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1 change: 1 addition & 0 deletions .Rbuildignore
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^_pkgdown\.yml$
^docs$
^pkgdown$
^revdep$
6 changes: 3 additions & 3 deletions CRAN-SUBMISSION
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Version: 1.0.0
Date: 2022-02-01 16:56:02 UTC
SHA: 93abf83e5b5f9043588f1e4b6dd2724a336fa889
Version: 1.0.2
Date: 2023-12-16 03:44:55 UTC
SHA: 0e4035d1f9998b6252e4c55152a9988ff6c6e805
5 changes: 5 additions & 0 deletions NEWS.md
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# baker 1.0.2

* fix an issue related to JAGS 4.3.x removed `cut()` function and only recognizes
`.Dim` not `dim` in array data objects stored in `jagsdata.txt` now.

# baker 1.0.0

* first public CRAN release
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4 changes: 2 additions & 2 deletions README.Rmd
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------
> An R Package for Fitting Bayesian [Nested Partially Latent Class Models](https://academic.oup.com/biostatistics/article/18/2/200/2555349/Nested-partially-latent-class-models-for-dependent)
[![R build status](https://github.com/zhenkewu/baker/workflows/R-CMD-check/badge.svg)](https://github.com/zhenkewu/baker/actions)
[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/zhenkewu/baker?branch=master&svg=true)](https://ci.appveyor.com/project/zhenkewu/baker)
[![R build status](https://github.com/zhenkewu/baker/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/zhenkewu/baker/actions)
<!-- [![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/zhenkewu/baker?branch=master&svg=true)](https://ci.appveyor.com/project/zhenkewu/baker) -->
`r badger::badge_cran_release("baker", "green")`
`r badger::badge_cran_download("baker", "grand-total", "green")`
`r badger::badge_cran_download("baker", "last-month", "green")`
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92 changes: 49 additions & 43 deletions README.md
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> Models](https://academic.oup.com/biostatistics/article/18/2/200/2555349/Nested-partially-latent-class-models-for-dependent)
[![R build
status](https://github.com/zhenkewu/baker/workflows/R-CMD-check/badge.svg)](https://github.com/zhenkewu/baker/actions)
[![AppVeyor build
status](https://ci.appveyor.com/api/projects/status/github/zhenkewu/baker?branch=master&svg=true)](https://ci.appveyor.com/project/zhenkewu/baker)
status](https://github.com/zhenkewu/baker/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/zhenkewu/baker/actions)
<!-- [![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/zhenkewu/baker?branch=master&svg=true)](https://ci.appveyor.com/project/zhenkewu/baker) -->
[![](https://www.r-pkg.org/badges/version/baker?color=green)](https://cran.r-project.org/package=baker)
[![](http://cranlogs.r-pkg.org/badges/grand-total/baker?color=green)](https://cran.r-project.org/package=baker)
[![](http://cranlogs.r-pkg.org/badges/last-month/baker?color=green)](https://cran.r-project.org/package=baker)
[![](http://cranlogs.r-pkg.org/badges/last-week/baker?color=green)](https://cran.r-project.org/package=baker)
[![](https://img.shields.io/badge/devel%20version-1.0.1-blue.svg)](https://github.com/zhenkewu/baker)
[![](https://img.shields.io/badge/devel%20version-1.0.2-blue.svg)](https://github.com/zhenkewu/baker)
[![](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html#maturing)

