Added OMOP CDM documentation data and books

Author: ParamThakkar123

data/OMOPCDM/Data Model Conventions.pdf

@@ -0,0 +1,68 @@
+# API
+
+This is a list of documentation associated with every single **exported** function from `OMOPCDMCohortCreator`.
+There are a few different sections with a brief explanation of what these sections are followed by relevant functions.
+
+```@contents
+Pages = ["api.md"]
+```
+
+
+## Getters
+
+This family of functions are dedicated to only getting information concerning a patient or OMOP CDM database.
+
+```@docs
+GetDatabasePersonIDs
+GetPatientState
+GetPatientGender
+GetPatientRace
+GetPatientEthnicity
+GetPatientAgeGroup
+GetPatientVisits
+GetMostRecentConditions
+GetMostRecentVisit
+GetVisitCondition
+GetDatabaseYearRange
+GetDrugExposureIDs
+GetDrugConceptIDs
+GetDrugAmounts
+GetDatabaseCohorts
+GetCohortSubjects
+GetCohortSubjectStartDate
+GetCohortSubjectEndDate
+GetVisitProcedure
+GetDrugExposureEndDate
+GetDrugExposureStartDate
+```
+
+## Filters
+
+These functions accepts parameters to produce queries that look for specific subpopulations or information given specific patient identifier(s) (i.e. `person_id`). 
+
+```@docs
+VisitFilterPersonIDs
+ConditionFilterPersonIDs
+RaceFilterPersonIDs
+GenderFilterPersonIDs
+StateFilterPersonIDs
+AgeGroupFilterPersonIDs
+```
+
+## Generators
+
+The generator functions are to set generate initial connections to an OMOP CDM database or to finalize resulting data from queries into various outputs. 
+
+```@docs
+GenerateDatabaseDetails
+GenerateGroupCounts
+GenerateTables
+```
+
+## Executors
+
+These functions perform quality assurance checks on data extracts genereated from OMOPCDMCohortCreator queries.
+
+```@docs
+ExecuteAudit
+```

data/OMOPCDM/OMOP CDM v5.pdf

@@ -0,0 +1,117 @@
+# Contributing to OMOPCDMCohortCreator 😁
+
+OMOPCDMCohortCreator is currently under heavy development as we push to a primary release version. 
+We follow a workflow pattern that is directly inspired by the [development workflow guide](http://docs.juliaplots.org/latest/contributing/#Development-Workflow-1) found in [`Plots.jl`](https://github.com/JuliaPlots/Plots.jl).
+The general workflow we expect contributors to adhere to is as follows:
+
+## 1. Create an Issue about the Problem 📝
+
+If you want to add functionality or to work on a bug you found, open an issue first.
+That'll save you from doing work that we may not support for OMOPCDMCohortCreator.
+
+## 2. Fork the repo to your account 🍴
+
+## 3. Create a branch based on what you are developing 🌳
+
+Before making a branch, make sure to check that you are even with master via the following commands within your fork:
+
+```sh
+git fetch origin
+git checkout master
+git merge --ff-only origin/master
+```
+
+> The `--ff-only` flag will "fast forward" to newer commits. It will not create new merge commits.
+
+Then, go ahead and create a branch that you could edit with the changes you want to see.
+This is done by going into the root and typing: `git branch -b [name of your branch]`
+
+## 4. Test, code, and commit ✏️
+
+Once you have a fork, it is useful to make sure the fork was successful.
+To verify that everything is operational, let's test it.
+The following procedure is as follows:
+
+1. Go into the root of your fork:
+
+`cd OMOPCDMCohortCreator`
+
+2. Open your Julia REPL and type the following within the repo:
+
+```julia-repl
+julia> ]
+(@v###) pkg> activate .
+(@v###) pkg> test
+```
+
+This might take some time, but if the installation on your computer is successful, it should say all tests passed.
+
+After making the changes you wanted to make, run the tests again to make sure you did not introduce any breaking changes.
+If everything passed, we can continue on to the next step.
+If not, it is the responsibility of the contributor to resolve any conflicts or failing tests.
+Don't worry!
+We're happy to help you resolve errors. 😄
+If you are stuck, go ahead and continue with this tutorial.
+
+The way we do this is in three steps:
+
+1. Add the files you have added or changed via `git add` 
+
+2. After adding the files, we need to say what you did to the files (i.e. commit the files). This can be accomplished thusly: `git commit -m "your message"` 
+
+3. Finally, let's push these changes to GitHub using `git push --set-upstream origin [name of the branch you made]`
+
+## 5. Submitting your changes to the main project ✅
+
+Almost done! Go to your fork and there should be a section that asks you to make a pull request (PR) from your branch. This allows the maintainers of OMOPCDMCohortCreator to see if they can add your changes to the main project. If not, you can click the "New pull request" button.
+
+Make sure the "base" branch is OMOPCDMCohortCreator `dev` and the "compare" branch is the branch on your fork. 
+To your PR, add an informative title and description, and link your PR to relevant issues or discussions. 
+Finally, click "Create pull request". 
+
+You may get some questions about it, and possibly suggestions of how to make it ready to go into the main project. 
+If you had test errors or problems, we are happy to help you. 
+Then, if all goes according to plan, it gets merged... **Thanks for the contribution!!** 🎉 🎉 🎉
+
+## Note on Adding Dependencies 📚
+
+As a rule, we try to avoid having too many dependencies.
+Therefore, we request that if you have a PR that adds a new dependency, please have opened an issue previously.
+
+### Adding Core Dependencies 📒
+
+If you are working on introducing a new core dependency, make sure to add that dependency to the main `Project.toml` for `OMOPCDMCohortCreator`.
+To do this, follow these steps:
+
+1. Enter the root of the `OMOPCDMCohortCreator` directory 
+
+```sh
+cd /path/to/OMOPCDMCohortCreator.jl
+```
+
+2. Activate the `OMOPCDMCohortCreator` environment and add the dependency:
+
+```julia-repl
+julia> ]
+(@v###) pkg> activate .
+(OMOPCDMCohortCreator) pkg> add [NAME OF DEPENDENCY]
+```
+
+### Adding Test Dependencies 📋
+
+If you are  introducing a new test dependency, make sure to add that dependency to the `Project.toml` located in the `OMOPCDMCohortCreator` test directory.
+To do this, follow these steps:
+
+1. Enter the test directory inside of the `OMOPCDMCohortCreator` directory 
+
+```sh
+cd /path/to/OMOPCDMCohortCreator.jl/test/
+```
+
+2. Activate the `OMOPCDMCohortCreator` test environment and add the dependency:
+
+```julia
+julia> ]
+(@v###) pkg> activate .
+(test) pkg> add [NAME OF DEPENDENCY]
+```

