R comes with a series of pre-installed packages in the “basic install”. There are however more than 4000 packages available and the list is growing continuously. To find more information about a package, just type R package and the name of the package in a google search. I have not tested all of them of course, nor even a small proportion of them but I can nevertheless recommend a few:
The plotting capabilities of R are excellent, but ggplot2 is of the few packages that brings scientific graphics to a new level and help create outstanding numerical representations. ggplot2 was created by Hadley Wickham and Winston Chang and follows the principle of the “Grammar of graphics” published by Leland Wilkinson.
dplyr is a very interesting package that allows for complex data manipulations in data frames : such as applying summary to groups of data, selecting variables or objects based on specific criteria/ There are 5 verbs that perform actions on the data frame:
filter: select rows according to various criteria
select: select variables according to various criteria
arrange: perform multiple sorting on the data
mutate: create new variables from existing ones
summarise: create summaries of the data selected.
tidyr was written by the same authors as dplyr and is designed to “tidy” datasets by regrouping the variables into variables. putting the data into vertical structure more suitable to further analysis. Like dplyr it is based on only 3 main function:
gather(): put variables spread across columns into a single column spread(): is used to transpose a single row of data into different columns.
separate(): separate a single complex columns into two or more columns.
rmarkdown is an addition to both R and R studio that allows the creation of dynamic documents that includes text, code and results of code (including graphics). The code example section in each test was created using rmarkdown.
circular is package entirely dedicated to the presentation and analysis of circular data (or statistics of periodic events: directions, time of day, time of year. A recent book (circular statistics in R) explains the variety of test and plots available from the package.
vegan was originally developed for plant community ecologist but of course can deal with a large variety of multivariate data sets. It includes tools for various form of diversity analysis, species accumulation, ordination and linkage with environment. It has also a series of function to carry out various dissimilarities (or similarities) based analysis such as ANOSIM, BIOENV, Mantel tests originally part of the PRIMER statistical package.
ggplot2
The plotting capabilities of R are excellent, but ggplot2 is of the few packages that brings scientific graphics to a new level and help create outstanding numerical representations. ggplot2 was created by Hadley Wickham and Winston Chang and follows the principle of the “Grammar of graphics” published by Leland Wilkinson.
dplyr
dplyr is a very interesting package that allows for complex data manipulations in data frames : such as applying summary to groups of data, selecting variables or objects based on specific criteria/ There are 5 verbs that perform actions on the data frame:
filter: select rows according to various criteria
select: select variables according to various criteria
arrange: perform multiple sorting on the data
mutate: create new variables from existing ones
summarise: create summaries of the data selected.
tidyr
tidyr was written by the same authors as dplyr and is designed to “tidy” datasets by regrouping the variables into variables. putting the data into vertical structure more suitable to further analysis. Like dplyr it is based on only 3 main function:
gather(): put variables spread across columns into a single column spread(): is used to transpose a single row of data into different columns.
separate(): separate a single complex columns into two or more columns.
rmarkdown
rmarkdown is an addition to both R and R studio that allows the creation of dynamic documents that includes text, code and results of code (including graphics). The code example section in each test was created using rmarkdown.
circular
circular is package entirely dedicated to the presentation and analysis of circular data (or statistics of periodic events: directions, time of day, time of year. A recent book (circular statistics in R) explains the variety of test and plots available from the package.
vegan
vegan was originally developed for plant community ecologist but of course can deal with a large variety of multivariate data sets. It includes tools for various form of diversity analysis, species accumulation, ordination and linkage with environment. It has also a series of function to carry out various dissimilarities (or similarities) based analysis such as ANOSIM, BIOENV, Mantel tests originally part of the PRIMER statistical package.