SPMCIIP

SPMCIIP: Severity Prediction Model for COVID-19 by Immune-inflammatory Parameters (https://spmciip.deepomics.org/)

Pre-requirements

• R3.6
• caret
• e1071
• gbm
• randomForest

Installation

Installation from Github

To clone the repository and install manually, run the following from a terminal:

git clone https://github.com/paprikachan/SPMCIIP.git
cd SPMCIIP

Usage

Help page

In command line:

Usage: predict_SPMCIIP.R [options]

Options:
        -i CHARACTER, --infile=CHARACTER
                Path of X input file

        -o CHARACTER, --outfile=CHARACTER
                Path of Y output file

        -h, --help
                Show this help message and exit

Quick start

The following code runs an example of SPMCIIP.

predict_SPMCIIP.R -i test_X.csv -o pred_y.csv

File format

Input file

Input file is a csv file, stores the measurements of six immune-inflammatory markers for each patient:

• Th/Ts
• T+B+NK count (per μl)
• IL-2R (U/mL)
• IL-6 (pg/mL)
• CRP (mg/L)
• PCT (ng/mL）

Note: Th/Ts,CD4+/CD8+. T+B+NK,CD3+CD19-;CD3-CD19+;CD3-CD16+CD56+. IL-2R, interleukin 2R. IL-6, interleukin 6. CRP, C reactive protein. PCT,Procalcitonin.

Output file

Out file is a csv file, stores the predicted results from CIRPMC:

• LR: The predicted critical illness probablity from logistic regression
• SVM: The predicted critical illness probablity from supported vector machine
• GBDT: The predicted critical illness probablity from gradient boosted decision tree
• KNN: The predicted critical illness probablity from k-nearest neighbor
• NN: The predicted critical illness probablity from neural network
• Probability: The predicted critical illness probablity from our ensemble model SPMCIIP
• Cluster: The predicted critical illness status, 0 or 1.
• Risk group: The stratified risk group, Non-critical or Critical.

Cite us

Help

If you have any questions or require assistance using SPMCIIP, please open an issue.