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USCCANA · May 4, 2021 · ad0e7f0 · ad0e7f0
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -18,7  18,6 @@
 .*\.pdf
 # Misc
 README[.]Rmd
-README[.]md
 ^README\_files$
 [.]travis[.]yml
 ^appveyor\.yml$

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6  1,6 @@
 Package: netdiffuseR
 Title: Analysis of Diffusion and Contagion Processes on Networks
-Version: 1.22.0
 Version: 1.22.1
 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")

diff --git a/Makefile b/Makefile
@@ -1,17  1,22 @@
 netdiffuseR.tar.gz: */*.R
-	rm netdiffuseR.tar.gz ; \
 	$(MAKE) clean ; \
 	R CMD build . && \
 		mv netdiffuseR*.tar.gz netdiffuseR.tar.gz
 
 inst/NEWS: NEWS.md
 	Rscript -e "rmarkdown::pandoc_convert('NEWS.md', 'plain', output='inst/NEWS')"&& \
 	head -n 80 inst/NEWS
 
 README.md: README.Rmd
 	Rscript -e 'rmarkdown::render("README.Rmd")'
 
 .PHONY: check checkv clean
 
 check: netdiffuseR.tar.gz
 	R CMD check --as-cran netdiffuseR.tar.gz
 
 checkv: netdiffuseR.tar.gz
 	R CMD check --as-cran --use-valgrind netdiffuseR.tar.gz
 
-README.md: README.Rmd
-	Rscript -e 'rmarkdown::render("README.Rmd")'
-
 clean:
 	rm -rf netdiffuseR.Rcheck ; rm -f netdiffuseR.tar.gz
diff --git a/NAMESPACE b/NAMESPACE
@@ -46,6  46,7 @@ S3method(image,diffnet_diffmap)
 S3method(plot,diffnet)
 S3method(plot,diffnet_adopters)
 S3method(plot,diffnet_bass)
 S3method(plot,diffnet_bootnet)
 S3method(plot,diffnet_degSeq)
 S3method(plot,diffnet_diffmap)
 S3method(plot,diffnet_hr)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4  1,11 @@
-# Changes in netdiffuseR version 1.21.0999 (2020-03-13)
 # Changes in netdiffuseR version 1.22.1 (2021-05-04)
 
 * netdiffuseR has now a logo!
 
 * Making updates after changes in knitr and Matrix.
 
 
 # Changes in netdiffuseR version 1.22.0 (2020-05-17)
 
 * Fixing a new issue regarding structural equivalence calculation. In the
   new version, the function has been fully ported to R, which should avoid

diff --git a/R/bootnet.r b/R/bootnet.r
@@ -60,12  60,14 @@
 #' \item{resample.args}{The list \code{resample.args} passed to \code{bootnet}.}
 #' @name bootnet
 #' @examples
-#' #
 #' # Computing edgecount -------------------------------------------------------
 #' set.seed(13)
 #' g <- rgraph_ba(t=99)
 #'
 #' ans <- bootnet(g, function(w, ...) length(w@x), R=100)
 #' ans
 #'
 #' # Generating
 NULL
 
 bootnet_fillselfR <- function(graph, index, E) {
@@ -368,3  370,12 @@ hist.diffnet_bootnet <- function(
 
   invisible(out)
 }
 
 #' @export
 #' @param y Ignored.
 #' @rdname bootnet
 #' @details The `plot.diffnet_bootnet` method is a wrapper for the
 #' `hist` method.
 plot.diffnet_bootnet <- function(x, y, ...) {
   hist.diffnet_bootnet(x = x, ...)
 }
diff --git a/R/formula.r b/R/formula.r
@@ -28,7  28,7 @@
 #' This is a wrapper of \code{\link[stats:glm]{glm}}. The function does the
 #' following steps:
 #' \enumerate{
-#'  \item Compute exposure by calling \code{exposure} on the LHS.
 #'  \item Compute exposure by calling \code{exposure} on the LHS (dependent variable).
 #'  \item Modify the formula so that the model is on adoption as a function of
 #'  exposure and whatever covariates the user specifies.
 #'  \item Selects either \code{"probit"} or \code{"logit"} and prepares the call
@@ -93,7  93,7 @@ diffreg <- function(model, type=c("logit", "probit")) {
   LHS <- attr(terms, "variables")[[2]]
 
   if (!inherits(eval(LHS), "diffnet"))
-    stop("The LHS of the formula is not a `diffnet` object. `diffreg` is only for `diffnet` objects.",
     stop("The LHS of the formula (dependent variable) is not a `diffnet` object. `diffreg` is only for `diffnet` objects.",
          call. = FALSE)
 
