README.md

In oslerinhealth/baker: Bayesian Analysis Kit for Etiology Research

baker: Bayesian Analysis Kit for Etiology Research

An R Package for Fitting Bayesian Nested Partially Latent Class Models

Maintainer: Zhenke Wu, [e-mail]

Issues Please click here to report reproducible issues.

References: If you are using baker for population and individual estimation from case-control data, please cite the following papers:

| | Citation | Paper Link | |--------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------| | partially Latent Class Models (pLCM) | Wu, Z., Deloria-Knoll, M., Hammitt, L. L., Zeger, S. L. and the Pneumonia Etiology Research for Child Health Core Team (2016), Partially latent class models for case–control studies of childhood pneumonia aetiology. J. R. Stat. Soc. C, 65: 97–114. | Link | | nested pLCM | Wu, Z., Deloria-Knoll, M., Zeger, S.L.; Nested partially latent class models for dependent binary data; estimating disease etiology. Biostatistics 2017; 18 (2): 200-213. doi: 10.1093/biostatistics/kxw037 | Link | | nested pLCM regression | Wu, Z., Chen, I (2020). Probabilistic Cause-of-disease Assignment using Case-control Diagnostic Tests: A Hierarchical Bayesian Approach. Statistics in Medicine. To Appear. . | Link | | 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 | Link | | 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, In press. | Link |

Table of content

- [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)

## Installation wzxhzdk:0 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!).

## Vignettes wzxhzdk:1

## Graphical User Interface (GUI) wzxhzdk:2 For developers interested in low-level details, here is a pretty awesome [visualization](https://stackoverflow.com/questions/44143110/visualizing-r-function-dependencies) of the function dependencies within the package: wzxhzdk:3 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`.

## 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.

## Details 1. Implements hierarchical Bayesian models to infer disease etiology for multivariate binary data. The package builds in functionalities for data cleaning, exploratory data analyses, model specification, model estimation, visualization and model diagnostics and comparisons, catalyzing vital effective communications between analysts and practicing clinicians. 2. `baker` has implemented models for dependent measurements given disease status, regression analyses of etiology, multiple imperfect measurements, different priors for true positive rates among cases with differential measurement characteristics, and multiple-pathogen etiology. 3. Scientists in [Pneumonia Etiology Research for Child Health](http://www.jhsph.edu/research/centers-and-institutes/ivac/projects/perch/) (PERCH) study usually refer to the etiology distribution as “*population etiology pie*” and “*individual etiology pie*” for their compositional nature, hence the name of the package.

## 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.

## Connect `R` to `JAGS`/`WinBUGS` #### Mac OSX 10.11 El Capitan 1. Use [Just Another Gibbs Sampler (JAGS)](http://mcmc-jags.sourceforge.net/) 2. Install JAGS 4.2.0; Download [here](https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/) 3. Install `R`; Download from [here](https://cran.r-project.org/) 4. Fire up `R`, run `R` command `install.packages("rjags")` 5. Run `R` command `library(rjags)` in R console; If the installations are successful, you’ll see some notes like this: wzxhzdk:4 - 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 wzxhzdk:5 #### Unix (Build from source without administrative privilege) Here we use [JHPCE](https://jhpce.jhu.edu/) as an example. [The complete installation guide](https://sourceforge.net/projects/mcmc-jags/files/Manuals/4.x/) offers extra information. 1. Download source code for [JAGS 4.2.0](https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.2.0.tar.gz/download); 2. Suppose you’ve downloaded it in `~/local/jags/4.2.0`. Follow the bash commands below: ``` bash # change to the directory with the newly downloaded source files: cd ~/local/jags/4.2.0 # create a new folder named "usr" mkdir usr # decompress files: tar zxvf JAGS-4.2.0.tar.gz # change to the directory with newly decompressed files: cd ~/local/jags/4.2.0/JAGS-4.2.0 # specify new JAGS home: export JAGS_HOME=$HOME/local/jags/4.2.0/usr export PATH=$JAGS_HOME/bin:$PATH # link to BLAS and LAPACK: # Here I have used "/usr/lib64/atlas/" and "/usr/lib64/" on JHPCE that give me # access to libblas.so.3 and liblapack.so.3. Please modify to paths on your system. LDFLAGS="-L/usr/lib64/atlas/ -L/usr/lib64/" ./configure --prefix=$JAGS_HOME --libdir=$JAGS_HOME/lib64 # if you have 8 cores: make -j8 make install # prepare to install R package, rjags: export PKG_CONFIG_PATH=$HOME/local/jags/4.2.0/usr/lib64/pkgconfig module load R R> install.packages("rjags") # or if the above fails, try: R>install.packages("rjags", configure.args="--enable-rpath") ``` 3. Also check out the [INSTALLATION](https://CRAN.R-project.org/package=rjags/INSTALL) file for `rjags` package.

## Submitting Jobs to Computing Cluster via a shell script Again, I use JHPCE as an example. wzxhzdk:6

#### Windows - JAGS 4.2.0 1. Install `R`; Download from [here](https://cran.r-project.org/) 2. Install [JAGS 4.2.0](https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/); Add the path to JAGS 4.2.0 into the environmental variable (essential for R to find the jags program). See [this](http://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 1. Fire up `R`, run `R` command `install.packages("rjags")` 2. Install [`Rtools`](https://cran.r-project.org/bin/windows/Rtools/) (for building and installing R pacakges from source); Add the path to `Rtools` (e.g. `C:\Rtools\`) into your environmental variables so that R knows where to find it.

#### Datasets We provide two datasets for exploratory use with the `baker` package. 1. `data_nplcm_reg`: a dataset containing BrS measurements, case-control status, and regression covariates (testing site and enrollment date). This dataset was generated using the `simulate_nplcm` function. We also provide the BrS measurements, case-control status, and regression covariates (testing site and enrollment date). Code to fit the NPLCM to this dataset is in the accompanying software paper and the full code used to produce this dataset is available upon request. Using this dataset and the functionality in `baker`, a user can reproduce Figures 7 and 8 in the accompanying software paper. 2. `baker_posterior_samples_example`: a folder which contains the output of an NPLCM fitted to real data. We are not able to provide the real data due to privacy restrictions. Instead, we provide: - 1. the posterior samples, which can be found in `CODAchain1.txt` and `CODAindex.txt`. - 1. the covariates used in fitting the model (`ENRLDATE` and `AGE`), which can be found in `data_nplcm.txt`. Note that this folder can be found here [to be added]() Using the posterior samples in this folder, Figure 10 of the software paper can be replicated. If you would like to use `baker` visualization functions on this data, please download the compressed folder directly to your local drive, so that the path to the folder containing these `.txt` files can be provided as an argument for the plotting functions.

oslerinhealth/baker documentation built on May 22, 2021, 12:05 p.m.