From 558b37114b441425467aef009df9f24fb130ab46 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Mon, 28 Apr 2025 09:47:25 +0200 Subject: [PATCH 1/6] docs: fix README CI badges ,and links --- README.Rmd | 13 ++++++------- README.md | 6 +++--- 2 files changed, 9 insertions(+), 10 deletions(-) diff --git a/README.Rmd b/README.Rmd index 3efd4e3..c86e050 100644 --- a/README.Rmd +++ b/README.Rmd @@ -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. @@ -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") diff --git a/README.md b/README.md index cc5795b..274956e 100644 --- a/README.md +++ b/README.md @@ -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. @@ -13,7 +13,7 @@ From CRAN: 
 install.packages("igraphdata")
-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): 
 devtools::install_github("igraph/igraphdata")
@@ -21,7 +21,7 @@ You can install the development version from Github, using the [devtools package ## Usage 
-library(igraphdata)
+library(igraphdata)
 data(package = "igraphdata")
 #> Data sets in package 'igraphdata':

From 558a0d7b391cd0499187efdd61a1eb056072b7b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= 
Date: Mon, 28 Apr 2025 10:33:23 +0200
Subject: [PATCH 2/6] docs: add some URLs for foodwebs

---
 R/foodweb.R     | 20 +++++++++++++-------
 man/foodwebs.Rd | 20 +++++++++++++-------
 2 files changed, 26 insertions(+), 14 deletions(-)

diff --git a/R/foodweb.R b/R/foodweb.R
index 8cada05..7b88957 100644
--- a/R/foodweb.R
+++ b/R/foodweb.R
@@ -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}.}
@@ -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,
@@ -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
@@ -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
@@ -134,7 +140,7 @@
 #' \sQuote{name}.
 #' @references See them above.
 #' @source See references for the individual webs above. The data itself
-#'   was downloaded from
-#'   .
+#'   was downloaded from the then webpage of the Pajek software
+#'  (link now broken).
 #' @keywords datasets
 NULL
diff --git a/man/foodwebs.Rd b/man/foodwebs.Rd
index df0948b..937a9bd 100644
--- a/man/foodwebs.Rd
+++ b/man/foodwebs.Rd
@@ -22,12 +22,15 @@ Reference: same as for \sQuote{ChesLower}.}
 \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}.}
@@ -36,7 +39,8 @@ Reference: same as for \sQuote{CrystalD}.}
 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,
@@ -49,7 +53,8 @@ Thesis. University of Coimbra, Coimbra, Portugal.}
 
 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
@@ -60,7 +65,8 @@ Edgewater, Maryland 21037-0028 USA.}
 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
@@ -129,8 +135,8 @@ The graphs also contain some informative graph attributes:
 }
 \source{
 See references for the individual webs above. The data itself
-was downloaded from
-\url{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).
 }
 \usage{
 foodwebs

From c8c23f57e015ab2616fe0daec6d22e0e38decf78 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= 
Date: Mon, 28 Apr 2025 10:33:35 +0200
Subject: [PATCH 3/6] docs: fix igraph url itself

---
 DESCRIPTION               | 4 ++--
 man/igraphdata-package.Rd | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ab84e63..e8a025f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -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)
@@ -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
diff --git a/man/igraphdata-package.Rd b/man/igraphdata-package.Rd
index eeeba15..a225016 100644
--- a/man/igraphdata-package.Rd
+++ b/man/igraphdata-package.Rd
@@ -11,7 +11,7 @@ A small collection of various network data sets, to use with the 'igraph' packag
 \seealso{
 Useful links:
 \itemize{
-  \item \url{http://igraph.org}
+  \item \url{https://igraph.org/}
   \item Report bugs at \url{https://github.com/igraph/igraphdata/issues}
 }
 

From 19f20c52a9c4da7b0636edbbbb27e07633a86ee2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= 
Date: Mon, 28 Apr 2025 10:37:53 +0200
Subject: [PATCH 4/6] docs: fix a few more links

---
 LICENSE           | 4 ++--
 R/USairports.R    | 4 ++--
 R/immuno.R        | 2 +-
 R/yeast.R         | 2 +-
 man/USairports.Rd | 4 ++--
 man/immuno.Rd     | 2 +-
 man/yeast.Rd      | 2 +-
 7 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/LICENSE b/LICENSE
index 45a946a..4b86091 100644
--- a/LICENSE
+++ b/LICENSE
@@ -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
 ------
@@ -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:
 
