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Correcting cran issues
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3 changes: 3 additions & 0 deletions .Rbuildignore
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^tutorials$
.*\.old
^doc$
^docker$
.*\.Rhistory$

# Binary files
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^vignettes/simulating. \.Rmd$
^vignettes/structural. \.Rmd$
^vignettes/rdiffnets\.Rmd$
^vignettes/large-simulation.Rmd$
# CRAN
^cran-comments\.md$
^next_release\.md$
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^netdiffuseR\.tar\.gz$
^\.github
netdiffuseR\.Rcheck

3 changes: 1 addition & 2 deletions R/rewire.r
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Expand Up @@ -407,8 407,7 @@ rewire_graph.array <-function(
#'
#' Mantel, N. (1967). The detection of disease clustering and a generalized
#' regression approach. Cancer Research, 27(2), 209–20.
#' \url{https://cancerres.aacrjournals.org/content/27/2_Part_1/209}
#'
#'
#' @seealso This function can be used as null distribution in \code{struct_test}
#' @family simulation functions
#' @export
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Expand Up @@ -48,7 48,6 @@ Changelog can be view [here](NEWS.md).
* [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://sunbelt2016.insna.org/program/)).

## Installation

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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)
[![](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)
[![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
Expand Down Expand Up @@ -46,44 44,41 @@ Health.
citation(package="netdiffuseR")
```

```

To cite netdiffuseR in publications use:
To cite netdiffuseR in publications use the following paper:

Valente TW, Vega Yon GG. Diffusion/Contagion Processes on Social
Networks. Health Education & Behavior. 2020;47(2):235-248.
doi:10.1177/1090198120901497
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>.
And the actual R package:

To see these entries in BibTeX format, use 'print(<citation>,
bibtex=TRUE)', 'toBibtex(.)', or set
'options(citation.bibtex.max=999)'.
```
Vega Yon G, Valente T (2022). _netdiffuseR: Analysis of Diffusion and
Contagion Processes on Networks_. doi:10.5281/zenodo.1039317
<https://doi.org/10.5281/zenodo.1039317>, R package version 1.22.4,
<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](https://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
Conference (checkout the full list of workshops
[here](http://sunbelt2016.insna.org/program/)).
- \[2016-02-18\] **netdiffuseR** vers 1.16.2 is now on CRAN!

## Installation

Expand Down Expand Up @@ -123,23 118,20 @@ before installing the package through `devtools`.

For the case of windows and mac users, they can find binary versions of
the package [here](https://github.com/USCCANA/netdiffuseR/releases),
netdiffuseR\_1…zip, and netdiffuseR\_1…tgz respectively. They can
install this directly as follows (using the 1.16.3.29 version):
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)
```
Expand All @@ -149,19 141,19 @@ 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/>
- 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

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seed.nodes = "random",
rgraph.args = list(m=3),
threshold.dist = function(x) runif(1, .3, .7))
```

## Warning in (function (graph, p, algorithm = "endpoints", both.ends = FALSE, :
## The option -copy.first- is set to TRUE. In this case, the first graph will be
## treated as a baseline, and thus, networks after T=1 will be replaced with T-1.

``` r
diffnet
```

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sessionInfo()
```

## R version 4.1.0 (2021-05-18)
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
## Running under: Ubuntu 20.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
## LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
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## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
## [1] stats graphics grDevices datasets utils methods base
##
## other attached packages:
## [1] netdiffuseR_1.22.2
## [1] netdiffuseR_1.22.4
##
## 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_4.1.0 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_3.1.2 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_2.8
## [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
## [1] Rcpp_1.0.9 sna_2.6 highr_0.9
## [4] compiler_4.2.1 pillar_1.8.1 tools_4.2.1
## [7] boot_1.3-28 digest_0.6.29 MatchIt_4.4.0
## [10] evaluate_0.16 tibble_3.1.8 lifecycle_1.0.2
## [13] lattice_0.20-45 viridisLite_0.4.0 pkgconfig_2.0.3
## [16] rlang_1.0.5 Matrix_1.5-0 igraph_1.3.2
## [19] cli_3.4.0 rstudioapi_0.14 yaml_2.3.5
## [22] SparseM_1.81 xfun_0.32 fastmap_1.1.0
## [25] coda_0.19-4 stringr_1.4.1 knitr_1.40
## [28] vctrs_0.4.1 networkDynamic_0.11.1 grid_4.2.1
## [31] glue_1.6.2 fansi_1.0.3 bspm_0.3.9
## [34] rmarkdown_2.16 magrittr_2.0.3 backports_1.4.1
## [37] htmltools_0.5.3 MASS_7.3-58.1 utf8_1.2.2
## [40] stringi_1.7.8 network_1.17.2 statnet.common_4.7.0

## 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)
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