Solving issues with URLs and adding paper citation

USCCANA · May 22, 2021 · 4cda66a · 4cda66a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6  1,6 @@
 Package: netdiffuseR
 Title: Analysis of Diffusion and Contagion Processes on Networks
-Version: 1.22.1
 Version: 1.22.2
 Authors@R: c(
   person("George", "Vega Yon", email="[email protected]", role=c("aut", "cre"),
     comment=c(ORCID = "0000-0002-3171-0844", what="Rewrite functions with Rcpp, plus new features")
@@ -22,6  22,7 @@ Depends:
     R (>= 3.1.1)
 License: MIT   file LICENSE
 LazyData: true
 Date: 2021-05-21
 Imports:
     Rcpp (>= 0.12.1),
     sna,

diff --git a/Makefile b/Makefile
@@ -1,7  1,10 @@
-netdiffuseR.tar.gz: */*.R
-	$(MAKE) clean ; \
-	R CMD build . && \
-		mv netdiffuseR*.tar.gz netdiffuseR.tar.gz
 VERSION:=$(shell Rscript -e 'x<-readLines("DESCRIPTION");cat(gsub(". [:]\\s*", "", x[grepl("^Vers", x)]))')
 
 install: netdiffuseR_$(VERSION).tar.gz
 	R CMD INSTALL netdiffuseR_$(VERSION).tar.gz
 
 netdiffuseR_$(VERSION).tar.gz: */*.R inst/NEWS README.md
 	R CMD build . 
 
 inst/NEWS: NEWS.md
 	Rscript -e "rmarkdown::pandoc_convert('NEWS.md', 'plain', output='inst/NEWS')"&& \
@@ -12,11  15,15 @@ README.md: README.Rmd
 
 .PHONY: check checkv clean
 
-check: netdiffuseR.tar.gz
-	R CMD check --as-cran netdiffuseR.tar.gz
 check: netdiffuseR_$(VERSION).tar.gz
 	R CMD check --as-cran netdiffuseR_$(VERSION).tar.gz
 
-checkv: netdiffuseR.tar.gz
-	R CMD check --as-cran --use-valgrind netdiffuseR.tar.gz
 checkv: netdiffuseR_$(VERSION).tar.gz
 	R CMD check --as-cran --use-valgrind netdiffuseR_$(VERSION).tar.gz
 
 clean:
-	rm -rf netdiffuseR.Rcheck ; rm -f netdiffuseR.tar.gz
 	rm -rf netdiffuseR.Rcheck
 
 man/moran.Rd: R/* src/*.cpp src/*.h
 	Rscript --vanilla -e 'roxygen2::roxygenize()'
 
diff --git a/R/random_graph.R b/R/random_graph.R
@@ -164,7  164,7 @@ rgraph_er <- function(n=10, t=1, p=0.01, undirected=getOption("diffnet.undirecte
 #' Networks. Science, 286(5439), 509–512. \doi{10.1126/science.286.5439.509}
 #'
 #' Albert-László Barabási. (2016). Network Science: (1st ed.). Cambridge University Press.
-#' Retrieved from \url{http://barabasi.com/book/network-science}
 #' Retrieved from \url{https://barabasi.com/book/network-science}
 #'
 #' De Almeida, M. L., Mendes, G. A., Madras Viswanathan, G., & Da Silva, L. R. (2013).
 #' Scale-free homophilic network. European Physical Journal B, 86(2).

diff --git a/README.Rmd b/README.Rmd
@@ -6,10  6,10 @@ output:
 
