add readme

.Rbuildignore

@@ -1,3 +1,5 @@
 ^OmopSketch\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^\.github$
+^README\.Rmd$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.gitignore

@@ -1,2 +1,5 @@
 .Rproj.user
 .Rhistory
+.Rdata
+.httr-oauth
+.DS_Store

DESCRIPTION

@@ -16,6 +16,7 @@ Config/testthat/parallel: true
 Imports: 
     CDMConnector (>= 1.3.0),
     checkmate,
+    cli,
     dplyr,
     IncidencePrevalence (>= 0.7.0),
     lubridate,

R/summariseOmopTable.R

@@ -55,6 +55,8 @@ getFunctions <- function(date, concept) {
   return(functions)
 }
 prepareTable <- function(omopTable, date, concept) {
+  cdm <- omopgenerics::cdmReference(omopTable)
+
   # domain_id
   if (concept != "cohort_definition_id") {
     omopTable <- omopTable |>

README.Rmd

@@ -0,0 +1,56 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# OmopSketch
+
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/oxford-pharmacoepi/OmopSketch/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/oxford-pharmacoepi/OmopSketch/actions/workflows/R-CMD-check.yaml)
+  <!-- badges: end -->
+
+The goal of OmopSketch is to ...
+
+## Installation
+
+You can install the development version of OmopSketch from [GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("oxford-pharmacoepi/OmopSketch")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+```{r example}
+library(OmopSketch)
+## basic example code
+```
+
+What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so:
+
+```{r cars}
+summary(cars)
+```
+
+You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. You could also use GitHub Actions to re-render `README.Rmd` every time you push. An example workflow can be found here: <https://github.com/r-lib/actions/tree/v1/examples>.
+
+You can also embed plots, for example:
+
+```{r pressure, echo = FALSE}
+plot(pressure)
+```
+
+In that case, don't forget to commit and push the resulting figure files, so they display on GitHub and CRAN.

README.md

@@ -0,0 +1,57 @@
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# OmopSketch
+
+<!-- badges: start -->
+
+[![R-CMD-check](https://github.com/oxford-pharmacoepi/OmopSketch/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/oxford-pharmacoepi/OmopSketch/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
+
+The goal of OmopSketch is to …
+
+## Installation
+
+You can install the development version of OmopSketch from
+[GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("oxford-pharmacoepi/OmopSketch")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+``` r
+library(OmopSketch)
+## basic example code
+```
+
+What is special about using `README.Rmd` instead of just `README.md`?
+You can include R chunks like so:
+
+``` r
+summary(cars)
+#>      speed           dist       
+#>  Min.   : 4.0   Min.   :  2.00  
+#>  1st Qu.:12.0   1st Qu.: 26.00  
+#>  Median :15.0   Median : 36.00  
+#>  Mean   :15.4   Mean   : 42.98  
+#>  3rd Qu.:19.0   3rd Qu.: 56.00  
+#>  Max.   :25.0   Max.   :120.00
+```
+
+You’ll still need to render `README.Rmd` regularly, to keep `README.md`
+up-to-date. `devtools::build_readme()` is handy for this. You could also
+use GitHub Actions to re-render `README.Rmd` every time you push. An
+example workflow can be found here:
+<https://github.com/r-lib/actions/tree/v1/examples>.
+
+You can also embed plots, for example:
+
+<img src="man/figures/README-pressure-1.png" width="100%" />
+
+In that case, don’t forget to commit and push the resulting figure
+files, so they display on GitHub and CRAN.