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docs: fix README CI badges ,and links #35

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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
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4 changes: 2 additions & 2 deletions DESCRIPTION
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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
4 changes: 2 additions & 2 deletions LICENSE
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Expand Up @@ -55,7 +55,7 @@ you use this data set:

D. Gfeller, Simplifying complex networks: from a clustering to a
coarse graining strategy, \emph{PhD Thesis EPFL}, no 3888, 2007.
http://library.epfl.ch/theses/?nr=3888
https://infoscience.epfl.ch/entities/publication/35db87cd-756f-42c5-b0a5-60f4de0eae69

karate
------
Expand Down Expand Up @@ -105,7 +105,7 @@ yeast
-----

The data was downloaded from
http://www.nature.com/nature/journal/v417/n6887/suppinfo/nature750.html
https://www.nature.com/articles/nature750#Sec8

Please cite the following paper if you use this data set:

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4 changes: 2 additions & 2 deletions R/USairports.R
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Expand Up @@ -43,9 +43,9 @@
#' \item{Distance}{The distance between the two airports, in miles.}
#' }
#' @source
#' Most of this information was downloaded from The Research and
#' Most of this information was downloaded from The (now dissolved) Research and
#' Innovative Technology Administration (RITA). See
#' <http://www.rita.dot.gov/about_rita/> for details. The airport
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@maelle maelle Apr 28, 2025

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@szhorvat a big issue is that CRAN will flag broken link even if they're not formatted as links.

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@maelle maelle Apr 28, 2025

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and this wikipedia page as a link to the web archive link of the RITA.

#' <https://en.wikipedia.org/wiki/Research_and_Innovative_Technology_Administration> for details. The airport
#' position information was collected from Wikipedia and other public
#' online sources.
#' @keywords datasets
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20 changes: 13 additions & 7 deletions R/foodweb.R
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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).
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@szhorvat szhorvat Apr 28, 2025

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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.

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@maelle maelle Apr 28, 2025

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

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@maelle maelle Apr 28, 2025

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

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@szhorvat szhorvat Apr 28, 2025

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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

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@maelle maelle Apr 28, 2025

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

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@maelle maelle May 13, 2025

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Friendly reminder 😁

#' @keywords datasets
NULL
2 changes: 1 addition & 1 deletion R/immuno.R
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Expand Up @@ -21,7 +21,7 @@
#' @references
#' D. Gfeller, Simplifying complex networks: from a clustering to a
#' coarse graining strategy, *PhD Thesis EPFL*, no 3888, 2007.
#' <http://library.epfl.ch/theses/?nr=3888>
#' <https://infoscience.epfl.ch/entities/publication/35db87cd-756f-42c5-b0a5-60f4de0eae69>
#' @source
#' See reference below.
#' @keywords datasets
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2 changes: 1 addition & 1 deletion R/yeast.R
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Expand Up @@ -61,6 +61,6 @@
#' Michael Cornell, Stephen G. Oliver, Stanley Fields and Peer
#' Bork. *Nature* 417, 399-403 (2002)
#' @source The data was downloaded from
#' <http://www.nature.com/nature/journal/v417/n6887/suppinfo/nature750.html>.
#' <https://www.nature.com/articles/nature750#Sec8>.
#' @keywords datasets
NULL
13 changes: 6 additions & 7 deletions README.Rmd
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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")
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6 changes: 3 additions & 3 deletions README.md
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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>
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