.Rhistory

############
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
)
pacman::p_load(rio,       # to import data
here,      # to locate files
tidyverse, # to clean, handle, and plot the data (includes ggplot2 package)
apyramid,  # a package dedicated to creating age pyramids
janitor,   # tables and cleaning data
stringr)   # working with strings for titles, captions, etc.
pacman::p_load(apyramid)
# Development version of epicontacts (for transmission chains with a time x-axis)
pacman::p_install_gh("reconhub/epicontacts@timeline")
# install/load packages
pacman::p_load(
stringr,    # many functions for handling strings
tidyverse,  # for optional data manipulation
tools)      # alternative for converting to title case
pacman::p_load(
rio,        # importing data
here,       # relative file pathways
janitor,    # data cleaning and tables
lubridate,  # working with dates
matchmaker, # dictionary-based cleaning
epikit,     # age_categories() function
tidyverse   # data management and visualization
)
pacman::p_load(
tidyverse,     # data management and visualization
UpSetR,        # special package for combination plots
ggupset)       # special package for combination plots
pacman::p_load(
rio,          # importing data
here,         # relative file pathways
janitor,      # data cleaning and tables
lubridate,    # working with dates
epikit,       # age_categories() function
apyramid,     # age pyramids
tidyverse,    # data manipulation and visualization
RColorBrewer, # color palettes
formattable,  # fancy tables
kableExtra    # table formatting
)
pacman::p_load(
rio,        # to import data
data.table, # to group and clean data
tidyverse,  # allows use of pipe (%>%) function in this chapter
here
)
pacman::p_load(
lubridate,  # general package for handling and converting dates
parsedate,   # has function to "guess" messy dates
aweek,      # another option for converting dates to weeks, and weeks to dates
zoo,        # additional date/time functions
tidyverse,  # data management and visualization
rio)        # data import/export
pacman::p_load(
tidyverse,   # deduplication, grouping, and slicing functions
janitor,     # function for reviewing duplicates
stringr)      # for string searches, can be used in "rolling-up" values
pacman::p_load(
rio,          # File import
here,         # File locator
skimr,        # get overview of data
tidyverse,    # data management + ggplot2 graphics,
gtsummary,    # summary statistics and tests
janitor,      # adding totals and percents to tables
flextable,    # converting tables to HTML
corrr         # correlation analayis for numeric variables
)
pacman::p_load(
DiagrammeR,     # for flow diagrams
networkD3,      # For alluvial/Sankey diagrams
tidyverse)      # data management and visualization
pacman::p_load(
fs,             # file/directory interactions
rio,            # import/export
here,           # relative file pathways
tidyverse)      # data management and visualization
pacman::p_load(
rio,          # file import/export
here,         # relative filepaths
lubridate,    # working with dates/epiweeks
aweek,        # alternative package for working with dates/epiweeks
incidence2,   # epicurves of linelist data
i2extras,     # supplement to incidence2
stringr,      # search and manipulate character strings
forcats,      # working with factors
RColorBrewer, # Color palettes from colorbrewer2.org
tidyverse     # data management + ggplot2 graphics
)
pacman::p_load(
rio,          # file import/export
here,         # relative filepaths
lubridate,    # working with dates/epiweeks
aweek,        # alternative package for working with dates/epiweeks
incidence2,   # epicurves of linelist data
i2extras,     # supplement to incidence2
stringr,      # search and manipulate character strings
forcats,      # working with factors
RColorBrewer, # Color palettes from colorbrewer2.org
tidyverse     # data management + ggplot2 graphics
)
pacman::p_load(
rio,          # File import
here,         # File locator
tidyverse,    # Data management + ggplot2 graphics
epicontacts,  # Analysing transmission networks
EpiNow2,      # Rt estimation
EpiEstim,     # Rt estimation
projections,  # Incidence projections
incidence2,   # Handling incidence data
epitrix,      # Useful epi functions
distcrete     # Discrete delay distributions
)
pacman::p_load(
rio,           # import/export
here,          # filepaths
lubridate,     # working with dates
forcats,       # factors
aweek,         # create epiweeks with automatic factor levels
janitor,       # tables
tidyverse      # data mgmt and viz
)
pacman::p_load(
rio,             # data import/export
here,            # locate files
tidyverse,       # data management and visualization
flexdashboard,   # dashboard versions of R Markdown reports
shiny,           # interactive figures
plotly           # interactive figures
)
pacman::p_load(
tidyverse,      # includes ggplot2 and other data management tools
rio,            # import/export
here,           # file locator
stringr         # working with characters
)
pacman::p_load(
tidyverse,      # includes ggplot2 and other
rio,            # import/export
here,           # file locator
stringr,        # working with characters
scales,         # transform numbers
ggrepel,        # smartly-placed labels
gghighlight,    # highlight one part of plot
RColorBrewer    # color scales
)
pacman::p_load(
rio,           # to import data
here,          # to locate files
tidyverse,     # to clean, handle, and plot the data (includes ggplot2 package)
sf,            # to manage spatial data using a Simple Feature format
tmap,          # to produce simple maps, works for both interactive and static maps
janitor,       # to clean column names
OpenStreetMap, # to add OSM basemap in ggplot map
spdep          # spatial statistics
)
pacman::p_load(
tidyverse,       # data manipulation and visualization
rio,             # importing data
lubridate        # working with dates
)
pacman::p_load(
rio,       # import/export
here,      # filepaths
lubridate, # working with dates
plotly,    # interactive plots
scales,    # quick percents
tidyverse  # data management and visualization
)
pacman::p_load(
rio,         # import/export
here,        # file locator