 [![R-CMD-check](https://github.com/USCCANA/netdiffuseR/actions/workflows/r.yml/badge.svg)](https://github.com/USCCANA/netdiffuseR/actions/workflows/r.yml)
 [![Build status](https://ci.appveyor.com/api/projects/status/6u48wgl1lqak2jum?svg=true)](https://ci.appveyor.com/project/gvegayon/netdiffuser)
-[![codecov.io](https://codecov.io/github/USCCANA/netdiffuseR/coverage.svg?branch=master)](https://codecov.io/github/USCCANA/netdiffuseR?branch=master) 
-[![](http://cranlogs.r-pkg.org/badges/netdiffuseR)](http://cran.r-project.org/package=netdiffuseR)
-[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/netdiffuseR)](http://cran.r-project.org/package=netdiffuseR)
-[![](http://cranlogs.r-pkg.org/badges/grand-total/netdiffuseR)](http://cran.rstudio.com/web/packages/netdiffuseR/index.html) 
 [![codecov.io](https://codecov.io/github/USCCANA/netdiffuseR/coverage.svg?branch=master)](https://codecov.io/github/USCCANA/netdiffuseR?branch=master)
 [![](https://cranlogs.r-pkg.org/badges/netdiffuseR)](https://cran.r-project.org/package=netdiffuseR)
 [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/netdiffuseR)](https://cran.r-project.org/package=netdiffuseR)
 [![](https://cranlogs.r-pkg.org/badges/grand-total/netdiffuseR)](https://cran.r-project.org/package=netdiffuseR)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1039317.svg)](https://doi.org/10.5281/zenodo.1039317)
 [![Dependencies](https://tinyverse.netlify.com/badge/netdiffuseR)](https://cran.r-project.org/package=netdiffuseR)
 [![USC's Department of Preventive Medicine](https://raw.githubusercontent.com/USCbiostats/badges/master/tommy-uscprevmed-badge.svg)](https://preventivemedicine.usc.edu)
@@ -21,7  21,7 @@ This package contains functions useful for analyzing network data for diffusion
 The package was developed as part of the paper Thomas W. Valente, Stephanie R.
 Dyal, Kar-Hai Chu, Heather Wipfli, Kayo Fujimoto, *Diffusion of innovations theory applied to global tobacco control treaty ratification*,
 Social Science & Medicine, Volume 145, November 2015, Pages 89-97, ISSN 0277-9536
-(available [here](http://www.sciencedirect.com/science/article/pii/S027795361530143X))
 (available [here](https://www.sciencedirect.com/science/article/pii/S027795361530143X))
 
 From the description:
 
@@ -36,15  36,19 @@ From the description:
 
 __Acknowledgements__:  netdiffuseR was created with the support of grant R01 CA157577 from the National Cancer Institute/National Institutes of Health. 
 
 ```{r, comment = ""}
 citation(package="netdiffuseR")
 ```
 
 ## News
 
 Changelog can be view [here](NEWS.md).
 
 * [2016-06-02] A video of the __netdiffuseR__ workshop at SUNBELT 2016 is now online on [youtube](https://www.youtube.com/playlist?list=PLT-GgRN1lFI4coHDqkRJm3flDw9e1gg2P), and the workshop materials can be found [here](https://github.com/USCCANA/netdiffuser-sunbelt2016/)
-* [2016-04-11] __netdiffuseR__ will be on [useR! 2016](https://user2016.r-project.org/) on as a presentation and on [IC2S2 2016](http://www.kellogg.northwestern.edu/news-events/conference/ic2s2/2016.aspx) in the posters session.
 * [2016-04-11] __netdiffuseR__ will be on [useR! 2016](https://user2016.r-project.org/) on as a presentation and on [IC2S2 2016](https://www.kellogg.northwestern.edu/news-events/conference/ic2s2/2016.aspx) in the posters session.
 * [2016-03-16] Next CRAN release scheduled for April 11th 2016 (after the workshop).
 * [2016-02-18] __netdiffuseR__ vers 1.16.2 is now on CRAN!
-* [2016-02-18] We will be offering a workshop at the 2016 SUNBELT Conference (checkout the full list of workshops [here](http://insna.org/sunbelt2016/program/)).
 * [2016-02-18] We will be offering a workshop at the 2016 SUNBELT Conference (checkout the full list of workshops [here](http://sunbelt2016.insna.org/program/)).
 
 ## Installation
 
@@ -103,8  107,8 @@ For the case of windows and mac users, they can find binary versions of the pack
 
 Since starting netdiffuseR, we have done a couple of workshops at Sunbelt and NASN. Here are the repositories:
 
-* Sunbelt 2018: https://USCCANA.github.io/netdiffuser-sunbelt2018 ([source code](https://github.com/USCCANA/netdiffuser-sunbelt2018))
-* NASN 2017: https://USCCANA.github.io/netdiffuser-nasn2017 ([source code](https://github.com/USCCANA/netdiffuser-nasn2017))
 * Sunbelt 2018: https://usccana.github.io/netdiffuser-sunbelt2018/ ([source code](https://github.com/USCCANA/netdiffuser-sunbelt2018))
 * NASN 2017: https://usccana.github.io/netdiffuser-nasn2017/ ([source code](https://github.com/USCCANA/netdiffuser-nasn2017))
 * Sunbelt 2016: https://github.com/USCCANA/netdiffuser-sunbelt2016
 
