Skip to content

docs: fix README CI badges ,and links #35

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
maelle wants to merge 7 commits into
base: main
Choose a base branch
from
Open

docs: fix README CI badges ,and links #35

Show file tree
Hide file tree
Changes from 3 commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
558b371
docs: fix README CI badges ,and links
maelle Apr 28, 2025
558a0d7
docs: add some URLs for foodwebs
maelle Apr 28, 2025
c8c23f5
docs: fix igraph url itself
maelle Apr 28, 2025
19f20c5
docs: fix a few more links
maelle Apr 28, 2025
737dfc2
Merge branch 'main' into urls
maelle Apr 28, 2025
b0964b6
more doi
maelle Apr 29, 2025
d39940c
this is a DOI too!
maelle Apr 29, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ Description: A small collection of various network data sets, to use with
Koenigsberg's bridges, visuotactile brain areas of the macaque monkey,
UK faculty friendship network, domestic US flights network, etc.
License: CC BY-SA 4.0 + file LICENSE
URL: http://igraph.org
URL: https://igraph.org/
BugReports: https://github.com/igraph/igraphdata/issues
Depends:
R (>= 2.10)
Expand All @@ -20,5 +20,5 @@ Suggests:
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
RoxygenNote: 7.3.2
Config/testthat/edition: 3
20 changes: 13 additions & 7 deletions R/foodweb.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,12 +28,15 @@
#' \item{\sQuote{Chesapeake}}{Chesapeake Bay Mesohaline Network.
#'
#' Reference: Baird D. & Ulanowicz R.E. (1989) The seasonal dynamics
#' of the Chesapeake Bay ecosystem. Ecological Monographs 59:329-364.}
#' of the Chesapeake Bay ecosystem. Ecological Monographs 59:329-364.
#' \doi{10.2307/1943071}
#' }
#' \item{\sQuote{CrystalC}}{Crystal River Creek (Control).
#'
#' Reference: Homer, M. and W.M. Kemp. Unpublished Ms. See also
#' Ulanowicz, R.E. 1986. Growth and Development: Ecosystems
#' Phenomenology. Springer, New York. pp 69-79.}
#' Phenomenology. Springer, New York. pp 69-79.
#' \url{https://link.springer.com/book/10.1007/978-1-4612-4916-0}}
#' \item{\sQuote{CrystalD}}{Crystal River Creek (Delta Temp).
#'
#' Reference: same as for \sQuote{CrystalD}.}
Expand All @@ -42,7 +45,8 @@
#' Reference: Almunia, J., G. Basterretxea, J. Aristegui, and
#' R.E. Ulanowicz. (1999) Benthic- Pelagic switching in a coastal
#' subtropical lagoon. Estuarine, Coastal and Shelf Science
#' 49:363-384.}
#' 49:363-384.
#' \doi{10.1006/ecss.1999.0503}}
#' \item{\sQuote{Michigan}}{Lake Michigan Control network.
#'
#' Reference: Krause, A. and D. Mason. (In preparation.) A. Krause,
Expand All @@ -55,7 +59,8 @@
#'
#' Reference: Monaco, M.E. and R.E. Ulanowicz. (1997) Comparative
#' ecosystem trophic structure of three U.S. Mid-Atlantic
#' estuaries. Mar. Ecol. Prog. Ser. 161:239-254.}
#' estuaries. Mar. Ecol. Prog. Ser. 161:239-254.
#' \doi{10.3354/meps161239}}
#' \item{\sQuote{Rhode}}{Rhode River Watershed - Water Budget.
#'
#' Reference: Correll, D. (Unpublished manuscript) Smithsonian
Expand All @@ -66,7 +71,8 @@
#' Reference: Baird, D., J. Luczkovich and R. R. Christian. (1998)
#' Assessment of spatial and temporal variability in ecosystem
#' attributes of the St Marks National Wildlife Refuge, Apalachee Bay,
#' Florida. Estuarine, Coastal, and Shelf Science 47: 329-349.}
#' Florida. Estuarine, Coastal, and Shelf Science 47: 329-349.
#' \doi{10.1006/ecss.1998.0360}}
#' \item{\sQuote{baydry}}{Florida Bay Trophic Exchange Matrix, dry season.
#'
#' Reference: Ulanowicz, R. E., C. Bondavalli, and
Expand Down Expand Up @@ -134,7 +140,7 @@
#' \sQuote{name}.
#' @references See them above.
#' @source See references for the individual webs above. The data itself
#' was downloaded from
#' <http://vlado.fmf.uni-lj.si/pub/networks/data/bio/foodweb/foodweb.htm>.
#' was downloaded from the then webpage of the Pajek software
#' (link now broken).
Copy link
Member

@szhorvat szhorvat Apr 28, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Please do not write "link now broken" in the documentation.

