Handbook v2.5 pt

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Automated pull request for pt handbook version v2.5

@Luccan97, please review changes and check the box when you finish

• Chapter contribution_guide_05-02-2021.qmd has changes in the following commit(s): 7638298.
• Chapter data/quarto/outbreak_dashboard.qmd has changes in the following commit(s): 2703d23, 4100e1a.
• Chapter data/quarto/outbreak_report.qmd has changes in the following commit(s): 2703d23.
• Chapter html_outputs/new_pages/descriptive_statistics.qmd has changes in the following commit(s): 29fb695, 05f7a6b, 4d4d472.
• Chapter index.qmd has changes in the following commit(s): 96f528b, d04e814, 0db3e99, 29fb695.
• Chapter new_pages/age_pyramid.qmd has changes in the following commit(s): 7638298, ddcd5e9, 1e6ac5a.
• Chapter new_pages/basics.qmd has changes in the following commit(s): 7638298, e6a4aa9, 3eb5e8e, 29fb695, ebfa021, 1f2bc63, e50caaf, 272c4a7, 076e264, 77b4ab4, 4a25f73, 6236817.
• Chapter new_pages/characters_strings.qmd has changes in the following commit(s): 7638298, e6a4aa9, 259560d, 29fb695, c300e6f.
• Chapter new_pages/cleaning.qmd has changes in the following commit(s): 7638298, e6a4aa9, 259560d, 29fb695, c300e6f.
• Chapter new_pages/collaboration.qmd has changes in the following commit(s): 7638298, eb248e2, e6a4aa9, 02d3990, c286b45.
• Chapter new_pages/combination_analysis.qmd has changes in the following commit(s): e6a4aa9, ddcd5e9, 1e6ac5a.
• Chapter new_pages/contact_tracing.qmd has changes in the following commit(s): 7638298, 29fb695, 7a4e68c.
• Chapter new_pages/data_table.qmd has changes in the following commit(s): b264728, 1a0854a, 5ac48f2, e6a4aa9, ddcd5e9, c286b45.
• Chapter new_pages/data_used.qmd has changes in the following commit(s): e6a4aa9, e3dbfbe, 7a4e68c, 1f2bc63, 093f435, e0ae901, a9ee323.
• Chapter new_pages/dates.qmd has changes in the following commit(s): 259560d, 29fb695, ebfa021, c300e6f.
• Chapter new_pages/deduplication.qmd has changes in the following commit(s): e6a4aa9, c5f136a.
• Chapter new_pages/descriptive_statistics.qmd has changes in the following commit(s): 29fb695, 4d4d472.
• Chapter new_pages/diagrams.qmd has changes in the following commit(s): e6a4aa9, ddcd5e9, e3dbfbe.
• Chapter new_pages/directories.qmd has changes in the following commit(s): c286b45.
• Chapter new_pages/editorial_style.qmd has changes in the following commit(s): 29fb695, 093f435, 0be7113.
• Chapter new_pages/epicurves.qmd has changes in the following commit(s): 136a8a8, e6a4aa9, e548cba, e3dbfbe, 224d203, 1e6ac5a.
• Chapter new_pages/epidemic_models.qmd has changes in the following commit(s): 29fb695, 7a4e68c.
• Chapter new_pages/errors.qmd has changes in the following commit(s): 136a8a8, c286b45, ebfa021.
• Chapter new_pages/factors.qmd has changes in the following commit(s): 29fb695, 3752295.
• Chapter new_pages/flexdashboard.qmd has changes in the following commit(s): ddcd5e9, ca573fc.
• Chapter new_pages/ggplot_basics.qmd has changes in the following commit(s): 259560d, ddcd5e9, ebfa021, 1e6ac5a.
• Chapter new_pages/ggplot_tips.qmd has changes in the following commit(s): 136a8a8, e6a4aa9, 259560d, ddcd5e9, ebfa021, 224d203, 1e6ac5a.
• Chapter new_pages/gis.qmd has changes in the following commit(s): ac0f112, e6a4aa9, 0db3e99, ddcd5e9, 29fb695, 744ef8b.
