Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
tools:r [2024/01/10 14:14] – [GNU R] willtools:r [2026/07/24 12:43] (current) – [GNU R] will
Line 2: Line 2:
  
  
-The [[https://www.r-project.org/|GNU R programming language]] is often paired with [[https://posit.co/download/rstudio-desktop/|posit's RStudio Desktop IDE]] and a suit of libraries (language packages) known as [[:tools:tidyverse|tidyverse]] (includes ''dplyr'' and ''ggplot2''). +The [[https://www.r-project.org/|GNU R programming language]] is often paired with [[https://posit.co/download/rstudio-desktop/|posit's RStudio Desktop IDE]] and a suit of libraries (language packages) known as [[:tools:tidyverse|tidyverse]] (includes ''dplyr'' and ''ggplot2''). R and RStudio (including Rmarkdown code cells) can use python interleaved with R code. See [[:tools:r:python]].
  
 You can also find a web interface to [[http://rhea.wpic.upmc.edu:8787/|Rstudio on rhea]] (also [[:admin:remoteaccess]]). You can also find a web interface to [[http://rhea.wpic.upmc.edu:8787/|Rstudio on rhea]] (also [[:admin:remoteaccess]]).
Line 8: Line 8:
 [[:tools:tutorials|Tutorials]] contains additional resources. [[:tools:tutorials|Tutorials]] contains additional resources.
  
-See [[:tools:r:issues]] for log of debugged problems.+See 
 +  * [[:tools:r:issues]] for log of debugged problems. 
 +  * [[:tools:r:versions]] for using specific older versions 
 ===== Notes ===== ===== Notes =====
-==== na.action ====+ 
 +==== Rstudio Chunk output in console ==== 
 +To use the panel for images instead of seeing them inlined within ''.Rmd'' use the "Chunk output in console" setting, either from the gear dropdown menu or in the yaml front matter.  (From Dan & Victoria) 
 + 
 +{{.:pasted:20251121-162226.png}} 
 +{{.:pasted:20251121-162127.png}} 
 + 
 +<code=R> 
 +--- 
 +editor_options: 
 +  chunk_output_type: console 
 +--- 
 +</code> 
 + 
 +==== na.action for residual ====
 When adding module residuals back to a dataframe, you need ''residuals()'' to return the same length as the input data.frame. use ''lm(na.action=na.exclude)''. When adding module residuals back to a dataframe, you need ''residuals()'' to return the same length as the input data.frame. use ''lm(na.action=na.exclude)''.
  
Line 18: Line 34:
 d <-  data.frame(x=c(1:4,NA),y=1:5); d <-  data.frame(x=c(1:4,NA),y=1:5);
 m <- lm(x~y,d,na.action=na.exclude); m <- lm(x~y,d,na.action=na.exclude);
-nrow(d);  +nrow(d);              # 5 
-length(m$residuals);  +length(m$residuals);  # 4 
-length(residuals(m)) +length(residuals(m))  # 5
-   [1] 5 +
-   [1] 4 +
-   [1] 5+
 </code> </code>
  
Line 33: Line 46:
  
  
 +==== MASS::select vs dplyr::select  ====
 +If you load MASS after dplyr, ''select'' will be ''MASS::select'' not ''dplyr::select'' and you're likely to encounter hard-to-debug errors about unused arguments
  
 +> Error in select ...  : unused arguments
 + 
 +**solutions** include 
 +  - load MASS first
 +  - force select to be ''dplyr'''s version, or 
 +  - unload MASS if you don't need it
 +
 +<code>
 +# load mass before dplyr to have 'select' be from dplyr
 +library(MASS)
 +library(dplyr)
 +
 +# force which select (if MASS was already loaded after dplyr and overwrite the function)
 +select <- dplyr::select
 +
 +# or unload MASS
 +detach("package:MASS", unload=TRUE)
 +
 +# check to see
 +environment(select) # if "MASS", you're in for a bad time
 +</code>
 ===== Backlinks ===== ===== Backlinks =====
  
  
 {{backlinks>.}} {{backlinks>.}}