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session-packages.qmd
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session-packages.qmd
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---
title: "Introduction to R and Rstudio"
subtitle: "Session - Packages"
---
## Package locations
### CRAN repository
[Comprehensive R Archive Network](https://cran.r-project.org/web/packages/)
19,291 packages (March 2023), free and structurally peer reviewed
### GitHub
Many useful packages in development or subject to a lot of change are not on CRAN and are available through GitHub including [{NHSRtheme}](https://github.com/nhs-r-community/NHSRtheme). These won't be peer reviewed.
### ROpenSci
ROpenSci offer a peer reviewed ecosystem of R packages through GitHub including UKHSA's [{fingertipsR}](https://github.com/ropensci/fingertipsR)
## Packages
::: columns
::: {.column width="40%"}
Quotations in R can be either double or single quotes but cannot be mixed or omitted:
```{r}
# either
install.packages("tidyverse")
# or
install.packages('tidyverse')
```
:::
::: {.column width="60"}
or use the RStudio wizard (only for published CRAN packages)
<img src="img/session-packages/package-wizard.PNG" alt="Screenshot of right panels in RStudio with the Packages tab highlighted" class="center"/>
:::
:::
::: notes
Explore searching for packages in this panel
:::
# Loading package
This needed for every new session/script and is often at the top
::: columns
::: {.column width="40%"}
```{r}
library(tidyverse)
```
Can be loaded from the packages panel and code appears in the Console
:::
::: {.column width="60%"}
<img src="img/session-packages/package-load.PNG" alt="Screenshot of the tick box next to tidyverse in the Packages tab that can be ticked" class="center"/>
:::
:::
::: notes
On work computer networks the packages get saved to personal files on C: drives so are not accessible to everyone
RStudio will pick up references to packages not yet loaded (on CRAN)
Also mention how quotations don't matter but case does in R
:::
## {tidyverse}
::: columns
::: {.column width="40%"}
Curly brackets around a {package} is used in text as many packages have "real names"
:::
::: {.column width="60%"}
<img src="img/session-packages/tidyverse.PNG" alt="The tidyverse name in a black screen with coloured dots like stars" class="center"/>
:::
:::
## What is the {tidyverse}?
The [tidyverse package](https://www.tidyverse.org/) collects (some of) the most popular\
R packages into one.
Also refers to a coding style in R.
## {tidyverse} debate
Should you use {tidyverse} when many of the packages are redundant?
Clashes occur with the packages which you are notified about, but not with those outside the package
```{r}
── Attaching core tidyverse packages ────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.0 ✔ readr 2.1.4
✔ forcats 1.0.0 ✔ stringr 1.5.0
✔ ggplot2 3.4.1 ✔ tibble 3.1.8
✔ lubridate 1.9.2 ✔ tidyr 1.3.0
✔ purrr 1.0.1
── Conflicts ──────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package to force all conflicts to become errors
```
::: notes
Might be best for beginners just to used {tidyverse} as it's easy to install and load altogether.
:::
## Errors, warnings & notifications
Warnings - not errors, just information on versions (from an older system)
Warning messages:
1: package ‘tidyverse’ was built under R version 4.0.4
2: package ‘tidyr’ was built under R version 4.0.3
3: package ‘readr’ was built under R version 4.0.3
4: package ‘purrr’ was built under R version 4.0.3
5: package ‘dplyr’ was built under R version 4.0.3
6: package ‘stringr’ was built under R version 4.0.3
Don't rely upon colour changes as all three are orange in the console!
::: notes
Errors will be where the code breaks and also says Error.
Warnings often mean the code has run, it's just giving information as something could break.
Red text is possibly avoided because of colour blindness.
{tidyverse} messages are very helpful and have been coded to give good information on errors.
:::
## End session