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4 changes: 2 additions & 2 deletions DESCRIPTION
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Expand Up @@ -5,9 +5,9 @@ Description: Synthesizes information across collaborating research. Created
Version: 0.2.0
Authors@R: c(person("Will", "Beasley", email="wibeasley@hotmail.com", role=c("aut", "cre"),
comment = c(ORCID = "0000-0002-5613-5006")),
person("Andrey", "Koval", email="andkov@uvic.ca", role = c("aut")),
person("Andriy", "Koval", email="andkov@uvic.ca", role = c("aut")),
person(given="Integrative Analysis of Longitudinal Studies of Aging (IALSA)", role = c("cph")))
URL: https://github.com/IALSA/IalsaSynthesis, https://www.maelstrom-research.org/mica/network/ialsa#/
URL: https://github.com/IALSA/IalsaSynthesis
BugReports: https://github.com/IALSA/IalsaSynthesis/issues
Depends:
R(>= 3.0.0)
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15 changes: 7 additions & 8 deletions R/IalsaSynthesis-package.r
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#'
#' @title Synthesizing Information Across Collaborating Research
#'
#' @description Synthesizing information across collaborating research. Created for \href{https://www.maelstrom-research.org/mica/network/ialsa#/}{Integrative Analysis of Longitudinal Studies of Aging} (IALSA).
#' @description Synthesizing information across collaborating research. Created for \href{https://www.ialsa.org/#team}{Integrative Analysis of Longitudinal Studies of Aging} (IALSA).
#'
#' @note The release version will be available through \href{https://cran.r-project.org/package=IalsaSynthesis}{CRAN}.
#' The most recent development version is available through \href{https://github.com/IALSA/IalsaSynthesis}{GitHub}.
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#' IALSA is funded through an NIH/NIA Program Project Grant (
#' \href{https://projectreporter.nih.gov/project_info_description.cfm?aid=8414933&icde=18870651&ddparam=&ddvalue=&ddsub=&cr=3&csb=default&cs=ASC}{P01AG043362}); 2013-2018) to Oregon Health & Science University
#' (Program Directors:
#' \href{https://www.maelstrom-research.org/mica/network/ialsa#/}{Scott Hofer},
#' \href{https://www.maelstrom-research.org/mica/network/ialsa#/}{Andrea Piccinin},
#' \href{https://www.maelstrom-research.org/mica/network/ialsa#/}{Jeffrey Kaye}, and
#' \href{https://www.maelstrom-research.org/mica/individual-study/mrc-nshd#/}{Diana Kuh})
#' \href{https://www.ialsa.org/#team}{Scott Hofer},
#' \href{https://www.ialsa.org/#team}{Andrea Piccinin},
#' \href{https://www.ialsa.org/#team}{Jeffrey Kaye}, and
#' \href{https://www.ialsa.org/#team}{Diana Kuh})
#' and previously funded by NIH/NIA (\href{https://projectreporter.nih.gov/project_info_description.cfm?aid=7210005&icde=19139556&ddparam=&ddvalue=&ddsub=&cr=5&csb=default&cs=ASC}{R01AG026453}; 2007-2013) and CIHR (103284; 2010-2013).
#'
#' @author
#' \href{http://scholar.google.com/citations?user=ffsJTC0AAAAJ}{William Howard Beasley}
#' --Associate Professor of Research, \href{http://find.ouhsc.edu/Faculty.aspx?FacultyID=1064}{University of Oklahoma Health Sciences Center},
#' \href{https://www.oumedicine.com/department-of-pediatrics}{Dept of Pediatrics}, Biomedical and Behavioral Methodology Core (\href{https://ouhsc.edu/bbmc/}{BBMC})
#' \href{https://medicine.ouhsc.edu/Academic-Departments/Pediatrics}{Dept of Pediatrics}, Biomedical and Behavioral Methodology Core (\href{https://www.ouhsc.edu/bbmc/}{BBMC})
#'
#'
#' \href{https://www.researchgate.net/profile/Andrey_Koval}{Andrey Koval}
#' \href{https://www.researchgate.net/profile/Andriy-Koval-2}{Andrey Koval}
#' --Post Doc, \href{http://www.uvic.ca/}{University of Victoria}, \href{http://www.uvic.ca/socialsciences/psychology/}{Department of Psychology}
#'
#' @examples
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25 changes: 12 additions & 13 deletions README.md
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<!-- rmarkdown v1 -->