• Chapter new_pages/grouping.qmd has changes in the following commit(s): e6a4aa9, 29fb695, c5f136a.
• Chapter new_pages/heatmaps.qmd has changes in the following commit(s): e6a4aa9, ddcd5e9, 1e6ac5a.
• Chapter new_pages/help.qmd has changes in the following commit(s): e6a4aa9, 61d38be, c286b45.
• Chapter new_pages/importing.qmd has changes in the following commit(s): e6a4aa9, 3eb5e8e, 29fb695, 410659b.
• Chapter new_pages/interactive_plots.qmd has changes in the following commit(s): ddcd5e9, 1e6ac5a.
• Chapter new_pages/iteration.qmd has changes in the following commit(s): e6a4aa9, 259560d, 29fb695, 4d4d472, c5f136a.
• Chapter new_pages/joining_matching.qmd has changes in the following commit(s): 29fb695, c5f136a.
• Chapter new_pages/missing_data.qmd has changes in the following commit(s): e6a4aa9, 29fb695, 61d38be, 1f2bc63.
• Chapter new_pages/moving_average.qmd has changes in the following commit(s): e6a4aa9, 29fb695, 1f2bc63.
• Chapter new_pages/network_drives.qmd has changes in the following commit(s): c286b45.
• Chapter new_pages/packages_suggested.qmd has changes in the following commit(s): 0db3e99, 29fb695, e50caaf.
• Chapter new_pages/phylogenetic_trees.qmd has changes in the following commit(s): 5ac48f2, ddcd5e9, 1e6ac5a.
• Chapter new_pages/pivoting.qmd has changes in the following commit(s): 29fb695, 7a4e68c, c5f136a.
• Chapter new_pages/quarto.qmd has changes in the following commit(s): e6a4aa9, 0db3e99, a53d14a, 3eb5e8e, 2703d23.
• Chapter new_pages/r_projects.qmd has changes in the following commit(s): 3eb5e8e, e50caaf.
• Chapter new_pages/regression.qmd has changes in the following commit(s): 3eb5e8e, 29fb695, ebfa021, 1f2bc63.
• Chapter new_pages/reportfactory.qmd has changes in the following commit(s): 02d3990.
• Chapter new_pages/rmarkdown.qmd has changes in the following commit(s): e6a4aa9, 259560d, ddcd5e9, 2703d23, 05f7a6b.
• Chapter new_pages/shiny_basics.qmd has changes in the following commit(s): ddcd5e9, 573cf62, ebfa021.
• Chapter new_pages/standardization.qmd has changes in the following commit(s): 259560d, 3eb5e8e, 29fb695, 61d38be, ebfa021, 1f2bc63.
• Chapter new_pages/stat_tests.qmd has changes in the following commit(s): 259560d, 29fb695, ebfa021, 1f2bc63.
• Chapter new_pages/survey_analysis.qmd has changes in the following commit(s): b208994, d04e814, ddcd5e9, 29fb695, 61d38be, ebfa021, 7a4e68c.
• Chapter new_pages/survival_analysis.qmd has changes in the following commit(s): ddcd5e9, 29fb695, 6c9bf82.
• Chapter new_pages/tables_descriptive.qmd has changes in the following commit(s): 29fb695, 05f7a6b, 4d4d472.
• Chapter new_pages/tables_presentation.qmd has changes in the following commit(s): ddcd5e9, 1e6ac5a.
• Chapter new_pages/time_series.qmd has changes in the following commit(s): 29fb695, 573cf62, 7a4e68c, 1f2bc63.
• Chapter new_pages/transition_to_R.qmd has changes in the following commit(s): 259560d, 29fb695, 1f2bc63, e50caaf.
• Chapter new_pages/transmission_chains.qmd has changes in the following commit(s): ddcd5e9, 1e6ac5a.
• Chapter new_pages/writing_functions.qmd has changes in the following commit(s): ddcd5e9, ebfa021.
• Chapter offline_long/index.qmd has changes in the following commit(s): a9ee323.