The goal of eq5d.plus is to run linear models on EQ-5D quality of life data that uses both the score and visual analogue scale (VAS).
You can install the released version of eq5d.plus from GitHub with:
# use the devtools library
library(devtools)
# Install the latest version from GitHub:
install_github("agbarnett/lmvas")Note that the INLA library also has to be installed from
GitHub.
This example runs a linear model with independent variables of age and sex:
library(eq5d.plus)
## example using the Spanish osteoarthritis data
model = lmvas(vas_name='EQ5D_VAS', eq_name='EQ5D', independent_vars = c('age','sex'), data=arthritis)
summary(model)
#>
#> Call:
#> "inla(formula = as.formula(formula), family = \"normal\", data =
#> for_model2)"
#> Time used:
#> Pre = 1.4, Running = 3.54, Post = 0.428, Total = 5.36
#> Fixed effects:
#> mean sd 0.025quant 0.5quant 0.975quant mode kld
#> (Intercept) 0.967 0.014 0.939 0.967 0.995 0.967 0
#> type_vas -0.153 0.006 -0.164 -0.153 -0.141 -0.153 0
#> age55-59 -0.047 0.018 -0.082 -0.047 -0.012 -0.047 0
#> age60-64 -0.046 0.019 -0.083 -0.046 -0.009 -0.046 0
#> age65-69 -0.056 0.019 -0.093 -0.056 -0.019 -0.056 0
#> age70-74 -0.067 0.021 -0.108 -0.067 -0.027 -0.067 0
#> age75-79 -0.104 0.022 -0.147 -0.104 -0.062 -0.104 0
#> age80-84 -0.122 0.025 -0.170 -0.122 -0.074 -0.122 0
#> age85+ -0.216 0.027 -0.269 -0.216 -0.163 -0.216 0
#> sexWoman -0.041 0.011 -0.063 -0.041 -0.020 -0.041 0
#>
#> Random effects:
#> Name Model
#> ID IID2D model
#>
#> Model hyperparameters:
#> mean sd 0.025quant 0.5quant
#> Precision for the Gaussian observations 2.21e+04 1.97e+04 2186.430 1.66e+04
#> Precision for ID (component 1) 2.42e+01 1.09e+00 22.114 2.42e+01
#> Precision for ID (component 2) 2.86e+01 1.29e+00 26.112 2.85e+01
#> Rho1:2 for ID 5.57e-01 2.20e-02 0.513 5.57e-01
#> 0.975quant mode
#> Precision for the Gaussian observations 7.41e+04 6311.739
#> Precision for ID (component 1) 2.64e+01 24.128
#> Precision for ID (component 2) 3.12e+01 28.494
#> Rho1:2 for ID 5.99e-01 0.558
#>
#> Expected number of effective parameters(stdev): 1994.00(7.35)
#> Number of equivalent replicates : 1.00
#>
#> Marginal log-Likelihood: 546.51The results show a reduced intercept for the VAS compared with the score of -0.153. Quality of life is lower on average for women and for older respondents.
The score and VAS are positively correlated with an estimated correlation of 0.557 (“rho” estimate in model hyperparameters).
The model may take a short while to run for very large data sets.