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index.Rmd
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---
title: "N8 CIR 'Northern Tour' ReproHack series"
output:
html_document:
theme: flatly
css: reprohack.css
params:
title: "N8 CIR 'Northern Tour' ReproHack series"
room_location: "Multiple locations"
address: "Newcastle, York, Leeds, Sheffield, Manchester"
date: "21 Jan - 12 Mar 2020"
time: "10:00am-17:00pm"
bannerurl: "reprohack-banner.png"
latitude: 53.38119
longitude: -1.48036
registration_url: https://n8cir.org.uk/news/reprohacks/
hackpad_url: https://bit.ly/remote-reprohack-hackpad
submission_url: https://forms.gle/vMk25vCevMg2QiYQ9
reprohack_repo_url: https://github.com/annakrystalli/n8cir-reprohacks
submission_form_title: "ReproHack Paper Submission Form - n8"
feedback_form_title: "ReproHack feedback form - n8"
runtime: shiny
---
# **`r params$title`**
## _A series of hands-on Reproducibility Hackathon_
<br>
#### **`r shiny::icon("clock")` `r params$time`**
#### **`r shiny::icon("calendar")` `r params$date`**
#### **`r shiny::icon("map-marker-alt")` `r params$room_location`**
#### **`r shiny::icon("map-marked-alt")` `r params$address`**
```{r out.width='100%', fig.height=6, eval=require('leaflet'), echo=FALSE, message=FALSE, warning=FALSE}
library(leaflet)
library(dplyr)
event_log <- readr::read_csv("data/event-log.csv") %>%
mutate(upcoming = date >= Sys.Date()) %>%
mutate(popup = glue::glue("<h3><a href={url} {title}></h3><br>{date}"),
date_f = format(date, format="%a %b %d %Y"))
plot_log <- event_log %>%
mutate(color = case_when(upcoming == TRUE ~ "green",
upcoming == FALSE ~ "orange"))
#pal <- colorFactor(c("green", "orange"), c(FALSE, TRUE))
make_popup <- function(df){
popup_row <- function(x){paste0(
"<h3><a href=", x["url"], "> ", x["title"],"</a></h3>", " <br>",
"<strong> Date: </strong>", x["date_f"], "<br>",
"<strong> Room: </strong>", x["room"], "<br>",
"<strong> Address: </strong>", x["address"], "<br>")}
apply(df, 1, popup_row)
}
icons <- awesomeIcons(
icon = 'ios-close',
iconColor = 'black',
library = 'ion',
markerColor = plot_log$color
)
plot_log %>%
leaflet() %>%
addProviderTiles("CartoDB.Positron") %>%
addAwesomeMarkers(icon = icons, popup = make_popup(plot_log))
```
***
```{r, echo = F, results='asis'}
if(!is.null(params$registration_url)){
cat(paste0("### [**REGISTER**](", params$registration_url, ")"))
}
```
[](https://reprohack-autoinvite.herokuapp.com/)
##### [ReproHack hackpad](`r params$hackpad_url`): containing details for participants
***
# **Welcome `r emo::ji("wave")` **
We are all excited by the progress made by many authors to **make their papers reproducible by publishing associated code and data**.
We know how challenging it can be so we **want to showcase the value of the practice**, both for original authors and as a learning experience for those who attempt to reproduce the work.
## **Event format**:
During a ReproHack, **participants attempt to reproduce published research of their choice from a list of proposed papers with publicly available associated code and data**. Participants get to work with other people's material in a low pressure environment and record their experiences on a number of key aspects, including reproducibility, transparency and reusability of materials. At the end of the day we regroup, share our experiences and give feedback to the authors.
It's imperative to note that **ReproHacks are by no means an attempt to criticise or discredit work**. We see reproduction as **beneficial scientific activity in itself**, with useful outcomes for authors and valuable learning experiences for the participants and the research community as a whole.
***
## **Ways to participate**
<br>
### `r shiny::icon("newspaper")` **Propose a paper**
##### You've put a lot of effort into making your work reproducible. Now let people learn from and engage with it!
Benefits to authors:
- **Feedback** on the reproducibility of your work.
- **Appreciation** for your efforts in making your work reproducible.
- Opportunity to **engage others with your research**.
<br>
### `r shiny::icon("redo-alt")` **Reproduce**
##### Join us at the ReproHack and get working with other people's material.
Benefits to participants:
- **Practical experience in reproducibility** with real published materials and the opportunity to explore different tools and strategies.
- **Inspiration** from working with other people’s code and data.
- An appreciation that **reproducibility is non trivial** but that opening up your work for more people to engage with is the best way to help improve it.
- An appreciation that **reproducibility has community value beyond just the validation of the results**. For example, access to such materials increases the potential for reuse and understanding of the work.
**Benefits to the whole research community:**
- Assessment of how reproducible papers are ‘out of the box’.
- Evaluation of how successful current practices are and for what purpose.
- Identification of what works and where the most pressing weaknesses in our approaches are.
<br>
Keep track of discussions and links to any outputs from our sessions on the event [**hackpad**](`r params$hackpad_url`)
***
# **PROPOSE**
### **Nominate a paper for Reproduction:**
We invite nominations for papers that have both associated **code** and **data** publicly available. We also encourage analyses based on open source tools as we cannot guarantee participants will have access to specialised licenced software.
