diff --git a/DESCRIPTION b/DESCRIPTION
index 73ea12d..0e11a01 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -17,7 +17,7 @@ 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)
diff --git a/LICENSE b/LICENSE
index 45a946a..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.
-http://library.epfl.ch/theses/?nr=3888
+https://doi.org/10.5075/epfl-thesis-3888
 
 karate
 ------
@@ -105,7 +105,7 @@ yeast
 -----
 
 The data was downloaded from 
-http://www.nature.com/nature/journal/v417/n6887/suppinfo/nature750.html
+https://doi.org/10.1038/nature750
 
 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
-#'   <http://www.rita.dot.gov/about_rita/> for details. The airport
+#'   <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
diff --git a/R/foodweb.R b/R/foodweb.R
index 8cada05..e5cde46 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 Unpublished Ms.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://doi.org/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
-#'   <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).
 #' @keywords datasets
 NULL
diff --git a/R/immuno.R b/R/immuno.R
index d485c0d..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.
-#'   <http://library.epfl.ch/theses/?nr=3888>
+#'   <https://doi.org/10.5075/epfl-thesis-3888>
 #' @source
 #'   See reference below.
 #' @keywords datasets
diff --git a/R/yeast.R b/R/yeast.R
index 3628b6d..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
-#'   <http://www.nature.com/nature/journal/v417/n6887/suppinfo/nature750.html>.
+#'   <https://doi.org/10.1038/nature750>.
 #' @keywords datasets
 NULL
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:
 <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>
@@ -21,7 +21,7 @@ You can install the development version from Github, using the [devtools package
 ## 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>
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/foodwebs.Rd b/man/foodwebs.Rd
index df0948b..1038261 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://doi.org/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
diff --git a/man/igraphdata-package.Rd b/man/igraphdata-package.Rd
index 7902410..118b931 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}
 }
 
diff --git a/man/immuno.Rd b/man/immuno.Rd
index e8e0e08..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{http://library.epfl.ch/theses/?nr=3888}
+\url{https://doi.org/10.5075/epfl-thesis-3888}
 }
 \keyword{datasets}
diff --git a/man/yeast.Rd b/man/yeast.Rd
index 4d5e484..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{http://www.nature.com/nature/journal/v417/n6887/suppinfo/nature750.html}.
+\url{https://doi.org/10.1038/nature750}.
 }
 \usage{
 yeast