early version of Rmd

ref #5

for-developers/sandbox/report-1.Rmd

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+---
+title: REDCapR Validator Example 1     # Change this value for new validators.
+date: "Date: `r Sys.time()`"
+output:
+  html_document:
+    keep_md: yes
+    toc: yes
+    toc_float: true
+    number_sections: true
+    # css: ../analysis/common/styles-1.css
+---
+
+
+<!--  Set the working directory to the repository's base directory; this assumes the report is nested inside of three directories.-->
+```{r, echo=F, message=F}
+# cat("Working directory: ", getwd())
+library(knitr)
+# Change this value for new validators.
+# opts_knit$set(root.dir='../')  #Don't combine this call with any other chunk -especially one that uses file paths.
+```
+
+<!-- Set the report-wide options, and point to the external code file. -->
+```{r set-options, echo=F}
+# cat("Working directory: ", getwd())
+report_render_start_time <- Sys.time()
+opts_chunk$set(
+  results    = 'show',
+  warning    = FALSE,
+  comment    = NA,
+  tidy       = FALSE,
+  fig.width  = 6.5,
+  fig.height = 4,
+  fig.path   = 'figure-png/'
+)
+# dpi = 400,
+# out.width = "650px", #This affects only the markdown, not the underlying png file.  The height will be scaled appropriately.
+
+echo_chunks <- FALSE
+options(width=100) #So the output is 25% wider than the default.
+
+# Change this value for new validators.
+# read_chunk("./analysis/validator-1.R") #This allows knitr to call chunks tagged in the underlying *.R file.
+```
+
+<!-- Load 'sourced' R files.  Suppress the output when loading packages. -->
+```{r load-packages, echo=echo_chunks, message=FALSE, warning=FALSE}
+requireNamespace("dplyr")
+requireNamespace("DT")
+```
+
+<!-- Load any global functions and variables declared in the R file.  Suppress the output. -->
+```{r declare-globals, echo=echo_chunks, results='show', message=FALSE}
+```
+
+<!-- Declare any global functions specific to a Rmd output.  Suppress the output. -->
+```{r, echo=echo_chunks, message=FALSE}
+  #Put presentation-specific code in here.  It doesn't call a chunk in the codebehind file.
+```
+
+<!-- Load the datasets.   -->
+```{r load-data, echo=echo_chunks, results='show', message=FALSE}
+```
+
+<!-- Tweak the datasets.   -->
+```{r tweak-data, echo=echo_chunks, results='show', message=TRUE}
+```
+
+```{r groom-rules, echo=echo_chunks, results='show', message=TRUE}
+```
+
+```{r groom-smells, echo=echo_chunks, results='show', message=TRUE}
+```
+
+Set Up {.tabset .tabset-fade}
+=============================
+
+Instructions
+-----------------------------
+
+1. Work through each line in the table to discover & correct entry mistakes in the database.  Be aware that a single mistake may manifest in multiple rows; fixing one value may clear several rows.
+1. Click the `record id` value in a row to be taken to the participant's Event Grid in REDCap (*i.e.*, the 'stop light page').
+1. Double-check that your manual corrections in REDCap are reflected in `r checks$path_output_rule`.  Be careful not to move this file to somewhere unsafe.
+1. To help discover the dataflow and problematic location, use the
+    * project's [codebook](`r checks$redcap_codebook`) in REDCap,
+    * [validator-1-arch](`r checks$github_link_arch`) file, and
+    * [validator-1](`r checks$github_link_report`) report.
+1. If you create a new rule or smell check, make sure the error message won't reveal any PHI.
+
+Execute Rules
+-----------------------------
+```{r execute-rules, echo=echo_chunks, message=TRUE, results='asis'}
+```
+
+Execute Smells
+-----------------------------
+```{r execute-smells, echo=echo_chunks, message=TRUE, results='asis'}
+```
+
+Inactive Rules
+-----------------------------
+
+`r nrow(ds_rule_inactive)` rules are defined, but disabled for this report:
+
+```{r  echo=echo_chunks, results='asis'}
+# glue::collapse(paste0("1. ", ds_rule_inactive$check_name), sep="; \n", last=", and \n")
+ds_rule_inactive |>
+  glue::glue_data("1. {check_name};")
+```
+
+Inactive Smells
+-----------------------------
+
+`r nrow(ds_smell_inactive)` smells are defined, but disabled for this report:
+
+```{r  echo=echo_chunks, results='asis'}
+ds_smell_inactive |>
+  glue::glue_data("1. {check_name};")
+# if( nrow(ds_smell_inactive) == 0L ) {
+#   cat("* *no smells are disabled*.")
+# } else {
+#   glue::collapse(paste0("1. ", ds_smell_inactive$smell_name), sep="; \n", last=", and \n")
+# }
+```
+
+Rules {.tabset .tabset-fade}
+=============================
+
+A *rule* is very exact.  Each record is examined, and determined if it passes each specific rule.
+
+Rule Detail
+-----------------------------
+```{r table-rule-detail, echo=echo_chunks, message=TRUE}
+```
+
+Rule Summary
+-----------------------------
+```{r table-rule-summary, echo=echo_chunks, message=TRUE}
+```
+
+Smells {.tabset .tabset-fade}
+=============================
+
+A *smell* test won't validate a given record (like the rules above), but it will make sure the dataset overall smells correct.
+
+Smell Summary
+-----------------------------
+```{r table-smell-summary, echo=echo_chunks, message=TRUE}
+```
+
+Termination {.tabset .tabset-fade}
+=============================
+
+### Save To Disk
+
+```{r verify-values, echo=echo_chunks, message=TRUE}
+```
+
+```{r specify-columns-to-upload, echo=echo_chunks, message=TRUE}
+```
+
+```{r save-to-disk, echo=echo_chunks, message=TRUE}
+```
+
+
+<!-- The footer that's common to all reports. -->
+<!--  ```{r, child = "analysis/common/footer-1.Rmd"}``` -->