IBEEM-MSU · billspat · Sep 26, 2025 · Mar 13, 2026 · Mar 13, 2026 · Mar 13, 2026
diff --git a/.gitignore b/.gitignore
@@ -6,8 +6,9 @@ renv/
 ~$*.xlsx
 *.json
 inst/doc
-int/credentials/*.json
+inst/credentials/
 *.csv
+L0
 
 
 
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,11 +2,19 @@ Package: collaboratR
 Title: validation and version control for level 0 data using Google Drive
 Version: 0.0.0.9100
 Authors@R: 
-    person("Patrick", "Bills", , "billspat@msu.edu", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0003-4235-255X"))
+    c(person("Patrick S.", "Bills", "", "billspat@msu.edu", role = c("aut", "cre"),
+        comment = c(ORCID = "0000-0003-4235-255X")),
+    person("Ashwini", "Ramesh", "", "ashwini.ramesh@yale.edu", role = c("aut","dtc"),
+        comment = c(ORCID = "0000-0003-1629-7024")),
+    person("Laís", "Petri", "", "petrila1@msu.edu", role = c("aut", "dtc"),
+        comment = c(ORCID = "0000-0001-9727-1939")),
+    person("Phoebe Lehman", "Zarnetske", "", "plz@msu.edu", role = c("aut","fnd"),
+        comment = c(ORCID = "0000-0001-6257-6951"))
+    )
 Description: Data management for Community Ecology RULES project of MSU IBEEM, 
-  using the EDI data package framework.  Reads data entered using from google drive
-  and validates using standard set of rules.   
+  using the EDI data package framework.  Reads data and schema from google drive,
+  validates using standard set of rules, and combines into CSV. 
+URL: https://ibeem-msu.github.io/collaboratR, https://github.com/IBEEM-MSU/collaboratR
 License: MIT + file LICENSE
 Suggests: 
     knitr,
@@ -20,10 +28,11 @@ Imports:
     gargle,
     googledrive,
     googlesheets4,
+    httpuv,
     readr,
     validate,
     dplyr
 VignetteBuilder: knitr
 Depends: 
-    R (>= 2.10)
+    R (>= 4.1.0)
 LazyData: true
diff --git a/R/install_dev_packages.r b/R/install_dev_packages.r
@@ -0,0 +1,3 @@
+
+dev_packages <- c('devtools', 'pkgdown', 'renv')
+install.packages(dev_packages, repos = "https://cran.rstudio.com")
diff --git a/vignettes/validating_commassemblyrules.Rmd → R/validating_commassemblyrules.Rmd b/vignettes/validating_commassemblyrules.Rmd → R/validating_commassemblyrules.Rmd
diff --git a/README.Rmd b/README.Rmd
@@ -15,37 +15,83 @@ knitr::opts_chunk$set(
 
 # collaboratR
 
-### [MSU IBEEM](https://ibeem.msu.edu) commRULES project
+**A package to support collaborative meta-analysis for [MSU IBEEM](https://ibeem.msu.edu)**
+
+### Authors: 
+
+- Patrick S Bills
+- Ashwini Ramesh
+- Laís Petri
+- Phoebe Lehman Zarnetske, PI and Director, IBEEM
+
+### Contributors: 
+
+- Kelly Kapsar, Data Scientist, IBEEM
+- Alejandra Martinez Blancas 
+- Amar Deep Tiwari
 
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
-[![CRAN status](https://www.r-pkg.org/badges/version/collaboratR)](https://CRAN.R-project.org/package=collaboratR)
 <!-- badges: end -->
 
-*This is very early version under heavy development.*
+### Motivation
 
-This R package is part of 3 repositories that support the data entry, validation and accumulation of a meta-analysis for the commRULES project.  
+Performing a Meta-analysis requires collating and harmonizing data extracted 
+from many different sources but most frequently scientific publications.  
+Collaborative meta-analysis requires a group of scientists to collectively develop
+and agree on their goals, type of data extracted, format of the those data, and to 
+do so extremely consistently across papers.  This package helps to support that 
+efficiently by the easy-to-use Google Sheets for data definition and data entry.
+The workflow in this project can read directly from Google sheets into CSVs and
+validate the structure of a google sheet as well as the data using the Validate package. 
 