<!-- [![Coverage status](https://codecov.io/gh/zhenkewu/baker/branch/master/graph/badge.svg)](https://codecov.io/github/zhenkewu/baker?branch=master) -->
Expand Down Expand Up @@ -43,24 +42,31 @@ estimation from case-control data, please cite the following papers:
| nested pLCM regression | Wu, Z., Chen, I (2021). Probabilistic Cause-of-disease Assignment using Case-control Diagnostic Tests: A Hierarchical Bayesian Approach. *Statistics in Medicine* 40(4):823-841. [![](https://img.shields.io/badge/doi-10.1002/sim.8804-yellow.svg)](https://doi.org/10.1002/sim.8804) |
| Application | Maria Deloria Knoll, Wei Fu, Qiyuan Shi, Christine Prosperi, Zhenke Wu, Laura L. Hammitt, Daniel R. Feikin, Henry C. Baggett, Stephen R.C. Howie, J. Anthony G. Scott, David R. Murdoch, Shabir A. Madhi, Donald M. Thea, W. Abdullah Brooks, Karen L. Kotloff, Mengying Li, Daniel E. Park, Wenyi Lin, Orin S. Levine, Katherine L. O’Brien, Scott L. Zeger; Bayesian Estimation of Pneumonia Etiology: Epidemiologic Considerations and Applications to the Pneumonia Etiology Research for Child Health Study, *Clinical Infectious Diseases*, Volume 64, Issue suppl_3, 15 June 2017, Pages S213–S227 [![](https://img.shields.io/badge/doi-10.1093/cid/cix144-yellow.svg)](https://doi.org/10.1093/cid/cix144) |
| Primary PERCH Analysis | The PERCH Study Group (2019). Aetiology of severe hospitalized pneumonia in HIV-uninfected children from Africa and Asia: the Pneumonia Aetiology Research for Child Health (PERCH) Case-Control Study. *The Lancet* 394(10200): 757-779. [![](https://img.shields.io/badge/doi-10.1016/S0140--6736(19)30721--4-yellow.svg)](https://doi.org/10.1016/S0140-6736(19)30721-4) |
| Software paper | Chen I, Shi Q, Zeger SL, Wu Z (2022+) `baker`: An `R` package for Nested Partially-Latent Class Models. [![](https://img.shields.io/badge/arxiv-preprint-red.svg)](https://arxiv.org/abs/2202.11778) [![](https://img.shields.io/badge/vignette-workflow-blue.svg)](https://zhenkewu.com/assets/html/baker_vignette.html) |
| Software paper | Chen I, Shi Q, Zeger SL, Wu Z (2022+) `baker`: An `R` package for Nested Partially-Latent Class Models. [![](https://img.shields.io/badge/arxiv-preprint-red.svg)](https://arxiv.org/abs/2202.11778) [![](https://img.shields.io/badge/vignette-workflow-blue.svg)](https://zhenkewu.com/assets/html/baker_vignette.html) [![](https://img.shields.io/badge/doi-10.1093/cid/cix144-yellow.svg)](https://doi.org/10.1093/cid/cix144) |

There are a number of scientific papers on global health and infectious diseases
that have used the model and some the software (in its earlier versions). Some notable
examples are listed below:

- Kubale et al. (2023). Etiology of acute lower respiratory illness hospitalizations among infants in four countries. Open Forum Infectious Diseases, ofad580. [![](https://img.shields.io/badge/doi-10.1093/ofid/ofad580 -yellow.svg)](https://doi.org/10.1093/ofid/ofad580)

- aha SK et al. (2018). Causes and incidence of community-acquired serious infections among young children in south Asia (ANISA): an observational cohort study. *The Lancet* 392(10142):145-159. [https://doi.org/10.1016/S0140-6736(18)31127-9)](https://doi.org/10.1016/S0140-6736(18)31127-9)

## Table of content

<div id='id-section1'/>

- [1. Installation](#id-section1)
- [2. Vignettes](#id-section2)
- [3. Graphical User Interface (GUI)](#id-section3)
- [4. Analytic Goal](#id-section4)
- [5. Comparison to Other Existing Solutions](#id-section5)
- [6. Details](#id-section6)
- [7. Platform](#id-section7)
- [8. Connect `R` to `JAGS` on Unix systems or OSX](#id-section8)
- [9. Submit Jobs to Computing Cluster via a shell
script](#id-section9)
- [10. Connect `R` to `JAGS` on Windows](#id-section10)
- [11. Example Datasets](#id-section11)
- [1. Installation](#id-section1)
- [2. Vignettes](#id-section2)
- [3. Graphical User Interface (GUI)](#id-section3)
- [4. Analytic Goal](#id-section4)
- [5. Comparison to Other Existing Solutions](#id-section5)
- [6. Details](#id-section6)
- [7. Platform](#id-section7)
- [8. Connect `R` to `JAGS` on Unix systems or OSX](#id-section8)
- [9. Submit Jobs to Computing Cluster via a shell script](#id-section9)
- [10. Connect `R` to `JAGS` on Windows](#id-section10)
- [11. Example Datasets](#id-section11)

<div id='id-section1'/>

Expand All @@ -73,12 +79,12 @@ devtools::install_github("zhenkewu/baker")

Note:

- run `install.packages("pbkrtest")` for `R(>=3.2.3)` if this package
is reported as missing.
- Windows User: use
`devtools::install_github("zhenkewu/baker",INSTALL_opts=c("--no-multiarch"))`
instead if you see an error message
`ERROR: loading failed for 'i386'` (Thanks Chrissy!).
- run `install.packages("pbkrtest")` for `R(>=3.2.3)` if this package is
reported as missing.
- Windows User: use
`devtools::install_github("zhenkewu/baker",INSTALL_opts=c("--no-multiarch"))`
instead if you see an error message `ERROR: loading failed for 'i386'`
(Thanks Chrissy!).

