bifurcatingr

Bifurcating autoregressive (BAR) models are commonly used to model binary tree-structured data that appear in many applications, most famously cell-lineage applications. The BAR model is an extension of the autoregressive (AR) model where each line of descent considers an AR process with the modification that the observations on the two sibling cells who share the same parent are correlated. In practice, the BAR model is used to explain the progression of single-cell proliferation. The goal of the bifurcatingr package is to provide a collection of functions that can be used for analyzing bifurcating autoregressive data. The package implements the least squares estimation of bifurcating autoregressive models of any order, p, BAR(p), and allows for executing several types of bias correction on the least-squares estimators of the autoregressive parameters including different types of confidence intervals. Currently, the bias correction methods supported include bootstrap (single, double, and fast-double) bias correction and linear-bias-function -based bias correction. The library also contains functions for generating and plotting bifurcating autoregressive data from any BAR(p) model.

Installation

You can install the development version of bifurcatingr like so: You can install the released version of bifurcatingr from CRAN with:

 install.packages("bifurcatingr")

Example

This is a basic example which shows you how to use bifurcatingr to fit a bifurcating autoregressive model to the ecoli dataset which contains the lifetimes of lineage E. coli cells.

library(bifurcatingr)
#> Loading required package: fMultivar
## basic example code
data("ecoli")
## Fitting a BAR(p=1) model to the `ecoli` dataset:

    bfa_ls(ecoli$lifetime, p = 1, conf = TRUE, conf_level = 0.95, 
           p_value = TRUE, cov_matrix = TRUE)
#> $coef
#>      Intercept  X_[t/2]
#> [1,]  17.61658 0.355198
#> 
#> $p_value
#>       Intercept  X_[t/2]
#> [1,] 0.01079535 0.181183
#> 
#> $error_cor
#> [1] 0.5836975
#> 
#> $cov_matrix
#>            Intercept    X_[t/2]
#> Intercept 1480.39874 -56.147524
#> X_[t/2]    -56.14752   2.187566
#> 
#> $asymptotic_ci
#>                 2.5%      97.5%
#> Intercept  4.0722831 31.1608852
#> X_[t/2]   -0.1654543  0.8758503
#> 
#> $bootstarp_ci
#>                2.5%     97.5%
#> Intercept  4.993058 30.240110
#> X_[t/2]   -0.105760  0.816156
#> 
#> $percentile_ci
#>                 2.5%      97.5%
#> Intercept  6.8659866 29.4617318
#> X_[t/2]   -0.1032912  0.7103112