-1. commRULES data: version controlled data collection for tracking provenance using git, this is the L0 and L1  layers in the EDI framework
-2. collaboratR: commRULES data management code for L0 and L0->L1 layer in EDI framework
-3. commRULES-analysis: R code for reproducible data analysis , L1->L2 layers in EDI framework
+<!-- insert description of the EDI data transform framework here -->
 
-## Installation - Package
+Originally, this This R package was part of 3 repositories that support the 
+data entry, validation and accumulation of a meta-analysis for a research project 
+sponsored by MSU IBEEM  
+
+
+1. collaboratR: data management code for L0 and L0->L1 layer in EDI framework
+1. data: version controlled data collection for tracking provenance using git, 
+   this is the L0 and L1  layers in the EDI framework. the collaboratR package
+   assists with data transfer and validation from Google drive into the data repository. 
+1. analysis: R code for reproducible data analysis , L1->L2 layers in EDI framework, 
+   using data in the data repository.  
 
-This package uses [renv](https://rstudio.github.io/renv/) to manage the packages you need to install, which creates an `renv.lock` file for you.  
+## Installation - Package
 
-- install RENV: this can go into your R environment used for all packages, so fire up R with now project select and `install.packages('renv')`
 - clone this repository into a [new Rstudio project](https://docs.posit.co/ide/user/ide/guide/code/projects.html) and open it
-- inside the Rstudio project in the R console, `renv::restore()`
 
-## Google Drive Project Setup
+- install required packages: 
+  This package uses [renv](https://rstudio.github.io/renv/) to manage the packages you need to install, which creates an `renv.lock` file for you.     1. install the renv package: this can go into your R environment used for all packages.  
+  2. in R run `renv::restore()` or if that complains about R versions
+
+*additional packages are required to build the package and this website, source the script*
+`R/install_dev_packages.R`
+
+### Installation/Testing
+
+Google drive in this package is set to interaction.  To run any building, installing or checking in R, 
+you must first manually connect to google drive, which must be set-up properly first.  
+
+See the vignette in this package "Google Sheets API setup using Google Cloud", 
+or in this source code see [Google Sheets Vignette RMD](vignettes/google_sheets_api.Rmd)
+
+Once set-up you may have to log-in manually prior to running tests or checks, 
+use 
+
+```r
+source("R/gdrive.R")
 
-Using google drive via MSU seems to require creating a Google Cloud project, enabling the proper
-APIs and and assigning permissions
+## Data Google Drive Project Setup
 
-Note that for safety, this package only reads from google drive and it never writes to google drive.  Therefore it only requests 'read-only' access.  
+See the Vignette ["Google Sheets API setup using Google Cloud"](vignettes/google_sheets_api.Rmd) 
+for details about setting up google sheets connection with R, which requires
+a google cloud project in your institution
 
-Full documentation for how to set this up is forthcoming
+Note that for safety, this package only reads from google drive and it never
+writes to google drive.  Therefore it only requests 'read-only' access.
 
 ## Usage
 

diff --git a/README.md b/README.md
@@ -3,39 +3,114 @@
 
 # collaboratR
 
-### [MSU IBEEM](https://ibeem.msu.edu) commRULES project
+**A package to support collaborative meta-analysis for [MSU
+IBEEM](https://ibeem.msu.edu)**
+
+### Authors:
+
+- Patrick S Bills
+- Ashwini Ramesh
+- Laís Petri
+- Phoebe Lehman Zarnetske, PI and Director, IBEEM
+
+### Contributors:
+
+- Kelly Kapsar, Data Scientist, IBEEM
+- Alejandra Martinez Blancas
+- Amar Deep Tiwari
 
 <!-- badges: start -->
 
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
-[![CRAN
-status](https://www.r-pkg.org/badges/version/collaboratR)](https://CRAN.R-project.org/package=collaboratR)
 <!-- badges: end -->
 
-*This is very early version under heavy development.*
+### Motivation
 
-This R package is part of 3 repositories that support the data entry,
-validation and accumulation of a meta-analysis for the commRULES
-project.
+Performing a Meta-analysis requires collating and harmonizing data
+extracted from many different sources but most frequently scientific
+publications.  
+Collaborative meta-analysis requires a group of scientists to
+collectively develop and agree on their goals, type of data extracted,
+format of the those data, and to do so extremely consistently across
+papers. This package helps to support that efficiently by the
+easy-to-use Google Sheets for data definition and data entry. The
+workflow in this project can read directly from Google sheets into CSVs
+and validate the structure of a google sheet as well as the data using
+the Validate package.
 