purrr,       # iteration
grates,      # scales in ggplot
tidyverse    # data management and visualization
)
pacman::p_load(
rio,            # import and export
here,           # locate files
tidyverse,      # data management and visualisation
RecordLinkage,  # probabilistic matches
fastLink        # probabilistic matches
)
pacman::p_load(
rio,           # import/export
tidyverse,     # data mgmt and viz
naniar,        # assess and visualize missingness
mice           # missing data imputation
)
pacman::p_load(
tidyverse,      # for data management and viz
slider,         # for calculating moving averages
tidyquant       # for calculating moving averages within ggplot
)
pacman::p_load(here, ggplot2, dplyr, ape, ggtree, treeio, ggnewscale)
pacman::p_load(
rio,             # import/export
here,            # relative file paths
tidyverse,       # general data management and visualization
ape,             # to import and export phylogenetic files
ggtree,          # to visualize phylogenetic files
treeio,          # to visualize phylogenetic files
ggnewscale)      # to add additional layers of color schemes
pacman::p_load(
rio,          # File import
here,         # File locator
kableExtra,   # Build and manipulate complex tables
tidyverse)    # data management + ggplot2 graphics
pacman::p_load(
rio,          # File import
here,         # File locator
tidyverse,    # data management + ggplot2 graphics,
stringr,      # manipulate text strings
purrr,        # loop over objects in a tidy way
gtsummary,    # summary statistics and tests
broom,        # tidy up results from regressions
lmtest,       # likelihood-ratio tests
parameters,   # alternative to tidy up results from regressions
see          # alternative to visualise forest plots
)
# Install and load the latest version of the package from Github
pacman::p_load_current_gh("reconverse/reportfactory")
pacman::p_load(tinytex)     # install tinytex package
pacman::p_load(rmarkdown)
## load packages from CRAN
pacman::p_load(here,         # File locator
randomNames,  # Generate random names
dplyr,		 # Data management
tidyr,		 # Switching from wide to long
ggplot2,      # Ggplot2 graphics
metR,         # Filled contours used with ggplot2
gridExtra,	 # Plotting ggplot2 graphs side by side
DT 			 # Interactive tables
)
pacman::p_load(shiny)
pacman::p_load(
rio,                 # import/export data
here,                # locate files
tidyverse,           # data management and visualization
stringr,             # cleaning characters and strings
frailtypack,         # needed for dsr, for frailty models
dsr,                 # standardise rates
PHEindicatormethods) # alternative for rate standardisation
## load packages from CRAN
pacman::p_load(rio,          # File import
here,         # File locator
tidyverse,    # data management + ggplot2 graphics
tsibble,      # handle time series datasets
survey,       # for survey functions
srvyr,        # dplyr wrapper for survey package
gtsummary,    # wrapper for survey package to produce tables
apyramid,     # a package dedicated to creating age pyramids
patchwork,    # for combining ggplots
ggforce       # for alluvial/sankey plots
)
## load packages from github
pacman::p_load_gh(
"R4EPI/sitrep"          # for observation time / weighting functions
)
# install/load the different packages needed for this page
pacman::p_load(
survival,      # survival analysis
survminer,     # survival analysis
rio,           # importing data
here,          # relative file pathways
janitor,       # tabulations
SemiCompRisks, # dataset examples and advanced tools for working with Semi-Competing Risks data
tidyverse,     # data manipulation and visualization
Epi,           # stat analyses in Epi
survival,      # survival analysis
survminer      # survival analysis: advanced KM curves
)
pacman::p_load(
rio,          # File import
here,         # File locator
skimr,        # get overview of data
tidyverse,    # data management + ggplot2 graphics
gtsummary,    # summary statistics and tests
rstatix,      # summary statistics and statistical tests
janitor,      # adding totals and percents to tables
scales,       # easily convert proportions to percents
flextable     # converting tables to pretty images
)
pacman::p_load(
rio,            # import/export
here,           # file pathways
flextable,      # make HTML tables
officer,        # helper functions for tables
tidyverse)      # data management, summary, and visualization
pacman::p_load(rio,          # File import
here,         # File locator
tidyverse,    # data management + ggplot2 graphics
tsibble,      # handle time series datasets
slider,       # for calculating moving averages
imputeTS,     # for filling in missing values
feasts,       # for time series decomposition and autocorrelation
forecast,     # fit sin and cosin terms to data (note: must load after feasts)
trending,     # fit and assess models
tmaptools,    # for getting geocoordinates (lon/lat) based on place names
ecmwfr,       # for interacting with copernicus sateliate CDS API
stars,        # for reading in .nc (climate data) files
units,        # for defining units of measurement (climate data)
yardstick,    # for looking at model accuracy
surveillance  # for aberration detection
)
# install development version of epicontacts
if(
!"epicontacts" %in% rownames(installed.packages()) |
packageVersion("epicontacts") != "1.2.0"
) remotes::install_github("reconhub/epicontacts@timeline")
## install and load packages
pacman::p_load(tidyverse,
#epicontacts,
magrittr, here, webshot, visNetwork)
pacman::p_load(
rio,          # File import
here,         # File locator
tidyverse,    # Data management + ggplot2 graphics
remotes       # Package installation from github
)
pacman::p_load(
rio,          # File import
here,         # File locator
skimr,        # get overview of data
tidyverse,    # data management + ggplot2 graphics,
gtsummary,    # summary statistics and tests
janitor,      # adding totals and percents to tables
scales,       # easily convert proportions to percents
flextable,     # converting tables to HTML
purrr,          #makes functional programming easier
readr,          #to read csv files
highcharter     #to create highchart object and draw particular plot
)
