Merge branch 'master' into vimc-4912_calculate_impact

Author: r-ash

.Rbuildignore

@@ -7,3 +7,4 @@
 ^\.Rproj\.user$
 ^TODO.md$
 ^.github$
+^vignettes_src$

.gitignore

@@ -4,3 +4,5 @@ docs
 .Rhistory
 .DS_Store
 .idea
+vignettes_src/*.md
+vignettes_src/*.html

DESCRIPTION

@@ -23,6 +23,7 @@ Imports:
     vaultr
 Suggests:
     ggplot2,
+    htmltools,
     knitr,
     mockery,
     testthat,

Makefile

@@ -36,4 +36,12 @@ pkgdown:
 website: pkgdown
 	./scripts/update_web.sh
 
+vignettes/internal-impact.Rmd: vignettes_src/internal-impact.Rmd
+	./scripts/build_impact_vignette
+
+vignettes: vignettes/using-vimpact.Rmd vignettes/vignette.Rmd
+	${RSCRIPT} -e 'tools::buildVignettes(dir = ".")'
+	mkdir -p inst/doc
+	cp vignettes/*.html vignettes/*.Rmd inst/doc
+
 .PHONY: all test document install vignettes

man/calculate_impact.Rd

@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+# We can't run the internal-impact vignette on a computer that doesn't
+# have access to montagu DB (including CI) so we pre-compile it
+# ocassinally here. The version in vignettes_src should be edited,
+# then this script run to create the version in vignettes
+(cd vignettes_src && Rscript -e 'knitr::knit("internal-impact.Rmd")')
+header="DO NOT EDIT THIS FILE - see vignettes_src and make changes there"
+widget=' \
+```{r} \
+htmltools::tags$iframe( \
+  src = "impact_comparisons.html", \
+  width = "100%", \
+  height = "400", \
+  scrolling = "no", \
+  seamless = "seamless", \
+  frameBorder = "0", \
+  `data-external` = "1" \
+)\
+```'
+sed -s 's/[[:space:]]*$//' vignettes_src/internal-impact.md |
+    sed 's/\r//g' |
+    sed "s/HEADER/$header/" |
+    sed "s/<!-- WIDGET -->/$widget/" > vignettes/internal-impact.Rmd
+cp vignettes_src/impact_comparisons.html vignettes/impact_comparisons.html

man/get_burden_estimate_set_ids.Rd

@@ -1,2 +1,3 @@
 *.html
+!impact_comparisons.html
 *.R