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Update README.md
Step by step instructions on how to add paper to the lab archive website
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‎README.md‎

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https://zipkinlab.github.io/#about
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# rqm-template
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[project] Webpage source code for Zipkin Lab code archive
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# Adding papers to the Zipkin Lab code archive front-facing page
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---
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Adapted from template developed by @auremoser for https://cbahlai.github.io/rqm-template/
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Here are the steps and information to add a new GitHub repository to the [Zipkin Lab Code Archive](https://zipkinlab.github.io/) front-face page, if you are one of the 'GitHub people'.
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The lab archive is the website where all our code and data can 'live through eternity', and where we can direct people who ask about our analysis or data. The [Lab Code Archive](https://github.com/zipkinlab/zipkinlab.github.io) is a single repository that lives within the [Zipkin Lab's GitHub](https://github.com/zipkinlab) page. It creates and links the [Zipkin Lab Archive website](https://zipkinlab.github.io/) to all other repositories that are stored in the lab GitHub.
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<div align="center">
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<img src="assets/images/lab_page.png" alt="lab_page" width="600">
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</div>
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---
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## These are the steps:
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### 1 - Fork personal repository to Zipkin Lab GitHub
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All repositories should be on the Zipkin Lab GitHub and linked from there (not from personal GitHub accounts) to the front-facing page. So step one is **forking** someone's repository into it.
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- Navigate to the repository you want to fork.
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- Click the **Fork** button (top-right of the page).
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- Choose the owner and name for the fork: it should be **ZIPKINLAB**, not your own.
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- You can also change the repository name at this stage.
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- Click **Create fork**.
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---
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### 2 - Gather required information
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There are two documents to use as references (available on the [Zipkin Lab Teams GitHub page](https://teams.microsoft.com/l/channel/19%3A15762ca26189456f989a45136b141e94%40thread.tacv2/GitHub?groupId=a1e331a0-3ad7-4671-a13e-3629dea6fd3b&tenantId=22177130-642f-41d9-9211-74237ad5687d)):
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- A checklist to track added papers:
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[GithubProjects.xlsx](https://michiganstate.sharepoint.com/:x:/r/sites/STUOT-ResearchGroup/Shared%20Documents/GitHub/GithubProjects.xlsx)
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- A document with detailed instructions:
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[Github Project Checklist.docx](https://michiganstate.sharepoint.com/:w:/r/sites/STUOT-ResearchGroup/Shared%20Documents/GitHub/Github%20Project%20Checklist.docx)
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---
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### 3 - Edit the front-facing page
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- Edits are done in the [index.html](https://github.com/zipkinlab/zipkinlab.github.io/blob/master/index.html) file.
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- Insert your new HTML block **within the appropriate paper category** (e.g., community models, unmarked population models).
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- New papers go at the top of the section.
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- You can add information manually, or use the code automation below:
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#### Automated version:
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- The paper metadata goes into the [github_dat.csv](https://michiganstate.sharepoint.com/:x:/r/sites/STUOT-ResearchGroup/Shared%20Documents/GitHub/github_dat.csv) file. Just download it and substitute the fields with the details of the paper you want to add.
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<details>
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<summary>Click to see code that creates github_dat.csv</summary>
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````r
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library(tidyverse)
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dat <- tibble(
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data = c("section", "citation", "title", "year", "journal", "fig_height", "fig_width", "abstract",
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"author1", "github1", "author2", "github2", "author3", "github3", "author4", "github4",
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"numb_authors", "doi", "doi_addr"),
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info = c("Data integration models", "Davis_etal_2025_EcoApps",
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"Evaluating environmental drivers and synchrony of Arctic shorebird demographic rates to inform conservation management",
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"2025", "Ecological Applications", "2128", "2193",
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"Environmental factors affect the population dynamics of migratory species throughout their annual cycles. However, identifying the",
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"Davis, K.L.", "https://github.com/davisk93", "Lanctot, R.B.", "NA", "Saalfeld, S.T.", "NA",
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"Zipkin, E.F.", "https://github.com/zipkinlab", "4", "10.1111/2041-210X.14282",
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"https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.14282")
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)
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````
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</details>
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<div align="center">
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<img src="assets/images/git_dat.png" alt="git_dat" width="400">
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</div>
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- Now that you have the new `github_dat.csv` file in your working directory, run [github_html.r](https://michiganstate.sharepoint.com/:u:/r/sites/STUOT-ResearchGroup/Shared%20Documents/GitHub/github_html.r) to create the HTML code snippets that should be added to [index.html](https://github.com/zipkinlab/zipkinlab.github.io/blob/master/index.html).
