": "print.review", "title": "Print Model Review Results", "topics": [ "print.review" ] }, { "page": "review", "title": "Creates a review object of regression model results for graphing purposes", "topics": [ "review" ] }, { "page": "unemployment", "title": "USA's unemployment rate between 1929 and 2024", "topics": [ "unemployment" ] } ], "_pkglogo": "https://github.com/szuniga07/ham/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/szuniga07/ham/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "Bayes.Rmd", "filename": "Bayes.html", "title": "Bayes", "engine": "knitr::rmarkdown", "headings": [ "1. Introduction", "Bayes()", "plot.Bayes()", "2. Diagnostics: 'dxa', 'dxd', 'dxg', 'dxt'", "interpretations", "3. Posterior summary: 'post'", "4a. Posterior Predictive Check: 'check'", "4b. Variation analysis: 'vary'", "4c. Checking the regression trend line: 'check'", "5. Hierarchical or Multilevel Model summary with multilevel/shrinkage plots: 'multi'", "6. Target setting: 'target'", "7. Gelamn's R^2: 'r2'" ], "created": "2026-03-13 05:16:47", "modified": "2026-10-08 00:42:11", "commits": 20 }, { "source": "control.Rmd", "filename": "control.html", "title": "control", "engine": "knitr::rmarkdown", "headings": [ "1. Introduction", "2. $\\bar{X}$ charts", "3. p-chart", "4. u-chart" ], "created": "2026-03-14 04:25:45", "modified": "2026-06-17 20:36:30", "commits": 4 }, { "source": "decide.Rmd", "filename": "decide.html", "title": "decide", "engine": "knitr::rmarkdown", "headings": [ "1. Introduction", "1. Model classification", "2. Decision Curve Analysis: Net Benefit", "3. Decision Curve Analysis (DCA): Interventions Saved" ], "created": "2026-03-14 04:25:45", "modified": "2026-03-19 01:26:40", "commits": 2 }, { "source": "ham-package.Rmd", "filename": "ham-package.html", "title": "ham-package", "engine": "knitr::rmarkdown", "headings": [ "Healthcare Analysis Methods (ham)", "1. Introduction", "2. Descriptive and inferential statistics", "Group level 95% confidence intervals over 12 months (t distribution)", "Rolling 6-month averages by quartiles of age (Q1 - Q4)", "Graph the results", "Between-group variance and within-group clustering", "Graph the confidence interval trend results", "3. Linear and logistic regression", "OLS or linear regression", "ham provides coefficient interpretations with interpret()", "Logistic regression", "Logistic regression interpretations", "Poisson regression", "Poisson regression interpretations", "Cox Proportional Hazards models", "OLS top-coding and propensity scores", "model results", "Inverse Probability of Treatment Weighting using the propensity score (IPW)", "Weighted least squares model results", "importance", "Graph importance", "Graph a summary of the coefficients", "Partial Prediction Plots", "4. Differences-in-Differences", "DID model for length of stay using assess()", "Code to view DID model results", "Code to get the coefficient interpretations", "View a partial prediction plot", "View DID 30-day readmissions results", "5. Interrupted Time Series", "ITS model 1", "View ITS model 1 results", "interpret coefficients", "Graph ITS model 1", "ITS model 2", "View ITS model 2 results", "interpret ITS 2 coefficients", "Graph ITS model 2", "ITS model 3", "Plot the summary coefficients", "View ITS model 3 results", "ITS model 4: 30-day death (mortality)", "View ITS model 4 results", "interpret ITS 4 coefficients", "Graph ITS model 4", "ITS model 5", "Graph ITS model 5 results", "An example of calculating Cronbach's alpha:", "Interpret Cronbach's alpha:", "7. Discussion", "8. References" ], "created": "2025-10-25 23:19:39", "modified": "2026-10-09 22:34:11", "commits": 29 } ], "_score": 5.993876914941211, "_indexed": true, "_nocasepkg": "ham", "_universes": [ "szuniga07" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4.0.9000", "date": "2026-11-03T01:55:45.000Z", "distro": "resolute", "commit": "c11131fb949bca66fa3e52a402f15467494d80a5", "fileid": "https://r2.ropensci.org/2c961a581027e264d8ed76cee652782beb88c3277cd8509d3a6c32a7073155ed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/szuniga07/actions/runs/41562373179" }, { "r": "4.6.2", "os": "linux", "version": "1.4.0.9000", "date": "2026-11-03T01:55:52.000Z", "distro": "resolute", "commit": "c11131fb949bca66fa3e52a402f15467494d80a5", "fileid": "https://r2.ropensci.org/94b3c3c4430da27357ee8f4e29161e84ea0fec0155cb29fe13dcc2b652421fa3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/szuniga07/actions/runs/41562373179" }, { "r": "4.5.3", "os": "mac", "version": "1.4.0.9000", "date": "2026-11-03T02:07:00.000Z", "commit": "c11131fb949bca66fa3e52a402f15467494d80a5", "fileid": "https://r2.ropensci.org/180cea661bd7972a70120e4dc7fb4e4af3ce48b7c48c81963196b1b61a0b447f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/szuniga07/actions/runs/41562373179" }, { "r": "4.6.2", "os": "mac", "version": "1.4.0.9000", "date": "2026-11-03T02:03:28.000Z", "commit": "c11131fb949bca66fa3e52a402f15467494d80a5", "fileid": "https://r2.ropensci.org/7177315e2196448df87a6e6b9acde21548e066bc9d0271ba256aa64a4e25c802", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/szuniga07/actions/runs/41562373179" }, { "r": "4.6.0", "os": "wasm", "version": "1.4.0.9000", "date": "2026-11-03T01:55:44.000Z", "commit": "c11131fb949bca66fa3e52a402f15467494d80a5", "fileid": "https://r2.ropensci.org/084a37ef2131d7cdf9bbc1b10797796d0d7ff0fecff6e4e330781e1a58f0a3ab", "status": "success", "buildurl": "https://github.com/r-universe/szuniga07/actions/runs/41562373179" }, { "r": "4.7.0", "os": "win", "version": "1.4.0.9000", "date": "2026-11-03T01:55:14.000Z", "commit": "c11131fb949bca66fa3e52a402f15467494d80a5", "fileid": "https://r2.ropensci.org/b67e97ba49a94eaf7d5c467da04bd2e8253c26fb3c9104b0c95bc12efce8eabd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/szuniga07/actions/runs/41562373179" }, { "r": "4.5.3", "os": "win", "version": "1.4.0.9000", "date": "2026-11-03T01:55:07.000Z", "commit": "c11131fb949bca66fa3e52a402f15467494d80a5", "fileid": "https://r2.ropensci.org/d8f03a9a7ea75b488aa894a3a85b51be058cf737be5471afe5b8ddcd78895dbf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/szuniga07/actions/runs/41562373179" }, { "r": "4.6.2", "os": "win", "version": "1.4.0.9000", "date": "2026-11-03T01:55:16.000Z", "commit": "c11131fb949bca66fa3e52a402f15467494d80a5", "fileid": "https://r2.ropensci.org/309e26ad244a3c4784aa2f25105f20f10bccd56d55425bb782cfbb3faab6b898", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/szuniga07/actions/runs/41562373179" } ] }