# PREVIEW ONLY ONE OR SOME PAGES
# !!! NOTE - sometimes running this command renders the entire book!
# !!! In this case, just stop the rendering and re-run the command. It should work the second time.
# Edit which pages to include in "_small_bookdown.yml"
# To view, navigate to the "preview" folder and open "index.html"
bookdown::render_book(
output_format = 'bookdown::bs4_book',
config_file = "_small_bookdown.yml")
# PREVIEW ONLY ONE OR SOME PAGES
# !!! NOTE - sometimes running this command renders the entire book!
# !!! In this case, just stop the rendering and re-run the command. It should work the second time.
# Edit which pages to include in "_small_bookdown.yml"
# To view, navigate to the "preview" folder and open "index.html"
bookdown::render_book(
output_format = 'bookdown::bs4_book',
config_file = "_small_bookdown.yml")
# Use these commands to actually render the handbook
# See format and content choices below
# test
################################################################################
# BS4 BOOKDOWN STYLE (WEBSITE VERSION) ##
#########################################
# WHOLE HANDBOOK
# for online viewing only - not available as a self-contained file
bookdown::render_book(
output_format = 'bookdown::bs4_book',
config_file = "_bookdown.yml")
remove.packages("bookdown")
install.packages("bookdown")
install.packages("bookdown")
# PREVIEW ONLY ONE OR SOME PAGES
# !!! NOTE - sometimes running this command renders the entire book!
# !!! In this case, just stop the rendering and re-run the command. It should work the second time.
# Edit which pages to include in "_small_bookdown.yml"
# To view, navigate to the "preview" folder and open "index.html"
bookdown::render_book(
output_format = 'bookdown::bs4_book',
config_file = "_small_bookdown.yml")
# PREVIEW ONLY ONE OR SOME PAGES
# !!! NOTE - sometimes running this command renders the entire book!
# !!! In this case, just stop the rendering and re-run the command. It should work the second time.
# Edit which pages to include in "_small_bookdown.yml"
# To view, navigate to the "preview" folder and open "index.html"
bookdown::render_book(
output_format = 'bookdown::bs4_book',
config_file = "_small_bookdown.yml")
# PREVIEW ONLY ONE OR SOME PAGES
# !!! NOTE - sometimes running this command renders the entire book!
# !!! In this case, just stop the rendering and re-run the command. It should work the second time.
# Edit which pages to include in "_small_bookdown.yml"
# To view, navigate to the "preview" folder and open "index.html"
bookdown::render_book(
output_format = 'bookdown::bs4_book',
config_file = "_small_bookdown.yml")
# PREVIEW ONLY ONE OR SOME PAGES
# !!! NOTE - sometimes running this command renders the entire book!
# !!! In this case, just stop the rendering and re-run the command. It should work the second time.
# Edit which pages to include in "_small_bookdown.yml"
# To view, navigate to the "preview" folder and open "index.html"
bookdown::render_book(
output_format = 'bookdown::bs4_book',
config_file = "_small_bookdown.yml")
# Use these commands to actually render the handbook
# See format and content choices below
# test
################################################################################
# BS4 BOOKDOWN STYLE (WEBSITE VERSION) ##
#########################################
# WHOLE HANDBOOK
# for online viewing only - not available as a self-contained file
bookdown::render_book(
output_format = 'bookdown::bs4_book',
config_file = "_bookdown.yml")
# PREVIEW ONLY ONE OR SOME PAGES
# !!! NOTE - sometimes running this command renders the entire book!
# !!! In this case, just stop the rendering and re-run the command. It should work the second time.
# Edit which pages to include in "_small_bookdown.yml"
# To view, navigate to the "preview" folder and open "index.html"
bookdown::render_book(
output_format = 'bookdown::bs4_book',
config_file = "_small_bookdown.yml")
# Use these commands to actually render the handbook
# See format and content choices below
# test
################################################################################
# BS4 BOOKDOWN STYLE (WEBSITE VERSION) ##
#########################################
# WHOLE HANDBOOK
# for online viewing only - not available as a self-contained file
bookdown::render_book(
output_format = 'bookdown::bs4_book',
config_file = "_bookdown.yml")
renv::status()