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Preparing for CRAN release (#54)
* Mostly refactoring and code cleaning * Cleaning * Reverting change to graph_data.r * Still a warning around plot_threshold method * Adding citer * Adding citer environment * Fixing plot_threshold * Fixing issue about threshold * Fixing citations * Adding qmd files to buildignore * Better warnings * Trying to address issues from CRAN * Using valgrind * Checking with valgrind * Adding citer properly * Adding artifact for automatic build
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‎.Rbuildignore‎

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.*\.doc
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.*\.pdf
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# Misc
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README[.]Rmd
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README[.](R|q)md
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^README\_files$
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[.]travis[.]yml
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^appveyor\.yml$
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^netdiffuseR\.tar\.gz$
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^\.github
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netdiffuseR\.Rcheck
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^\.devcontainer$
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^\.vscode$

‎.devcontainer/.vscode/settings.json‎

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{
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"r.plot.useHttpgd": true,
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"r.alwaysUseActiveTerminal": true
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}

‎.devcontainer/Dockerfile‎

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FROM rocker/tidyverse:4.4.0
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# RUN \
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# echo 'options(repos=c(CRAN="https://packagemanager.posit.co/cran/__linux__/bookworm/latest"))' >> ~/.Rprofile && \
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# Rscript --vanilla -e 'getOption("repos")'
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# Adding R packages
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RUN install2.r Rcpp sna network networkDynamic Matrix MASS MatchIt SparseM igraph \
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viridisLite covr testthat knitr rmarkdown ape RSiena survival RcppArmadillo
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RUN install2.r languageserver httpgd
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RUN apt-get update && apt-get install --no-install-recommends -y valgrind gdb \
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libglpk-dev
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CMD ["bash"]

‎.devcontainer/devcontainer.json‎

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// For format details, see https://aka.ms/devcontainer.json. For config options, see the
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// README at: https://github.com/devcontainers/templates/tree/main/src/cpp
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{
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"name": "epiworldR",
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"build": {
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"dockerfile": "Dockerfile"
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},
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"customizations": {
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"vscode": {
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"extensions": [
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"reditorsupport.r",
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"rdebugger.r-debugger",
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"quarto.quarto",
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"tianyishi.rmarkdown"
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]
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}
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},
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"mounts": [
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// Mount the .vscode configuration into the container
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"source=${localWorkspaceFolder}/.devcontainer/.vscode,target=/workspaces/${localWorkspaceFolderBasename}/.vscode,type=bind,consistency=cached"
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]
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// Features to add to the dev container. More info: https://containers.dev/features.
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// "features": {},
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// Use 'forwardPorts' to make a list of ports inside the container available locally.
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// "forwardPorts": [],
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// Use 'postCreateCommand' to run commands after the container is created.
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// "postCreateCommand": "gcc -v",
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// Configure tool-specific properties.
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// "customizations": {},
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// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
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// "remoteUser": "root"
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}

‎.github/workflows/r.yml‎

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- {os: macOS-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-latest, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-latest, r: 'devel', valgrind: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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shell: Rscript {0}
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- name: Check
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if: ${{ matrix.config.valgrind != true }}
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env:
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_R_CHECK_CRAN_INCOMING_REMOTE_: false
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run: |
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options(crayon.enabled = TRUE)
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rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
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shell: Rscript {0}
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- name: Setup valgrind
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if: ${{ matrix.config.valgrind == true }}
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run: |
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sudo apt-get update
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sudo apt-get install -y valgrind --no-install-recommends
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shell: bash
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- name: Check with Valgrind
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if: ${{ matrix.config.valgrind == true }}
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env:
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_R_CHECK_CRAN_INCOMING_REMOTE_: false
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run: |
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options(crayon.enabled = TRUE)
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rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--use-valgrind"), error_on = "error", check_dir = "check")
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shell: Rscript {0}
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@main
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with:
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name: ${{ runner.os }}-r${{ matrix.config.r }}-results
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path: check
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- name: Build the package
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if: ${{ matrix.config.os == 'ubuntu-latest' && (matrix.config.r == 'release' || matrix.config.r == 'devel') && (matrix.config.valgrind != true) }}
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run: R CMD build .
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- uses: actions/upload-artifact@v4
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if: ${{ matrix.config.os == 'ubuntu-latest' && (matrix.config.r == 'release' || matrix.config.r == 'devel') && (matrix.config.valgrind != true) }}
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with:
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name: netdiffuseR-built-package-${{ matrix.config.os }}-${{ matrix.config.r }}
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path: netdiffuseR_*.tar.gz
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retention-days: 7

