Update README.md

README.md

@@ -1,35 +1,55 @@
+# DARt
+[![DOI](https://zenodo.org/badge/306890959.svg)](https://zenodo.org/badge/latestdoi/306890959)
+[![GitHub license](https://img.shields.io/github/license/Naereen/StrapDown.js.svg)](https://github.com/Kerr93/DARt/blob/master/LICENSE)
+![Safe](https://img.shields.io/badge/Stay-Safe-red?logo=data:image/svg%2bxml;base64,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)
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-### A tool to estimate Instantaneous Reproduction Number(Rt) 
-cal_r()provide real-time estimation of time-varying distribution of 
-Rt and infected numbers from a range of epidemic observations (e.g., number of onsets and confirmed cases).
-
-test DARtTool via https://dsi-dart.shinyapps.io/covidrt/.
+**DARt: Estimate Real-time Infection and the Time-varying Epidemiological Parameter R<sub>t**
 
+Online platform: https://dsi-dart.shinyapps.io/covidrt/.
 
 ## Installation
 ```{r, eval = FALSE}
 pip install DARtTool
 ```
-## Usage
-dart = DARt(GT,D_s,Filename)
+
+## Quick Start
+`DARtTool` is designed to be used with simple function calls, the core
+functions of `DARtTool`are `DARt()` and `car_r()`. In the following section we give an overview of the simple use case for`DARt()`and`cal_r()`.
 
-cal_r()
+`DARt()` and `cal_r()` are the two single-call functions can be used on its own to infer the underlying infection case curve from reported cases and estimate Rt.
 
-## Arguments
-GT: generation time distribution
+Firstly we need to define a DARt class, and initialize with three parameters: gt (generation time), ds(report of incubation delay) and an inputfile in csv format.
 
-D_s: delay time distribution
+```
+import DARtTool
+dart = DARtTool.DARt(filename='./inputfile.csv')
+```
 
-Filename:input file
+The function cal_r() represents the core functionality of the package aiming to:
 
-## References:
-This tool is described in the following paper:
+1. infer the underlying infection case curve from observations and estimate Rt.
+2. provides visualisations of results.
 
-## Examples
+```
+dart.cal_r()
+```
+
+Estimating the underlying infection cases and Rt curve via smoothing is substantially computationally demanding than using filter but can provide reliable estimate.
+
+## Citation
+If you use this tool in your research, please cite our paper.
+```bibtex
+@misc{yang2020revealing,
+      title={Revealing the Transmission Dynamics of COVID-19: A Bayesian Framework for $R_t$ Estimation}, 
+      author={Xian Yang and Shuo Wang and Yuting Xing and Ling Li and Richard Yi Da Xu and Karl J. Friston and Yike Guo},
+      year={2020},
+      eprint={2101.01532},
+      archivePrefix={arXiv},
+      primaryClass={stat.AP}
+}
+```
 
-    GT = [0, 0, 0.165720874545241, 0.226350757019051, 0.245007574714227, 0.213515210247327,
-          0.149405583474155]  # 1:7; non-zero index 3:7
-    D_s = [0, 0, 0, 0, 0, 0, 0.0996906, 0.1130266, 0.1143032, 0.1069238, 0.0937167999999999]
-    dart = DARt(GT=GT, D_s=D_s, filename='uk_report_1011.csv')
-    dart.cal_r()
+## License
+This source code is licensed under the [MIT](https://github.com/Kerr93/DARt/blob/master/LICENSE) license.