The BC Chronic Disease Registry (CDR) is a data product that captures information about the rate of new and persistent cases of chronic diseases across the province. Age-standardized rates of disease are studied for different regions, including HAs (Health Authorities) and CHSAs (Community Health Service Areas), as well as for demographic variables such as sex.
In this project we aim to create an interactive dashboard that will allow users of all technical expertise to explore and visualize spatial and temporal information of the disease rates in the data, and to develop an analysis pipeline that will describe the temporal trends in the data.
Our data product is currently available for internal use only. Please contact the CDR Working Group to request access to the data. To re-run the analysis and run the dashboard, please ensure that R (version 4.2.0) and RStudio are installed, then follow the respective instructions below.
opho-cdr-shiny.Rproject
file in RStudio. Run the
following command in the R console to install the package
dependencies or manually as listed below: renv::restore()
make all
rmarkdown::run('src/model/02_visualize.Rmd')
rmarkdown::run('src/joinpoint/joinpoint_method.rmd')
data/
directory within the src/dashboard/
director, and
save the original and modeled data inside in folders named “raw” and
“model” respectively. The data inside the raw
folder should be
saved from the “Data_MFT_HA_CHSA” dataset, and the data inside the
model
folder should be saved from running the Models (Both
Temporal and Joinpoint Regression) above. The folder structure
should look as follows:.
├── ...
├── src
│ ├── dashboard
| │ ├── data
| │ | ├── model # Modeled Data from Modelling
| │ | | ├── HSCPrevalence
| │ | | | ├── AMI_EPI.csv
| │ | | | ├── ASTHMA_EPI.csv
| │ | | | └── ...
| │ | | ├── IncidenceRate
| │ | | | ├── ALZHEIMER_DEMENTIA.csv
| │ | | | ├── AMI.csv
| │ | | | └── ...
| │ | | └── LifePrevalence
| │ | | | ├── ALZHEIMER_DEMENTIA.csv
| │ | | | ├── AMI.csv
| │ | | | └── ...
| │ | | └── joinpoint_for_shiny_df.fst
| │ | | └── joinpoint_results.csv
| │ | └── raw # Original Data from "Data_MFT_HA_CHSA'
| │ | ├── HSCPrevalence
| │ | | ├── AMI_EPI.csv
| │ | | ├── ASTHMA_EPI.csv
| │ | | └── ...
| │ | ├── IncidenceRate
| │ | | ├── ALZHEIMER_DEMENTIA.csv
| │ | | ├── AMI.csv
| │ | | └── ...
| │ | └── LifePrevalence
| │ | ├── ALZHEIMER_DEMENTIA.csv
| │ | ├── AMI.csv
| │ | └── ...
│ | └── ...
│ └── ...
└── ...
shiny::runApp('src/dashboard')
R version 4.2.0 and R packages:
GNU make 3.81
To report bugs/issues/feature requests, please file an issue.
If you would like to contribute, please see our CONTRIBUTING guidelines.
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
Copyright 2022 Province of British Columbia
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.
This project was created using the bcgovr package.