Merge pull request #94 from marton-balazs-kovacs/main

alexholcombe · web-flow · commit 9d12268724e4 · 2025-01-27T10:11:03.000+11:00
trying fresh checkout of main from github
diff --git a/R/app_server.R b/R/app_server.R
@@ -23,7 +23,7 @@ if (show_popup) {
     # Show a non-aggressive pop-up notification using shinyjs
     shinyjs::runjs("
       const div = document.createElement('div');
-      div.innerHTML = 'Please support tenzing &#x1F60A; <br>Donate <a href=\"https://opencollective.com/tenzing\" target=\"_blank\">here</a>!';
+      div.innerHTML = 'Please support tenzing &#x1F60A; by <br>donating <a href=\"https://opencollective.com/tenzing\" target=\"_blank\">here</a>.';
       div.style.position = 'fixed';
       div.style.top = '75%';
       div.style.left = '16%';
diff --git a/R/app_ui.R b/R/app_ui.R
@@ -77,7 +77,7 @@ app_ui <- function() {
                    class = "main-steps-title-container",
                    h1("3.",
                       class = "main-steps-title-number"),
-                   h3("Download the output",
+                   h3("Generate an output",
                       class = "main-steps-title"),
                    div(
                      class = "help-icon-container",
@@ -104,7 +104,7 @@ app_ui <- function() {
                     ),
                # Privacy notice
                HTML("<p><b>Privacy:</b><BR>
-                    To get a sense of how many users we have, we log a masked version of IP addresses. You are not identifiable by the logged information.</p>")
+                    To get a sense of how many use tenzing, we log a masked version of IP addresses. You are not identifiable by the logged information.</p>")
                ),
         column(2)
         ),
diff --git a/R/mod_conflict_statement.R b/R/mod_conflict_statement.R
@@ -13,7 +13,7 @@ mod_conflict_statement_ui <- function(id){
     div(class = "out-btn",
         actionButton(
           NS(id, "show_report"),
-          label = "Show conflict of interest statement",
+          label = "Conflict of interest statement",
           class = "btn btn-primary btn-validate")
         ) %>% 
       tagAppendAttributes(
diff --git a/R/mod_create_table.R b/R/mod_create_table.R
@@ -18,7 +18,7 @@ mod_create_table_ui <- function(id) {
     p("Duplicate and edit the ",
       style = "display: inline; margin-bottom: 0;"),
     a(
-      href = "https://docs.google.com/spreadsheets/d/1Gl0cwqN_nTsdFH9yhSvi9NypBfDCEhViGq4A3MnBrG8/edit?usp=sharing",
+      href = "https://docs.google.com/spreadsheets/d/1ay8pS-ftvfzWTrKCZr6Fa0cTLg3n8KxAOOleZmuE7Hs/edit?usp=sharing",
       "contributors table template",
       target = "_blank",
       style = "display: inline; color: #ffdf57; text-decoration: underline;",
diff --git a/R/mod_credit_roles.R b/R/mod_credit_roles.R
@@ -19,7 +19,7 @@ mod_credit_roles_ui <- function(id){
     div(class = "out-btn",
         actionButton(
           NS(id, "show_report"),
-          label = "Show contributor contributions text",
+          label = "Contributions text",
           class = "btn btn-primary btn-validate")
         ) %>% 
       tagAppendAttributes(
diff --git a/R/mod_funding_information.R b/R/mod_funding_information.R
@@ -13,7 +13,7 @@ mod_funding_information_ui <- function(id){
     div(class = "out-btn",
         actionButton(
           NS(id, "show_report"),
-          label = "Show funding information",
+          label = "Funding information",
           class = "btn btn-primary btn-validate")
         ) %>% 
       tagAppendAttributes(
diff --git a/R/mod_show_yaml.R b/R/mod_show_yaml.R
@@ -20,7 +20,7 @@ mod_show_yaml_ui <- function(id) {
     div(class = "out-btn",
         actionButton(
           inputId = NS(id, "show_yaml"),
-          label = HTML("Show <i>papaja</i> YAML"),
+          label = HTML("<i>papaja</i> YAML"),
           class = "btn btn-primary btn-validate")
         ) %>% 
       tagAppendAttributes(
diff --git a/R/mod_title_page.R b/R/mod_title_page.R
@@ -19,7 +19,7 @@ mod_title_page_ui <- function(id){
     div(class = "out-btn",
         actionButton(
           NS(id, "show_report"),
-          label = "Show contributor list with affiliations",
+          label = "Contributor list with affiliations",
           class = "btn btn-primary btn-validate")
         ) %>% 
       tagAppendAttributes(
diff --git a/R/mod_xml_report.R b/R/mod_xml_report.R
@@ -18,7 +18,7 @@ mod_xml_report_ui <- function(id){
   tagList(
     div(class = "out-btn",
         actionButton(NS(id, "show_report"),
-                       label = "Show XML file (for publisher use)",
+                       label = "JATS-XML (for publisher use)",
                        class = "btn btn-primary btn-validate")
         ) %>% 
       tagAppendAttributes(
diff --git a/README.md b/README.md
@@ -63,7 +63,6 @@ Running the app.
 ``` r
 tenzing::run_app()
 ```
-If working in RStudio, after opening the .Rproj file and then "app.R", click on "Run app" in the top right of the app window.
 
