Epi_R_handbook：现场流行病学家的R手册

style-and-editorial-notes style text-style tidyverse code-readability editorial-decisions datasets-used r-basics overview why-use-r install tinytex pandoc rtools rstudio rstudio-orientation rstudio-settings scripts rmd rnotebooks shinyscripts workingdirectory filepaths set-by-command set-manually in-an-r-project objects everything-is-an-object defining-objects-- objectstructure objectclasses dollarsign brackets remove-objects functions simple-functions functions-with-multiple-arguments packages piping pipes define-intermediate-objects operators assignment-operators relational-and-logical-operators missing-values mathematics-and-statistics mathematical-operators mathematical-functions statistical-functions other-useful-functions in errors-warnings error-versus-warning general-syntax-tips code-assists recommended-training cheatsheets courses importing-and-exporting overview-1 packages-1 here importing import-from-filepath excel-sheet select-file-manually google-sheets websites skip-rows removing-a-second-header-row manual-data-entry entry-by-columns entry-by-rows pasting-from-clipboard rdata-files r-projects creating-an-r-project settings organization resources suggested-packages cleaning-data overview-2 cleaning-pipeline load-packages import-data skip-import-of-rows remove-a-second-header-row create-a-data-dictionary combine-two-header-rows column-names automatic-name-cleaning manual-name-cleaning other-name-challenges select-or-re-order-columns keep-columns helper-functions remove-columns standalone deduplication column-creation-and-transformation new-columns add-or-transform-columns-using-base-r add-to-pipe-chain convert-column-class re-code-values re-code-by-logic re-code-with-a-cleaning-dictionary other-transformations special-re-coding-tools num_cats age_categories cut case_when add-to-pipe-chain-2 add-rows filter-rows a-simple-filter a-complex-filter filter-stand-alone-command filter-to-quickly-review-observations add-to-pipe-chain-3 rowwise-dplyr transformations-across-multiple-columns working-with-dates overview-3 packages-2 converting-objects-to-date-class converting-to-datetime-classes lubridate guess_dates excel-dates how-dates-are-displayed calculating-distance-between-dates converting-datestime-zones epidemiological-weeks dates-in-epicurves lagging-and-leading-calculations dates-miscellaneous missing-data overview-4 preparation useful-functions assess-missingness-in-a-dataframe statistics visualizing-missingness explore-and-visualize-missingness-relationships filter-out-rows-with-missing-values handling-na-in-ggplot imputation types-of-missing-data useful-packages mean-imputation regression-imputation locf-and-bocf multiple-imputation resources-1 grouping-data overview-5 preparation-1 grouping unique-groups new-columns-1 replaceadd-grouping-columns un-group summarise summarise-across-multiple-columns count-and-tally add-totals arranging-grouped-data filter-on-grouped-data filter slice-rows-per-group filter-on-group-size mutate-on-grouped-data select-on-grouped-data base-r resources-2 joining-matching-datasets overview-6 preparation-2 datasets pre-cleaning dplyr-joins general-syntax section add-columns-left-right-joins full-join inner-join semi-join anti-join probabalistic-matching resources-3 charactersstrings overview-7 preparation-3 handle-by-position extract-by-character-position extract-by-word-position replace-by-character-position evaluate-length unite-split-and-arrange combine-strings dynamic-strings unite-columns split split-columns arrange base-r-functions adjust-length pad truncate standardize-length remove-leadingtrailing-whitespace remove-repeated-whitespace-within wrap-into-paragraphs change-case patterns detect-a-pattern replace-all detect-within-logic locate-pattern-position extract-a-match subset-and-count regex-groups regex-and-special-characters special-characters regular-expressions-regex resources-4 de-duplication overview-8 preparation-4 deduplication-1 examine-duplicate-rows