cohortBuilder

Overview

cohortBuilder provides common API for creating cohorts on multiple data sources, such as local data frame, database schema or external data api.

With only two steps:

Configuring data source with set_source.
Initializing cohort with cohort.

You can operate on data using common methods, such as:

filter - to define and run to apply filtering rules,
step - to perform multi-stage filtering,
get_data, stat, attrition, plot_data - to extract, sum up or visualize your cohort data.

With cohortBuilder you can share the cohort easier with useful methods:

code - to get reproducible cohort creation code,
get_state - to get cohort state (e.g. in JSON) that can be then easily restored with restore.

Or modify the cohort configuration with:

add_filter, rm_filter, update_filter - to manage filters definition
add_step, rm_step - to manage filtering steps,
update_source - to manage the cohort source.

Data sources and extensions

The goal of cohortBuilder is to provide common API for creating data cohorts, but also to be easily extendable for working on different data sources (and interactive dashboards).

cohortBuilder allows to operate on local data frames (or list of data frames), yet you may easily switch to a database source by loading cohortBuilder.db layer.

As a standalone R package, you use cohortBuilder to perform all the operations in non-interactive R script, but its shiny layer shinyCohortBuilder package helps you to easily switch to intuitive gui mode. More to that you may integrate cohortBuilder with your custom Shiny application.

If you want to learn how to write custom source extension, please check vignette("custom-extensions").

Installation

# CRAN version
install.packages("cohortBuilder")

# Latest development version
remotes::install_github("https://github.com/r-world-devs/cohortBuilder")

Usage

librarian_source <- set_source(
  as.tblist(librarian)
)

coh <- librarian_source %>% 
  cohort(
    filter(
      "discrete", id = "author", dataset = "books", 
      variable = "author", value = "Dan Brown"
    ),
    filter(
      "range", id = "copies", dataset = "books", 
      variable = "copies", range = c(5, 10)
    ),
    filter(
      "date_range", id = "registered", dataset = "borrowers", 
      variable = "registered", range = c(as.Date("2010-01-01"), Inf)
    ) 
  ) %>% 
  run()

get_data(coh)
#> $books
#> # A tibble: 1 × 6
#>   isbn          title             genre                       publisher 
#>   <chr>         <chr>             <chr>                       <chr>     
#> 1 0-385-50420-9 The Da Vinci Code Crime, Thriller & Adventure Transworld
#>   author    copies
#>   <chr>      <int>
#> 1 Dan Brown      7
#> 
#> $borrowers
#> # A tibble: 8 × 6
#>   id     registered address                                         
#>   <chr>  <date>     <chr>                                           
#> 1 000013 2011-09-30 534 Iroquois Ave. Watertown, MA 02472           
#> 2 000014 2013-01-12 7968 Victoria Drive Dearborn, MI 48124          
#> 3 000015 2013-12-24 9484 Somerset Road Romeoville, IL 60446         
#> 4 000016 2014-01-20 48 Prairie Ave. Palos Verdes Peninsula, CA 90274
#> 5 000017 2014-04-07 8501 Lawrence Rd. Terre Haute, IN 47802         
#>   name                    phone_number program 
#>   <chr>                   <chr>        <chr>   
#> 1 Dr. Sharif Kunde        104-832-8013 premium 
#> 2 Marlena Reichert PhD    044-876-8419 vip     
#> 3 Mr. Brandan Oberbrunner 568-044-7463 vip     
#> 4 Lloyd Adams III         001-017-0211 standard
#> 5 Randy Ziemann           895-995-2326 premium 
#> # ℹ 3 more rows
#> 
#> $issues
#> # A tibble: 50 × 4
#>   id     borrower_id isbn              date      
#>   <chr>  <chr>       <chr>             <date>    
#> 1 000001 000019      0-676-97976-9     2015-03-17
#> 2 000002 000010      978-0-7528-6053-4 2008-09-13
#> 3 000003 000016      0-09-177373-3     2014-09-28
#> 4 000004 000005      0-224-06252-2     2005-11-14
#> 5 000005 000004      0-340-89696-5     2006-03-19
#> # ℹ 45 more rows
#> 
#> $returns
#> # A tibble: 30 × 2
#>   id     date      
#>   <chr>  <date>    
#> 1 000001 2015-04-06
#> 2 000003 2014-10-23
#> 3 000004 2005-12-29
#> 4 000005 2006-03-26
#> 5 000006 2016-08-30
#> # ℹ 25 more rows
#> 
#> attr(,"class")
#> [1] "tblist"
#> attr(,"call")
#> as.tblist(librarian)

