setting up style and datat for anvil

Author: kweav

_site.yml

@@ -1,29 +1,23 @@
-name: metricminer dashboard
+name: AnVIL Outreach Metric Dashboard
 output_dir: 'docs'
 navbar:
-  title: metricminer dashboard
+  title: AnVIL Outreach Metric Dashboard
   left:
   - text: Home
     href: index.html
     icon: fa-home
-  - text: Calendly
-    href: calendly.html
-    icon: fa-calendar
   - text: Citations
     href: citations.html
     icon: fa-scroll
-  - text: CRAN
-    href: cran.html
-    icon: fa-r
+  #- text: Bioconductor
+  #  href: bioconductor.html
+  #  icon: fa-r
   - text: GitHub
     href: github.html
     icon: fa-github
   - text: Google Analytics
     href: googleanalytics.html
     icon: fa-google
-  #- text: Slido
-  #  href: slido.html
-  #  icon: a-square-poll-vertical
   - text: Youtube
     href: youtube.html
     icon: fa-play

bioconductor.Rmd

@@ -0,0 +1,46 @@
+---
+title: "Bioconductor"
+output:
+  html_document:
+    toc: true
+    toc_float: true
+    toc_collapsed: true
+date: "`r format(Sys.time(), '%d %B, %Y')`"
+---
+
+## Preview
+
+```{r, eval = FALSE, echo = FALSE, hide = TRUE, message = FALSE}
+library(tidyverse)
+
+root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
+yaml <- yaml::read_yaml(file.path(root_dir, "_config_automation.yml"))
+
+## For github
+cran <- readr::read_tsv(file.path("metricminer_data", "cran", "cran.tsv"))
+```
+
+Total Bioconductor downloads for all packages:
+
+```{r, eval = FALSE}
+cran %>% dplyr::summarize(download_total = sum(count))
+```
+CRAN package downloads over time, summarized by month.
+
+```{r, eval = FALSE, message = FALSE}
+cran_stats <- cran %>%
+  separate(date, into=c("year", "month name", "day"), sep = "-") %>%
+  unite("Month", c("year", "month name"), sep='-', remove=TRUE) %>%  
+  group_by(Month, package) %>%
+  summarise(monthly_downloads = sum(count)) %>% #summarize monthly downloads by package
+  filter(monthly_downloads > 0) #drop the 0's
+
+ggplot(cran_stats, aes(Month, monthly_downloads, group=package, color = package)) +
+  geom_line() +
+  geom_point() +
+  theme(panel.background = element_blank(), panel.grid = element_blank()) +
+  theme(axis.text.x = element_text(angle = 90)) +
+  labs(x = NULL,
+       y = "Monthly Downloads",
+       color = "R Packages")
+```

calendly.Rmd

@@ -8,6 +8,8 @@ output:
 date: "`r format(Sys.time(), '%d %B, %Y')`"
 ---
 
+Currently this is capped at reporting 10 citations per paper. But this will be fixed soon.
+
 ## Preview
 
 ```{r, echo = FALSE, hide = TRUE, message = FALSE}
@@ -44,31 +46,3 @@ Column information:
 ```{r, message = FALSE}
 knitr::kable(citations)
 ```
-
-## Setting up Citations
-
-1. Go to: https://scholar.google.com/scholar
-2. Search for the paper you are looking for the citation count.
-3. Then click the `Cited by ___` button below the title of the paper
-4. Copy and paste this in the `_config_automation.yml` file in the `citation_papers` section.
-
-```
-###### Citations ######
-refresh-citations: yes
-citation_papers: [
-  "https://scholar.google.com/scholar?cites=6140457238337460780",
-  "https://scholar.google.com/scholar?cites=15945159957067506879" ]
-citation_googlesheet:
-```
-- [ ] In the `_config_automation.yml` file, make sure that `refresh-citations` is set to "yes".
-- [ ] Optionally, if you are saving data to google, specify a googlesheet ID in `citation_googlesheet` if you'd like the citation data to be saved to. This will only be relevant if you've set `data_dest` to `google`.
-
-
-## Customizing Citation Data
-
-In order to customize the data you are downloading from Google Scholar you can modify the
-`refresh-scripts/refresh-citations.R` script in your repository.
-
-You can take a look at the [`metricminer` R package documentation](https://hutchdatascience.org/metricminer/articles/getting-started.html) for more details about the functions and what is possible.
-
-If you have a metric need that is not currently fulfilled by `metricminer` or `metricminer-dashboard` we encourage you to [file a GitHub issue with us and let us know about your new feature idea (or bug report)](https://github.com/fhdsl/metricminer/issues/new/choose).

citations.Rmd

@@ -1,6 +1,6 @@
 ---
 title: "GitHub"
-output: 
+output:
   html_document:
     toc: true
     toc_float: true
@@ -21,39 +21,35 @@ yaml <- yaml::read_yaml(file.path(root_dir, "_config_automation.yml"))
 ## For github
 github_overall <- readr::read_tsv(file.path("metricminer_data", "github", "github.tsv"))
 github_timecourse <- readr::read_tsv(file.path("metricminer_data", "github", "github_timecourse.tsv"))
-
-## For google
-# github_overall <- googlesheets4::read_sheet(yaml$github_googlesheet, sheet = "overall_stats")
-# github_timecourse <- googlesheets4::read_sheet(yaml$github_googlesheet, sheet = "timecourse")
 ```
 
