README.md

In resplab/accept: The Acute COPD Exacerbation Prediction Tool (ACCEPT)

accept

R package for the ACute COPD Exacerbation Prediction Tool (ACCEPT)

ACCEPT is a prediction model for predicting probability, rate, and severity of exacerbations (also known as lung attacks) in patients with Chronic Obstructive Pulmonary Disease.

ACCEPT has been developed by researchers at the University of British Columbia. 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')

You can install the development version of accept from GitHub with:

# install.packages("pak")
pak::pak("resplab/accept")

Usage

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.

Example

Exacerbation Prediction

To get a prediction for exacerbation rate, you will need to pass in a patient vector. The accept package comes with a sample patient data tibble called samplePatients:

library(accept)
accept(samplePatients) #accept uses the latest updated prediction model
#>   predicted_exac_probability predicted_exac_rate
#> 1                  0.8327888           1.7884977
#> 2                  0.4366622           0.5738758
#>   predicted_severe_exac_probability predicted_severe_exac_rate
#> 1                         0.6026383                  0.9229084
#> 2                         0.1085515                  0.1149076

accept2() and accept1() functions return a more detailed dataframe with the predictions for different treatment options with measures of uncertainty.

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.

results <- accept2(samplePatients[1,])

plotExacerbations(results, type="probability")

plotExacerbations(results, type="rate")

Probability of N Exacerbations (Poisson)

You can also calculate the predicted number of exacerbations in a year:

results <- accept2(samplePatients[1,]) 
exacerbationsMatrix <- predictCountProb(results, n = 10, shortened = TRUE)
print(exacerbationsMatrix)
#>                         none severe   1 severe   2 severe 3 or more severe
#> no exacerbations         0.16721119 0.00000000 0.00000000       0.00000000
#> 1 exacerbation           0.11883372 0.18022310 0.00000000       0.00000000
#> 2 exacerbations          0.04222640 0.12808103 0.09712378       0.00000000
#> 3 or more exacerbations  0.01206628 0.05851757 0.10055944       0.07102149

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(results, n = 10, shortened = FALSE)
print(exacerbationsMatrix)
#>                       0 severe     1 severe     2 severe     3 severe
#> 0 exacerbation(s) 1.672112e-01 0.000000e+00 0.000000e+00 0.000000e+00
#> 1 exacerbation(s) 1.188337e-01 1.802231e-01 0.000000e+00 0.000000e+00
#> 2 exacerbation(s) 4.222640e-02 1.280810e-01 9.712378e-02 0.000000e+00
#> 3 exacerbation(s) 1.000316e-02 4.551234e-02 6.902397e-02 3.489389e-02
#> 4 exacerbation(s) 1.777262e-03 1.078158e-02 2.452699e-02 2.479841e-02
#> 5 exacerbation(s) 2.526131e-04 1.915564e-03 5.810285e-03 8.811872e-03
#> 6 exacerbation(s) 2.992120e-05 2.722708e-04 1.032314e-03 2.087475e-03
#> 7 exacerbation(s) 3.037773e-06 3.224959e-05 1.467291e-04 3.708819e-04
#> 8 exacerbation(s) 2.698608e-07 3.274164e-06 1.737958e-05 5.271571e-05
#> 9 exacerbation(s) 2.130942e-08 2.908606e-07 1.764475e-06 6.244004e-06
#>                       4 severe     5 severe     6 severe     7 severe
#> 0 exacerbation(s) 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> 1 exacerbation(s) 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> 2 exacerbation(s) 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> 3 exacerbation(s) 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> 4 exacerbation(s) 9.402310e-03 0.000000e+00 0.000000e+00 0.000000e+00
#> 5 exacerbation(s) 6.682038e-03 2.026794e-03 0.000000e+00 0.000000e+00
#> 6 exacerbation(s) 2.374397e-03 1.440403e-03 3.640856e-04 0.000000e+00
#> 7 exacerbation(s) 5.624791e-04 5.118332e-04 2.587485e-04 5.605968e-05
#> 8 exacerbation(s) 9.993573e-05 1.212499e-04 9.194377e-05 3.984052e-05
#> 9 exacerbation(s) 1.420447e-05 2.154249e-05 2.178088e-05 1.415694e-05
#>                       8 severe     9 severe
#> 0 exacerbation(s) 0.000000e+00 0.000000e+00
#> 1 exacerbation(s) 0.000000e+00 0.000000e+00
#> 2 exacerbation(s) 0.000000e+00 0.000000e+00
#> 3 exacerbation(s) 0.000000e+00 0.000000e+00
#> 4 exacerbation(s) 0.000000e+00 0.000000e+00
#> 5 exacerbation(s) 0.000000e+00 0.000000e+00
#> 6 exacerbation(s) 0.000000e+00 0.000000e+00
#> 7 exacerbation(s) 0.000000e+00 0.000000e+00
#> 8 exacerbation(s) 7.552761e-06 0.000000e+00
#> 9 exacerbation(s) 5.367600e-06 9.044996e-07

To visualize the matrix as a heatmap, we can use the function plotHeatMap:

plotHeatMap(results, shortened = FALSE)

Web App for ACCEPT

ACCEPT is also available as web app, accessible at http://resp.core.ubc.ca/ipress/accept

API using vetiver and plumber

You can use vetiver and plumber packages to create, deploy, and monitor an API for ACCEPT:

library(vetiver)
v_accept <- vetiver_model(accept, 
                   "accept-model")

To test to API locally, you can use

library(plumber)
pr() |> 
    vetiver_api(v_accept) |>
  pr_run()

Cloud-based API Access through Peer Models Network

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/run

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

resplab/accept documentation built on July 5, 2023, 2:25 p.m.