| [GitHub](https://github.com/IALSA/IalsaSynthesis) | [Travis-CI](https://travis-ci.org/IALSA/IalsaSynthesis/builds) | [AppVeyor](https://ci.appveyor.com/project/wibeasley/ialsasynthesis/history) | [Coveralls](https://coveralls.io/r/IALSA/IalsaSynthesis) |
| [GitHub](https://github.com/IALSA/IalsaSynthesis) | [Travis-CI](https://travis-ci.org/IALSA/IalsaSynthesis/builds) | [AppVeyor](https://ci.appveyor.com/project/wibeasley/ialsasynthesis/history) | [Coveralls](https://coveralls.io/github/IALSA/IalsaSynthesis) |
| :----- | :---------------------------: | :------------: | :-------:
| [Master](https://github.com/IALSA/IalsaSynthesis/tree/master) | [![Travis-CI Build Status](https://travis-ci.org/IALSA/IalsaSynthesis.png?branch=master)](https://travis-ci.org/IALSA/IalsaSynthesis) | [![Build status](https://ci.appveyor.com/api/projects/status/8u5m65k0rr2veahx/branch/master?svg=true)](https://ci.appveyor.com/project/wibeasley/ialsasynthesis/branch/master) | [![Coverage Status](https://coveralls.io/repos/IALSA/IalsaSynthesis/badge.svg?branch=master)](https://coveralls.io/r/IALSA/IalsaSynthesis?branch=master) |
| [Dev](https://github.com/IALSA/IalsaSynthesis/tree/dev) | [![Travis-CI Build Status](https://travis-ci.org/IALSA/IalsaSynthesis.png?branch=dev)](https://travis-ci.org/IALSA/IalsaSynthesis) | [![Build status](https://ci.appveyor.com/api/projects/status/8u5m65k0rr2veahx/branch/dev?svg=true)](https://ci.appveyor.com/project/wibeasley/ialsasynthesis/branch/dev) | [![Coverage Status](https://coveralls.io/repos/IALSA/IalsaSynthesis/badge.svg?branch=dev)](https://coveralls.io/r/IALSA/IalsaSynthesis?branch=dev) |
| [Master](https://github.com/IALSA/IalsaSynthesis/tree/master) | [![Travis-CI Build Status](https://travis-ci.org/IALSA/IalsaSynthesis.png?branch=master)](https://travis-ci.org/IALSA/IalsaSynthesis) | [![Build status](https://ci.appveyor.com/api/projects/status/8u5m65k0rr2veahx/branch/master?svg=true)](https://ci.appveyor.com/project/wibeasley/ialsasynthesis/branch/master) | [![Coverage Status](https://coveralls.io/repos/IALSA/IalsaSynthesis/badge.svg?branch=master)](https://coveralls.io/github/IALSA/IalsaSynthesis?branch=master) |
| [Dev](https://github.com/IALSA/IalsaSynthesis/tree/dev) | [![Travis-CI Build Status](https://travis-ci.org/IALSA/IalsaSynthesis.png?branch=dev)](https://travis-ci.org/IALSA/IalsaSynthesis) | [![Build status](https://ci.appveyor.com/api/projects/status/8u5m65k0rr2veahx/branch/dev?svg=true)](https://ci.appveyor.com/project/wibeasley/ialsasynthesis/branch/dev) | [![Coverage Status](https://coveralls.io/repos/IALSA/IalsaSynthesis/badge.svg?branch=dev)](https://coveralls.io/github/IALSA/IalsaSynthesis?branch=dev) |
| | *Ubuntu LTS* | *Windows Server* | *Travis Test Coverage* |


IalsaSynthesis
====================

An [R](http://www.r-project.org/) package for synthesizing information across collaborating research.
An [R](https://www.r-project.org/) package for synthesizing information across collaborating research.