data/OMOPCDM/OMOP Common Data Model.pdf

@@ -0,0 +1,48 @@
+# Welcome to the `OMOPCDMCohortCreator.jl` Docs! 👋
+
+> Create cohorts from databases utilizing the OMOP CDM.
+
+This package uses a functional approach to query databases in the [OMOP Common Data Model format](https://www.ohdsi.org/data-standardization/the-common-data-model/) whereby you could build rapidly lines of inquiry into the database.
+Furthermore, this package is a companion to those tools found in the [HADES](https://ohdsi.github.io/Hades/) ecosystem.
+To get started, visit the [Tutorials](@ref) section as well as visit the [API](@ref) section to see all the functions available.
+If you want to contribute, please check out our [Contributing](@ref) guide!
+
+## Main Features 🔧
+
+The biggest features of this package are:
+
+- Incremental building blocks for creating an analysis pipeline in the form of (more information in [API](@ref)):
+  - "Getter" functions to "get" information from a database 
+  - "Filter" functions to "filter" information from a database 
+  - "Generator" functions to "generate" database information and connections
+  - "Executor" functions to "execute" on retrieved information 
+- Automatic targeting and support for the SQL flavors (via [FunSQL.jl](https://mechanicalrabbit.github.io/FunSQL.jl/)):
+  - `postgresql`
+  - `sqlite`
+  - `redshift`
+- Prepare SQL queries if unable to connect to database via OMOPCDMCohortCreator that could then be run on a given SQL database directly
+- Does not mutate database or require temp tables
+- Interoperable with the R language via [JuliaConnectoR](https://github.com/stefan-m-lenz/JuliaConnectoR) to work directly within R syntax (see [Tutorials](@ref))
+- Readily parallelizable via [Distributed.jl](https://docs.julialang.org/en/v1/manual/distributed-computing/)
+- Complementary to [OHDSI HADES](https://ohdsi.github.io/Hades/) ecosystem tools
+- Extensive [test suite](https://github.com/JuliaHealth/OMOPCDMCohortCreator.jl/tree/main/test) to ensure correctness and compliance with privacy preserving methods (HITECH, etc.)
+
+## Why? 🤔
+
+This package was created as the result of work in the [MentalHealthEquity](https://github.com/ohdsi-studies/MentalHealthEquity) network study.
+Phenotype definitions work alongside this package and OMOPCDMCohortCreator allows an investigator to quickly iterate and build on top of phenotype definitions and/or concept sets.
+Where I personally see this being of use is when an investigator needs to quickly pull information out of a database, iterate and test ideas for a formal phenotype definition rapidly, and reason simply about queries.
+
+## Why Julia? 🤓
+
+Julia itself is built for High Performance Computing and readability.
+We wanted to work in a language that could handle the high amounts of data that could manifest in working with OMOP CDM databases.
+Julia not only made sense for "big data" operations and readability but also was attractive due to it's ability to work with other programming languages such as R or Python.
+Therefore, the benefit is:
+
+- High performance more easily reached on all ranges of hardware
+- Lower barrier to entry for new contributors
+- Interoperation with other programming languages
+
+In our eyes, we do not see anything lost by choosing Julia as we can easily bridge to other languages.
+The idea is that this approach can keep users in the language they are comfortable with while working with a flexible package to quickly perform analyses.

data/OMOPCDM/OMOPCDM_FAQ.pdf

@@ -0,0 +1,10 @@
+# Tutorials
+
+```@contents
+Pages = ["tutorials.md"]
+```
+
+These tutorials are designed to equip new users with how to get started with OMOPCDMCohortCreator:
+
+- [Beginner Tutorial](tutorials/beginner_tutorial.md) - a step by step guide on using OMOPCDMCohortCreator to run a mini characterization study with minimal Julia knowledge required! **Difficulty: Easy**
+- [Using OMOPCDMCohortCreator with R](tutorials/r_tutorial.md) - a guide on how to use OMOPCDMCohortCreator within R to run a mini characterization study. **Difficulty: Medium**