initial plumbing files

ref #4

.gitignore

@@ -1,10 +1,20 @@
+# bookdown temp files & directories
+#   from https://github.com/rstudio/bookdown/blob/main/inst/examples/.gitignore
+_bookdown_files
+_book
+docs
+redcap-manual-v1.log
+images/dedication.lyx
+redcap-manual-v1.rds
+
+/.quarto/
+
 # History files
 .Rhistory
 .Rapp.history
 
 # Session Data files
 .RData
-.RDataTmp
 
 # User-specific files
 .Ruserdata
@@ -39,11 +49,7 @@ vignettes/*.pdf
 # R Environment Variables
 .Renviron
 
-# pkgdown site
-docs/
-
-# translation temp files
-po/*~
+# R Environment Variables
+*.DS_Store
 
-# RStudio Connect folder
-rsconnect/
+/.luarc.json

.markdownlint.json

@@ -0,0 +1,22 @@
+{
+    "header-style": { "style": "atx" },
+    "MD007": { "indent": 2 },
+    "MD013": { "line_length": 600 },
+    "MD022": {
+        "lines_above": 1,
+        "lines_below": 1
+    },
+    "MD024": { "siblings_only": true },
+    "MD033": {
+        "allowed_elements": [
+            "a",
+            "br",
+            "details",
+            "div",
+            "img",
+            "span",
+            "sub",
+            "sup"
+        ]
+    }
+}

.vscode/settings.json

@@ -0,0 +1,232 @@
+{
+    "cSpell.words": [
+        "adminpr",
+        "AHRQ",
+        "analyte",
+        "annualization",
+        "anonymization",
+        "Anschutz",
+        "Anzalone",
+        "apalike",
+        "biblio",
+        "Bioinformatics",
+        "Bionetworks",
+        "biostatisticians",
+        "bookdown",
+        "booktabs",
+        "bslib",
+        "Cahan",
+        "callout",
+        "CAMC",
+        "CDIS",
+        "Charlson",
+        "CITI",
+        "CNAME",
+        "codeset",
+        "Codesets",
+        "colwidths",
+        "comorbid",
+        "comorbidities",
+        "consortial",
+        "contributorship",
+        "COPD",
+        "covariate",
+        "covariates",
+        "CTSA",
+        "Deacy",
+        "deidentification",
+        "deidentified",
+        "deps",
+        "discoverability",
+        "documentclass",
+        "downlit",
+        "dplyr",
+        "ecmo",
+        "EHDEN",
+        "embeddable",
+        "epub",
+        "Eskenazi",
+        "estimand",
+        "ethnicities",
+        "eval",
+        "explainability",
+        "favicon",
+        "FHIR",
+        "flowsheet",
+        "fullnote",
+        "Gelman",
+        "generalizability",
+        "ghpagescname",
+        "gtsummary",
+        "Hadley",
+        "HCPCS",
+        "heatmaps",
+        "hsrp",
+        "hydroxychloroquine",
+        "ICMJE",
+        "inclusivity",
+        "informatic",
+        "informatician",
+        "informaticians",
+        "informaticist",
+        "informaticists",
+        "JHU's",
+        "kable",
+        "kableExtra",
+        "knitcitations",
+        "knitr",
+        "Kolmogorov-Smirnov",
+        "Kuplicki",
+        "Laraway",
+        "LHBA",
+        "lightbox",
+        "Lise",
+        "Ljazouli",
+        "LOINC",
+        "Loomba",
+        "macrovisit",
+        "Mariam",
+        "MCAR",
+        "McMurry",
+        "meds",
+        "methodologists",
+        "Microvisit",
+        "microvisits",
+        "missingness",
+        "mkdir",
+        "MNAR",
+        "mosio",
+        "natbib",
+        "NCATS",
+        "NCBI",
+        "Nephrology",
+        "NIDDK",
+        "NIGMS",
+        "ocri",
+        "OHDSI",
+        "Olex",
+        "OMOP",
+        "oneils",
+        "operationalizing",
+        "orcid",
+        "OU's",
+        "pagedown",
+        "pandoc",
+        "pango",
+        "PCOR",
+        "pdftools",
+        "pfaff",
+        "PHASTR",
+        "phenotyping",
+        "PPRL",
+        "prepended",
+        "preprocess",
+        "printr",
+        "Raton",
+        "reactable",
+        "referenceable",
+        "reidentification",
+        "remdesivir",
+        "reseachers",
+        "retinopathy",
+        "rmarkdown",
+        "Rscript",
+        "Saad",
+        "SDOH",
+        "setext",
+        "sidky",
+        "SNOMED",
+        "stoudt",
+        "Suver",
+        "svglite",
+        "Synpuf",
+        "Synthea",
+        "telehealth",
+        "templatization",
+        "templatized",
+        "tibble",
+        "tidyverse",
+        "tikz",
+        "tinytex",
+        "trackdown",
+        "unbillable",
+        "Universidad",
+        "Unmutes",
+        "unvalidated",
+        "usethis",
+        "vapply",
+        "Vehtari",
+        "Walonski",
+        "webshot",
+        "Wickham",
+        "workflowr",
+        "Workstream",
+        "workstreams",
+        "xelatex",
+        "Yihui",
+        "Yihui's",
+        "Zenodo",
+        "Zhou"
+    ],
+    "grammarly.selectors": [
+        {
+            "language": "markdown",
+            "scheme": "file",
+            "pattern": "chapters/story.md"
+        },
+        {
+            "language": "markdown",
+            "scheme": "file",
+            "pattern": "chapters/access.md"
+        },
+        {
+            "language": "markdown",
+            "scheme": "file",
+            "pattern": "chapters/advanced.md"
+        },
+        {
+            "language": "markdown",
+            "scheme": "file",
+            "pattern": "chapters/cycle.md"
+        },
+        {
+            "language": "markdown",
+            "scheme": "file",
+            "pattern": "chapters/governance.md"
+        },
+        {
+            "language": "markdown",
+            "scheme": "file",
+            "pattern": "chapters/intro.md"
+        },
+        {
+            "language": "markdown",
+            "scheme": "file",
+            "pattern": "chapters/onboarding.md"
+        },
+        {
+            "language": "markdown",
+            "scheme": "file",
+            "pattern": "chapters/publishing.md"
+        },
+        {
+            "language": "markdown",
+            "scheme": "file",
+            "pattern": "chapters/support.md"
+        },
+        {
+            "language": "markdown",
+            "scheme": "file",
+            "pattern": "chapters/tools.md"
+        },
+        {
+            "language": "markdown",
+            "scheme": "file",
+            "pattern": "chapters/understanding.md"
+        },
+        {
+            "language": "markdown",
+            "scheme": "file"
+        }
+    ]
+}

raise-manual-v1.Rproj

@@ -0,0 +1,20 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: No
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+UseNativePipeOperator: Yes
+
+MarkdownCanonical: No