coh <- librarian_source %>% 
  cohort() %->% 
  step(
    filter(
      "discrete", id = "author", dataset = "books", 
      variable = "author", value = "Dan Brown"
    ),
    filter(
      "date_range", id = "registered", dataset = "borrowers", 
      variable = "registered", range = c(as.Date("2010-01-01"), Inf)
    )
  ) %->% 
  step(
    filter(
      "range", id = "copies", dataset = "books", 
      variable = "copies", range = c(5, 10)
    )
  ) %>% 
  run()

get_data(coh, step_id = 1)
#> $books
#> # A tibble: 2 × 6
#>   isbn          title             genre                       publisher 
#>   <chr>         <chr>             <chr>                       <chr>     
#> 1 0-385-50420-9 The Da Vinci Code Crime, Thriller & Adventure Transworld
#> 2 0-671-02735-2 Angels and Demons Crime, Thriller & Adventure Transworld
#>   author    copies
#>   <chr>      <int>
#> 1 Dan Brown      7
#> 2 Dan Brown      4
#> 
#> $borrowers
#> # A tibble: 8 × 6
#>   id     registered address                                         
#>   <chr>  <date>     <chr>                                           
#> 1 000013 2011-09-30 534 Iroquois Ave. Watertown, MA 02472           
#> 2 000014 2013-01-12 7968 Victoria Drive Dearborn, MI 48124          
#> 3 000015 2013-12-24 9484 Somerset Road Romeoville, IL 60446         
#> 4 000016 2014-01-20 48 Prairie Ave. Palos Verdes Peninsula, CA 90274
#> 5 000017 2014-04-07 8501 Lawrence Rd. Terre Haute, IN 47802         
#>   name                    phone_number program 
#>   <chr>                   <chr>        <chr>   
#> 1 Dr. Sharif Kunde        104-832-8013 premium 
#> 2 Marlena Reichert PhD    044-876-8419 vip     
#> 3 Mr. Brandan Oberbrunner 568-044-7463 vip     
#> 4 Lloyd Adams III         001-017-0211 standard
#> 5 Randy Ziemann           895-995-2326 premium 
#> # ℹ 3 more rows
#> 
#> $issues
#> # A tibble: 50 × 4
#>   id     borrower_id isbn              date      
#>   <chr>  <chr>       <chr>             <date>    
#> 1 000001 000019      0-676-97976-9     2015-03-17
#> 2 000002 000010      978-0-7528-6053-4 2008-09-13
#> 3 000003 000016      0-09-177373-3     2014-09-28
#> 4 000004 000005      0-224-06252-2     2005-11-14
#> 5 000005 000004      0-340-89696-5     2006-03-19
#> # ℹ 45 more rows
#> 
#> $returns
#> # A tibble: 30 × 2
#>   id     date      
#>   <chr>  <date>    
#> 1 000001 2015-04-06
#> 2 000003 2014-10-23
#> 3 000004 2005-12-29
#> 4 000005 2006-03-26
#> 5 000006 2016-08-30
#> # ℹ 25 more rows
#> 
#> attr(,"class")
#> [1] "tblist"
#> attr(,"call")
#> as.tblist(librarian)