```{r, echo=FALSE}
library("shiny")
wellPanel(a("Nominate Paper", class = "btn btn-primary btn-md",
href = params$submission_url))
```
## **Proposed papers:**
<br>
```{r, echo=FALSE, message=FALSE, warning=FALSE, eval=require('googlesheets4')}
library(googlesheets4)
options(gargle_oauth_cache = ".secrets",
gargle_oauth_email = "annakrystalli@googlemail.com")
```
```{r, echo=FALSE}
print_contact_links <- function(responses, i){
row <- responses[i, ]
twitter <- if(!is.na(row[,"Twitter handle (optional)"])){
twitter_url <- paste0("https://twitter.com/", gsub(" *@ *", "", row[,"Twitter handle (optional)"]))
paste0("[<i class='fa fa-twitter'/>](", twitter_url,")")}else{NULL}
github <- if(!is.na(row[,"GitHub username (optional)"])){
github_url <- paste0("https://github.com/", gsub(" *@ *", "", row[,"GitHub username (optional)"]))
paste0("[<i class='fa fa-github'/>](", github_url,")")}else{NULL}
feedback <- if(row[, "Would you like to receive a copy of any feedback on the paper?"] == "Yes"){
"<i class='fa fa-comment-dots'/>"}else{NULL}
public <- if(row[,"Can feedback on your paper be made public?"] == "Yes"){
"<i class='fa fa-globe'/>"}else{NULL}
return(paste(twitter, github, feedback, public))
}
```
```{r, message=FALSE, results='asis', warning=FALSE, echo=FALSE}
match_length <- 30
responses_gs <- sheets_find(paste(params$submission_form_title))
responses <- sheets_read(responses_gs) %>%
dplyr::mutate(match_name = stringr::str_trunc(.data$`Paper title`, match_length) )
# load feedback
feedback_gs <- sheets_find(paste(params$feedback_form_title))
feedback <- sheets_read(feedback_gs) %>%
dplyr::mutate(match_name = stringr::str_trunc(.data$`Which paper did you attempt?`, match_length) )
responses_joined <- fuzzyjoin::stringdist_left_join(feedback, responses,
by = c(match_name = "match_name"),
max_dist = 10,
method = "qgram",
#method = "cosine",
ignore_case = TRUE) %>%
dplyr::select(.data$`Paper title`,
.data$`Which paper did you attempt?`, dplyr::everything()) %>%
assertr::verify(!is.na(.data$`Which paper did you attempt?`))
stats <- dplyr::group_by(responses_joined, .data$`Paper title`) %>%
dplyr::summarise(no_attempts = dplyr::n(),
mean_repro = mean(.data$`On a scale of 1 to 10, how much of the paper did you manage to reproduce?`) %>%
round())
responses <- dplyr::left_join(responses, stats)
row_n <- nrow(responses)
set.seed(params$latitude * params$longitude)
if(row_n > 0){
random_ids <- sample.int(row_n)
for(j in seq_len(row_n)){
i <- random_ids[j]
cat("<div class='card'>")
cat('\n')
cat('\n')
cat('\n')
cat("### **", j,". ", as.character(responses[i, "Paper title"]), "**", "\n", "\n", sep = "")
cat("**", gsub("\n", "", gsub("[*]", "", as.character(responses[i, "Paper citation"]))), "\n**", "\n", "\n", sep = "")
cat("##### *submitted by ", as.character(responses[i, "Name"]), print_contact_links(responses, i), "*", "\n")
if(!is.na(responses[i, "no_attempts"])){
cat("*No. attempts <i class='fa fa-recycle'/>* ", as.character(responses[i, "no_attempts"]), "\n")
cat("*Mean Repro Score <i class='fas fa-check-circle' />* ", as.character(responses[i, "mean_repro"]), "/10 \n\n")
}
cat('\n')
cat('\n')
cat("**Why should we attempt to reproduce this paper?**", "\n", "\n")
cat(as.character(responses[i, "Why should we attempt to reproduce this paper?"]), "\n")
cat('\n')
cat("**Paper URL:** [", as.character(responses[i, "Paper URL"]),"](",as.character(responses[i, "Paper URL"]) ,")", "\n")
cat('\n')
cat("**Data URL:**", as.character(responses[i, "Data URL"]), "\n")
cat('\n')
cat("**Code URL:**", as.character(responses[i, "Code URL"]), "\n")
cat('\n', "\n")
cat("**Useful programming skills:**", as.character(responses[i, "Useful programming skills"]), "\n")
cat("</div>")
cat('\n', "\n",'\n')
}
}
```
```{r, echo=FALSE}
wellPanel(a("Refresh proposal list", class = "btn btn-primary btn-md",
href = "javascript:history.go(0)"))
```
***
### ReproHack History
ReproHacks were inspired by **Owen Petchey's** [**Reproducible Research in Ecology, Evolution, Behaviour, and Environmental Studies course**](https://github.com/opetchey/RREEBES), where students attempt to reproduce the analyses and figures of a paper from the raw data. We wanted to attempt to do the same but, while they take a few months over a number of sessions, for our first event we only had one day. So to condense that activity into one day we set the challenge to be: **reproduce results from published data AND code**.
We've run **two ReproHacks so far** as part of satellite OpenCon events (Berlin 2016, [London 2017](https://rse.shef.ac.uk/blog/opencon-london/)) with **a [series of them planned for 2019-2020](https://rse.shef.ac.uk/blog/ssi-fellowships-2019/) using funding provided through the [Software Sustainability Institute Fellowship programme](https://www.software.ac.uk/blog/2019-04-11-announcing-2019-software-sustainability-institute-fellows)**.
#### If you would like to host a ReproHack at your institution please get in touch!
***
<div class="pull-left">
### Get in touch
Chat to us on [Slack](https://reprohack-autoinvite.herokuapp.com/) or email [reprohack@googlegroups.com](mailto:reprohack@googlegroups.com).
</div>
<div class="pull-right">
<img src="https://www.software.ac.uk/sites/default/files/images/content/SSI_Big300dpi.png" width="100%">
</div>