Documentation request: how to use ezknitr with Shiny and paramaterised R markdown reports #15
Description
I have a parameterised R markdown report which creates some tables and figures after querying a database and fetching data for the genus or species specified by the user.
My YAML header for a file called AlertReport.Rmd looks like this:
---
params:
genus: NA
species: NA
title: "Alert report"
date: "`r format(Sys.time(), '%d %B %Y')`"
output:
orgcharts::html_org:
includes:
in_header: org_logo.html
---
(orgcharts is a local package that produces a HTML template with my organisation's branding on it).
If I run this .Rmd directly from 'knit with parameters' it will output the resultant HTML to the same directory as the .Rmd and will call it AlertReport.html, such that when I choose different species via the parameters, this file will be over-written.
I therefore want to:
a) change the name of the output file to paste0("AlertReport_", params$species, "_", Sys.Date(), ".html");
b) change the directory that the file will be saved in to a completely different network drive;
c) wrap all this in a shiny app which would call ezknitr() to do (a) and (b) above.
First getting ezknitr() to do (a) and (b):
- I can't figure out how to pass multiple elements to
out_suffixas currently it seems just to take one? - - For the specifications above I want the species name that has been provided as a parameter by the user to be included in the output report name, but couldn't figure out how to do this since the current readme/example forezknitrnames the parameter value and deals with each separately and in my case I won't know what the user has entered (there are literally thousands of options so I'm not providing a menu, they will just type in the species as free text). - (b) is straight-forward as presumably I can just supply the full path to
out_dir.
Next putting this in a shiny app:
- I'm presuming this goes in the
contentslot of thedownloadHandler(), but then what do I do with the 'filename' slot so that it doesn't over-write the changes I am making to the file name with theout_suffixargument? - Also the parameters have already been provided as input$genus and input$species, respectively in the ui - how do I pass these to the
paramsargument ofezknit()?
See my (not working) attempt below:
###############################
# Set directories:
library(shiny)
library(here)
library(lubridate)
library(ezknitr)
# Define the path to the .Rmd file:
rmdwd <- here::here()
# Define the path to the root directory to save the report to (dummy example):
repwd <- "//MyNetworkDrive/Myfolder"
# Auto-calculate the reporting week and year:
repdate <- Sys.Date() - weeks(1)
ryear <- year(repdate)
rweek <- isoweek(repdate)
ryw <- paste0(ryear, rweek)
# Create the year/week sub-directory to save the report in:
outwd <- paste(repwd, "/", ryear, "/", ryw, sep = "")
###############################
# Create user interface:
ui = fluidPage(
textInput(inputId = "genus", label = "Pathogen genus", value = "NA", placeholder = "To generate an alert report at the genus level, enter the pathogen genus in this box"),
textInput(inputId = "species", label = "Pathogen species", value = "NA", placeholder = "To generate an alert report at the species level, enter the pathogen genus and species in this box"),
downloadButton("report", "Generate report")
)
###############################
# Create server logic:
server <- function(input, output) {
# Create the output:
output$report = downloadHandler(
# Set up parameters to pass to Rmd document
params = list(genus = input$genus, species = input$species),
# Create the temp file name:
filename = function() {
ifelse(params$genus == "NA",
paste0("AlertReport_", params$species, "_", Sys.Date(), ".html"),
paste0("AlertReport_", params$genus, "_", Sys.Date(), ".html"))
},
# Define the content of the temp file:
content = function(file) {
# Knit the document, defining the destination path and file name:
ezknitr::ezknit(file = "ExceedanceReports.Rmd",
wd = rmdwd,
out_dir = outwd,
fig_dir = "figs",
params = list(genus = "NA", species = "NA"),
keep_md = FALSE,
keep_html = TRUE)
}
)
}
###############################
# Run app:
shinyApp(ui, server)
So in summary:
- getting out_suffix to take a list of things to be appended, and specifically parameters for parameterised R markdown reports would be really handy (feature request unless there is already a way to do this)?
- having some documentation to show how to use ezknit with parameterised reports in combination with Shiny would be a great help.