[![logo](man/figures/ialsa-wide.png)](https://www.maelstrom-research.org/mica/network/ialsa#/)
[![logo](man/figures/ialsa-wide.png)](https://www.ialsa.org/)

[IALSA](https://www.nia.nih.gov/research/resource/integrative-analysis-longitudinal-studies-aging-ialsa) (Integrative Analysis of Longitudinal Studies of Aging) research network unites approximately 100 longtidinal studies from all over the world. IALSA makes primary use of a [coordinated analysis approach](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773828/) and various [harmonization methods](https://www.maelstrom-research.org/repository/methods_library). Our projects involve dealing with multiple longitudinal studies, each of which may count numerous statistical models, making the synthesis of results particularly arduous. The `IalsaSynthesis` package offers software tools for extracting, pooling, evaluating, and reporting the results of a large number of statistical models. See out [flagship project](https://github.com/IALSA/IALSA-2015-Portland), stemming from coordinated analysis workshop in Portland in February of 2015.
[IALSA](https://www.nia.nih.gov/research/resource/integrative-analysis-longitudinal-studies-aging-ialsa) (Integrative Analysis of Longitudinal Studies of Aging) research network unites approximately 100 longtidinal studies from all over the world. IALSA makes primary use of a [coordinated analysis approach](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773828/) and various harmonization methods. Our projects involve dealing with multiple longitudinal studies, each of which may count numerous statistical models, making the synthesis of results particularly arduous. The `IalsaSynthesis` package offers software tools for extracting, pooling, evaluating, and reporting the results of a large number of statistical models. See out [flagship project](https://github.com/IALSA/IALSA-2015-Portland), stemming from coordinated analysis workshop in Portland in February of 2015.

### Package Crew

[Will Beasley](https://www.researchgate.net/profile/William_Beasley2) (*[University of Oklahoma Health Sciences Center](https://ouhsc.edu/), [Department of Pediatrics](https://www.oumedicine.com/department-of-pediatrics), [Biomedical & Behavioral Research Core](http://ouhsc.edu/BBMC/)*)
[Will Beasley](https://www.researchgate.net/profile/William-Beasley-5) (*[University of Oklahoma Health Sciences Center](https://www.ouhsc.edu/), [Department of Pediatrics](https://medicine.ouhsc.edu/Academic-Departments/Pediatrics), [Biomedical & Behavioral Research Core](http://ouhsc.edu/BBMC/)*)

[Andriy Koval](https://www.researchgate.net/profile/Andrey_Koval) ([University of Victoria](http://www.uvic.ca/), [Institute on Aging and Lifelong Health](http://www.uvic.ca/aging/)*).
[Andriy Koval](https://www.researchgate.net/profile/Andriy-Koval-2) ([University of Victoria](http://www.uvic.ca/), [Institute on Aging and Lifelong Health](http://www.uvic.ca/aging/)*).


### Download and Installation Instructions

| [CRAN](http://cran.rstudio.com/) | [Version](https://cran.r-project.org/package=IalsaSynthesis) | [Rate](http://cranlogs.r-pkg.org/) | [Zenodo](https://zenodo.org/search?ln=en&p=ialsasynthesis) |
| [CRAN](https://cran.r-project.org/) | [Version](https://cran.r-project.org/package=IalsaSynthesis) | [Rate](https://cranlogs.r-pkg.org/) | [Zenodo](https://zenodo.org/search?ln=en&p=ialsasynthesis) |
| :---- | :----: | :----: | :----: |
| [Latest](https://cran.r-project.org/package=IalsaSynthesis) | [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/IalsaSynthesis)](https://cran.r-project.org/package=IalsaSynthesis) | ![CRANPace](http://cranlogs.r-pkg.org/badges/IalsaSynthesis) | [![DOI](https://zenodo.org/badge/34798650.svg)](https://zenodo.org/badge/latestdoi/34798650) |
| [Latest](https://cran.r-project.org/package=IalsaSynthesis) | [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/IalsaSynthesis)](https://cran.r-project.org/package=IalsaSynthesis) | ![CRANPace](http://cranlogs.r-pkg.org/badges/IalsaSynthesis) | [![DOI](https://zenodo.org/badge/34798650.svg)](https://zenodo.org/badge/latestdoi/34798650) |
| | *Latest CRAN version* | *CRAN Downloads* | *Independently-hosted Archive* |

