R4PH: Epidemiology R packages
R4PH24 : 23 - 28 Sept 2024
| Learning R |
| learnr interactive tutorials in RStudio Tutorial pane |
| swirl interactive tutorials in R console |
| Project and file management |
| here file paths relative to R project root folder |
| rio import/export of many types of data |
| openxlsx import/export of multi-sheet Excel workbooks |
| Package install and management |
| pacman package install/load |
| renv managing versions of packages when working in collaborative groups |
| remotes install from github |
| General data management |
| tidyverse dplyr data management |
| tidyverse tidyr data management |
| tidyverse ggplot2 data visualization |
| tidyverse stringr work with strings and characters |
| tidyverse forcats work with factors |
| tidyverse lubridate work with dates |
| tidyverse purrr iteration and working with lists |
| linelist cleaning linelists |
| naniar assessing missing data |
| Power and Sample Size |
| epiR Tools for the Analysis of Epidemiological Data |
| pwrss Statistical Power and Sample Size Calculation Tools |
| WebPower Basic and Advanced Statistical Power Analysis |
| Statistics |
| janitor tables and data cleaning |
| gtsummary making descriptive and statistical tables |
| rstatix quickly run statistical tests and summaries |
| broom tidy up results from regressions |
| lmtest likelihood-ratio tests |
| easystats NA |
| parameters alternative to tidy up results from regressions |
| see alternative to visualise forest plots |
| Epidemic Modeling |
| epicontacts Analysing transmission networks |
| EpiNow2 Rt estimation |
| EpiEstim Rt estimation |
| projections Incidence projections |
| incidence2 Make epicurves and handle incidence data |
| i2extras Extra functions for the incidence2 package |
| epitrix Useful epi functions |
| distcrete Discrete delay distributions |
| Plots - General |
| ggplot2 included in tidyverse |
| cowplot combining plots |
| patchwork combining plots (alternative) |
| RColorBrewer color scales |
| ggnewscale to add additional layers of color schemes |
| Plots - Specific |
| DiagrammeR diagrams using DOT language |
| incidence2 epidemic curves |
| gghighlight highlight a subset |
| ggrepel smart labels |
| plotly interactive graphics |
| gganimate animated graphics |
| Maps |
| sf to manage spatial data using a Simple Feature format |
| tmap to produce simple maps, works for both interactive and static maps |
| OpenStreetMap to add OSM basemap in ggplot map |
| spdep spatial statistics |
| Reports |
| rmarkdown produce PDFs, Word Documents, Powerpoints, and HTML files |
| reportfactory auto-organization of R Markdown outputs |
| officer powerpoints |
| quarto produce PDFs, Word Documents, Powerpoints, and HTML files |
| Dashboard |
| flexdashboard convert an R Markdown script into a dashboard |
| shiny interactive web apps |
| Tables |
| knitr R Markdown report generation and html tables |
| flextable HTML tables |
| DT HTML tables (alternative) |
| gt HTML |
| huxtable HTML tables (alternative) |
| Phylogenetics |
| ggtree visualization and annotation of trees |
| ape analysis of phylogenetics and evolution |
| treeio to visualize phylogenetic files |
- adopted from The Epidemiologist R Handbook