I Installed the package "vegan" but cant seem to run it. When I use the command library(vegan) I get this message
.
Any ideas? I normally just use R cmdr so excuse me if this is a silly question.
Also: Is there any plugin to cmdr for NMDS ordination that I can use instead?
That wasn't a "problem". It was only a "message" and not even a particularly dangerous message. It was telling you that the vegan package had a function of the same name as another function in the pls package. If you know that you will be using the scores function with the syntax of the pls::scores function at a later time, then you will need to use it with that form. If you just use scores you will get the function as it exists in pkg:vegan.
I'm being mute about the second part (although it may be premised incorrectly on your anxiety about the message, in which case the question is moot). Multipart questions are discouraged on SO.
To answer your question about Rcmdr plugin for NMDS: check BiodiversityR package that provides an Rcmdr GUI to a part of vegan (plus more).
Related
After forming the matrix( which is my resultant image ) from certain data I am trying to display the image using the "imagesc" in r. The same thing I already had done in Matlab. To do the same in r I found out "imagesc" in r. but when I use this function it is showing the following error message
No documentation for ‘imagesc’ in specified packages and libraries:
you could try ‘??imagesc’
Even I already incorporated
library(R.matlab)
please help me to resolve the issue? I am a beginner in r programming.
You are looking for the function imagesc in the wrong package.
The package R.matlab doesn't have such function (see R.matlab).
You can find it in the matlab package, though.
So just do:
install.packages("matlab")
library(matlab)
and you'll be good to go with imagesc.
That said, if your task is going to be a recurrent one, I think it's a good idea to use native R solutions, instead of Matlab's. In such case, you may want to check ggplot2::geom_tile.
Check this image, for instance:
I'm writing an R package and I'd like to use one function from another package (plotKML). This external package has so many dependencies that I don't want my users to be required to download etc. If I use importFrom(plotKML, readGPX) in the NAMESPACE file it will load all of plotKML into the namespace and download all dependencies which I don't want.
So the question is: is it appropriate to copy the code for the one function I need (ensuring that all the dependencies in that one function are included)? If so what is appropriate for the attribution/documentation -- do I copy the documentation from the original?
There is a great discussion of this issue in this post and the answer by Brian Diggs is very helpful. But he ends with "For your example, you may be better off copying the code for memisc::describe into your package, although that approach has its own problems and caveats" so I'm left with some uncertainty about what the problems are and whether it's appropriate from a attribution perspective.
Questions about the appropriate attribution would probably be best resolved by contacting the package author directly. As noted in the comments above, that package appears to use GPL-3, which should mean that you can include the function in your package but your package must then also be GPL-3 licensed. (As always, probably no one here is a lawyer so that's on you to check...)
The primary downside to copying just the function you need is that then you are responsible for maintaining it. This probably also means maintaining it in a way that keeps it in sync with the original version from plotKML. Depending on the package, surrounding code and how often it is updated that could be fairly simple or it could be horrible.
colorout is no longer on CRAN. As #user2647661 points out below, the package is still being maintained and can be downloaded from the author's website.
My question: Is there another R package that provides similar functionality or at least a quick hack that shows errors in red? (I use R inside a Gnome Terminal on Ubuntu.)
I am aware of Alex's question about printing errors in red. #Eric Fail's answer suggests that something like this can be build using error handling functions. However, I am not familiar enough with R to fully understand his suggestion. Has anybody implemented something like this yet?
The package is no longer on CRAN but it's still being maintained. Please, look at http://www.lepem.ufc.br/jaa/colorout.html
Does anybody know where I can download the R package "cart" that can help create Gastner's
"Mapping with Diffusion-based Cartograms" ? I tried a install.package on R and says it's not available
for R 2.15. There is a page on R-forge about it but it doesn't explain how to download the package.
Thanks.
Way late to the game, but from what I can tell there's not much happening for the cart package; my recent efforts with cartogramming in R have pushed me towards two alternatives: Rcartogram within R (available from the GitHub repository) and ScapeToad, a program written in JS.
Advantage of the former is that you don't have to leave R (better for long-term project management), however it's a bit arcane to use (requires converting your shapefile to a density grid & then figuring out how to use an interpolation method, etc.).
Advantage of the latter is that it's got a very simple point-and-click GUI--add shapefile, create cartogram wizard, export shapefile, voila.
Both are based on the Gastner-Newman diffusion-based algorithm.
If you check the build page you'll see that at the moment the package fails to build. I thought it might be something minor but I've put in a little bit of work so far and it's still failing to build on my machine.
You might want to email the authors and ask them. You could also try their forum but it looks like it hasn't seen much activity lately.
I'm looking for a an R package which can be used to train a Dirichlet prior from counts data. I'm asking for a colleague who's using R, and don't use it myself, so I'm not too sure how to look for packages. It's a bit hard to search for, because "R" is such a nonspecific search string. There doesn't seem to be anything on CRAN, but are there any other places to look?
I've only come across both R and the Dirichlet distribution in passing, so I hope I'm not too much off the mark.
This mailing list message seems to answer your question:
Scrolling through the results of
RSiteSearch("dirichlet") suggests some useful tools
in the VGAM package. The gtools package and
MCMC packages also have ddirichlet() functions
that you could use to construct a (negative log) likelihood
function and optimize with optim/nlmin/etc.
The deal, DPpackage and mix packages also may or may not provide what you need.
Then again, these are all still CRAN packages, so I'm not sure if you already found these and found them unsuitable.
As for searching for R, the R project site itself already provides a few links on its search page.