 Contributions to a repository example:
 
 ```{r echo = FALSE, hide = TRUE, message=FALSE, warning = FALSE}
-github_overall %>% 
-  ggplot(aes(x = repo_name, y = total_contributions)) + 
-  geom_bar(stat = "identity", fill = "lavender") + 
+github_overall %>%
+  ggplot(aes(x = repo_name, y = total_contributions)) +
+  geom_bar(stat = "identity", fill = "lavender") +
   theme_classic()
 ```
 
-Views of a GitHub Repository over time 
+Views of a GitHub Repository over time
 
 ```{r echo = FALSE, hide = TRUE, message=FALSE}
-github_timecourse %>% 
-  ggplot(aes(x = timestamp, y = count_views, fill = repo, color = repo)) + 
-  geom_line(stat = "identity") + 
-  theme_classic() + 
+github_timecourse %>%
+  ggplot(aes(x = timestamp, y = count_views, fill = repo, color = repo)) +
+  geom_line(stat = "identity") +
+  theme_classic() +
   ylab("date")
 ```
 
-## Data information 
+## Data information
 
 Data information for `github overall data`:
 
-- `num_forks` shows the number of times this repo has been forked. NA means it has never been forked. 
+- `num_forks` shows the number of times this repo has been forked. NA means it has never been forked.
 - `num_contributors` how many people have contributed to this repo
 - `num_stars` how many people have starred this repo?
-- `health_percentage` what percentage of ["good software health" items as described by GitHub](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/about-community-profiles-for-public-repositories) does this repo have? 
+- `health_percentage` what percentage of ["good software health" items as described by GitHub](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/about-community-profiles-for-public-repositories) does this repo have?
 
 ```{r, message=FALSE}
 knitr::kable(github_overall)
@@ -62,36 +58,11 @@ knitr::kable(github_overall)
 Data information for `github timecourse`:
 
 - `timestamp` shows the date the counts correspond to
-- `count_clones` tells the number of clones made on this day. NAs generally indicate no one cloned the repository that day. 
+- `count_clones` tells the number of clones made on this day. NAs generally indicate no one cloned the repository that day.
 - `unique_clones` tells how many people did these clones come from? NAs generally indicate no one cloned the repository that day.
 - `count_views` how many views did the repo get on this day? NAs generally indicate no one viewed the repository that date
 - `unique_views` how many people were those views from? NAs generally indicate no one viewed the repository that date
 
 ```{r, message=FALSE}
 knitr::kable(github_timecourse)
 ```
-
-## Setting up GitHub
-
-At this point you should already have your GitHub authorization set up for your metricminer dashboard by having [followed the instructions above.](#setting-up-your-dashboard-repository).
-
-In the `_config_automation.yml` you will need to specify items in the GitHub section.
-```
-###### GitHub ######
-refresh-github: yes
-github_repos: [ fhdsl/metricminer, fhdsl/metricminer.org ]
-github_googlesheet:
-```
-
-- [ ] In the `_config_automation.yml` file, make sure that `refresh-github` is set to "yes".
-- [ ] In `github_repos` of your `_config_automation.yml`, specify the names of the repositories you'd like to collect data from in `github_repos`. Make sure it includes the `owner/repository` e.g. `fhdsl/metricminer` not just `metricminer`. Commas need to separate the repositories. Delete the example repositories we put there.
-- [ ] Optionally, if you are saving data to Google, specify a googlesheet ID in `github_googlesheet` you'd like the GitHub data to be saved to. This will only be relevant if you've set `data_dest` to `google`.
-
-## Customizing GitHub Data 
-
-In order to customize the data you are downloading from GitHub you can modify the 
-`refresh-scripts/refresh-github.R` script in your repository. 
-
-You can take a look at the [`metricminer` R package documentation](https://hutchdatascience.org/metricminer/articles/getting-started.html) for more details about the functions and what is possible. 
-
-If you have a metric need that is not currently fulfilled by `metricminer` or `metricminer-dashboard` we encourage you to [file a GitHub issue with us and let us know about your new feature idea (or bug report)](https://github.com/fhdsl/metricminer/issues/new/choose).