keep-only-unique-rows duplicate-elements-in-a-vector with-base-r slicing slice-with-groups keep-all-but-mark-them calculate-row-completeness roll-up-values roll-up-values-into-one-row overwrite-valueshierarchy resources-5 iteration-and-loops preparation-5 for-loops tracking-progress-of-a-loop purrr apply-functions resources-6 descriptive-analysis overview-9 preparation-6 packages-3 load-data clean-data browse-data base-r-1 skimr-package summarystats gtsummary-package mean median range standard-deviation percentile combined-table dplyr-package mean-1 median-1 range-1 standard-deviation-1 percentile-1 combined-table-1 frequencycross-tabs gtsummary-package-1 one-way-table multiple-variable-one-way-table two-way-table three-way-table dplyr-package-1 one-way-table-1 two-way-table-1 three-way-table-1 statistical-tests gtsummary-package-2 t-tests wilcoxon-rank-sum-test kruskal-wallis-test chi-squared-test dplyr-package-2 t-tests-1 wilcoxon-rank-sum-test-1 kruskal-wallis-test-1 chi-squared-test-1 base-package t-tests-2 wilcoxon-rank-sum-test-2 kruskal-wallis-test-2 chi-squared-test-2 correlations resources-7 simple-statistical-tests overview-10 preparation-7 packages-4 load-data-1 clean-data-1 univariate gtsummary-package-3 base stratified gtsummary-package-4 base-1 multivariable gtsummary-package-5 base-2 forest-plot ggplot2-package easystats-packages resources-8 standardization overview-11 preparation-8 load-packages-1 load-data-2 one-row-per-stratum add-mortality-numbers prepare-reference-population dsr-package standardized-rates standardized-rate-ratios standardized-rate-difference pheindicatormethods-package directly-standardized-rates resources-9 moving-averages overview-12 preparation-9 calculate-then-display calculate-on-the-fly resources-10 outbreak-detection overview-13 preparation-10 sub-tab-1 sub-tab-2 option-1 option-1-sub-tab option-2 option-2-sub-tab resources-11 time-series-analysis overview-14 preparation-11 sub-tab-1-1 sub-tab-2-1 option-1-1 option-1-sub-tab-1 option-2-1 option-2-sub-tab-1 resources-12 epidemicmodels overview-15 preparation-12 sub-tab-1-2 sub-tab-2-2 option-1-2 option-1-sub-tab-2 option-2-2 option-2-sub-tab-2 resources-13 modeling overview-16 preparation-13 overview-17 logistic-regression multi-level-modeling-regression survival-analysis multi-stage-markov-models tables-of-model-results causal-diagrams survey-analysis overview-18 preparation-14 sub-tab-1-3 sub-tab-2-3 from-data-frame overview-19 weighting random-selection resources-14 survival-analysis-1 overview-20 preparation-15 option-1-3 option-1-sub-tab-3 option-2-3 option-2-sub-tab-3 resources-15 gis-basics overview-21 preparation-16 plotting-coordinates polygons-and-shapefiles time-series-heatmap health-facility-catchment-area resources-16 ggplot-tips overview-22 preparation-17 highlighting faceting dual-axes smart-labeling time-axes dual-axes-1 adding-shapes animations epidemic-curves overview-23 preparation-18 packages-5 load-data-3 set-parameters verify-dates incidence-package intro modifications plot-modifications filtered-data date-axis-labelsgridlines option-1-scale_x_incidence-only option-2-scale_x_date-and-make_breaks option-3-use-scale_x_date-only a-sunday-week-example show-individual-cases color-by-value change-colors-and-legend facetssmall-multiples ggplot intro-1 modifications-1 modify-axes color-by-groups facetingsmall-multiples moving-averages-1 using-slider using-tidyquant tentative-data using-annotate using-geom_segment-and-geom_rect dual-axis multi-level-date-labels aggregating-linelist-data weeks months days aggregated-data dual-axis-1 resources-17 plotting-continuous-data overview-24 preparation-19 plotting-with-base-graphics plotting-with-ggplot resources-18 plotting-categorical-variables overview-25 preparation-20 plotting-with-base-graphics-1 plotting-with-ggplot-1 resources-19 tables overview-26 preparation-21 basic-flextable conditional-flextable-formatting saving-your-table resources-20 age-pyramids overview-27 preparation-22 apyramid-pa