 ## Presentations

diff --git a/README.md b/README.md
@@ -3,17  3,19 @@
 [![Build
 status](https://ci.appveyor.com/api/projects/status/6u48wgl1lqak2jum?svg=true)](https://ci.appveyor.com/project/gvegayon/netdiffuser)
 [![codecov.io](https://codecov.io/github/USCCANA/netdiffuseR/coverage.svg?branch=master)](https://codecov.io/github/USCCANA/netdiffuseR?branch=master)
-[![](http://cranlogs.r-pkg.org/badges/netdiffuseR)](http://cran.r-project.org/package=netdiffuseR)
-[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/netdiffuseR)](http://cran.r-project.org/package=netdiffuseR)
-[![](http://cranlogs.r-pkg.org/badges/grand-total/netdiffuseR)](http://cran.rstudio.com/web/packages/netdiffuseR/index.html)
 [![](https://cranlogs.r-pkg.org/badges/netdiffuseR)](https://cran.r-project.org/package=netdiffuseR)
 [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/netdiffuseR)](https://cran.r-project.org/package=netdiffuseR)
 [![](https://cranlogs.r-pkg.org/badges/grand-total/netdiffuseR)](https://cran.r-project.org/package=netdiffuseR)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1039317.svg)](https://doi.org/10.5281/zenodo.1039317)
 [![Dependencies](https://tinyverse.netlify.com/badge/netdiffuseR)](https://cran.r-project.org/package=netdiffuseR)
 [![USC’s Department of Preventive
 Medicine](https://raw.githubusercontent.com/USCbiostats/badges/master/tommy-uscprevmed-badge.svg)](https://preventivemedicine.usc.edu)
 
 <h1>
 
 netdiffuseR: Analysis of Diffusion and Contagion Processes on
 Networks<img src="man/figures/netdiffuser-logo.svg" style="max-width:200px;width:50%;" align="right">
 
 </h1>
 
 This package contains functions useful for analyzing network data for
@@ -24,7  26,7 @@ Stephanie R. Dyal, Kar-Hai Chu, Heather Wipfli, Kayo Fujimoto,
 *Diffusion of innovations theory applied to global tobacco control
 treaty ratification*, Social Science & Medicine, Volume 145, November
 2015, Pages 89-97, ISSN 0277-9536 (available
-[here](http://www.sciencedirect.com/science/article/pii/S027795361530143X))
 [here](https://www.sciencedirect.com/science/article/pii/S027795361530143X))
 
 From the description:
 
@@ -40,26  42,48 @@ From the description:
 R01 CA157577 from the National Cancer Institute/National Institutes of
 Health.
 
 ``` r
 citation(package="netdiffuseR")
 ```
 
 ``` 
 
 To cite netdiffuseR in publications use:
 
   Valente TW, Vega Yon GG. Diffusion/Contagion Processes on Social
   Networks. Health Education & Behavior. 2020;47(2):235-248.
   doi:10.1177/1090198120901497
 
 Vega Yon G, Valente T (2021). _netdiffuseR: Analysis of Diffusion and
 Contagion Processes on Networks_. doi: 10.5281/zenodo.1039317 (URL:
 https://doi.org/10.5281/zenodo.1039317), R package version 1.22.2,
 <URL: https://github.com/USCCANA/netdiffuseR>.
 
 To see these entries in BibTeX format, use 'print(<citation>,
 bibtex=TRUE)', 'toBibtex(.)', or set
 'options(citation.bibtex.max=999)'.
 ```
 
 ## News
 
 Changelog can be view [here](NEWS.md).
 
--   \[2016-06-02\] A video of the **netdiffuseR** workshop at SUNBELT
   - \[2016-06-02\] A video of the **netdiffuseR** workshop at SUNBELT
     2016 is now online on
     [youtube](https://www.youtube.com/playlist?list=PLT-GgRN1lFI4coHDqkRJm3flDw9e1gg2P),
     and the workshop materials can be found
     [here](https://github.com/USCCANA/netdiffuser-sunbelt2016/)
--   \[2016-04-11\] **netdiffuseR** will be on [useR!
-    2016](https://user2016.r-project.org/) on as a presentation and on
-    [IC2S2
-    2016](http://www.kellogg.northwestern.edu/news-events/conference/ic2s2/2016.aspx)
   - \[2016-04-11\] **netdiffuseR** will be on
     [useR\! 2016](https://user2016.r-project.org/) on as a presentation
     and on
     [IC2S2 2016](https://www.kellogg.northwestern.edu/news-events/conference/ic2s2/2016.aspx)
     in the posters session.
--   \[2016-03-16\] Next CRAN release scheduled for April 11th 2016
   - \[2016-03-16\] Next CRAN release scheduled for April 11th 2016
     (after the workshop).
--   \[2016-02-18\] **netdiffuseR** vers 1.16.2 is now on CRAN!
--   \[2016-02-18\] We will be offering a workshop at the 2016 SUNBELT
   - \[2016-02-18\] **netdiffuseR** vers 1.16.2 is now on CRAN\!
   - \[2016-02-18\] We will be offering a workshop at the 2016 SUNBELT
     Conference (checkout the full list of workshops
-    [here](http://insna.org/sunbelt2016/program/)).
     [here](http://sunbelt2016.insna.org/program/)).
 
