diff --git a/README.Rmd b/README.Rmd index e46c78f..0600f37 100644 --- a/README.Rmd +++ b/README.Rmd @@ -5,7 +5,6 @@ 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://app.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) diff --git a/README.md b/README.md index 1be3d6a..b5287d9 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,5 @@ [![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://app.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) @@ -12,6 +10,7 @@ status](https://ci.appveyor.com/api/projects/status/6u48wgl1lqak2jum?svg=true)]( Medicine](https://raw.githubusercontent.com/USCbiostats/badges/master/tommy-uscprevmed-badge.svg)](https://pphs.usc.edu/center/cana/)

+ netdiffuseR: Analysis of Diffusion and Contagion Processes on Networks

@@ -44,7 +43,6 @@ Health. citation(package="netdiffuseR") ``` - To cite netdiffuseR in publications use the following paper: Valente TW, Vega Yon GG. Diffusion/Contagion Processes on Social @@ -53,9 +51,9 @@ citation(package="netdiffuseR") And the actual R package: - Vega Yon G, Valente T (2022). _netdiffuseR: Analysis of Diffusion and + Vega Yon G, Valente T (2023). _netdiffuseR: Analysis of Diffusion and Contagion Processes on Networks_. doi:10.5281/zenodo.1039317 - , R package version 1.22.4, + , R package version 1.22.6, . To see these entries in BibTeX format, use 'print(, @@ -66,19 +64,19 @@ citation(package="netdiffuseR") 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](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! +- \[2016-06-02\] 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) + 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! ## Installation @@ -141,19 +139,19 @@ 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: - ([source code](https://github.com/USCCANA/netdiffuser-sunbelt2018)) -- NASN 2017: - ([source code](https://github.com/USCCANA/netdiffuser-nasn2017)) -- Sunbelt 2016: +- Sunbelt 2018: + ([source code](https://github.com/USCCANA/netdiffuser-sunbelt2018)) +- NASN 2017: ([source + code](https://github.com/USCCANA/netdiffuser-nasn2017)) +- Sunbelt 2016: ## Presentations -- ic2s2 2016 Evanston, IL: - (poster) -- useR! 2016 Stanford, CA: - (slides) -- useR! 2016: +- ic2s2 2016 Evanston, IL: + (poster) +- useR! 2016 Stanford, CA: + (slides) +- useR! 2016: ## Examples @@ -305,8 +303,8 @@ plot_threshold( ) ``` - ## Warning in (function (graph, expo, toa, include_censored = FALSE, t0 = - ## min(toa, : -vertex.sides- will be coerced to integer. + ## Warning in (function (graph, expo, toa, include_censored = FALSE, t0 = min(toa, + ## : -vertex.sides- will be coerced to integer. ![](README_files/figure-gfm/NiceThreshold-1.png) @@ -414,69 +412,67 @@ par(oldpar) sessionInfo() ``` - ## R version 4.2.1 (2022-06-23) - ## Platform: x86_64-pc-linux-gnu (64-bit) - ## Running under: Ubuntu 20.04.5 LTS + ## R version 4.4.1 (2024-06-14) + ## Platform: aarch64-apple-darwin23.4.0 + ## Running under: macOS Sonoma 14.6.1 ## ## Matrix products: default - ## 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 + ## BLAS: /opt/homebrew/Cellar/openblas/0.3.27/lib/libopenblasp-r0.3.27.dylib + ## LAPACK: /opt/homebrew/Cellar/r/4.4.1/lib/R/lib/libRlapack.dylib; LAPACK version 3.12.0 ## ## locale: - ## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C - ## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 - ## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 - ## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C - ## [9] LC_ADDRESS=C LC_TELEPHONE=C - ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C + ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 + ## + ## time zone: America/Denver + ## tzcode source: internal ## ## attached base packages: - ## [1] stats graphics grDevices datasets utils methods base + ## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: - ## [1] netdiffuseR_1.22.4 + ## [1] netdiffuseR_1.22.6 ## ## loaded via a namespace (and not attached): - ## [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 + ## [1] Matrix_1.7-0 highr_0.11 dplyr_1.1.4 + ## [4] compiler_4.4.1 tidyselect_1.2.1 Rcpp_1.0.12 + ## [7] networkLite_1.0.5 boot_1.3-30 yaml_2.3.8 + ## [10] fastmap_1.2.0 lattice_0.22-6 coda_0.19-4.1 + ## [13] R6_2.5.1 generics_0.1.3 MatchIt_4.5.5 + ## [16] igraph_2.0.3 knitr_1.47 MASS_7.3-60.2 + ## [19] backports_1.5.0 tibble_3.2.1 statnet.common_4.9.0 + ## [22] pillar_1.9.0 rlang_1.1.4 utf8_1.2.4 + ## [25] xfun_0.45 viridisLite_0.4.2 cli_3.6.3 + ## [28] magrittr_2.0.3 network_1.18.2 digest_0.6.36 + ## [31] grid_4.4.1 lifecycle_1.0.4 vctrs_0.6.5 + ## [34] sna_2.7-2 evaluate_0.24.0 SparseM_1.84-2 + ## [37] glue_1.7.0 fansi_1.0.6 rmarkdown_2.27 + ## [40] tools_4.4.1 pkgconfig_2.0.3 networkDynamic_0.11.4 + ## [43] htmltools_0.5.8.1 ## To-do list -- 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, - 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 - use the ones stored in meta instead.