add readme

.Rbuildignore

@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 ^extras$
 ^LICENSE\.md$
+^README\.Rmd$

.Rhistory

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+x <- c(1, 2, 3, 4, 5)
+expand.grid(c)
+expand.grid(x)
+expand.grid(rep(list(x), length(x)))
+5*5*5*5*5
+lapply(names, c(0, 1))
+lapply(names, function(x){c(0, 1)})
+names
+names <- c("cohort1", "cohort2", "cohort3", "cohort3")
+names <- c("cohort1", "cohort2", "cohort3", "cohort4")
+lapply(names, function(x){c(0, 1)})
+lapply(names, function(x){c(0, 1)}) |>
+expand.grid()
+lapply(names, function(x){c(0, 1)}) |>
+expand.grid() |>
+rlang::set_names(name)
+lapply(names, function(x){c(0, 1)}) |>
+expand.grid() |>
+rlang::set_names(names)
+lapply(names, function(x){c(0, 1)}) |>
+expand.grid() |>
+rlang::set_names(names) |>
+dplyr::as_tibble()
+lapply(names, function(x){c(0, 1)}) |>
+expand.grid() |>
+rlang::set_names(names) |>
+dplyr::as_tibble() %>%
+dplyr::mutate("cohort_definition_id" = dplyr::row_number())
+lapply(names, function(x){c(0, 1)}) |>
+expand.grid() |>
+rlang::set_names(names) |>
+dplyr::as_tibble() |>
+dplyr::mutate("cohort_definition_id" = dplyr::row_number())
+getCohortSetMutuallyEclusive <- function(names) {
+lapply(names, function(x){c(0, 1)}) |>
+expand.grid() |>
+rlang::set_names(names) |>
+dplyr::as_tibble() |>
+dplyr::mutate("cohort_definition_id" = dplyr::row_number())
+}
+getCohortSetMutuallyEclusive(names)

.gitignore

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

README.Rmd

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+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# CohortConstructor
+
+<!-- badges: start -->
+[![CRAN status](https://www.r-pkg.org/badges/version/CohortConstructor)](https://CRAN.R-project.org/package=CohortConstructor)
+[![codecov.io](https://codecov.io/github/oxford-pharmacoepi/CohortConstructor/coverage.svg?branch=main)](https://app.codecov.io/github/oxford-pharmacoepi/CohortConstructor?branch=main)
+[![R-CMD-check](https://github.com/oxford-pharmacoepi/CohortConstructor/workflows/R-CMD-check/badge.svg)](https://github.com/oxford-pharmacoepi/CohortConstructor/actions)
+[![Lifecycle:Experimental](https://img.shields.io/badge/Lifecycle-Experimental-339999)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+<!-- badges: end -->
+
+The goal of CohortConstructor is to help on the creation of cohorts in the OMOP Common Data Model.
+
+## Installation
+
+You can install the development version of CohortConstructor from [GitHub](https://github.com/) with:
+
+``` {r, eval = FALSE}
+# install.packages("devtools")
+devtools::install_github("oxford-pharmacoepi/CohortConstructor")
+```
+
+## Example
+
+Generate a combination cohort.
+
+```{r}
+library(PatientProfiles)
+library(CohortConstructor)
+library(CDMConnector)
+
+cdm <- mockPatientProfiles()
+cdm <- generateCombinationCohortSet(cdm = cdm, name = "cohort3", targetCohortName = "cohort2")
+
+cdm$cohort3
+
+cohortSet(cdm$cohort3)
+
+cdmDisconnect(cdm)
+```
+

README.md

@@ -0,0 +1,64 @@
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# CohortConstructor
+
+<!-- badges: start -->
+
+[![CRAN
+status](https://www.r-pkg.org/badges/version/CohortConstructor)](https://CRAN.R-project.org/package=CohortConstructor)
+[![codecov.io](https://codecov.io/github/oxford-pharmacoepi/CohortConstructor/coverage.svg?branch=main)](https://app.codecov.io/github/oxford-pharmacoepi/CohortConstructor?branch=main)
+[![R-CMD-check](https://github.com/oxford-pharmacoepi/CohortConstructor/workflows/R-CMD-check/badge.svg)](https://github.com/oxford-pharmacoepi/CohortConstructor/actions)
+[![Lifecycle:Experimental](https://img.shields.io/badge/Lifecycle-Experimental-339999)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+<!-- badges: end -->
+
+The goal of CohortConstructor is to help on the creation of cohorts in
+the OMOP Common Data Model.
+
+## Installation
+
+You can install the development version of CohortConstructor from
+[GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("oxford-pharmacoepi/CohortConstructor")
+```
+
+## Example
+
+Generate a combination cohort.
+
+``` r
+library(PatientProfiles)
+#> Warning: package 'PatientProfiles' was built under R version 4.2.3
+library(CohortConstructor)
+library(CDMConnector)
+
+cdm <- mockPatientProfiles()
+cdm <- generateCombinationCohortSet(cdm = cdm, name = "cohort3", targetCohortName = "cohort2")
+
+cdm$cohort3
+#> # Source:   table<cohort3> [4 x 4]
+#> # Database: DuckDB 0.7.1 [martics@Windows 10 x64:R 4.2.1/:memory:]
+#>   cohort_definition_id subject_id cohort_start_date cohort_end_date
+#>                  <int>      <dbl> <date>            <date>         
+#> 1                    2          1 2020-05-25        2020-05-25     
+#> 2                    1          1 2019-12-30        2019-12-30     
+#> 3                    1          1 2020-05-25        2020-05-25     
+#> 4                    3          1 2020-05-25        2020-05-25
+
+cohortSet(cdm$cohort3)
+#> # A tibble: 7 × 6
+#>   cohort_definition_id cohort_name cohort_1 cohort_2 cohort_3 mutually_exclusive
+#>                  <int> <chr>          <dbl>    <dbl>    <dbl> <lgl>             
+#> 1                    1 cohort_1           1       NA       NA FALSE             
+#> 2                    2 cohort_2          NA        1       NA FALSE             
+#> 3                    3 cohort_1+c…        1        1       NA FALSE             
+#> 4                    4 cohort_3          NA       NA        1 FALSE             
+#> 5                    5 cohort_1+c…        1       NA        1 FALSE             
+#> 6                    6 cohort_2+c…       NA        1        1 FALSE             
+#> 7                    7 cohort_1+c…        1        1        1 FALSE
+
+cdmDisconnect(cdm)
+```