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sleev

sleev: An R Package for Semiparametric Likelihood Estimation with Errors in Variables - Published in JOSS (2025)

https://github.com/dragontaoran/sleev

Science Score: 87.0%

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    CITATION.cff file
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    .zenodo.json file
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    DOI references
    Found 14 DOI reference(s) in README and JOSS metadata
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    Links to: joss.theoj.org
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    Academic email domains
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    JOSS paper metadata
    Published in Journal of Open Source Software

Scientific Fields

Materials Science Physical Sciences - 40% confidence
Last synced: 4 months ago · JSON representation

Repository

Combination of logreg2ph and TwoPhaseReg

Basic Info
  • Host: GitHub
  • Owner: dragontaoran
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Size: 11.7 MB
Statistics
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Fork of Epic-Doughnut/sleev
Created almost 4 years ago · Last pushed 4 months ago

https://github.com/dragontaoran/sleev/blob/main/ 


  
    
SLEEV: Semiparametric Likelihood Estimation with Errors in Variables

    


License: file `/inst/LICENSE_sleev.txt`

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.07320/status.svg)](https://doi.org/10.21105/joss.07320)

HTML:

  DOI badge


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](https://doi.org/10.1111/biom.13512). 
  
Part of the R package `TwoPhaseReg` as described in [this paper](https://doi.org/10.1002/sim.8876).

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](https://github.com/dragontaoran/sleev/blob/main/inst/article/sleev_vignette.pdf).
  
### Install
To install the package for GitHub, run the following in your `R` console: 
    
```{r}
  devtools::install_github("dragontaoran/sleev")
```
or install from CRAN:
```
install.packages("sleev")
```
  
Load package:
    
```{r}
  library(sleev)
```
  
### `mock.vccc` data
  
This data is a simulated two-phase sampling dataset based on VCCC data. To load this dataset, run:
    
```{r}
  data(mock.vccc)
```
  
### Preprocessing
  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)
```
  
### Construct B-spline Basis
  
```
sn=20
data.linear <- spline2ph(x = "VL_unval_l10", data = mock.vccc, size = sn,
                         degree = 3,  group = "Sex")
```
  
### Model fitting 
  
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)
```

Owner

  • Name: Ran Tao
  • Login: dragontaoran
  • Kind: user
  • Location: Nashville, TN
  • Company: Vanderbilt University Medical Center

Assistant Professor, Department of Biostatistics and Vanderbilt Genetics Institute, Vanderbilt University Medical Center

JOSS Publication

sleev: An R Package for Semiparametric Likelihood Estimation with Errors in Variables
Published
August 05, 2025
DOI
Volume 10, Issue 112, Page 7320
Authors
Jiangmei Xiong ORCID
Department of Biostatistics, Vanderbilt University Medical Center, USA
Sarah C. Lotspeich ORCID
Department of Statistical Sciences, Wake Forest University, USA
Joey B. Sherrill ORCID
Brigham Young University, USA
Gustavo Amorim ORCID
Department of Biostatistics, Vanderbilt University Medical Center, USA
Bryan E. Shepherd ORCID
Department of Biostatistics, Vanderbilt University Medical Center, USA
Ran Tao ORCID
Department of Biostatistics, Vanderbilt University Medical Center, USA, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, USA
Editor
Mehmet Hakan Satman ORCID
Tags
measurement error two-phase sampling nonparametric statistics B-splines
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Packages

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  • Total versions: 10
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cran.r-project.org: sleev

Semiparametric Likelihood Estimation with Errors in Variables

  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 295 Last month
Rankings
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Average: 48.2%
Downloads: 79.3%
Maintainers (1)
r.tao@vanderbilt.edu
Last synced: 4 months ago