-1.  commRULES data: version controlled data collection for tracking
-    provenance using git, this is the L0 and L1 layers in the EDI
-    framework
-2.  collaboratR: commRULES data management code for L0 and L0-\>L1 layer
-    in EDI framework
-3.  commRULES-analysis: R code for reproducible data analysis , L1-\>L2
-    layers in EDI framework
+<!-- insert description of the EDI data transform framework here -->
+
+Originally, this This R package was part of 3 repositories that support
+the data entry, validation and accumulation of a meta-analysis for a
+research project sponsored by MSU IBEEM
 
-## Installation
+1.  collaboratR: data management code for L0 and L0-\>L1 layer in EDI
+    framework
+2.  data: version controlled data collection for tracking provenance
+    using git, this is the L0 and L1 layers in the EDI framework. the
+    collaboratR package assists with data transfer and validation from
+    Google drive into the data repository.
+3.  analysis: R code for reproducible data analysis , L1-\>L2 layers in
+    EDI framework, using data in the data repository.
 
-This package uses [renv](https://rstudio.github.io/renv/) to manage the
-packages you need to install, which creates an `renv.lock` file for you.
+## Installation - Package
 
-- install RENV: this can go into your R environment used for all
-  packages, so fire up R with now project select and
-  `install.packages('renv')`
 - clone this repository into a [new Rstudio
   project](https://docs.posit.co/ide/user/ide/guide/code/projects.html)
   and open it
-- inside the Rstudio project in the R console, `renv::restore()`
+
+- install required packages: This package uses
+  [renv](https://rstudio.github.io/renv/) to manage the packages you
+  need to install, which creates an `renv.lock` file for you. 1. install
+  the renv package: this can go into your R environment used for all
+  packages.
+
+  2.  in R run `renv::restore()` or if that complains about R versions
+
+*additional packages are required to build the package and this website,
+source the script* `R/install_dev_packages.R`
+
+### Installation/Testing
+
+Google drive in this package is set to interaction. To run any building,
+installing or checking in R, you must first manually connect to google
+drive, which must be set-up properly first.
+
+See the vignette in this package “Google Sheets API setup using Google
+Cloud”, or in this source code see [Google Sheets Vignette
+RMD](vignettes/google_sheets_api.Rmd)
+
+Once set-up you may have to log-in manually prior to running tests or
+checks, use
+
+``` r
+source("R/gdrive.R")
+
+## Data Google Drive Project Setup
+
+See the Vignette ["Google Sheets API setup using Google Cloud"](vignettes/google_sheets_api.Rmd) 
+for details about setting up google sheets connection with R, which requires
+a google cloud project in your institution
+
+Note that for safety, this package only reads from google drive and it never
+writes to google drive.  Therefore it only requests 'read-only' access.
+
+## Usage
+
+When reading in data sheets, you provide a URL for a datasheet that exists in any folder that you have access to.   The system will attempt to log you into to google drive and requests your permission for this code to access files on your behalf.   
+
+```R
+gurl<- 'https://docs.google.com/spreadsheets/d/1w6sYozjybyd53eeiTdigrRTonteQW2KXUNZNmEhQyM8/edit?gid=0#gid=0'
+study_data<- read_commrules_sheet(gurl)
+```
+
+### 
+
+## References
+
+@article{van2021data, title={Data validation infrastructure for R},
+author={van der Loo, Mark PJ and de Jonge, Edwin}, journal={Journal of
+Statistical Software}, year={2021}, volume ={97}, issue = {10}, pages =
+{1-33}, doi={10.18637/jss.v097.i10}, url =
+{<https://www.jstatsoft.org/article/view/v097i10>} }
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -0,0 +1,4 @@
+url: https://github.com/IBEEM-MSU/collaboratR
+template:
+  bootstrap: 5
+  bootswatch: lumen
diff --git a/docs/.nojekyll b/docs/.nojekyll
@@ -0,0 +1 @@
+
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/404.md b/docs/404.md
@@ -0,0 +1,3 @@
+Content not found. Please use links in the navbar.
+
+# Page not found (404)
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@

		dev_packages <- c('devtools', 'pkgdown', 'renv')
		install.packages(dev_packages, repos = "https://cran.rstudio.com")
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		Content not found. Please use links in the navbar.

		# Page not found (404)