Goals of Care Site Reports

An R package and command line tool to generate goals of care conversation reports for VA sites.

Prerequisites

This project makes use of R, Rscript,pandoc, and pdflatex. All should be in the PATH of the user. Ensure the R Packages listed in this section are installed and available for the user.

LaTeX

For Windows users MikTex is suggested https://miktex.org/ Additionally, the latex-extras packages will need to be present on the system.

• texlive-latex-extra (deb)
• texlive-collection-latexextra (rpm)

Pandoc

Home Page https://www.pandoc.org Pandoc is a requirement of the knitr package. For command line Rscript, pandoc needs to be included in PATH.

R

Home Page https://cran.r-project.org/ Optionally, use RStudio to get a GUI. https://www.rstudio.com/

R Packages

The DESCRIPTION file lists the packages GoCC needs to import in order to run. Using devtools::install_deps should download and install these.

Installation

Installation instructions are inteneted to be run from the directory that contains the gocc directory. For example, if /home/joe/projects/gocc is where the gocc source directory will reside, then the commands below should be run from /home/joe/projects.

1. Install Prequisites (details below)
2. Clone repository into directory named gocc

   git clone https://github.com/Display-Lab/goals-of-care gocc

3. Install gocc package dependencies

   Rscript --vanilla -e 'install.packages("devtools", repos="http://cran.us.r-project.org")'
   Rscript --vanilla -e 'devtools::install_deps(pkg="gocc", dependencies=TRUE)'

4. Install gocc package from source directory

   R CMD INSTALL --preclean --no-multiarch --with-keep.source gocc

Update

1. Navigate to gocc source directory

   cd /path/to/gocc

2. Pull latest source code

   git pull

3. Navidate on directory up and follow final two steps from installation instructions above.

   cd ..
   Rscript --vanilla -e 'install.packages("devtools", repos="http://cran.us.r-project.org")'
   Rscript --vanilla -e 'devtools::install_deps(pkg="gocc", dependencies=TRUE)'
   R CMD INSTALL --preclean --no-multiarch --with-keep.source gocc

Configuration

Various strings that appear in the reports need to be changed per recipient. To facilitate this, those strings are specified in a yaml configuration file config/report_settings.yml.

• YAML overview: https://en.wikipedia.org/wiki/YAML
• YAML technical specification: yaml.org

Important Config Notes

• The config file must exist
• The config must be filled out for each id that exists in the input data.
• The config must start with the key default
• The config should contain a config for clc, hbpc, $ dementia.

Example:

---
default:
  clc:
    title: Title of the Report
    assists:
      - Data collected quarterly.
      - Data is analyzed in aggregate.
      - Your millage may vary.
    sites:
      nTR:
        name: No Trend Location
        contacts:
          - Jane Smith, Product Owner (555-555-5555)
          - John Jones, No Trend Manager (555-222-9101)
        provider: Reporting Committe for Reporting Reports
      9984: 
        name: Randal Trenderson Building
        contacts: John Jones, Random Manager (555-222-1121)
        provider: Friendly Neighborhood Feedback Provider

Package Use

The package comes with a command line utility script in bin/gocc.sh

1. Gather input data.
2. Make a configuration file. An example config with defaults settings exists in the package source directory under config/report_settings.yml.sample
3. Run the report generation script supplying the path to your inputs directory and config file.

An Example Directory Structure and Use

A example directory structure and command

• gocc.sh is a symlink to the shell script in the package
• report_settings.yml is the configuration file

example/
├── config
│   └── report_settings.yml
├── gocc.sh -> /home/grosscol/workspace/gocc/bin/gocc.sh
└── input
    ├── clc.csv
    └── hbpc.csv

From within example, the command that would generate clc & hbpc reports is:

./gocc.sh -c config/report_settings.yml --clc input/clc.csv --hbpc input/hbpc.csv

Input Codebook

The meaning and values of the various input csv files is documented in the codebook markdown.

Creating full set of reports.

bin/gocc.sh -c config/report_settings.yml --clc input/clc.csv --hbpc input/hbpc.csv --dementia input/dementia.csv

License

Copyright 2018 Regents of the University of Michigan

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.