Bio300b packages

Annotated list of packages used in Bio300B, showing how we have used the package in this course (some of the packages have functionality we have not explored).

• Packages marked (tv) are installed when tidyverse is installed
• Packages marked (TV) are installed when tidyverse is installed and loaded into memory when library(tidyverse) is run.
• Packages marked (gh) are available from github

General

• Base R packages, base, stats, utils etc
• tidyverse meta package that loads tidyr, dplyr, ggplot2 etc.

data

• palmerpenguins penguins

help

• introverse Resources for learning R and tidyverse (gh)

Data manipulation

• tibble improved data frames (TV)
• readr importing data (TV)
• janitor cleaning data
• tidyr tidying data (TV)
• dplyr manipulating data in data.frames/tibbles (TV)
• lubridate manipulating dates (tv)

Modelling

• pwr power tests
• car type II anova
• lme4 mixed effect models
• lmerTest forces lme4 models to give approximate p-values
• nlme alternative package for fitting mixed effect models
• broom convenient predictions etc from lm, glm etc models (tv)
• broom.mixed convenient predictions etc from mixed effect models
• MuMIn dredging data to find the best model in exploratory analyses
• multcomp multiple comparisons

Visualisation

• ggplot2 data visualisation (TV)
• ggbeeswarm ggplot geoms for violin-plot shaped jitter
• gghighlight highlight points and lines in ggplot
• ggfortify lm model diagnostics
• GGally pairs plot
• patchwork combine plots
• colorBlindness simulate colour-blindness

Maps

• rnaturalearth map data
• ggOceanMap ocean map data
• ggmap make a map with tiles
• terra import and process raster data
• sf import, process and plot geospatial data
• ggspatial help plot and annotate geospatial data

Communication

• quarto dynamic, executable, reproducible documents with markdown
• knitr helper functions for quarto documents
• english numbers as words
• gt publication ready tables

Reproducibility

• conflicted settle conflicts between packages
• here finding your project root for importing/exporting files
• remotes install packages from github
• usethis help set-up R and RStudio