diff --git a/R/USairports.R b/R/USairports.R
index 75edf30..d337e2b 100644
--- a/R/USairports.R
+++ b/R/USairports.R
@@ -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
-#'    for details. The airport
+#'    for details. The airport
 #'   position information was collected from Wikipedia and other public
 #'   online sources.
 #' @keywords datasets
diff --git a/R/immuno.R b/R/immuno.R
index d485c0d..5268f90 100644
--- a/R/immuno.R
+++ b/R/immuno.R
@@ -21,7 +21,7 @@
 #' @references
 #'   D. Gfeller, Simplifying complex networks: from a clustering to a
 #'   coarse graining strategy, *PhD Thesis EPFL*, no 3888, 2007.
-#'   
+#'   
 #' @source
 #'   See reference below.
 #' @keywords datasets
diff --git a/R/yeast.R b/R/yeast.R
index 3628b6d..6382bd4 100644
--- a/R/yeast.R
+++ b/R/yeast.R
@@ -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
-#'   .
+#'   .
 #' @keywords datasets
 NULL
diff --git a/man/USairports.Rd b/man/USairports.Rd
index 0f72cc6..415a7d5 100644
--- a/man/USairports.Rd
+++ b/man/USairports.Rd
@@ -31,9 +31,9 @@ carried out by a given airline, using a given aircraft type.}
 }
 }
 \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
-\url{http://www.rita.dot.gov/about_rita/} for details. The airport
+\url{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.
 }
diff --git a/man/immuno.Rd b/man/immuno.Rd
index e8e0e08..21c13b0 100644
--- a/man/immuno.Rd
+++ b/man/immuno.Rd
@@ -25,6 +25,6 @@ is smaller than the threshold value \eqn{\theta=8}{theta=8} Angstrom.
 \references{
 D. Gfeller, Simplifying complex networks: from a clustering to a
 coarse graining strategy, \emph{PhD Thesis EPFL}, no 3888, 2007.
-\url{http://library.epfl.ch/theses/?nr=3888}
+\url{https://infoscience.epfl.ch/entities/publication/35db87cd-756f-42c5-b0a5-60f4de0eae69}
 }
 \keyword{datasets}
diff --git a/man/yeast.Rd b/man/yeast.Rd
index 4d5e484..1b30152 100644
--- a/man/yeast.Rd
+++ b/man/yeast.Rd
@@ -46,7 +46,7 @@ attributes are \code{NA} for these.
 }
 \source{
 The data was downloaded from
-\url{http://www.nature.com/nature/journal/v417/n6887/suppinfo/nature750.html}.
+\url{https://www.nature.com/articles/nature750#Sec8}.
 }
 \usage{
 yeast

From b0964b61ee9ad1d551024933c39061f448508376 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= 
Date: Tue, 29 Apr 2025 13:01:30 +0200
Subject: [PATCH 5/6] more doi

---
 LICENSE       | 4 ++--
 R/immuno.R    | 2 +-
 R/yeast.R     | 2 +-
 man/immuno.Rd | 2 +-
 man/yeast.Rd  | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/LICENSE b/LICENSE
index 4b86091..c2130d2 100644
--- a/LICENSE
+++ b/LICENSE
@@ -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.
-https://infoscience.epfl.ch/entities/publication/35db87cd-756f-42c5-b0a5-60f4de0eae69
+https://doi.org/10.5075/epfl-thesis-3888
 
 karate
 ------
@@ -105,7 +105,7 @@ yeast
 -----
 
 The data was downloaded from 
-https://www.nature.com/articles/nature750#Sec8
+https://doi.org/10.1038/nature750
 
 Please cite the following paper if you use this data set:
 
diff --git a/R/immuno.R b/R/immuno.R
index 5268f90..cd14331 100644
--- a/R/immuno.R
+++ b/R/immuno.R
@@ -21,7 +21,7 @@
 #' @references
 #'   D. Gfeller, Simplifying complex networks: from a clustering to a
 #'   coarse graining strategy, *PhD Thesis EPFL*, no 3888, 2007.
-#'   
+#'   
 #' @source
 #'   See reference below.
 #' @keywords datasets
diff --git a/R/yeast.R b/R/yeast.R
index 6382bd4..6db34d9 100644
--- a/R/yeast.R
+++ b/R/yeast.R
@@ -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
-#'   .
+#'   .
 #' @keywords datasets
 NULL
diff --git a/man/immuno.Rd b/man/immuno.Rd
index 21c13b0..72ce0fc 100644
--- a/man/immuno.Rd
+++ b/man/immuno.Rd
@@ -25,6 +25,6 @@ is smaller than the threshold value \eqn{\theta=8}{theta=8} Angstrom.
 \references{
 D. Gfeller, Simplifying complex networks: from a clustering to a
 coarse graining strategy, \emph{PhD Thesis EPFL}, no 3888, 2007.
-\url{https://infoscience.epfl.ch/entities/publication/35db87cd-756f-42c5-b0a5-60f4de0eae69}
+\url{https://doi.org/10.5075/epfl-thesis-3888}
 }
 \keyword{datasets}
diff --git a/man/yeast.Rd b/man/yeast.Rd
index 1b30152..a70b982 100644
--- a/man/yeast.Rd
+++ b/man/yeast.Rd
@@ -46,7 +46,7 @@ attributes are \code{NA} for these.
 }
 \source{
 The data was downloaded from
-\url{https://www.nature.com/articles/nature750#Sec8}.
+\url{https://doi.org/10.1038/nature750}.
 }
 \usage{
 yeast

From d39940caab7472c6027dedc3aae96205a97b1652 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= 
Date: Tue, 29 Apr 2025 13:03:19 +0200
Subject: [PATCH 6/6] this is a DOI too!

---
 R/foodweb.R     | 2 +-
 man/foodwebs.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/foodweb.R b/R/foodweb.R
index 7b88957..e5cde46 100644
--- a/R/foodweb.R
+++ b/R/foodweb.R
@@ -36,7 +36,7 @@
 #'   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.
-#'   \url{https://link.springer.com/book/10.1007/978-1-4612-4916-0}}
+#'   \url{https://doi.org/10.1007/978-1-4612-4916-0}}
 #'   \item{\sQuote{CrystalD}}{Crystal River Creek (Delta Temp).
 #'
 #'   Reference: same as for \sQuote{CrystalD}.}
diff --git a/man/foodwebs.Rd b/man/foodwebs.Rd
index 937a9bd..1038261 100644
--- a/man/foodwebs.Rd
+++ b/man/foodwebs.Rd
@@ -30,7 +30,7 @@ of the Chesapeake Bay ecosystem. Ecological Monographs 59:329-364.
 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.
-\url{https://link.springer.com/book/10.1007/978-1-4612-4916-0}}
+\url{https://doi.org/10.1007/978-1-4612-4916-0}}
 \item{\sQuote{CrystalD}}{Crystal River Creek (Delta Temp).
 
 Reference: same as for \sQuote{CrystalD}.}