<div id='id-section2'/>

Expand Down Expand Up @@ -118,19 +124,19 @@ You will get a dynamic figure. A snapshot is below:

## Analytic Goal

- To study disease etiology from case-control data from multiple
sources that have measurement errors. If you are interested in
estimating the population etiology pie (fraction), and the
probability of each cause for individual case, try `baker`.
- To study disease etiology from case-control data from multiple sources
that have measurement errors. If you are interested in estimating the
population etiology pie (fraction), and the probability of each cause
for individual case, try `baker`.

<div id='id-section5'/>

## Comparison to Other Existing Solutions

- Acknowledges various levels of measurement errors and combines
multiple sources of data for optimal disease diagnosis.
- Main function: `nplcm()` that fits the model with or without
covariates.
- Acknowledges various levels of measurement errors and combines
multiple sources of data for optimal disease diagnosis.
- Main function: `nplcm()` that fits the model with or without
covariates.

<div id='id-section6'/>

Expand All @@ -157,11 +163,11 @@ You will get a dynamic figure. A snapshot is below:

## Platform

- The `baker` package is compatible with OSX, Linux and Windows
systems, each requiring a slightly different setup as described
below. If you need to speed up the installation and analysis, please
contact the maintainer or chat by clicking the `gitter` button at
the top of this README file.
- The `baker` package is compatible with OSX, Linux and Windows systems,
each requiring a slightly different setup as described below. If you
need to speed up the installation and analysis, please contact the
maintainer or chat by clicking the `gitter` button at the top of this
README file.

<div id='id-section8'/>

Expand All @@ -185,10 +191,10 @@ Linked to JAGS 4.x.0
Loaded modules: basemod,bugs
```

- Run `R` command `library(baker)`. If the package `ks` cannot be
loaded due to failure of loading package `rgl`, first install X11 by
going [here](https://www.xquartz.org/releases/XQuartz-2.7.11.html),
followed by
- Run `R` command `library(baker)`. If the package `ks` cannot be loaded
due to failure of loading package `rgl`, first install X11 by going
[here](https://www.xquartz.org/releases/XQuartz-2.7.11.html), followed
by

``` r
install.packages("http://download.r-forge.r-project.org/src/contrib/rgl_0.95.1504.tar.gz",repo=NULL,type="source")
Expand Down Expand Up @@ -287,7 +293,7 @@ date

#### Windows

- JAGS 4.2.0
- JAGS 4.2.0

1. Install `R`; Download from [here](https://cran.r-project.org/)
2. Install [JAGS
Expand All @@ -297,8 +303,8 @@ date
[this](https://superuser.com/questions/949560/how-do-i-set-system-environment-variables-in-windows-10)
for setting environmental variables;

- alternatives are `brew install -v jags` for OSX,
`sudo apt-get install jags` for Ubuntu/Debian
- alternatives are `brew install -v jags` for OSX,
`sudo apt-get install jags` for Ubuntu/Debian

3. Fire up `R`, run `R` command `install.packages("rjags")`
4. Install [`Rtools`](https://cran.r-project.org/bin/windows/Rtools/)
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## Resubmission
This is a resubmission. In this version I have:

* updated to fix an issue in the example of `nplcm` (Package was archived on CRAN because of a tricky interfacing issue between JAGS 4.3.x and R 4.3.x)
* updated to fix an issue in the example of `nplcm` (Package was archived on CRAN because of a tricky interfacing issue between JAGS 4.3.x and R 4.3.x was not corrected in time)

* [only appeared on Windows Server 2022, R-devel, x64] Lost braces; missing escapes or markup?

Expand All @@ -14,21 +14,22 @@ This is a resubmission. In this version I have:
al (17:49, 19:11)
et (17:46, 19:8)

## Reverse dependencies
## Reverse dependencies; revdecp_check result `OK: 0` `BROKEN: 0`

This is a precise fix to a previously a short and archived release taken down on 2022-06-08 (https://cran.r-project.org/web/packages/baker/index.html), so there are no reverse dependencies
given the short life of the previous release.



## Test environments
* local OS X install, R 4.3.1
* ubuntu latest release (on Github-Action), R 4.1.2
* win-builder (devel and release), R 4.1.2
* local macOS X Sonoma 14.2 install, R 4.3.2
* ubuntu latest release (on Github-Action), R latest release
* windows latest release (on Github-Action), R latest release
* macOS latest release (on Github-Action), R latest release
* win-builder (devel and release)

## R CMD check results

0 errors | 0 warnings | 1 note
0 errors | 0 warnings | 0 note


---
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# Platform

|field |value |
|:--------|:----------------------------------------|
|version |R version 4.3.2 (2023-10-31) |
|os |macOS Sonoma 14.2 |
|system |aarch64, darwin20 |
|ui |RStudio |
|language |(EN) |
|collate |en_US.UTF-8 |
|ctype |en_US.UTF-8 |
|tz |America/Detroit |
|date |2023-12-15 |
|rstudio |2023.09.1+494 Desert Sunflower (desktop) |
|pandoc |3.1.10 @ /opt/homebrew/bin/pandoc |