   # Updating the formula -------------------------------------------------------

diff --git a/README.Rmd b/README.Rmd
@@ -4,7  4,7 @@ output:
     html_preview: false
 ---
 
-[![Build Status](https://travis-ci.org/USCCANA/netdiffuseR.svg?branch=master)](https://travis-ci.org/USCCANA/netdiffuseR)
 [![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.rstudio.com/web/packages/netdiffuseR/index.html)

diff --git a/README.md b/README.md
@@ -1,6  1,5 @@
 
-[![Build
-Status](https://travis-ci.org/USCCANA/netdiffuseR.svg?branch=master)](https://travis-ci.org/USCCANA/netdiffuseR)
 [![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)
@@ -13,10  12,8 @@ status](https://ci.appveyor.com/api/projects/status/6u48wgl1lqak2jum?svg=true)](
 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">
-
 Networks<img src="man/figures/netdiffuser-logo.png" style="max-width:200px;width:50%;" align="right">
 </h1>
 
 This package contains functions useful for analyzing network data for
@@ -50,19  47,19 @@ Health.
 
 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/tree/master/doc/conferences/20160400_sunbelt2016/)
-  - \[2016-04-11\] **netdiffuseR** will be on
-    [useR\! 2016](http://user2016.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](http://user2016.org) on as a presentation and on [IC2S2
     2016](http://www.kellogg.northwestern.edu/news-events/conference/ic2s2/2016.aspx)
     in the posters session.
-  - \[2016-03-16\] 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/)).
 
@@ -108,19  105,16 @@ 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)
     ```
@@ -130,19  124,19 @@ 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
 -   NASN 2017: <https://USCCANA.github.io/netdiffuser-nasn2017> ([source
     code](https://github.com/USCCANA/netdiffuser-nasn2017))
-  - Sunbelt 2016: <https://github.com/USCCANA/netdiffuser-sunbelt2016>
 -   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
 
@@ -421,7  415,7 @@ sessionInfo()
     ## loaded via a namespace (and not attached):
     ##  [1] igraph_1.2.6          Rcpp_1.0.6            knitr_1.30           
     ##  [4] magrittr_2.0.1        networkDynamic_0.10.1 network_1.16.1       
-    ##  [7] MASS_7.3-53.1         viridisLite_0.3.0     lattice_0.20-41      
     ##  [7] MASS_7.3-53.1         viridisLite_0.3.0     lattice_0.20-44      
     ## [10] rlang_0.4.10          stringr_1.4.0         tools_4.0.5          
     ## [13] MatchIt_4.1.0         grid_4.0.5            rle_0.9.2            
     ## [16] xfun_0.20             sna_2.6               coda_0.19-4          
@@ -435,29  429,29 @@ sessionInfo()
 
 ## 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/NEWS b/inst/NEWS
@@ -1,6  1,15 @@
 
 
-CHANGES IN NETDIFFUSER VERSION 1.22.0 (2020-05-06)
 CHANGES IN NETDIFFUSER VERSION 1.22.1 (2021-05-04)
 
 
 -   netdiffuseR has now a logo!
 
 -   Making updates after changes in knitr and Matrix.
 
 
 
 CHANGES IN NETDIFFUSER VERSION 1.22.0 (2020-05-17)
 
 
 -   Fixing a new issue regarding structural equivalence calculation. In

diff --git a/man/bootnet.Rd b/man/bootnet.Rd
diff --git a/man/diffreg.Rd b/man/diffreg.Rd
diff --git a/man/figures/netdiffuser-logo.png b/man/figures/netdiffuser-logo.png