stopadforms

stopadforms is an R package and Shiny application to allow reviewers to view and score submissions to the STOP-AD Compound Submission Portal.

The application is hosted at https://shinypro.synapse.org/users/kwoo/stopadforms/. To use it, you must be a member of the STOP-AD_Reviewers Synapse team and be logged in to Synapse. To save reviews, you must be a Certified User on Synapse.

Installation

devtools::install_github("Sage-Bionetworks/stopadforms")

Calculating scores for a submission

Below is an example of how to calculate scores for a submission outside of the Shiny app (i.e. in an R script). This example uses sample data included in the package.

library("stopadforms")

## Create a list with the form data id as the name, and the path to the included
## JSON file as the value
sample_sub <- list(
  "242" = system.file("extdata", "testdata.json", package = "stopadforms")
)

## Load the JSON data and convert to a data frame
dat <- process_submissions(sample_sub, lookup_table = lookup_table)

## Append clinical multiplier used in calculations
submission <- append_clinical_to_submission(dat)

## Load weighted scores. The contents of this file correspond to the output of
## the `pull_reviews_table()` function.
scores <- read.csv(
  system.file("extdata", "weighted_scores.csv", package = "stopadforms"),
  stringsAsFactors = FALSE
)

## Calculate overall score
calculate_submission_score(submission, scores)
#> [1] 0.2631988

See vignette("scoring", package = "stopadforms") for a detailed description of the scoring process and an example of how to score real submissions that are stored in Synapse.

Running the application locally

library("stopadforms")
run_app()

Scores entered while running the application locally will persist on Synapse.

See vignette("deploying-stopadforms", package = "stopadforms") for information on how we deploy the app on the Sage Bionetworks Shiny Pro server.

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Please note that the stopadforms project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.