Resources
Remms:
Refining Evaluation Methodology on Stage System
T (extent of the primary tumor), N (absence or presence and extent of regional lymph node metastasis) and M (absence or presence of distant metastasis) are three components to describe the anatomical tumor extent. TNM stage is important in treatment decision-making and outcome predicting. The existing oropharyngeal Cancer (OPC) TNM stages have not made distinction of the two sub sites of Human papillomavirus positive (HPV+) and Human papillomavirus negative (HPV-) diseases. We developed novel criteria to assess performance of the TNM stage grouping schemes based on parametric modeling adjusting on important clinical factors. These criteria evaluate the TNM stage grouping scheme in five different measures: hazard consistency, hazard discrimination, explained variation, likelihood difference, and balance. The methods are described in Xu, W., et al. (2015)
https://www.austinpublishinggroup.com/biometrics/fulltext/biometrics-v2-id1014.php
reportRmd:
reporting biostatistics + R Markdown
The goal of reportRmd is to automate the reporting of clinical data in R Markdown environments. Functions include table one-style summary statistics, compilation of multiple univariate models, tidy output of multivariable models and side by side comparisons of univariate and multivariable models. Plotting functions include customisable survival curves, forest plots, and automated bivariate plots.
https://github.com/biostatsPMH/reportRmd
reportRx: - deprecated
report + R(language) + R(yan) + x(docx) + Rx (prescription (clinical)) + more
https://github.com/biostatsPMH/reportRx
swimplot:
Tools for Creating Swimmers Plots using 'ggplot2'
Used for creating swimmers plots with functions to customize the bars, add points, add lines, add text, and add arrows.
https://cran.r-project.org/web/packages/swimplot/
xlink:
Genetic Association Models for X-Chromosome SNPS on Continuous, Binary and Survival Outcomes
The expression of X-chromosome undergoes three possible biological processes: X-chromosome inactivation (XCI), escape of the X-chromosome inactivation (XCI-E),and skewed X-chromosome inactivation (XCI-S). To analyze the X-linked genetic association for phenotype such as continuous, binary, and time-to-event outcomes with the actual process unknown, we propose a unified approach of maximizing the likelihood or partial likelihood over all of the potential biological processes. The methods are described in Wei Xu, Meiling Hao (2017) <doi:10.1002/gepi.22097>. And also see Dongxiao Han, Meiling Hao, Lianqiang
Qu, Wei Xu (2019) <doi:10.1177/0962280219859037>
https://cran.r-project.org/package=xlink
exceldata:
Streamline Data Import, Cleaning and Recoding from 'Excel'
A small group of functions to read in a data dictionary and the corresponding data table from 'Excel' and to automate the cleaning, re-coding and creation of simple calculated variables. This package was designed to be a companion to the macro-enabled 'Excel' template available on the GitHub site, but works with any similarly-formatted 'Excel' data.
https://cran.r-project.org/package=exceldata