I have a problem with package stars when trying to use split function to split a stars raster object. I use the stars version 0.5-4 (that one is automatically installed when asking for installing stars). According to the package documentation, there should be a function split (in fact, it's probably a method for the generic R function split) for splitting stars object. However, when I try to use it, my R says there is no such function in the stars namespace. Is the function really missing and the documentation wrong? Or could that be caused by some other problem with namespaces?
> library(stars)
> split.stars
Error: object 'split.stars' not found
> stars::split
Error: 'split' is not an exported object from 'namespace:stars'
But when I type
> ?stars
I get the help for the split function from stars. Can someone explain that?
Thanks in advance!
Edit: It works now, not sure what the problem was.
split is a base R function. It’s an S3 generic, and the ‘stars’ package provides its own method implementation for a custom S3 class.
To use the method, use it as any other, regular function from base R. That is, write split. Don’t write split.stars, nor stars::split.
Related
I'm attempting to scale a dataset by its unit variance using the scaling_UV() function in R from the santaR package. I have installed and loaded the santaR library but I am still being told that the scaling_UV() function could not be found.
How can I use this function or is there another function that performs the same operation? I will even perform the scaling manually if necessary.
I assume you have already used library(santaR) without errors.
If the function is exported by the package, santaR::scaling_UV() should work.
You can also try santar:::scaling_UV() (notice the three colons).
According to the documentation, the function should be present in version 1.2.3
I had written some R functions that I wanted to convert to an R package. One of them is called for example print.pretty.values and another print.empty.line. Package builds and installs alright, but when I run the check function I get this warning:
Found the following apparent S3 methods exported but not registered
I have read the relevant documentation and I don't want to have a print function of my class someClass. I just need to export nicely (and without warning) a function that is called print.something or plot.something.else without it being understood as an S3 method and without me having to change the name. Is there a way to define this (in the function documentation or the NAMESPACE file?)
I changed all the names of the functions to have the underscore separator (_) instead of the dot (.), following the tidyverse guidelines: https://style.tidyverse.org/syntax.html
Note that the only case that they 'allow' dots in functions are when you write function.class or class.name and in my case it wasn't like that (print.pretty.values wasn't an S3 function - I just wanted to use the dot as a separator for words in general and thus I got warnings).
What is the possible documentation available for R package? For example I try to understand sp package.
In addition to help(sp), what are the other functions for searching through help and documentation?
Getting help on a function that you know the name of
Use ? or, equivalently, help.
?mean
help(mean) # same
For non-standard names use quotes or backquotes; see An Introduction to R: Getting help with functions and features:
For a feature specified by special characters, the argument must be enclosed in double or single quotes, making it a “character string”: This is also necessary for a few words with syntactic meaning including if, for and function."
?`if`
?"if" # same
help("if") # same
There are also help pages for datasets, general topics and some packages.
?iris
?Syntax
?lubridate
Use the example function to see examples of how to use it.
example(paste)
example(`for`)
The demo function gives longer demonstrations of how to use a function.
demo() # all demos in loaded pkgs
demo(package = .packages(all.available = TRUE)) # all demos
demo(plotmath)
demo(graphics)
Finding a function that you don't know the name of
Use ?? or, equivalently, help.search.
??regression
help.search("regression")
Again, non-standard names and phrases need to be quoted.
??"logistic regression"
apropos finds functions and variables in the current session-space (but not in installed but not-loaded packages) that match a regular expression.
apropos("z$") # all fns ending with "z"
rseek.org is an R search engine with a Firefox plugin.
RSiteSearch searches several sites directly from R.
findFn in sos wraps RSiteSearch returning the results as a HTML table.
RSiteSearch("logistic regression")
library(sos)
findFn("logistic regression")
Finding packages
available.packages tells you all the packages that are available in the repositories that you set via setRepositories. installed.packages tells you all the packages that you have installed in all the libraries specified in .libPaths. library (without any arguments) is similar, returning the names and tag-line of installed packages.
