Bivariate Alternating Recurrent Event Data Analysis

Alternating recurrent event data arise frequently in biomedical and social sciences where 2 types of events such as hospital admissions and discharge occur alternatively over time. As such we implement a collection of non-parametric and semiparametric methods to analyze such data. The main functions are biv.rec.fit() and biv.rec.np(). Use biv.rec.fit() for estimation of covariate effects on the two alternating event gap times (xij and yij) using semiparametric methods. The method options are "Lee.et.al" and "Chang". Use biv.rec.np() for estimation of the joint cumulative distribution function (cdf) for the two alternating events gap times (xij and yij) as well as the marginal survival function for type I gap times (xij) and the conditional cdf of the type II gap times (yij) given an interval of type I gap times (xij) in a non-parametric fashion. The package also provides options to simulate and visualize the data and results of analysis.


Bivariate Alternating Recurrent Event Data Analysis (BivRec)

Alternating recurrent event data arise frequently in biomedical and social sciences where two types of events such as hospital admissions and discharge occur alternatively over time. BivRec implements a collection of non-parametric and semiparametric methods to analyze such data.

The main functions are:
- biv.rec.fit: Use for the estimation of covariate effects on the two alternating event gap times (Xij and Yij) using semiparametric methods. The method options are “Lee.et.al” and “Chang”.
- biv.rec.np: Use for the estimation of the joint cumulative distribution funtion (cdf) for the two alternating events gap times (Xij and Yij) as well as the marginal survival function for type I gap times (Xij) and the conditional cdf of the type II gap times (Yij) given an interval of type I gap times (Xij) in a non-parametric fashion.

The package also provides options to simulate and visualize the data and results of analysis.

BivRec depends on the following system requirements:
- Rtools. Download Rtools 35 from https://cran.r-project.org/bin/windows/Rtools/

Once those requirements are met you can install BivRec from github as follows:

#Installation requires devtools package.
#install.packages("devtools")
library(devtools)
install_github("SandraCastroPearson/BivRec")

Example

This is an example using a simulated data set.

# Simulate bivariate alternating recurrent event data
library(BivRec)
#> Loading required package: survival
set.seed(1234)
biv.rec.data <- biv.rec.sim(nsize=150, beta1=c(0.5,0.5), beta2=c(0,-0.5), tau_c=63, set=1.1)
head(biv.rec.data)
#>   id epi      xij      yij       ci d1 d2 a1        a2
#> 1  1   1 2.411938 1.608223 40.41911  1  1  0 0.4390421
#> 2  1   2 1.405158 1.358592 40.41911  1  1  0 0.4390421
#> 3  1   3 2.188781 1.633935 40.41911  1  1  0 0.4390421
#> 4  1   4 2.045351 1.071826 40.41911  1  1  0 0.4390421
#> 5  1   5 5.047795 2.175306 40.41911  1  1  0 0.4390421
#> 6  1   6 2.503392 1.324126 40.41911  1  1  0 0.4390421
 
# Plot gap times
biv.rec.plot(formula = id + epi ~ xij + yij, data = biv.rec.data)

 
# Apply the non-parametric method of Huang and Wang (2005) and visualize marginal and conditional results
 
# To save plots in a pdf file un-comment the following line of code: 
# pdf("nonparamplots.pdf")
 
nonpar.result <- biv.rec.np(formula = id + epi + xij + yij + d1 + d2 ~ 1,
           data=biv.rec.data, ai=1, u1 = seq(2, 25, 1), u2 = seq(1, 20, 1),
           conditional = TRUE, given.interval=c(0, 10), jointplot=TRUE,
           marginalplot = TRUE, condiplot = TRUE)
#> [1] "Original number of observations: 856 for 150 individuals"
#> [1] "Observations to be used in analysis: 856 for 150 individuals"
#> [1] "Estimating joint cdf and marginal survival"

#> [1] "Estimating conditional CDF with 95% CI using 100 Bootstrap samples"

