UQRUG 47

meeting
Overview: Webscraping with rvest.
Questions: loading packages, time series data, reading data into R, ggpicrust, dealing with windows file paths.
Published

February 28, 2024

2024-02-28: UQRUG 47

R Overview of the Month

This month at UQRUG, before we jump into our help session for everyone to ask questions, this month Nick will be looking at some basics of scraping data from Bing results and Wikipedia (or any other webpage) using the rvest package.

You can download the R script here.

Attendees

Add your name, where you’re from, and why you’re here:

Name Where are you from? What brings you here?
Nicholas Wiggins UQ Library Here to help!
Pradeepa Korale-Gedara QAAFI Here to learn
jeffery agri sci learn something about R to deal with my research project
Andy Cui ITEE/EECS/ISB Here to plot data
Jove UQ Herston Here to learn
Wei Weng Computer science Here to learn
Ryan Economics Here to learn
Jessica Hintzsche i
Erda Rame Hau UQ Vet School Here to learn ggpicrust

Questions

Q1 - Andy - Problems with loading packages

Previously, I never needed to install packages everytime I start RStudio. Now, it seems that I get these errors whenever I run a line of code such as:

> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
> library(dplyr)
Error: package or namespace load failed for ‘dplyr’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace ‘lifecycle’ 1.0.0 is already loaded, but >= 1.0.1 is required

Here’s an error that will appear when I try to install tidyverse: Execution halted ERROR: lazy loading failed for package ‘ggplot2’ removing ‘C:/Users/s4434877/Documents/R/win-library/4.0/ggplot2’

Answers

  • Looks like it’s related to the Library location found via .libPaths()
  • Recommended installing a newer version of R, as the current version

Q2 - Pradeepa - Time series data

I am trying to build a network using time series data. I use tsnet_vg funcion.One of the issues I encounted is the software consider date variable also as a node. Example

Answers

  • Run the plot again.
  • Then try changing some of the theming variables/arguments to make the text change
  • You can export the matrix you’ve created using write.csv()

Q3 - How to read data in to R

How can I read a csv into R for example?

Answers

  • you can use the base read.csv() function, or the tidyverse read_csv()
  • The UQ Library Training team regularly runs training sessions that cover this: https://web.library.uq.edu.au/library-services/training

Q4 - Erda- would like to ask if I can get help using ggpicrust package. thank you

Error in ggpicrust2(data = abundance_data, metadata = metadata_Nepal_kath,  : 
Notice: There are no statistically significant biomarkers in the dataset. This is not an error, but it might indicate that the data do not contain any biomarkers passing the set significance threshold (p<=0.05). You may refer to the tutorial's FAQ for further help and suggestions

Answers

  • Look through the FAQ and Issues on the github, and if those don’t help, raise an issue yourself. https://github.com/cafferychen777/ggpicrust2

Q5 - AC - I am trying to scrape the athletes with their country and DOB from a page. How do I know which elements to get? (As in what to put in my code)

https://www.worldaquatics.com/swimming/athletes?gender=&discipline=SW&nationality=&name=.

Answers

  • Use the inspect tool to find the class associated with the table you want to extract. Then use the html_table() function to make it look nice.

Q6 - Elegant way to paste windows paths in R by reversing the slashes

snippet pp
    "`r gsub('"', "", gsub("\\\\", "/", readClipboard()))`"

Copied from Josh Gilfillan at stackoverflow