View(available.packages())
View(installed.packages())
library()
.libPaths()
Similarly, data with no arguments tells you which datasets are available on your machine.
data()
search tells you which packages have been loaded.
search()
packageDescription shows you the contents of a package's DESCRIPTION file. Likewise news read the NEWS file.
packageDescription("utils")
news(package = "ggplot2")
Getting help on variables
ls lists the variables in an environment.
ls() # global environment
ls(all.names = TRUE) # including names beginning with '.'
ls("package:sp") # everything for the sp package
Most variables can be inspected using str or summary.
str(sleep)
summary(sleep)
ls.str is like a combination of ls and str.
ls.str()
ls.str("package:grDevices")
lsf.str("package:grDevices") # only functions
For large variables (particularly data frames), the head function is useful for displaying the first few rows.
head(sleep)
args shows you the arguments for a function.
args(read.csv)
General learning about R
The Info page is a very comprehensive set of links to free R resources.
Many topics in R are documented via vignettes, listed with browseVignettes.
browseVignettes()
vignette("intro_sp", package = "sp")
By combining vignette with edit, you can get its code chunks in an editor.
edit(vignette("intro_sp",package="sp"))
This answer already gives you a very comprehensive list.
I would add that findFn("some search terms") in package sos is extremely helpful, if you only have an idea/keywords of what you are looking for and don't already have a package or function in mind.
And also the task views on CRAN: not really a search process but a great place to wander as you wonder.
This thread contains many good suggestions. Let me add one more.
For finding which packages are loaded, plus extra goodies, ?sessionInfo is quite nice.
help(package="<package-name>") where of course <package-name> is the name of the package you want help for.
Often the same function name is used by several packages. To get help on a function from a specific package, use:
help(aggregate, package="stats")
help(aggregate, package="sp")
In the RStudio IDE you can click on any function name and press F1, which will directly open the associated function help text in its pane. Like you would have called help() or ?fun().
I'm building an R package for the first time and am having some trouble. I am doing an R CMD Check and am getting the following error:
get.AlignedPositions: no visible global function definition for 'subject'
I am not sure what is causing this. I don't even have a "subject" variable in my code. The code is rather lengthy so I rather not paste all of it unless someone asks in a comment. Is there something specific I should look for? The only thing I can think of is that I have a line like this:
alignment <-pairwiseAlignment(pattern = canonical.protein, subject=protein.extracted, patternQuality=patternQuality,
subjectQuality=subjectQuality,type = type, substitutionMatrix= substitutionMatrix,
fuzzyMatrix=fuzzyMatrix,gapOpening=gapOpening,gapExtension=gapExtension,
scoreOnly=scoreOnly)
but subject is defined by the pairwiseAlignment function in the Biostrings package. Thank you for your help!
R spotted a function, subject, being used without a function called subject being available. One possible reason for this is explained in this discussion on R-devel. In that case code is used conditionally, e.g. if a certain package is installed we use its functionality. When checking the package on a system which does not have this package installed, we run in to these kinds of warnings. So please check if this might be the case. Alternatively, you might have made a mistake by calling subject while no function existed, e.g. subject was not a function but just an object.
I'm trying to debug my first R script and I came across this line:
data <- read.data(dir, indiv, label)
I've been googling "R read.data" for the past 30 minutes and absolutely nothing is coming up. Am I doing something wrong? Is there a good way to look up things I see in R scripts that I don't know what they are?
And what is this particular line doing anyway?
It's probably a function defined by the author of the script. Search for it in the code you have.
A couple of things to check:
Does your script define the function 'read.data' somewhere? read.data <- function(...
Does your script use library() or require() to load another package? In that case, the read.data function can be defined in that package.
Does your script use source to read another script? Check that script then...
package sos to the rescue:
read.data is a deprecated function in the rjags package
> library(sos)
> findFn("read.data")
Finds this result:
http://finzi.psych.upenn.edu/R/library/rjags/html/read.data.html
From this page:
Read data for a JAGS model from a file.
Usage
read.jagsdata(file)
read.bugsdata(file)
Note
Earlier versions of the rjags package had a read.data function which read data
in either format, but the function name was ambiguous (There are many data file
format in R) so this is now deprecated.
There isn't a base function named read.data. If you want to find help for an R function (for example read.table), simply type ?read.table at the interactive prompt.
This line calls a read.data function which is either defined in that script or in something else it loads (such as libraries with the library() or require(), other scripts with source()). You'll need to search those sources to find this function.