 ## Installation
 
@@ -103,16  127,19 @@ netdiffuseR\_1…zip, and netdiffuseR\_1…tgz respectively. They can
 install this directly as follows (using the 1.16.3.29 version):
 
 1.  Install dependencies from CRAN
-    `r     > install.packages(c("igraph", "Matrix", "SparseM", "RcppArmadillo", "sna"), dependencies=TRUE)`
 
     ``` r
     > install.packages(c("igraph", "Matrix", "SparseM", "RcppArmadillo", "sna"), dependencies=TRUE)
     ```
 
 2.  Download the binary version and install it as follows:
-
     
     ``` r
     > install.packages("netdiffuseR_1.16.3.29.zip", repos=NULL)
     ```
-
     
     For windows users, and for Mac users:
-
     
     ``` r
     > install.packages("netdiffuseR_1.16.3.29.tgz", repos=NULL)
     ```
@@ -122,19  149,19 @@ install this directly as follows (using the 1.16.3.29 version):
 Since starting netdiffuseR, we have done a couple of workshops at
 Sunbelt and NASN. Here are the repositories:
 
--   Sunbelt 2018: <https://USCCANA.github.io/netdiffuser-sunbelt2018>
   - Sunbelt 2018: <https://usccana.github.io/netdiffuser-sunbelt2018/>
     ([source code](https://github.com/USCCANA/netdiffuser-sunbelt2018))
--   NASN 2017: <https://USCCANA.github.io/netdiffuser-nasn2017> ([source
-    code](https://github.com/USCCANA/netdiffuser-nasn2017))
--   Sunbelt 2016: <https://github.com/USCCANA/netdiffuser-sunbelt2016>
   - NASN 2017: <https://usccana.github.io/netdiffuser-nasn2017/>
     ([source code](https://github.com/USCCANA/netdiffuser-nasn2017))
   - Sunbelt 2016: <https://github.com/USCCANA/netdiffuser-sunbelt2016>
 
 ## Presentations
 
--   ic2s2 2016 Evanston, IL:
   - ic2s2 2016 Evanston, IL:
     <https://github.com/USCCANA/netdiffuser-ic2s22016> (poster)
--   useR! 2016 Stanford, CA:
   - useR\! 2016 Stanford, CA:
     <https://github.com/USCCANA/netdiffuser-user2016> (slides)
--   useR! 2016: <https://github.com/USCCANA/netdiffuser-user2016>
   - useR\! 2016: <https://github.com/USCCANA/netdiffuser-user2016>
 
