accept
R package for the ACute COPD Exacerbation Prediction Tool (ACCEPT)
The function accept() provides predictions from the latest version of the accept prediction model. accept1() provides predictions of exacerbations for COPD patients per original published manuscript. accept2() is an updated version of ACCEPT that is fine tuned for improved predictions in patients who do not have a prior history of exacerbations. Please refer to the published papers for more information:
Adibi A, Sin DD, Safari A, Jonhson KM, Aaron SD, FitzGerald JM, Sadatsafavi M. The Acute COPD Exacerbation Prediction Tool (ACCEPT): a modelling study. The Lancet Respiratory Medicine, 8(10), pp.1013-1021; doi:10.1016/S2213-2600(19)30397-2
Safari, A., Adibi, A., Sin, D.D., Lee, T.Y., Ho, J.K., Sadatsafavi, M. and IMPACT study team, 2022. ACCEPT 2· 0: Recalibrating and externally validating the Acute COPD exacerbation prediction tool (ACCEPT). EClinicalMedicine, 51, p.101574. doi:10.1016/j.eclinm.2022.101574
The following animation explains the accept model in 90 seconds:
Installation
The latest stable version can be downloaded from CRAN:install.packages ('accept')
Alternatively, you can download the latest development version from GitHub:
install.packages("remotes")
remotes::install_github("resplab/accept")Web App for ACCEPT
ACCEPT is also available as web app, accessible at http://resp.core.ubc.ca/ipress/accept
ACCEPT in R
Sample Data
To get started, there is an R data frame with the package of sample patient data. I have printed columns 1-13 and 14-19 separately because there isn't enough space:
library(accept)
samplePatients <- accept::samplePatients
Exacerbation Prediction
To get a prediction for exacerbation rate, you will need to pass in a patient vector:
results <- accept(samplePatients[1,]) #accept uses the latest updated prediction model
print(t(results))The accept() function returns a data frame with the patient data used for prediction, along with the predictions for different treatment options.
To visualize the data, there is a graphing function called plotExacerbations(), which creates a Plotly bar graph. You have the option of selecting probability or rate for which prediction you want to see, and either CI or PI to select the confidence interval or prediction interval respectively.
plotExacerbations(results, type="probability", interval = "CI")plotExacerbations(results, type="probability", interval = "PI")plotExacerbations(results, type="rate", interval = "CI")Probability of N Exacerbations (Poisson)
We can also calculate the predicted number of exacerbations in a year:
patientResults = accept1(samplePatients[1,]) #accept uses the original prediction model
exacerbationsMatrix = predictCountProb(patientResults, n = 10, shortened = TRUE)
print(exacerbationsMatrix)The shortened parameter groups the probabilities from 3-10 exacerbations into one category, "3 or more exacerbations." To see all n exacerbation probabilities:
exacerbationsMatrix = predictCountProb(patientResults, n = 10, shortened = FALSE)
print(exacerbationsMatrix)To visualize the matrix as a heatmap, we can use the function plotHeatMap:
plotHeatMap(patientResults, shortened = FALSE)Cloud-based API Access
The Peer Models Network allows users to access ACCEPT through the cloud. A MACRO-enabled Excel-file can be used to interact with the model and see the results. To download the PRISM Excel template file for ACCEPT, please refer to the Peer Models Network model repository.
Python
import json
import requests
url = 'https://prism.peermodelsnetwork.com/route/accept/run'
headers = {'x-prism-auth-user': YOUR_API_KEY}
model_run = requests.post(url, headers=headers,
json = {"func":["prism_model_run"],"model_input":[{"ID": "10001","male": 1,"age": 57,"smoker": 0,"oxygen": 0,"statin": 0,"LAMA": 1,"LABA": 1,"ICS": 1,"FEV1": 51,"BMI": 18,"SGRQ": 63,"LastYrExacCount": 2,"LastYrSevExacCount": 1,"randomized_azithromycin": 0,"randomized_statin": 0,"randomized_LAMA": 0,"randomized_LABA": 0,"randomized_ICS": 0, "random_sampling_N" : 100, "calculate_CIs" : "TRUE"}]})
print(model_run)
results = json.loads(model_run.text)
print(results)Linux Bash
In Ubuntu, you can call the API with curl:
curl \
-X POST \
-H "x-prism-auth-user: REPLACE_WITH_API_KEY" \
-H "Content-Type: application/json" \
-d '{"func":["prism_model_run"],"model_input":[{"ID": "10001","male": 1,"age": 57,"smoker": 0,"oxygen": 0,"statin": 0,"LAMA": 1,"LABA": 1,"ICS": 1,"FEV1": 51,"BMI": 18,"SGRQ": 63,"LastYrExacCount": 2,"LastYrSevExacCount": 1,"randomized_azithromycin": 0,"randomized_statin": 0,"randomized_LAMA": 0,"randomized_LABA": 0,"randomized_ICS": 0, "random_sampling_N" : 100,
"calculate_CIs" : "TRUE"}]}' \
https://prism.peermodelsnetwork.com/route/accept/runUser Manual
An interactive user manual that describes the study, the web app, the API, and the R package is available here.
Citation
Please cite:
Adibi A, Sin DD, Safari A, Jonhson KM, Aaron SD, FitzGerald JM, Sadatsafavi M. The Acute COPD Exacerbation Prediction Tool (ACCEPT): a modelling study. The Lancet Respiratory Medicine. Published Online First 2020 March 13th; doi:10.1016/S2213-2600(19)30397-2
Safari, A., Adibi, A., Sin, D.D., Lee, T.Y., Ho, J.K., Sadatsafavi, M. and IMPACT study team, 2022. ACCEPT 2· 0: Recalibrating and externally validating the Acute COPD exacerbation prediction tool (ACCEPT). EClinicalMedicine, 51, p.101574. doi:10.1016/j.eclinm.2022.101574