get_data(coh, step_id = 2)
#> $books
#> # A tibble: 1 × 6
#>   isbn          title             genre                       publisher 
#>   <chr>         <chr>             <chr>                       <chr>     
#> 1 0-385-50420-9 The Da Vinci Code Crime, Thriller & Adventure Transworld
#>   author    copies
#>   <chr>      <int>
#> 1 Dan Brown      7
#> 
#> $borrowers
#> # A tibble: 8 × 6
#>   id     registered address                                         
#>   <chr>  <date>     <chr>                                           
#> 1 000013 2011-09-30 534 Iroquois Ave. Watertown, MA 02472           
#> 2 000014 2013-01-12 7968 Victoria Drive Dearborn, MI 48124          
#> 3 000015 2013-12-24 9484 Somerset Road Romeoville, IL 60446         
#> 4 000016 2014-01-20 48 Prairie Ave. Palos Verdes Peninsula, CA 90274
#> 5 000017 2014-04-07 8501 Lawrence Rd. Terre Haute, IN 47802         
#>   name                    phone_number program 
#>   <chr>                   <chr>        <chr>   
#> 1 Dr. Sharif Kunde        104-832-8013 premium 
#> 2 Marlena Reichert PhD    044-876-8419 vip     
#> 3 Mr. Brandan Oberbrunner 568-044-7463 vip     
#> 4 Lloyd Adams III         001-017-0211 standard
#> 5 Randy Ziemann           895-995-2326 premium 
#> # ℹ 3 more rows
#> 
#> $issues
#> # A tibble: 50 × 4
#>   id     borrower_id isbn              date      
#>   <chr>  <chr>       <chr>             <date>    
#> 1 000001 000019      0-676-97976-9     2015-03-17
#> 2 000002 000010      978-0-7528-6053-4 2008-09-13
#> 3 000003 000016      0-09-177373-3     2014-09-28
#> 4 000004 000005      0-224-06252-2     2005-11-14
#> 5 000005 000004      0-340-89696-5     2006-03-19
#> # ℹ 45 more rows
#> 
#> $returns
#> # A tibble: 30 × 2
#>   id     date      
#>   <chr>  <date>    
#> 1 000001 2015-04-06
#> 2 000003 2014-10-23
#> 3 000004 2005-12-29
#> 4 000005 2006-03-26
#> 5 000006 2016-08-30
#> # ℹ 25 more rows
#> 
#> attr(,"class")
#> [1] "tblist"
#> attr(,"call")
#> as.tblist(librarian)

update_filter(
  coh, step_id = 1, filter_id = "author",
  range = c(5, 6)
)
run(coh)

get_data(coh, step_id = 2)
#> $books
#> # A tibble: 1 × 6
#>   isbn          title             genre                       publisher 
#>   <chr>         <chr>             <chr>                       <chr>     
#> 1 0-385-50420-9 The Da Vinci Code Crime, Thriller & Adventure Transworld
#>   author    copies
#>   <chr>      <int>
#> 1 Dan Brown      7
#> 
#> $borrowers
#> # A tibble: 8 × 6
#>   id     registered address                                         
#>   <chr>  <date>     <chr>                                           
#> 1 000013 2011-09-30 534 Iroquois Ave. Watertown, MA 02472           
#> 2 000014 2013-01-12 7968 Victoria Drive Dearborn, MI 48124          
#> 3 000015 2013-12-24 9484 Somerset Road Romeoville, IL 60446         
#> 4 000016 2014-01-20 48 Prairie Ave. Palos Verdes Peninsula, CA 90274
#> 5 000017 2014-04-07 8501 Lawrence Rd. Terre Haute, IN 47802         
#>   name                    phone_number program 
#>   <chr>                   <chr>        <chr>   
#> 1 Dr. Sharif Kunde        104-832-8013 premium 
#> 2 Marlena Reichert PhD    044-876-8419 vip     
#> 3 Mr. Brandan Oberbrunner 568-044-7463 vip     
#> 4 Lloyd Adams III         001-017-0211 standard
#> 5 Randy Ziemann           895-995-2326 premium 
#> # ℹ 3 more rows
#> 
#> $issues
#> # A tibble: 50 × 4
#>   id     borrower_id isbn              date      
#>   <chr>  <chr>       <chr>             <date>    
#> 1 000001 000019      0-676-97976-9     2015-03-17
#> 2 000002 000010      978-0-7528-6053-4 2008-09-13
#> 3 000003 000016      0-09-177373-3     2014-09-28
#> 4 000004 000005      0-224-06252-2     2005-11-14
#> 5 000005 000004      0-340-89696-5     2006-03-19
#> # ℹ 45 more rows
#> 
#> $returns
#> # A tibble: 30 × 2
#>   id     date      
#>   <chr>  <date>    
#> 1 000001 2015-04-06
#> 2 000003 2014-10-23
#> 3 000004 2005-12-29
#> 4 000005 2006-03-26
#> 5 000006 2016-08-30
#> # ℹ 25 more rows
#> 
#> attr(,"class")
#> [1] "tblist"
#> attr(,"call")
#> as.tblist(librarian)