 ## Examples
 
@@ -388,7  415,7 @@ par(oldpar)
 sessionInfo()
 ```
 
-    ## R version 4.0.5 (2021-03-31)
     ## R version 4.1.0 (2021-05-18)
     ## Platform: x86_64-pc-linux-gnu (64-bit)
     ## Running under: Ubuntu 18.04.5 LTS
     ## 
@@ -408,49  435,49 @@ sessionInfo()
     ## [1] stats     graphics  grDevices utils     datasets  methods   base     
     ## 
     ## other attached packages:
-    ## [1] netdiffuseR_1.22.0
     ## [1] netdiffuseR_1.22.2
     ## 
     ## loaded via a namespace (and not attached):
     ##  [1] igraph_1.2.6          Rcpp_1.0.6            knitr_1.33           
     ##  [4] magrittr_2.0.1        networkDynamic_0.10.1 network_1.16.1       
     ##  [7] MASS_7.3-54           viridisLite_0.4.0     lattice_0.20-44      
     ## [10] rlang_0.4.11          fansi_0.4.2           highr_0.9            
-    ## [13] stringr_1.4.0         tools_4.0.5           MatchIt_4.1.0        
-    ## [16] grid_4.0.5            rle_0.9.2             xfun_0.22            
     ## [13] stringr_1.4.0         tools_4.1.0           MatchIt_4.1.0        
     ## [16] grid_4.1.0            rle_0.9.2             xfun_0.23            
     ## [19] utf8_1.2.1            sna_2.6               coda_0.19-4          
     ## [22] htmltools_0.5.1.1     ellipsis_0.3.2        yaml_2.2.1           
-    ## [25] digest_0.6.27         tibble_3.1.1          lifecycle_1.0.0      
     ## [25] digest_0.6.27         tibble_3.1.2          lifecycle_1.0.0      
     ## [28] crayon_1.4.1          Matrix_1.3-3          vctrs_0.3.8          
-    ## [31] evaluate_0.14         statnet.common_4.4.1  rmarkdown_2.7        
-    ## [34] stringi_1.5.3         compiler_4.0.5        pillar_1.6.0         
     ## [31] evaluate_0.14         statnet.common_4.4.1  rmarkdown_2.8        
     ## [34] stringi_1.6.2         compiler_4.1.0        pillar_1.6.1         
     ## [37] backports_1.2.1       boot_1.3-28           SparseM_1.81         
     ## [40] pkgconfig_2.0.3
 
 ## To-do list
 
--   Import/Export functions for interfacing other package’s clases, in
   - Import/Export functions for interfacing other package’s clases, in
     particular: `statnet` set (specially the packages `networkDynamic`
     and `ndtv`), ~~`igraph`~~ and `Rsiena`.
--   Populate the tests folder.
--   ~~Use spells? (`select_egoalter` would use this)~~
--   ~~Classify individuals by adoption category using early adopters,
   - Populate the tests folder.
   - ~~Use spells? (`select_egoalter` would use this)~~
   - ~~Classify individuals by adoption category using early adopters,
     adopters, and laggards, and by threshold using very low, low, high
     and very high threshold (Valente 95’ p. 94).~~
--   ~~Double check all functions using adjacency matrix values.~~
--   ~~Remove dimnames from matrices and vectors. It is more efficient to
   - ~~Double check all functions using adjacency matrix values.~~
   - ~~Remove dimnames from matrices and vectors. It is more efficient to
     use the ones stored in meta instead.~~
--   Implement the Bass model
--   ~~Include function to import survey data (as shown on the
   - Implement the Bass model
   - ~~Include function to import survey data (as shown on the
     vignettes)~~
--   Exposure based on Mahalanobis distances and also Roger Leenders on
   - Exposure based on Mahalanobis distances and also Roger Leenders on
     weighting exposure (internal note).
--   (2016-03-30): use `xspline` for drawing polygons & edges.
--   ~~(2016-04-04): Add more options to `exposure`, namely, `self` (so
-    removes diagonal or not!).~~
--   (2016-04-19): animal behaviorists.
--   (2016-10-18): Review language throughout the manual (more than
   - (2016-03-30): use `xspline` for drawing polygons & edges.
   - ~~(2016-04-04): Add more options to `exposure`, namely, `self` (so
     removes diagonal or not\!).~~
   - (2016-04-19): animal behaviorists.
   - (2016-10-18): Review language throughout the manual (more than
     innovation).
--   (2016-10-18): Evaluate and eventually use a standard graph format
   - (2016-10-18): Evaluate and eventually use a standard graph format
     (`network` for instance?).
--   (2016-10-18): Standarize graph plot methods (choose either
   - (2016-10-18): Standarize graph plot methods (choose either
     statnet/igraph/own)
diff --git a/inst/CITATION b/inst/CITATION
@@ -1,6  1,29 @@
 year <- sub("-.*", "", meta$Date)
 note <- sprintf("R package version %s", meta$Version)
 
 citHeader("To cite netdiffuseR in publications use the following paper:")
 
 citEntry(
   entry  = "Article",
   title = "Diffusion/Contagion Processes on Social Networks",
   author = c(
     person("Thomas", "Valente"),
     person("George", "Vega Yon")
     ),
   journal = "Health Education & Behavior",
   year    = "2020",
   month   = "feb",
   volume  = 42,
   issue   = 2,
   doi     = "10.1177/1090198120901497",
   url     = "https://doi.org/10.1177/1090198120901497",
   issn    = "1367-4803",
   pages   = "235-248",
   note    = "{PMID: 32090655}",
  textVersion = "Valente TW, Vega Yon GG. Diffusion/Contagion Processes on Social Networks. Health Education & Behavior. 2020;47(2):235-248. doi:10.1177/1090198120901497"
 )
 
 
 bibentry(bibtype = "Manual",
          title = "{{netdiffuseR: Analysis of Diffusion and Contagion Processes on Networks}}",
          author = c(
@@ -10,4  33,6 @@ bibentry(bibtype = "Manual",
          year = year,
          note = note,
          url = "https://github.com/USCCANA/netdiffuseR",
-         doi = "10.5281/zenodo.1039317")
          doi = "10.5281/zenodo.1039317", 
          header = "And the actual R package:")
 
diff --git a/man/rgraph_ba.Rd b/man/rgraph_ba.Rd