‎DESCRIPTION‎

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Package: netdiffuseR
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Title: Analysis of Diffusion and Contagion Processes on Networks
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Version: 1.22.7
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Version: 1.23.0
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Authors@R: c(
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person("George", "Vega Yon", email="[email protected]", role=c("aut", "cre"),
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comment=c(ORCID = "0000-0002-3171-0844", what="Rewrite functions with Rcpp, plus new features")
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survival
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VignetteBuilder: knitr
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LinkingTo: Rcpp, RcppArmadillo
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RoxygenNote: 7.3.1
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RoxygenNote: 7.3.2
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Encoding: UTF-8
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URL: https://github.com/USCCANA/netdiffuseR,
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https://USCCANA.github.io/netdiffuseR/
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'adjmat.r'
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'bass.r'
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'bootnet.r'
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'citer_environment.R'
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'data.r'
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'diffnet-c.R'
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'diffnet-class.r'

‎Makefile‎

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VERSION:=$(shell Rscript -e 'x<-readLines("DESCRIPTION");cat(gsub(".+[:]\\s*", "", x[grepl("^Vers", x)]))')
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install: netdiffuseR_$(VERSION).tar.gz
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R CMD INSTALL netdiffuseR_$(VERSION).tar.gz
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netdiffuseR_$(VERSION).tar.gz: */*.R inst/NEWS README.md
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help:
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@echo "Makefile for netdiffuseR package"
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@echo "Usage:"
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@echo " make install - Install the package"
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@echo " make build - Build the package source tarball"
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@echo " make check - Check the package with R CMD check"
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@echo " make checkv - Check the package with R CMD check using Valgrind"
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@echo " make clean - Clean up the build artifacts"
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@echo " make docs - Generate documentation"
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install:
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R CMD INSTALL .
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build:
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R CMD build .
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inst/NEWS: NEWS.md
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Rscript -e "rmarkdown::pandoc_convert('NEWS.md', 'plain', output='inst/NEWS')"&& \
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head -n 80 inst/NEWS
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README.md: README.Rmd
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Rscript -e 'rmarkdown::render("README.Rmd")'
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.PHONY: check checkv clean
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check: netdiffuseR_$(VERSION).tar.gz
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R CMD check --as-cran netdiffuseR_$(VERSION).tar.gz
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checkv: netdiffuseR_$(VERSION).tar.gz
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R CMD check --as-cran --use-valgrind netdiffuseR_$(VERSION).tar.gz
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clean:
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rm -rf netdiffuseR.Rcheck
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rm -rf netdiffuseR.Rcheck src/*.so src/*.o
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man/moran.Rd: R/* src/*.cpp src/*.h
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Rscript --vanilla -e 'roxygen2::roxygenize()'
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docs:
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Rscript --vanilla -e 'devtools::document()'
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.PHONY: check checkv clean install docs

‎NEWS.md‎

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# Changes in netdiffuseR version 1.23.0 (2025-06-10)
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* New methods for simulating multi-diffusion models.
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* It is now possible to simulate diffusions with general disadoption functions.
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# Changes in netdiffuseR version 1.22.7 (2024-09-18)
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* Minor changes to testing (skip warnings).

‎R/citer_environment.R‎

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# file_version: f6ffa5cc103728c81c977e9101df287d
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# citer_version: 0.0.9000
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# DO NOT EDIT THIS BY HAND!
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# This document was automatically generated by the `citer` package.
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# tools::md5sum()
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# Citer Environment Setup
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citation_on_load <- function() {
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pkg_name <- "netdiffuseR"
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packageStartupMessage(
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"Thank you for using ", pkg_name, "! ",
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"Please consider citing it in your work.\n",
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"You can find the citation information by running\n citation(\"",
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pkg_name,
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"\")"
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)
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}

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