 You can read more on how to use the `tenzing` app in
 `vignette("app_use")`.
diff --git a/inst/app/www/about.Rmd b/inst/app/www/about.Rmd
@@ -5,30 +5,30 @@ output: html_document
 
 <i>tenzing</i> is a project of the <a href="https://contributorshipcollaboration.github.io/" class="link" target='_blank'>Contributorship Collaboration</a>.
 
-_tenzing_ is named after the Nepali-Indian Sherpa Tenzing Norgay, who was one of the first two people to reach the summit of Mount Everest. Despite his essential contribution, the achievement is often credited less to him than to his partner, the New Zealand mountaineer Edmund Hillary.
+_tenzing_ is named after the Nepali-Indian Sherpa Tenzing Norgay, whose achievement in climbing Everest is often credited less to him than to his partner, the New Zealand mountaineer Edmund Hillary.
 
 ### About CRediT
 
 <a href="http://credit.niso.org/" class="link" target='_blank'>CRediT</a> (Contributor Roles Taxonomy) is a high-level taxonomy of 14 roles that indicate some of the roles played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output.
 
-### Contributors
+### Some who have recommended <i>tenzing</i>
 
-Marton Kovacs, Alex Holcombe, Balazs Aczel, Frederik Aust, Julien Colomb.
+<a href="https://sfdora.org/resource-library/?_resource_type=tools" class="link" target='_blank'>DORA</a>
+<br>
+<a href="https://www.collabra.org/" class="link" target='_blank'>Collabra: Psychology</a>
+<br>
+<a href="https://ukrn.org" class="link" target='_blank'>UKRN</a>
 
 ### Related papers
 
 Holcombe, A. O., Kovacs, M., Aust, F., & Aczel, B. (2020). <a href="https://doi.org/10.1371/journal.pone.0244611" class="link" target='_blank'>Documenting contributions to scholarly articles using CRediT and tenzing</a>. *Plos one, 15*(12), e0244611. DOI:10.1371/journal.pone.0244611
 
 Kovacs, M., Holcombe, A., Aust, F., & Aczel, B. (2021). <a href="https://doi.org/10.3233/ISU-210109" class="link" target='_blank'>Tenzing and the importance of tool development for research efficiency</a>. *Information Services & Use, 41*, 123–130. DOI:10.3233/ISU-210109
 
-### Groups that recommend <i>tenzing</i>
+### Contributors
 
-<a href="https://www.collabra.org/" class="link" target='_blank'>Collabra: Psychology</a>
-<br>
-<a href="https://sfdora.org/resource-library/?_resource_type=tools" class="link" target='_blank'>DORA</a>
-<br>
-<a href="https://ukrn.org" class="link" target='_blank'>UKRN</a>
+Marton Kovacs, Alex O. Holcombe, [et al.](https://github.com/marton-balazs-kovacs/tenzing/graphs/contributors)
 
 ### Contact
 
-If you have any questions or comments, please add to the <a href="https://github.com/marton-balazs-kovacs/tenzing" class="link" target='_blank'>issues on Github</a>, email Marton: marton.balazs.kovacs at gmail.com, or message us <a href="https://neuromatch.social/@tenzingContrib" class="link" target="_blank">on Mastodon</a>.
+If you have any questions or comments, please add an <a href="https://github.com/marton-balazs-kovacs/tenzing" class="link" target='_blank'>issue on Github</a>, email Marton: marton.balazs.kovacs at gmail.com, or message us <a href="https://neuromatch.social/@tenzingContrib" class="link" target="_blank">on Mastodon</a>.
diff --git a/inst/app/www/introduction.Rmd b/inst/app/www/introduction.Rmd
@@ -3,24 +3,22 @@ title: ""
 output: html_document
 ---
 
-#### 1. Create your contributors table
-* Copy the contributors table template in your Google Drive _File -> Make a copy_
-* Fill out your copy of the contributors table
-+ You can share it with your collaborators to make the process faster
+### 1. Create your contributors table
+* Duplicate the contributors table template into your Google Drive: _File -> Make a copy_. Alternatively, you can download it.
+* Fill out your copy of the contributors table (consider sharing it with your collaborators to do so).
 
