psotob91 / kfre-ckd-reba-peru

Kidney Failure Prediction: Multicenter External Validation of the KFRE Model in Patients with CKD Stages 3-4 in Peru

R code repository to reproduce the result of the manuscript Kidney Failure Prediction: Multicenter External Validation of the KFRE Model in Patients with CKD Stages 3-4 in Peru (in review).

Journal version of the manuscript is not available yet because the mansucript is in review.
A preprint version of the manuscript is here.

The repository contains the following code:

• Code/: Folder with reproducible code for the analysis

  • 1_Analysis_Code_Minimal_Results.qmd contains the code to reproduce the main results showed in the manuscript. Results of rendering this code is found on 1_Analysis_Code_Minimal_Results.md.

  • 2_Sensitivity_Analysis01_wo_outliers.qmd contains the code to reproduce the analysis excluding outliers trough winzoring of ACR. Results of rendering this code is found on 2_Sensitivity_Analysis01_wo_outliers.md.

  • 3_Sensitivity_Analysis02_Cox.qmd contains the code to reprdocue teh analysis disregarding competing risks. Results of rendering this code is found on 3_Sensitivity_Analysis02_Cox.md.

• Figures/: Folder with figures of the manuscript.

  • plot_flowchart.png is Figure 1 of the manuscript.

  • Plot_CIF.png is Figure 2 of the manuscript.

  • Plot_Calibration.png is Figure 3 of the manuscript.

  • plot_dist_risks.png is Figure S1 of the manuscript.

  • plot_dist_vars.png is Figure S2 of the manuscript.

  • plot_dist_vars_sens_outlier.png is Figure S3 of the manuscript.

  • plot_dist_risks_sens_outlier.png is Figure S4 of the manuscript.

  • Plot_Calibration_sens_outlier.png is Figure S5 of the manuscript.

  • plot_km_compet.png is Figure S6 of the manuscript.

  • Plot_Calibration_cox.png is Figure S7 of the manuscript.

• Tables/: Folder with tables generated by code.

  • Table1.docx: Table 1 of the manuscript.

  • Table2.docx: Table 2 of the manuscript.

  • TableS3.docx: Table S3 of the manuscript.

  • TableS4.docx: Table S4 of the manuscript.

  • TableS5.docx: Table S5 of the manuscript.

  • TableS6.docx: Table S6 of the manuscript.

  • TableS7.docx: Table S7 of the manuscript.

  • TableS8.docx: Table S8 of the manuscript.

  • TableS9.docx: Table S9 of the manuscript.

  • TableS10.docx: Table S10 of the manuscript.

  • TableS11.docx: Table S11 of the manuscript.

  • TableS12.docx: Table S12 of the manuscript.

  • TableS12.docx: Table S13 of the manuscript.

• renv.lock: File renv.

Usage

You can either download a zip file containing the directory, or you can clone it by using

git clone https://github.com/psotob91/kfre-ckd-reba-peru

In either case, you can then use the kfre-ckd-reba-peru.Rproj file to open and Rstudio session in the directory you have just downloaded. You may then knit both quarto files, or run them line-by-line.

Contributions

Name	Affiliation	Role
Percy Soto Becerra	Universidad Continental, Huancayo, Perú	Author/maintainer and creator of R code

Licence

MIT