License: file /inst/LICENSE_sleev.txt
reStructuredText: .. image:: https://joss.theoj.org/papers/10.21105/joss.07320/status.svg :target: https://doi.org/10.21105/joss.07320
The complete R package logreg2ph and code for the
simulation settings included in this paper.
Part of the R package TwoPhaseReg as described in this paper.
If you wish to make suggestions, report a problem, or need more support with package use, please email Dr. Ran Tao (r DOT tao AT vumc DOT org) or Dr. Sarah Lotspeich (lotspes AT wfu DOT edu).
Below is a simple example for running a linear regression with
sleev. The complete vignette detailing all uses of example
in sleev can be found as an article.
To install the package for GitHub, run the following in your
R console:
devtools::install_github("dragontaoran/sleev")
or install from CRAN:
install.packages("sleev")
Load package:
library(sleev)
mock.vccc dataThis data is a simulated two-phase sampling dataset based on VCCC data. To load this dataset, run:
data(mock.vccc)
Because of skewness, we often transform both CD4 and VL. In our analysis, CD4 was divided by 10 and square-root transformed and VL was log_10 transformed:
mock.vccc$CD4_val_sq10 <- sqrt(mock.vccc$CD4_val/10)
mock.vccc$CD4_unval_sq10 <- sqrt(mock.vccc$CD4_unval/10)
mock.vccc$VL_val_l10 <- log10(mock.vccc$VL_val)
mock.vccc$VL_unval_l10 <- log10(mock.vccc$VL_unval)
Load splines package
library(splines)
sn=20
data.linear <- spline2ph(x = "VL_unval_l10", data = mock.vccc, size = sn,
degree = 3, group = "Sex")
The SMLEs can be obtained by running
res_linear <- linear2ph(y_unval = "CD4_unval_sq10", y = "CD4_val_sq10",
x_unval = "VL_unval_l10",x = "VL_val_l10",z = "Sex",
b_spline = paste0("bs", 1:sn), data = data.linear,
hn_scale = 1, se = TRUE, tol = 1e-04,
max_iter = 1000, verbose = FALSE)
Check convergence:
c(res_linear$converge, res_linear$converge_cov)