# Dependencies

|package |old |new |Δ |
|:-------------|:---|:----------|:--|
|baker |NA |1.0.2 |* |
|bslib |NA |0.6.1 |* |
|cowplot |NA |1.1.2 |* |
|data.table |NA |1.14.10 |* |
|dplyr |NA |1.1.4 |* |
|e1071 |NA |1.7-14 |* |
|fpc |NA |2.2-11 |* |
|haven |NA |2.5.4 |* |
|htmltools |NA |0.5.7 |* |
|httpuv |NA |1.6.13 |* |
|later |NA |1.3.2 |* |
|lme4 |NA |1.1-35.1 |* |
|MatrixModels |NA |0.5-3 |* |
|mclust |NA |6.0.1 |* |
|mvtnorm |NA |1.2-4 |* |
|R2WinBUGS |NA |2.1-21 |* |
|ranger |NA |0.16.0 |* |
|RcppArmadillo |NA |0.12.6.6.1 |* |
|RcppEigen |NA |0.3.3.9.4 |* |
|sass |NA |0.4.8 |* |
|scales |NA |1.3.0 |* |
|shiny |NA |1.8.0 |* |
|sp |NA |2.1-2 |* |
|stringi |NA |1.8.3 |* |
|stringr |NA |1.5.1 |* |
|testthat |NA |3.2.1 |* |
|vroom |NA |1.6.5 |* |
|waldo |NA |0.5.2 |* |

# Revdeps

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package,old,new,delta
baker,NA,1.0.2,*
bslib,NA,0.6.1,*
cowplot,NA,1.1.2,*
data.table,NA,1.14.10,*
dplyr,NA,1.1.4,*
e1071,NA,1.7-14,*
fpc,NA,2.2-11,*
haven,NA,2.5.4,*
htmltools,NA,0.5.7,*
httpuv,NA,1.6.13,*
later,NA,1.3.2,*
lme4,NA,1.1-35.1,*
MatrixModels,NA,0.5-3,*
mclust,NA,6.0.1,*
mvtnorm,NA,1.2-4,*
R2WinBUGS,NA,2.1-21,*
ranger,NA,0.16.0,*
RcppArmadillo,NA,0.12.6.6.1,*
RcppEigen,NA,0.3.3.9.4,*
sass,NA,0.4.8,*
scales,NA,1.3.0,*
shiny,NA,1.8.0,*
sp,NA,2.1-2,*
stringi,NA,1.8.3,*
stringr,NA,1.5.1,*
testthat,NA,3.2.1,*
vroom,NA,1.6.5,*
waldo,NA,0.5.2,*
7 changes: 7 additions & 0 deletions revdep/cran.md
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## revdepcheck results

We checked 0 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.

* We saw 0 new problems
* We failed to check 0 packages

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*Wow, no problems at all. :)*
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Package: MatrixModels
Version: 0.5-3
Date: 2023-11-06
Title: Modelling with Sparse and Dense Matrices
Author: Douglas Bates <bates@stat.wisc.edu> and Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Contact: Matrix-authors@R-project.org
Description: Modelling with sparse and dense 'Matrix' matrices, using
modular prediction and response module classes.
Depends: R (>= 3.6.0)
Imports: stats, methods, Matrix (>= 1.6-0)
ImportsNote: _not_yet_stats4
Encoding: UTF-8
LazyLoad: yes
License: GPL (>= 2)
URL: https://Matrix.R-forge.R-project.org/,
https://r-forge.r-project.org/R/?group_id=61
BugReports: https://R-forge.R-project.org/tracker/?func=add&atid=294&group_id=61
NeedsCompilation: no
Packaged: 2023-11-06 13:43:15 UTC; maechler
Repository: CRAN
Date/Publication: 2023-11-06 14:30:02 UTC
Built: R 4.3.1; ; 2023-11-14 02:45:14 UTC; unix
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Model-class Mother Class "Model" of all S4 Models
glm4 Fitting Generalized Linear Models (using S4)
glpModel-class Class "glpModel" of General Linear Prediction
Models
lm.fit.sparse Fitter Function for Sparse Linear Models
mkRespMod Create a respModule object
model.Matrix Construct Possibly Sparse Design or Model
Matrices
modelMatrix-class Class "modelMatrix" and SubClasses
predModule-class Class "predModule" and SubClasses
resid,ANY-method Aliases for Model Extractors
respModule-class "respModule" and derived classes
reweightPred Reweight Prediction Module Structure Internals
solveCoef Solve for the Coefficients or Coefficient
Increment
updateMu Update 'mu', the Fitted Mean Response
updateWts Update the Residual and X Weights - Generic and
Methods
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