-
Notifications
You must be signed in to change notification settings - Fork 11
/
README.Rmd
132 lines (88 loc) · 6.67 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# joineRML <img src="man/figures/hex.png" width = "175" height = "200" align="right" />
<!-- badges: start -->
[](https://github.com/graemeleehickey/joineRML/actions)
[](https://ci.appveyor.com/project/graemeleehickey/joineRML)
<!--[](http://www.gnu.org/licenses/gpl-3.0.html)-->
[](https://CRAN.R-project.org/package=joineRML)
[](https://CRAN.R-project.org/package=joineRML)
[](https://CRAN.R-project.org/package=joineRML)
[](https://app.codecov.io/gh/graemeleehickey/joineRML)
[](http://depsy.org/package/r/joineRML)
[](https://doi.org/10.5281/zenodo.1158231)
<!-- badges: end -->
`joineRML` is an extension of the joineR package for fitting joint models of time-to-event data and multivariate longitudinal data. The model fitted in joineRML is an extension of the Wulfsohn and Tsiatis (1997) and Henderson et al. (2000) models, which is comprised of $(K+1)$-sub-models: a Cox proportional hazards regression model (Cox, 1972) and a $K$-variate linear mixed-effects model - a direct extension of the Laird and Ware (1982) regression model. The model is fitted using a Monte Carlo Expectation-Maximization (MCEM) algorithm, which closely follows the methodology presented by Lin et al. (2002).
## Why use joineRML?
As noted in Hickey et al. (2016), there is a lack of statistical software available for fitting joint models to multivariate longitudinal data. This is contrary to a growing methodology in the statistical literature. `joineRML` is intended to fill this void.
# Example
The main workhorse function is `mjoint`. As a simple example, we use the `heart.valve` dataset from the package and fit a bivariate joint model.
```r
library(joineRML)
data(heart.valve)
hvd <- heart.valve[!is.na(heart.valve$log.grad) & !is.na(heart.valve$log.lvmi), ]
set.seed(12345)
fit <- mjoint(
formLongFixed = list("grad" = log.grad ~ time + sex + hs,
"lvmi" = log.lvmi ~ time + sex),
formLongRandom = list("grad" = ~ 1 | num,
"lvmi" = ~ time | num),
formSurv = Surv(fuyrs, status) ~ age,
data = list(hvd, hvd),
timeVar = "time")
```
The fitted model is assigned to `fit`. We can apply a number of functions to this object, e.g. `coef`, `logLik`, `plot`, `print`, `ranef`, `fixef`, `summary`, `AIC`, `getVarCov`, `vcov`, `confint`, `sigma`, `update`, `formula`, `resid`, and `fitted`. In addition, several special functions have been added, including `dynSurv`, `dynLong`, and `baseHaz`, as well as plotting functions for objects inheriting from the `dynSurv`, `dynLong`, `ranef`, and `mjoint` functions. For example,
```r
summary(fit)
plot(fit, param = 'gamma')
```
`mjoint` automatically estimates approximate standard errors using the empirical information matrix (Lin et al., 2002), but the `bootSE` function can be used as an alternative.
# Errors and updates
If you spot any errors or wish to see a new feature added, please file an issue at https://github.com/graemeleehickey/joineRML/issues or email [Graeme Hickey](mailto:graeme.hickey@liverpool.ac.uk).
# Further learning
For an overview of the model estimation being performed, please see the technical vignette, which can be accessed by
```r
vignette('technical', package = 'joineRML')
```
For a demonstration of the package, please see the introductory vignette, which can be accessed by
```r
vignette('joineRML', package = 'joineRML')
```
# Funding
This project is funded by the [Medical Research Council](https://mrc.ukri.org) (Grant number MR/M013227/1).
# Using the latest developmental version
To install the latest **developmental version**, you will need R version (version 3.3.0 or higher) and some additional software depending on what platform you are using.
## Windows
If not already installed, you will need to install [Rtools](https://cran.r-project.org/bin/windows/Rtools/). Choose the version that corresponds to the version of R that you are using.
## Mac OSX
If not already installed, you will need to install Xcode Command Line Tools. To do this, open a new terminal and run
```bash
$ xcode-select --install
```
## From R
The latest developmental version will not yet be available on CRAN. Therefore, to install it, you will need `devtools`. You can check you are using the correct version by running
Once the prerequisite software is installed, you can install `joineRML` by running the following command in an R console
```r
library('devtools')
install_github('graemeleehickey/joineRML')
```
# Compatibility with [`broom`](https://github.com/tidymodels/broom/)
Tidiers methods for objects of class `mjoint` (i.e. models fit with `joineRML`) are included in the [`broom`](https://github.com/tidymodels/broom/) package; this provides methods that allow extracting model estimates, predictions, and comparing models in a straightforward way.
See `vignette(topic = "joineRML-broom", package = "joineRML")` for further details and examples.
# References
1. Cox DR. Regression models and life-tables. *J R Stat Soc Ser B Stat Methodol.* 1972; **34(2)**: 187-220.
2. Henderson R, Diggle PJ, Dobson A. Joint modelling of longitudinal measurements and event time data. *Biostatistics.* 2000; **1(4)**: 465-480.
3. Hickey GL, Philipson P, Jorgensen A, Kolamunnage-Dona R. Joint modelling of time-to-event and multivariate longitudinal outcomes: recent developments and issues. *BMC Med Res Methodol.* 2016; **16(1)**: 117.
4. Laird NM, Ware JH. Random-effects models for longitudinal data. *Biometrics.* 1982; **38(4)**: 963-974.
5. Lin H, McCulloch CE, Mayne ST. Maximum likelihood estimation in the joint analysis of time-to-event and multiple longitudinal variables. *Stat Med.* 2002; **21**: 2369-2382.
6. Wulfsohn MS, Tsiatis AA. A joint model for survival and longitudinal data measured with error. *Biometrics.* 1997; **53(1)**: 330-339.