The released CRAN version of IalsaSynthesis can be installed through R. (The *release* version will be available on [CRAN](https://cran.rstudio.com/) closer to the Gothenburg conference.)

```R
install.packages("IalsaSynthesis")
Expand All @@ -46,10 +45,10 @@ devtools::install_github(repo="IALSA/IalsaSynthesis")
The package documentation for the [development version](documentation-peek.pdf) on GitHub can be viewed without installing the package.

### Collaborative Development
Consistent with IALSA goals, we encourage input and collaboration from the overall community. If you're familar with GitHub and R packages, feel free to submit a [pull request](https://github.com/IALSA/IalsaSynthesis/pulls). If you'd like to report a bug or make a suggestion, please create a GitHub [issue](https://github.com/IALSA/IalsaSynthesis/issues); issues are a usually a good place to ask public questions too. However, feel free to email Andrey or Will privately (<andkov@uvic.ca> or <wibeasley@hotmail.com>).
Consistent with IALSA goals, we encourage input and collaboration from the overall community. If you're familar with GitHub and R packages, feel free to submit a [pull request](https://github.com/IALSA/IalsaSynthesis/pulls). If you'd like to report a bug or make a suggestion, please create a GitHub [issue](https://github.com/IALSA/IalsaSynthesis/issues); issues are a usually a good place to ask public questions too. However, feel free to email Andriy or Will privately (<andkov@uvic.ca> or <wibeasley@hotmail.com>).

### Thanks to Funders
IALSA is funded through an NIH/NIA Program Project Grant ([P01AG043362](https://projectreporter.nih.gov/project_info_description.cfm?aid=8414933&icde=18870651&ddparam=&ddvalue=&ddsub=&cr=3&csb=default&cs=ASC); 2013-2018) to Oregon Health & Science University (Program Directors: [Scott Hofer](https://www.maelstrom-research.org/mica/network/ialsa#/users/hofer), [Andrea Piccinin](https://www.maelstrom-research.org/mica/network/ialsa#/users/piccinin), [Jeffrey Kaye](https://www.maelstrom-research.org/mica/network/ialsa#/users/kaye), and [Diana Kuh](https://www.maelstrom-research.org/mica/network/ialsa#/users/kuh)) and previously funded by NIH/NIA ([R01AG026453](https://projectreporter.nih.gov/project_info_description.cfm?aid=7210005&icde=19139556&ddparam=&ddvalue=&ddsub=&cr=5&csb=default&cs=ASC); 2007-2013) and CIHR (103284; 2010-2013).
IALSA is funded through an NIH/NIA Program Project Grant ([P01AG043362](https://projectreporter.nih.gov/project_info_description.cfm?aid=8414933&icde=18870651&ddparam=&ddvalue=&ddsub=&cr=3&csb=default&cs=ASC); 2013-2018) to Oregon Health & Science University (Program Directors: [Scott Hofer](https://www.ialsa.org/#team), [Andrea Piccinin](https://www.ialsa.org/#team), [Jeffrey Kaye](https://www.ialsa.org/#team), and [Diana Kuh](https://www.ialsa.org/#team) and previously funded by NIH/NIA ([R01AG026453](https://projectreporter.nih.gov/project_info_description.cfm?aid=7210005&icde=19139556&ddparam=&ddvalue=&ddsub=&cr=5&csb=default&cs=ASC); 2007-2013) and CIHR (103284; 2010-2013).

### Code Coverage Over Time

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## Description
This submission introduces the package to CRAN. It will contain the workhorse functions for [IALSA](https://github.com/IALSA) conferences (eg, https://github.com/IALSA/IALSA-2015-Portland).

At Kurt's request, I modified last night's submission and removed `VignetteBuilder: knitr` from the description file. Sorry that never appeared in any of the checks I ran.
This submission has some minor modifications to comply with updated CRAN checks and package dependencies

Please tell me if there's something else I should do for CRAN. -Will Beasley

## Test environments
* Local Win8, R 3.2.2 patched