code(coh)
#> .pre_filtering <- function(source, data_object, step_id) {
#>     for (dataset in names(data_object)) {
#>         attr(data_object[[dataset]], "filtered") <- FALSE
#>     }
#>     return(data_object)
#> }
#> .run_binding <- function(source, binding_key, data_object_pre, data_object_post,
#>     ...) {
#>     binding_dataset <- binding_key$update$dataset
#>     dependent_datasets <- names(binding_key$data_keys)
#>     active_datasets <- data_object_post %>%
#>         purrr::keep(~attr(., "filtered")) %>%
#>         names()
#>     if (!any(dependent_datasets %in% active_datasets)) {
#>         return(data_object_post)
#>     }
#>     key_values <- NULL
#>     common_key_names <- paste0("key_", seq_along(binding_key$data_keys[[1]]$key))
#>     for (dependent_dataset in dependent_datasets) {
#>         key_names <- binding_key$data_keys[[dependent_dataset]]$key
#>         tmp_key_values <- dplyr::distinct(data_object_post[[dependent_dataset]][,
#>             key_names, drop = FALSE]) %>%
#>             stats::setNames(common_key_names)
#>         if (is.null(key_values)) {
#>             key_values <- tmp_key_values
#>         } else {
#>             key_values <- dplyr::inner_join(key_values, tmp_key_values, by = common_key_names)
#>         }
#>     }
#>     data_object_post[[binding_dataset]] <- dplyr::inner_join(switch(as.character(binding_key$post),
#>         `FALSE` = data_object_pre[[binding_dataset]], `TRUE` = data_object_post[[binding_dataset]]),
#>         key_values, by = stats::setNames(common_key_names, binding_key$update$key))
#>     if (binding_key$activate) {
#>         attr(data_object_post[[binding_dataset]], "filtered") <- TRUE
#>     }
#>     return(data_object_post)
#> }
#> source <- list(dtconn = as.tblist(librarian))
#> data_object <- source$dtconn
#> step_id <- "1"
#> pre_data_object <- data_object
#> data_object <- .pre_filtering(source, data_object, "1")
#> data_object[["books"]] <- data_object[["books"]] %>%
#>     dplyr::filter(author %in% c("Dan Brown", NA))
#> attr(data_object[["books"]], "filtered") <- TRUE
#> data_object[["borrowers"]] <- data_object[["borrowers"]] %>%
#>     dplyr::filter((registered <= Inf & registered >= 14610) | is.na(registered))
#> attr(data_object[["borrowers"]], "filtered") <- TRUE
#> data_object <- .post_filtering(source, data_object, "1")
#> for (binding_key in binding_keys) {
#>     data_object <- .run_binding(source, binding_key, pre_data_object, data_object)
#> }
#> step_id <- "2"
#> data_object <- .pre_filtering(source, data_object, "2")
#> data_object[["books"]] <- data_object[["books"]] %>%
#>     dplyr::filter((copies <= 10 & copies >= 5) | is.na(copies))
#> attr(data_object[["books"]], "filtered") <- TRUE
#> data_object <- .post_filtering(source, data_object, "2")

attrition(coh, dataset = "books")

get_state(coh, json = TRUE)
#> [{"step":"1","filters":[{"range":[5,6],"type":"discrete","id":"author","name":"author","variable":"author","value":"Dan Brown","dataset":"books","keep_na":true,"description":null,"active":true},{"type":"date_range","id":"registered","name":"registered","variable":"registered","range":["2010-01-01","Inf"],"dataset":"borrowers","keep_na":true,"description":null,"active":true}]},{"step":"2","filters":[{"type":"range","id":"copies","name":"copies","variable":"copies","range":[5,10],"dataset":"books","keep_na":true,"description":null,"active":true}]}]

Acknowledgement

Special thanks to:

Kamil Wais for highlighting the need for the package and its relevance to real-world applications.
Adam Foryś for technical support, numerous suggestions for the current and future implementation of the package.
Paweł Kawski for indication of initial assumptions about the package based on real-world medical data.

Getting help

In a case you found any bugs, have feature request or general question please file an issue at the package Github. You may also contact the package author directly via email at [email protected].

Name		Name	Last commit message	Last commit date
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R		R
data		data
examples		examples
inst		inst
man		man
pkgdown/favicon		pkgdown/favicon
renv		renv
tests		tests
vignettes		vignettes
.Rbuildignore		.Rbuildignore
.gitignore		.gitignore
.gitmodules		.gitmodules
.publish_rpackage		.publish_rpackage
DESCRIPTION		DESCRIPTION
LICENSE		LICENSE
NAMESPACE		NAMESPACE
NEWS.md		NEWS.md
README.Rmd		README.Rmd
README.md		README.md
_pkgdown.yml		_pkgdown.yml
cohortBuilder.Rproj		cohortBuilder.Rproj
meta_data.yaml		meta_data.yaml
renv.lock		renv.lock

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