| output | bibliography |
|---|---|
github_document |
paper/paper.bib |
Internal package for costings
library(CTUCosting)
devtools::load_all()run_costing_app()The app is deployed on CTUs shiny server. The shiny server requires creating a docker container with the app.
The docker/Dockerfile file defines the code to create the docker container.
This needs to be run on an ubuntu system (the server uses version 20.04, so that is a suitable version to use to build the container on.
Set up a virtual machine with it).
In order to make the container, clone this repository, copy the Dockerfile to the directory where you cloned this repository and
create a .Renviron file with the REDCap token containing CTUCosting_token = "xxxxxxxx", where xxxxxxxx is the REDCap token.
The directory should then contain (at least)
+ CTUCosting
| + R
| | + get_data.R
| | + ...
| + inst
| + ...
+ Dockerfile
+ .Renviron
In the ubuntu VM, start a terminal from the above folder, and build the container via sudo docker build -t ctucosting.
Test it via sudo docker run --rm -p 3838:3838 ctucosting and open the app in a guest OS browser by going to localhost:3838.
Create the docker image to be transferred to the shiny server via sudo docker image save ctucosting | gzip > ctucosting-vx.y.z.tar.gz.
Transfer the image to the shiny server via scp ctucosting-vx.y.z.tar.gz [email protected]:/home/shiny
(you need to have a log in to the server for this).
token <- Sys.getenv("CTUCosting_token")
record <- 4
costing <- 1
meta <- get_metadata(token = token)
d <- get_data(record = record, costing = costing, token = token)
info <- costing_info(d, meta$metadata)
wp <- get_workpackage_data(d, meta)
selected_workpackages <- summ_workpackages <- summarize_by_wp(wp)
selected_expenses <- expenses <- d$expenses %>% #names
mutate(wp = sprintf("%05.1f", exp_pf)) %>%
left_join(wp_codes(meta$metadata), by = c(wp = "val")) %>% #names
left_join(redcaptools::singlechoice_opts(meta$metadata) %>% #names()
filter(var == "exp_budget_pos") %>%
select(val, lab) %>%
mutate(val = as.numeric(val)),
by = c(exp_budget_pos = "val")) %>%
mutate(total_cost = exp_units * exp_cost) %>%
relocate(Division = lab, Description = exp_desc, Amount = total_cost, wp_lab)
discount <- calc_discount(selected_workpackages,
initcosting = info$initcosting,
discount_db = info$discount_db)
overhead_tab <- overhead(selected_workpackages)
totals(workpackages = selected_workpackages,
expenses = selected_expenses,
discount = discount,
overhead = overhead_tab,
internal = info$internal,
dlf = TRUE)
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