* win-builder (version="R-devel"); http://win-builder.r-project.org/4E2w7357xxGX
* Travis CI, Ubuntu 12.04 LTS; https://travis-ci.org/IALSA/IalsaSynthesis/builds
* AppVeyor, Windows Server 2012; https://ci.appveyor.com/project/wibeasley/ialsasynthesis/history
* Wercker, Docker; https://app.wercker.com/#applications/5562b43349f5656573003aab
* Local Ubuntu, R 4.0.5
* Local Windows, R 4.0.4 patched
* win-builder (version="R-devel"); <not responding>
* Travis CI, Ubuntu LTS; https://travis-ci.org/IALSA/IalsaSynthesis/builds
* AppVeyor, Windows Server; https://ci.appveyor.com/project/wibeasley/ialsasynthesis/history
* R-hub (https://builder.r-hub.io/status/IalsaSynthesis_0.2.0.tar.gz-6de26f7bcd3e4d3d9b5a3d2bbfa09905)

## R CMD check results
* No ERRORs or WARNINGs on any builds.
* No NOTEs on win-builder.
* No other unexplainable NOTEs on the other builds.

* The checks on some builds catch a 404 http error with `https://cran.r-project.org/package=IalsaSynthesis` in the home page in the reference manual. This shouldn't be a problem once the package is accepted on CRAN for the first time.
* No ERRORs, WARNINGs, or NOTEs on any builds.

## Downstream dependencies
No other packages depend/import this one.
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---
title: Proposed Architecture of Synthesis Ecosystem for [IALSA](https://www.maelstrom-research.org/mica/network/ialsa#/)
title: Proposed Architecture of Synthesis Ecosystem for [IALSA](https://www.ialsa.org/)
date: 2015-05-21
output:
html_document:
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#### A2 Reports: Overall Conference Progress
Whereas an A1 report displays only one study at a time, an A2 tracks the progress of all participants. The hope is that this continually-updated material (possibly shown on an overhead projector) emphasizes the collective goals of the conference, and therefore increase the sense of camaraderie. By showing which studies are on each stage, we hope that the leaders are more willing to help those behind, and those behind are more likely to ask for help from the leaders.

UVic staff can more quickly identify who needs assistance, and decide whether to help them directly, or suggest one of the leading participants help them. This type of collaboration is championed by [Jim Mold](https://find.ouhsc.edu/Faculty.aspx?FacultyID=363) (who was a big influence on the way the [BBMC](http://www.ouhsc.edu/bbmc/) operates its research investigations and QA projects). One of the basic ideas is that even high-performing nurses/providers can learn better techniques from inexperienced and low-performing ones, if the environment is collaborative and safe. It sounds like IALSA already posses strong cohesion, and the A2 reports will be designed to increase the members' awareness of who needs help, and who can provide help.
UVic staff can more quickly identify who needs assistance, and decide whether to help them directly, or suggest one of the leading participants help them. This type of collaboration is championed by [Jim Mold](https://medicine.ouhsc.edu/Academic-Departments/Family-and-Preventive-Medicine/Faculty/jim-mold-mph-md) (who was a big influence on the way the [BBMC](http://www.ouhsc.edu/bbmc/) operates its research investigations and QA projects). One of the basic ideas is that even high-performing nurses/providers can learn better techniques from inexperienced and low-performing ones, if the environment is collaborative and safe. It sounds like IALSA already posses strong cohesion, and the A2 reports will be designed to increase the members' awareness of who needs help, and who can provide help.


#### B1 Reports: Single Study Analysis
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