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<details>
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<summary>Click to see code from github_html.r</summary>
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````r
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## code to create html file for the lab front-facing page
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library(glue)
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library(tidyverse)
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dat <- read_csv("github_dat.csv")
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# Match section name to ID
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id_codes <- c("icm", "dataintegration", "other", "community", "unmarked")
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id_names <- c("Integrated community models", "Data integration models", "Other projects", "Community analyses", "Unmarked population models")
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id_cd <- cbind(id_codes, id_names) %>% as_tibble()
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this_id <- pull(dat[which(dat$data == "section"),2])
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id <- paste0(gsub(" ", "",tolower(id_cd[which(id_cd$id_names == this_id),1])),
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dat[which(dat$data == "year"),2],
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toupper(substr(dat[which(dat$data == "author1"),2],1,1)))
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citation <- dat[which(dat$data == "citation"),2] %>% pull()
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figure <- glue("assets/images/{citation}.png")
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git_repo <- glue("https://github.com/zipkinlab/{citation}")
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title <- pull(dat[which(dat$data == "title"),2])
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fig_height <- as.numeric(pull(dat[which(dat$data == "fig_height"),2]))
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fig_width <- as.numeric(pull(dat[which(dat$data == "fig_width"),2]))
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FigSize <- function(OriginalWidth, OriginalHeight, OutputWidth = 200){
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WidthRatio <- OutputWidth / OriginalWidth
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OutputHeight <- OriginalHeight * WidthRatio
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return(list(round(OutputWidth), round(OutputHeight)))
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}
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res_fig <- FigSize(fig_width, fig_height)
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fig_width2 <- res_fig[[1]][1]
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fig_height2 <- res_fig[[2]][1]
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journal <- pull(dat[which(dat$data == "journal"),2])
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year <- pull(dat[which(dat$data == "year"),2])
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doi <- pull(dat[which(dat$data == "doi"),2])
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doi_addr <- pull(dat[which(dat$data == "doi_addr"),2])
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abstract <- pull(dat[which(dat$data == "abstract"),2])
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numb_authors <- as.numeric(pull(dat[which(dat$data == "numb_authors"),2]))
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# Build author list with optional GitHub links
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ht2 <- c()
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for(i in 1:numb_authors){
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author <- pull(dat[dat$data == paste0("author", i), 2])
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github <- pull(dat[dat$data == paste0("github", i), 2])
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if (is.na(github)) {
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ht2 <- c(ht2, paste0(author, ifelse(i < numb_authors, ", ", "")))
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} else {
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link <- glue("<a href='{github}'>{author}</a>")
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ht2 <- c(ht2, ifelse(i == numb_authors && i > 1, paste0("and ", link), paste0(link, ", ")))
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}
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}
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authors_html <- paste(ht2, collapse = "")
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html_content <- glue("
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<h3 id='{id}'>{citation}</h3>
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<section class='example'>
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<section class='title'>
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<h1>{title}</h1>
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<img class='modal-img' src='{figure}' alt='{citation}' height='{fig_height2}' width='{fig_width2}' style='background-color:white;' >
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</section>
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<section class='content'>
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<p><strong>Citation</strong> - {authors_html} ({year}) {title}. <em>{journal}</em>. <a href='{doi_addr}'>DOI: {doi}</a></p>
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<p><strong>Abstract</strong> - {abstract}</p>
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<p><strong>Code and Data</strong> - <a href='{git_repo}'>Link to repo</a></p>
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</section>
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</section>
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")
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writeLines(html_content, "git_text.txt")
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writeLines(glue("<em> <a href='#{id}'>{citation}</a></em> |"), "git_title.txt")
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````
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</details><br>
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- Paste the text from `git_text.txt` and `git_title.txt` into the `index.html` file (you have to hit 'edit' and commit it!).
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<br>
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- Add a figure (.PNG) to the [assets/images/](https://github.com/zipkinlab/zipkinlab.github.io/tree/master/assets/images) folder on GitHub. The figure name should match the citation (e.g., `Zipkin_etal_2025_MEE.png`).
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---
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### 4 - Add metadata to the `Archived-data` repository
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- Upload the relevant data/code links to the [Archived-data repo](https://github.com/zipkinlab/Archived-data).
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---
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#### Open the [Zipkin Lab Code Archive](https://zipkinlab.github.io/) to check if your edits are correct and...
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## 🎉 YAY, you are done!!!
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---
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**Author:** Bruna Amaral

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