diff --git a/DESCRIPTION b/DESCRIPTION index 7859773a..eb66ac57 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,7 +28,7 @@ Description: This package was developed in order to provide researchers the abil table. Users are also able to export and reimport data in .ris, and csv. files. The package includes a shiny application for interactive use. License: GPL (>= 3) -URL: https://www.eshackathon.org/CiteSource +URL: https://eshackathon.github.io/CiteSource/ BugReports: https://github.com/ESHackathon/CiteSource/issues Imports: ASySD (>= 0.3.0), diff --git a/README.md b/README.md index 47df2428..7ccda520 100644 --- a/README.md +++ b/README.md @@ -53,7 +53,7 @@ Install CiteSource in R with remotes::install_github("ESHackathon/CiteSource") **Vignettes** -Vignettes covering various use cases can be found on the [CiteSource web page](https://www.eshackathon.org/CiteSource/articles). +Vignettes covering various use cases can be found on the [CiteSource web page](https://eshackathon.github.io/CiteSource/articles/). ## Feedback diff --git a/_pkgdown.yml b/_pkgdown.yml index a05f32b6..3b1d8522 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,4 +1,4 @@ -url: http://www.eshackathon.org/CiteSource/ +url: https://eshackathon.github.io/CiteSource/ template: bootstrap: 5 @@ -12,4 +12,3 @@ articles: - citesource_vignette_db-pre-screen_validation - citesource_vignette_db-topic-coverage - citesource_analysis_across_screening_phases - \ No newline at end of file diff --git a/inst/shiny-app/CiteSource/www/about.md b/inst/shiny-app/CiteSource/www/about.md index d793304c..2e0eb314 100644 --- a/inst/shiny-app/CiteSource/www/about.md +++ b/inst/shiny-app/CiteSource/www/about.md @@ -84,4 +84,4 @@ CiteSource is built for anyone involved in evidence synthesis. It helps you: --- -*CiteSource is available both as this interactive Shiny application and as a full R package with detailed vignettes. For more information on the R package, visit the [CiteSource Website](https://www.eshackathon.org/CiteSource/).* \ No newline at end of file +*CiteSource is available both as this interactive Shiny application and as a full R package with detailed vignettes. For more information on the R package, visit the [CiteSource Website](https://eshackathon.github.io/CiteSource/).* \ No newline at end of file diff --git a/inst/shiny-app/CiteSource/www/user_guide.md b/inst/shiny-app/CiteSource/www/user_guide.md index 01197c29..de75fb0b 100644 --- a/inst/shiny-app/CiteSource/www/user_guide.md +++ b/inst/shiny-app/CiteSource/www/user_guide.md @@ -2,7 +2,7 @@ -> CiteSource has a number of applications. This guide walks users through the step-wise process of uploading, deduplicating and analyzing data > within the shiny application. For step by step instructions for running CiteSource in R, [check out our vignettes](https://www.eshackathon.org/CiteSource/articles/) +> CiteSource has a number of applications. This guide walks users through the step-wise process of uploading, deduplicating and analyzing data within the shiny application. For step by step instructions for running CiteSource in R, [check out our vignettes](https://eshackathon.github.io/CiteSource/articles/). --- ### Using CiteSource: Step-by-Step diff --git a/man/CiteSource-package.Rd b/man/CiteSource-package.Rd index 19a730d8..6bc35376 100644 --- a/man/CiteSource-package.Rd +++ b/man/CiteSource-package.Rd @@ -14,7 +14,7 @@ found and then enables users to compare the contribution of different sources \seealso{ Useful links: \itemize{ - \item \url{https://www.eshackathon.org/CiteSource} + \item \url{https://eshackathon.github.io/CiteSource/} \item Report bugs at \url{https://github.com/ESHackathon/CiteSource/issues} } @@ -24,6 +24,7 @@ Useful links: Authors: \itemize{ + \item Trevor Riley \email{trevor.riley@noaa.gov} (\href{https://orcid.org/0000-0002-6834-9802}{ORCID}) \item Kaitlyn Hair \email{kaitlyn.hair@ed.ac.uk} (\href{https://orcid.org/0000-0003-0180-7343}{ORCID}) \item Lukas Wallrich \email{lukas.wallrich@gmail.com} (\href{https://orcid.org/0000-0003-2121-5177}{ORCID}) \item Matthew Grainger \email{matthewjamesgrainger@gmail.com} (\href{https://orcid.org/0000-0001-8426-6495}{ORCID}) diff --git a/man/plot_source_overlap_upset.Rd b/man/plot_source_overlap_upset.Rd index c5a5b9be..f96e4f1a 100644 --- a/man/plot_source_overlap_upset.Rd +++ b/man/plot_source_overlap_upset.Rd @@ -44,6 +44,7 @@ will be the specific intersections listed.} \item{\code{main.bar.color}}{Color of the main bar plot} \item{\code{mainbar.y.max}}{The maximum y value of the intersection size bar plot scale. May be useful when aligning multiple UpSet plots horizontally.} \item{\code{sets.bar.color}}{Color of set size bar plot} + \item{\code{plot.title}}{Title of UpSetR plot} \item{\code{point.size}}{Size of points in matrix plot} \item{\code{line.size}}{Width of lines in matrix plot} \item{\code{mb.ratio}}{Ratio between matrix plot and main bar plot (Keep in terms of hundredths)} @@ -53,6 +54,7 @@ will be the specific intersections listed.} \item{\code{decreasing}}{How the variables in order.by should be ordered. "freq" is decreasing (greatest to least) and "degree" is increasing (least to greatest)} \item{\code{show.numbers}}{Show numbers of intersection sizes above bars} \item{\code{number.angles}}{The angle of the numbers atop the intersection size bars} + \item{\code{number.colors}}{The colors of the numbers atop the intersection size bars} \item{\code{group.by}}{How the data should be grouped ("degree" or "sets")} \item{\code{cutoff}}{The number of intersections from each set (to cut off at) when aggregating by sets} \item{\code{queries}}{Unified query of intersections, elements, and custom row functions. Entered as a list that contains a list of