~~ -- 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 - 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 - innovation). -- (2016-10-18): Evaluate and eventually use a standard graph format - (`network` for instance?). -- (2016-10-18): Standarize graph plot methods (choose either - statnet/igraph/own) +- 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, + 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 + use the ones stored in meta instead.~~ +- 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 + 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 + innovation). +- (2016-10-18): Evaluate and eventually use a standard graph format + (`network` for instance?). +- (2016-10-18): Standarize graph plot methods (choose either + statnet/igraph/own) diff --git a/README_files/figure-gfm/Adopters-1.png b/README_files/figure-gfm/Adopters-1.png index bcbbfc7..09fd020 100644 Binary files a/README_files/figure-gfm/Adopters-1.png and b/README_files/figure-gfm/Adopters-1.png differ diff --git a/README_files/figure-gfm/BoringThreshold, plot_threshold-1.png b/README_files/figure-gfm/BoringThreshold, plot_threshold-1.png index 8c91bdd..7309b7f 100644 Binary files a/README_files/figure-gfm/BoringThreshold, plot_threshold-1.png and b/README_files/figure-gfm/BoringThreshold, plot_threshold-1.png differ diff --git a/README_files/figure-gfm/Hazard-1.png b/README_files/figure-gfm/Hazard-1.png index 14797a1..1ae2dd3 100644 Binary files a/README_files/figure-gfm/Hazard-1.png and b/README_files/figure-gfm/Hazard-1.png differ diff --git a/README_files/figure-gfm/NiceThreshold-1.png b/README_files/figure-gfm/NiceThreshold-1.png index c2f16aa..62b9cc3 100644 Binary files a/README_files/figure-gfm/NiceThreshold-1.png and b/README_files/figure-gfm/NiceThreshold-1.png differ diff --git a/README_files/figure-gfm/mosaic-1.png b/README_files/figure-gfm/mosaic-1.png index a4234ca..07ce77c 100644 Binary files a/README_files/figure-gfm/mosaic-1.png and b/README_files/figure-gfm/mosaic-1.png differ diff --git a/README_files/figure-gfm/plot_diffnet-1.png b/README_files/figure-gfm/plot_diffnet-1.png index 8f377a3..8451a4f 100644 Binary files a/README_files/figure-gfm/plot_diffnet-1.png and b/README_files/figure-gfm/plot_diffnet-1.png differ diff --git a/README_files/figure-gfm/plot_diffnet2 with map-1.png b/README_files/figure-gfm/plot_diffnet2 with map-1.png index 7401839..802503b 100644 Binary files a/README_files/figure-gfm/plot_diffnet2 with map-1.png and b/README_files/figure-gfm/plot_diffnet2 with map-1.png differ diff --git a/README_files/figure-gfm/plot_diffnet2-1.png b/README_files/figure-gfm/plot_diffnet2-1.png index 232798e..91bc1ee 100644 Binary files a/README_files/figure-gfm/plot_diffnet2-1.png and b/README_files/figure-gfm/plot_diffnet2-1.png differ diff --git a/README_files/figure-gfm/plot_infectsuscept-1.png b/README_files/figure-gfm/plot_infectsuscept-1.png index 5e37064..3746c70 100644 Binary files a/README_files/figure-gfm/plot_infectsuscept-1.png and b/README_files/figure-gfm/plot_infectsuscept-1.png differ diff --git a/README_files/figure-gfm/plot_infectsuscept-2.png b/README_files/figure-gfm/plot_infectsuscept-2.png index 2ed060b..ff55eae 100644 Binary files a/README_files/figure-gfm/plot_infectsuscept-2.png and b/README_files/figure-gfm/plot_infectsuscept-2.png differ diff --git a/appveyor.yml b/appveyor.yml deleted file mode 100644 index cc57348..0000000 --- a/appveyor.yml +++ /dev/null @@ -1,56 +0,0 @@ -# DO NOT CHANGE the "init" and "install" sections below - -# Download script file from GitHub -init: - ps: | - $ErrorActionPreference = "Stop" - Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" - Import-Module '..\appveyor-tool.ps1' - -install: - ps: Bootstrap - -# Adapt as necessary starting from here -# https://github.com/krlmlr/r-appveyor/issues/81 - -environment: - global: - WARNINGS_ARE_ERRORS: 1 - - matrix: - - R_VERSION: release - R_ARCH: x64 - - - R_VERSION: oldrel - - - R_VERSION: devel - - -build_script: - - travis-tool.sh r_install RSiena survival - - travis-tool.sh install_deps - -test_script: - - travis-tool.sh run_tests - -on_failure: - - travis-tool.sh dump_logs - -artifacts: - - path: '*.Rcheck\**\*.log' - name: Logs - - - path: '*.Rcheck\**\*.out' - name: Logs - - - path: '*.Rcheck\**\*.fail' - name: Logs - - - path: '*.Rcheck\**\*.Rout' - name: Logs - - - path: '\*_*.tar.gz' - name: Bits - - - path: '\*_*.zip' - name: Bits