I have successfully installed Orca using Method 4 on the github page. However, I am unsure how best to proceed to export a static plot I have made in Plotly.
I have tried calling Orca in my R script using the syntax shown on the github page, but it returns "Error: The orca command-line utility is required to use the 'orca()' function".
I would appreciate if someone is able to explain the best way to proceed. I am inexperienced with the command-line, and do not understand the syntax shown for the command-line on the previously linked github page.
Related
I am learning R. I have install "seqinr package" successfully. But when I load the "seqinr" package, it is something wrong. Does anyone know how to resolve it?
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I have tried to install package ade4，but it was shown like
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Hopefully this helps the first part of your question.
For the seqinr package, I utilize the following code:
install.packages("seqinr")
#https://www.rdocumentation.org/packages/seqinr/versions/4.2-8
library(seqinr)
It seems old school but I always put the install and call for the library embedded within the code. Also are you using R Studio or just R? I have been dabbling in this same library myself.
Update
Issue resolved
Update, still not working
Tried the following in R file
(1) deleted both library(...) packages
(2) Added #import jpeg before ShowPalettePhoto() and #import tidyverse before RanglaPunjab() so roxygen automatically adds to NAMESPACE.
After running devtools::document(), ran devtools::use_package("jpeg") and devtools::use_package("tidyverse") to automatically add to DESCRIPTION.
Unfortunately, even in testing, I cannot get JPEG photo.
Here is GitHub repository, https://github.com/ArtieLadie/RanglaPunjab
I created R package according to this tutorial
It worked and I was able to execute all commands, including a function to display photo in another directory.
I uploaded to my GitHub account. Anyone can install package in R environment with install_github("ArtieLadie/RanglaPunjab")
I am able to run functions by adding RanglaPunjab:: in front of it, i.e.
RanglaPunjab::PaintPalette("Jutti")
?RanglaPunjab::MergePalette
However, when I try to run ?RanglaPunjab::ShowPalettePhoto("Teej") I get
Error in readJPEG(x, native = TRUE) : could not find function "readJPEG"
Before creating the package I added function to set working directory to file location, but it was creating errors when I ran install("RanglaPunjab"), i.e. "Cannot execute"
Here are the exact commands I had, which I had to delete from code
library(rstudioapi)
current_path <- getActiveDocumentContext()$path
setwd(dirname(current_path ))
Please help
Your dependencies are not handled correctly. Here you explicitly load packages with library(...). That is not how one does that in an R package. You should add your dependencies to the Imports: section of the DESCRIPTION file and use the package::function() syntax when calling the function. c.f. http://r-pkgs.had.co.nz/description.html#dependencies.
In addition, if you want the images to be installed with your package, you should place them for example in inst/pics. You can then get the path to these files with
system.file("pics", <file-name>, package = "RanglaPunjab")
R noobie here.
I'm am trying to use a package that I download off of github using source_gist, but it appears that I need to re-download it every time I quit R (I'm using RStudio).
To clarify, the function that I'm using is part of plotrix package and is called barp. Someone made a modified version of it (called barp2) and put it up on github. That's what I want to use.
So my question is this: is there anyway to have this modified code saved inside the plotrix package, so I wouldn't have to download it every time?
I hope I'm explaining this correctly.
So, let's get some quick terminology straight: the function you're getting off of github isn't a package, it's just a single function. If it was a package, you could use devtools::install_github once and then load it with require() or library() like any other package.
A good solution isn't too different. Just go to the gist, copy the code, paste it into your R editor, and save it somewhere as a .R script file. Something like C:/path/to/barp2.R (adjusting, of course, based on where you actually want to keep it and based on your OS). Then you can read it locally using source("C:/path/to/barp2.R") instead of devtools::source_gist().
If you always want to load it, you could load plotrix and then source this file every time R starts with a couple lines in your R profile, see ?Startup as #BondedDust suggests for details on this.
Reading it off of github every time does have the advantage that, if the author fixes bugs or otherwise improves it, you'll always be using the up-to-date version. It has several disadvantages too: requiring an internet connection, losing access if the gist is deleted, or being unable to access old versions if the author changes it in a way you don't like. Keeping a copy of a version you like is a smart move.
I am fitting a GLMM and I had seen some examples where is used the function: overdisp_fun, defined in glmm_funs.R, but I don't know which package contain them or how can I call it from R, can somebody help me?
Thanks,
If you google for glmm_funs.R, you'll find links to the script (eg here: http://glmm.wdfiles.com/local--files/trondheim/glmm_funs.R).
You can save the file on your local machine, then call it in your R session with source("path to file/glmm_funs.R").
You will then be able to use the functions contained in the script, including overdisp_fun().
You can think of it a little bit like loading a package, except the functions are just presented in a script.
I have installed a library that contains lot of functions. I want to see calculations done in those functions. How to reach man page of these function in R prompt ?
I only know library(help="name of library") command to seek help.
The shortcut is:
?command
The longer version, for commands such as if for which the shortcut won't work, is:
help("command")
If you need to find a command in installed packages:
help.search("command")
If you need to find a command in all possible packages, the sos library is the ticket.
If you were using the ggplot2 package, go to google, type in something like :
'r ggplot2'
In the results look for the sites that look like this:
cran.r-project.org/package=ggplot2
and start with 'cran.r-project.org/....'
Click on that link and you will see a page for the package. You want to click on either the Reference Manual or for some packages there are Vignettes with more involved explanations and examples. However, the Reference Manual is usually pretty good for examples of how to use the package functions.