In this case, Google still finds the page and there is only a timeout. This suggests that the server is only down temporarily and will come back.

When this is not the case, it is best to get the last good snapshot of the page from archive.org. To do this, one needs the original link, another argument not to remove it.

Copy link
Contributor Author

@maelle maelle Apr 28, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

in my case the webpage never loaded. Do you want to link to the archive.dot snapshots for broken links then?

Copy link
Contributor Author

@maelle maelle Apr 28, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I can't find a snapshot for this page on the wayback machine.

Copy link
Member

@szhorvat szhorvat Apr 28, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

In this case I think we should wait for a couple of days and see if comes back online (or just email Vlado and ask).

That said, this page is present on the Wayback Machine and the datasets are downloadable:

https://web.archive.org/web/20230930092030/http://vlado.fmf.uni-lj.si/pub/networks/data/bio/foodweb/foodweb.htm

Copy link
Contributor Author

@maelle maelle Apr 28, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Do you mind emailing Vlado? It'd be nice to link to an https not http page. 😸

Copy link
Contributor Author

@maelle maelle May 13, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Friendly reminder 😁

#' @keywords datasets
NULL
13 changes: 6 additions & 7 deletions README.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,17 +13,16 @@ knitr::opts_chunk$set(

```{r, echo = FALSE, results = 'hide'}
options(pager = function(files, header, title, delete.file) {
for (f in files) {
l <- readLines(f)
cat(l, sep = "\n")
}
for (f in files) {
l <- readLines(f)
cat(l, sep = "\n")
}
})
```

# Data sets for the igraph R package

[![Linux build status](https://travis-ci.org/igraph/igraphdata.png)](https://travis-ci.org/igraph/igraphdata)
[![Windows build status](https://ci.appveyor.com/api/projects/status/6wov9hh8oprrpkhs?svg=true)](https://ci.appveyor.com/project/gaborcsardi/igraphdata)
[![rcc](https://github.com/igraph/igraphdata/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/igraph/igraphdata/actions/workflows/R-CMD-check.yaml)

This is a data R package, that contains network data sets,
to be used with the igraph R package.
Expand All @@ -37,7 +36,7 @@ install.packages("igraphdata")
```

You can install the development version from Github, using the
[devtools package](https://github.com/hadley/devtools):
[devtools package](https://github.com/r-lib/devtools):

```{r, eval = FALSE}
devtools::install_github("igraph/igraphdata")
Expand Down
6 changes: 3 additions & 3 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

# Data sets for the igraph R package

[![Linux build status](https://travis-ci.org/igraph/igraphdata.png)](https://travis-ci.org/igraph/igraphdata) [![Windows build status](https://ci.appveyor.com/api/projects/status/6wov9hh8oprrpkhs?svg=true)](https://ci.appveyor.com/project/gaborcsardi/igraphdata)
[![rcc](https://github.com/igraph/igraphdata/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/igraph/igraphdata/actions/workflows/R-CMD-check.yaml)

This is a data R package, that contains network data sets, to be used with the igraph R package.

Expand All @@ -13,15 +13,15 @@ From CRAN:
<pre class='chroma'>
<span><span class='nf'><a href='https://rdrr.io/r/utils/install.packages.html'>install.packages</a></span><span class='o'>(</span><span class='s'>"igraphdata"</span><span class='o'>)</span></span></pre>

You can install the development version from Github, using the [devtools package](https://github.com/hadley/devtools):
You can install the development version from Github, using the [devtools package](https://github.com/r-lib/devtools):

<pre class='chroma'>
<span><span class='nf'>devtools</span><span class='nf'>::</span><span class='nf'><a href='https://remotes.r-lib.org/reference/install_github.html'>install_github</a></span><span class='o'>(</span><span class='s'>"igraph/igraphdata"</span><span class='o'>)</span></span></pre>

## Usage

<pre class='chroma'>
<span><span class='kr'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='o'>(</span><span class='nv'><a href='http://igraph.org'>igraphdata</a></span><span class='o'>)</span></span>
<span><span class='kr'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='o'>(</span><span class='nv'><a href='https://igraph.org/'>igraphdata</a></span><span class='o'>)</span></span>
<span><span class='nf'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='o'>(</span>package <span class='o'>=</span> <span class='s'>"igraphdata"</span><span class='o'>)</span></span></pre>
<pre class='chroma'>
<span><span class='c'>#&gt; Data sets in package 'igraphdata':</span></span>
Expand Down
20 changes: 13 additions & 7 deletions man/foodwebs.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion man/igraphdata-package.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.