-#### 2. Upload your contributors table
-* Use the share URL of your contributors table and click "Upload from URL" OR
-  - The share links should be made viewable
-* Upload your contributors table in a .csv, .tsv or .xlsx format
-  - Download your filled out contributors table to your computer (if you use .xlsx format the contributorship information should be on the first sheet)
-  - Click the “Browse” button, locate your contributors table on your computer, and click "Upload from local file"
-* To verify that your contributors table was imported correctly click “Review contributors table”
+### 2. A) Upload your contributors table file, or B) Paste its URL
+A. Upload your contributors table in a .csv, .tsv or .xlsx format.
+  - Click "Local file", then “Browse”, and locate your contributors table on your computer.
+
+B. Share the URL via Google Drive, and click "Upload from URL".
+  - To ensure the URL is public so tenzing can access it, in your copy go to _File->Share with others_. Set _General access_ to _Anyone with the link_.
   
-#### 3. Download the output
+### 3. Generate an output
 * Select the associated button to choose one of the available outputs, which are:
-  - "author Contributions text": A human-readable report of the contributions with the 
-  - "author list with affiliations": The author names and affiliation information
-  - "XML file": JATS XML, the machine-readable version of the contributions
-  - `papaja` compatible YAML code of the contributor roles
-  - "funding information" for pasting into a manuscript
-  - "conflict of interest statement"
+  - "contributions text": A list of the contributions 
+  - "contributor list with affiliations": The contributor names and affiliations (useful for your manuscript's title page)
+  - "JATS-XML": JATS XML, the machine-readable version of the contributions
+  - [papaja](https://github.com/crsh/papaja)-compatible YAML code of the contributor roles
+  - "funding information", useful for pasting into a manuscript
+  - "conflict of interest statement", useful for pasting into a manuscript
diff --git a/rsconnect/shinyapps.io/alexholcombe/tenzing-master.dcf b/rsconnect/shinyapps.io/alexholcombe/tenzing-master.dcf
@@ -0,0 +1,12 @@
+name: tenzing-master
+title: tenzing-master
+username: alexholcombe
+account: alexholcombe
+server: shinyapps.io
+hostUrl: https://api.shinyapps.io/v1
+appId: 8701446
+bundleId: 9691969
+url: https://alexholcombe.shinyapps.io/tenzing-master/
+version: 1
+asMultiple: FALSE
+asStatic: FALSE
diff --git a/rsconnect/shinyapps.io/rollercoaster/tenzing-master.dcf b/rsconnect/shinyapps.io/rollercoaster/tenzing-master.dcf
@@ -0,0 +1,12 @@
+name: tenzing-master
+title: tenzing-master
+username: rollercoaster
+account: rollercoaster
+server: shinyapps.io
+hostUrl: https://api.shinyapps.io/v1
+appId: 8633777
+bundleId: 9700340
+url: https://rollercoaster.shinyapps.io/tenzing-master/
+version: 1
+asMultiple: FALSE
+asStatic: FALSE
diff --git a/rsconnect/shinyapps.io/rollercoaster/tenzing.dcf b/rsconnect/shinyapps.io/rollercoaster/tenzing.dcf
@@ -0,0 +1,12 @@
+name: tenzing
+title: tenzing
+username: rollercoaster
+account: rollercoaster
+server: shinyapps.io
+hostUrl: https://api.shinyapps.io/v1
+appId: 4527698
+bundleId: 9700369
+url: https://rollercoaster.shinyapps.io/tenzing/
+version: 1
+asMultiple: FALSE
+asStatic: FALSE
diff --git a/tenzing.Rproj b/tenzing.Rproj
@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 82b54835-4604-46a7-a546-35d967112cb1
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`Version: 1.0`
	`2`	`+ProjectId: 82b54835-4604-46a7-a546-35d967112cb1`
`2`	`3`
`3`	`4`	`RestoreWorkspace: Default`
`4`	`5`	`SaveWorkspace: Default`