README.md

In alexmarzel/svisits: Shared Clinic Visit Dates Identify Steady HIV Positive Partnerships for Research

R package: svisits

Using mathematical approximations and a shuffling approach to derive the probabilities of sharing a given number of visits by chance the package helps to identify couples that may represent either transmission pairs or serosorting couples in a stable relationship, for biological and epidemiologcial HIV research.

Installation

Make sure the most updated version of R is installed.

The packages "compiler" and "parallel" should be included by default. If not, update R.

Install dependencies

install.packages(c("Rcpp", "chron","data.table")) 

Install the "svisits" package

install.packages("svisits_1.2.0.tar.gz",
                 repos = NULL, type = "source")  

Note: Place "svisits_1.2.0.tar.gz" into the working directory or provide the full path.

Fastest use, an example

library(svisits) 

data("simulated_data") 

pairs <- find_pairs(simulated_data, 
                    ids_column = "subject",
                    dates_column = "sim_dates")

head(pairs$Bonferroni_pairs)

alexmarzel/svisits documentation built on May 12, 2019, 1:36 a.m.