 
# To close the pdf file with the saved plots un-comment the following line of code
# dev.off()
 
head(nonpar.result$joint.cdf)
#>   x y Joint.Probability         SE     0.025%    0.975%
#> 1 2 1        0.07765854 0.01916368 0.04009842 0.1152187
#> 2 2 2        0.12390735 0.02288661 0.07905041 0.1687643
#> 3 2 3        0.13381917 0.02345172 0.08785464 0.1797837
#> 4 2 4        0.13694252 0.02348318 0.09091634 0.1829687
#> 5 2 5        0.13928503 0.02373745 0.09276048 0.1858096
#> 6 2 6        0.13928503 0.02373745 0.09276048 0.1858096
head(nonpar.result$marginal.survival)
#>        Time Marginal.Survival           SE    0.025%    0.975%
#> 1 0.2697386         0.9998851 9.383939e-06 0.9998667 0.9999034
#> 2 0.2759313         0.9997701 1.149293e-04 0.9995449 0.9999954
#> 3 0.2912704         0.9996552 2.292833e-04 0.9992058 1.0000000
#> 4 0.3055601         0.9995402 3.437648e-04 0.9988665 1.0000000
#> 5 0.3203637         0.9994253 4.582784e-04 0.9985271 1.0000000
#> 6 0.3229318         0.9993103 5.728047e-04 0.9981877 1.0000000
head(nonpar.result$conditional.cdf)
#>     Time Conditional.Probability  Bootstrap SE Bootstrap 0.025%
#> 1 0.0112                  0.0000        0.0000             0.00
#> 2 0.1358                  0.0060        0.0040             0.00
#> 3 0.2604                  0.0197        0.0112             0.00
#> 4 0.3850                  0.0267        0.0133             0.00
#> 5 0.5095                  0.0401        0.0160             0.01
#> 6 0.6341                  0.0660        0.0201             0.02
#>   Bootstrap 0.975%
#> 1             0.00
#> 2             0.01
#> 3             0.04
#> 4             0.05
#> 5             0.07
#> 6             0.10
 
# Apply Lee C, Huang CY, Xu G, Luo X (2017) method using multiple covariates
fit.lee <- biv.rec.fit(formula = id + epi + xij + yij + d1 + d2 ~ a1 + a2,
                data=biv.rec.data, method="Lee.et.al", CI=0.99)
#> [1] "Original number of observations: 856 for 150 individuals"
#> [1] "Observations to be used in analysis: 856 for 150 individuals"
#> [1] "Fitting model with covariates: a1,a2"
#> [1] "Estimating standard errors/confidence intervals"
fit.lee$covariate.effects
#>          Estimate        SE     0.005%    0.995%
#> xij a1  0.5744414 0.1306845  0.2378204 0.9110623
#> xij a2  0.5128054 0.2707497 -0.1845995 1.2102103
#> yij a1  0.2888306 0.1985364 -0.2225653 0.8002266
#> yij a2 -0.6207422 0.3842713 -1.6105596 0.3690751
 
# To apply Chang (2004) method use method="Chang".
# biv.rec.chang<- biv.rec.fit(formula = id + epi + xij + yij + d1 + d2 ~ a1 + a2, 
# data=biv.rec.data, method="Chang", CI=0.99)

News

BivRec 1.0.0

Submitted to CRAN 10/26/18

Reference manual

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install.packages("BivRec")

1.0.0 by Sandra Castro-Pearson, 10 months ago


Report a bug at https://github.com/SandraCastroPearson/BivRec/issues


Browse source code at https://github.com/cran/BivRec


Authors: Sandra Castro-Pearson [aut, cre] , Chi-Hyun Lee [aut] , Chiung-Yu Huang [aut] , Xianghua Luo [ctb]


Documentation:   PDF Manual  


GPL-3 license


Imports MASS, stringr, utils, knitr, rmarkdown, Rcpp, graphics, grDevices

Depends on survival, stats

Linking to Rcpp


See at CRAN