Merge 6e0178c into 1e7115a

IALSA · Jun 29, 2018 · 40763a4 · 40763a4
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -4,14 +4,11 @@ Description: Synthesizes information across collaborating research. Created
     specifically for Integrative Analysis of Longitudinal Studies of Aging (IALSA).
 Version: 0.1.8.9001
 Date: 2018-08-23
-Authors@R: c(person("Will", "Beasley", email="wibeasley@hotmail.com", role=c("aut", "cre")),
+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(given="Integrative Analysis of Longitudinal Studies of Aging (IALSA)", role = c("cph")))
-Author: Will Beasley [aut, cre],
-    Andrey Koval [aut],
-    Integrative Analysis of Longitudinal Studies of Aging (IALSA) [cph]
-Maintainer: Will Beasley <wibeasley@hotmail.com>
-URL: https://github.com/IALSA/IalsaSynthesis, http://www.ialsa.org/
+URL: https://github.com/IALSA/IalsaSynthesis, https://www.maelstrom-research.org/mica/network/ialsa#/
 BugReports: https://github.com/IALSA/IalsaSynthesis/issues
 Depends:
     R(>= 3.0.0),

diff --git a/R/IalsaSynthesis-package.r b/R/IalsaSynthesis-package.r
@@ -1,42 +1,42 @@
 #' @name IalsaSynthesis-package
 #' @docType package
-#' 
+#'
 #' @title Synthesizing Information Across Collaborating Research
-#' 
-#' @description Synthesizing information across collaborating research. Created for \href{http://www.ialsa.org/}{Integrative Analysis of Longitudinal Studies of Aging} (IALSA).
-#' 
+#'
+#' @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).
+#'
 #' @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}.
 #' Please see the installation examples below.
-#' 
+#'
 #' If you're having trouble with the package, please install the development version.  If this doesn't solve
 #' your problem, please create a \href{https://github.com/IALSA/IalsaSynthesis/issues}{new issue}, or email Will or Andrey.
-#' 
-#' @references 
-#' 
+#'
+#' @references
+#'
 #' IALSA is funded through an NIH/NIA Program Project Grant (
-#' \href{http://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{http://www.ialsa.org/users/hofer}{Scott Hofer}, 
-#' \href{http://www.ialsa.org/users/piccinin}{Andrea Piccinin}, 
-#' \href{http://www.ialsa.org/users/kaye}{Jeffrey Kaye}, and 
-#' \href{http://www.ialsa.org/users/kuh}{Diana Kuh})
-#' and previously funded by NIH/NIA (\href{http://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} 
-#'  --Assistant Professor of Research, \href{http://find.ouhsc.edu/Faculty.aspx?FacultyID=1064}{University of Oklahoma Health Sciences Center}, 
-#'  \href{http://www.oumedicine.com/pediatrics}{Dept of Pediatrics}, Biomedical and Behavioral Methodology Core (\href{http://ouhsc.edu/bbmc/}{BBMC})
-#'  
-#'  
+#' \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})
+#' 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://www.researchgate.net/profile/Andrey_Koval}{Andrey Koval}
 #'  --Post Doc, \href{http://www.uvic.ca/}{University of Victoria}, \href{http://www.uvic.ca/socialsciences/psychology/}{Department of Psychology}
-#'  
+#'
 #' @examples
 #' \dontrun{
 #' # Install/update IalsaSynthesis with the release version from CRAN.
 #' install.packages('IalsaSynthesis')
-#' 
+#'
 #' # Install/update IalsaSynthesis with the development version from GitHub
 #' #install.packages('devtools') #Uncomment if `devtools` isn't installed already.
 #' devtools::install_github('IALSA/IalsaSynthesis')

diff --git a/README.md b/README.md
@@ -12,13 +12,13 @@ IalsaSynthesis
 
 An [R](http://www.r-project.org/) package for synthesizing information across collaborating research.
 
-[![logo](man/figures/ialsa-wide.png)](http://www.ialsa.org/)
+[![logo](man/figures/ialsa-wide.png)](https://www.maelstrom-research.org/mica/network/ialsa#/)
 
-[IALSA](http://www.ialsa.org/) (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](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.
 
 ### Package Crew
 
-[Will Beasley](https://www.researchgate.net/profile/William_Beasley2) (*[University of Oklahoma Health Sciences Center](http://ouhsc.edu/), [Department of Pediatrics](http://www.oumedicine.com/pediatrics), [Biomedical & Behavioral Research Core](http://ouhsc.edu/BBMC/)*)
+[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/)*)
 
 [Andrey 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/)*).
 
@@ -30,7 +30,7 @@ An [R](http://www.r-project.org/) package for synthesizing information across co
 | [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 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](http://cran.rstudio.com/) closer to the Gothenburg conference.)
+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")
@@ -49,7 +49,7 @@ The package documentation for the [development version](documentation-peek.pdf)
 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>).
 
 ### Thanks to Funders
-IALSA is funded through an NIH/NIA Program Project Grant ([P01AG043362](http://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](http://www.ialsa.org/users/hofer), [Andrea Piccinin](http://www.ialsa.org/users/piccinin), [Jeffrey Kaye](http://www.ialsa.org/users/kaye), and [Diana Kuh](http://www.ialsa.org/users/kuh)) and previously funded by NIH/NIA ([R01AG026453](http://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.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).
 
 ### Code Coverage Over Time
 

diff --git a/libs/documents/architecture.html b/libs/documents/architecture.html
@@ -61,7 +61,7 @@
 
 
 <div id="header">
-<h1 class="title">Proposed Architecture of Synthesis Ecosystem for <a href="http://www.ialsa.org/">IALSA</a></h1>
+<h1 class="title">Proposed Architecture of Synthesis Ecosystem for <a href="https://www.maelstrom-research.org/mica/network/ialsa#/">IALSA</a></h1>
 <h4 class="date"><em>2015-05-21</em></h4>
 </div>
 

diff --git a/libs/documents/architecture.md b/libs/documents/architecture.md
@@ -1,5 +1,5 @@
 ---
-title: Proposed Architecture of Synthesis Ecosystem for [IALSA](http://www.ialsa.org/)
+title: Proposed Architecture of Synthesis Ecosystem for [IALSA](https://www.maelstrom-research.org/mica/network/ialsa#/)
 date: 2015-05-21
 output:
   html_document:

diff --git a/man/IalsaSynthesis-package.Rd b/man/IalsaSynthesis-package.Rd
diff --git a/utility/create-package.R b/utility/create-package.R
@@ -1,7 +1,7 @@
 library(devtools)
 devtools::create(path=file.path(getwd(), "seed") ,check=TRUE, description=list(
   "Title" = "Synthesizing Information Across Collaborating Research",
-  "Description" = "Synthesizing information across collaborating research. Created for Integrative Analysis of Longitudinal Studies of Aging (http://www.ialsa.org/).",
+  "Description" = "Synthesizing information across collaborating research. Created for Integrative Analysis of Longitudinal Studies of Aging (https://www.maelstrom-research.org/mica/network/ialsa#/).",
   "Date" = "2015-04-29",
   "Author" = "Will Beasley",
   "Maintainer" = "'Will Beasley' <wibeasley@hotmail.com>"