##########################################
# List of useful epidemiology R packages #
##########################################

# This script uses the p_load() function from pacman R package, 
# which installs if package is absent, and loads for use if already installed


# Ensures the package "pacman" is installed
if (!require("pacman")) install.packages("pacman")


# Packages available from CRAN
##############################
pacman::p_load(
     
     # 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,    # includes many packages for tidy data wrangling and presentation
          #dplyr,      # data management
          #tidyr,      # data management
          #ggplot2,    # data visualization
          #stringr,    # work with strings and characters
          #forcats,    # work with factors 
          #lubridate,  # work with dates
          #purrr       # iteration and working with lists
     linelist,     # cleaning linelists
     naniar,       # assessing missing data
     
     # 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,
          # 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 types
     ########################
     DiagrammeR,       # diagrams using DOT language
     incidence2,       # epidemic curves
     gghighlight,      # highlight a subset
     ggrepel,          # smart labels
     plotly,           # interactive graphics
     gganimate,        # animated graphics 

     
     # gis
     ######
     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 
     
     # routine reports
     #################
     rmarkdown,        # produce PDFs, Word Documents, Powerpoints, and HTML files
     reportfactory,    # auto-organization of R Markdown outputs
     officer,          # powerpoints
     
     # dashboards
     ############
     flexdashboard,    # convert an R Markdown script into a dashboard
     shiny,            # interactive web apps
     
     # tables for presentation
     #########################
     knitr,            # R Markdown report generation and html tables
     flextable,        # HTML tables
     #DT,              # HTML tables (alternative)
     #gt,              # HTML tables (alternative)
     #huxtable,        # HTML tables (alternative) 
     
     # phylogenetics
     ###############
     ggtree,           # visualization and annotation of trees
     ape,              # analysis of phylogenetics and evolution
     treeio            # to visualize phylogenetic files
 
)

# Packages to download from Github (not available on CRAN)
##########################################################

# Development version of epicontacts (for transmission chains with a time x-axis)
pacman::p_install_gh("reconhub/epicontacts@timeline")

# The package for this handbook, which includes all the example data  
pacman::p_install_gh("appliedepi/epirhandbook")