gjuggler/ggphylo

Phylogenetic plots for R and ggplot

ggphylo's Issues

updates for R version 3.3.2

Any expectation for further development of this package? I was unable to download for R version 3.3.2, and installation failed for devtools::install_github("gjuggler/ggphylo")

Problem installing and using - `could not find function "is.linear"`

Hi there

I'm having difficulty using ggphylo. First, when I tried building and installing the package, I got an error during the construction of vignettes:

could not find function "is.linear"

I was able to get past this by bypassing the vignettes, but once I tried actually running some simple code, I got the same error. Is it possible that there is a dependency that isn't being specified properly?

We're running R 2.14.2 (64 bit Linux), for what it's worth.

Please let me know if you have any suggestions, and thank you for your time.

Chris

Error in eval(expr, envir, enclos) : could not find function "eval"

When I try to install ggphylo I get the following

githubinstall('gjuggler/ggphylo')

[...]

* installing *source* package 'ggphylo' ...
** R
** inst
** preparing package for lazy loading
Error in eval(expr, envir, enclos) : 
  could not find function "eval"
Error : unable to load R code in package 'ggphylo'
ERROR: lazy loading failed for package 'ggphylo'
* removing 'C:/Users/Francisco/Documents/R/win-library/3.3/ggphylo'
Error: Command failed (1)

Conflict with other packages

Hey @gjuggler,

I've run into a conflict using ggphylo with the R package Shiny.

Your S3 method tags

function(object, ...) {
  UseMethod("tags")
}

is also in Shiny. I am using these together in a Shiny app. I wonder if you think it's possible to change tags to something else? Like ggtags or something else that won't conflict.

Shorten multi-sentence titles to one short phrase

This issue stems from the Roxygen convention that the first LaTeX-paragraph of the roxygen header become the title. The package's function index expects relatively short sentences/phrases here, or the rendering looks pretty bad in the index. I think the title ends-up being a run-on when you read the documentation in a GUI as well.

The fix:
Easy. Put a space between the short phrase you want to keep as the title, and the rest of the paragraph(s) that you want to use for additional details. The first paragraph after the title in the roxygen header becomes the summary, and any additional paragraphs beyond that get dropped into "additional details" or whatever it's called.

Consider hiding internal functions

Many of the smaller functions in this package might be considered "internal", and useful to others in only a small minority of special cases. In these cases, there is no need for the @export tag in the rox-header, and even better to add an explicit

#' @keywords internal

tag to the header. The documentation will still be built, but it won't show up in the normal package index. This will help the largest fraction of the intende audience find the main functions we really want them to use. Not-exporting these internal functions helps others import our package without having to worry about name-clashes with other packages. A motivated user will still have access to our functions, and these internal functions can still be directly accessed via

pkgname:::funname()

In general this should feel less like a convention and more like a helpful organizing principle to make it easier on the users.

Error: processing vignette 'ggphylo.Rnw' failed with diagnostics:

HI,

When attempting to install ggphylo using install_github('ggphylo', 'gjuggler')

I received the error message:
Error: processing vignette 'ggphylo.Rnw' failed with diagnostics:
chunk 7 (label = phylo5)
Error in coord_polar(expand = F, theta = "y") :
unused argument(s) (expand = F)
Execution halted

Does anyone know what might be the issue?

Thanks,
:)

Bipartite networks?

Maybe you have already done this. If not, it would be great to have the option of plotting bipartite networks, sort of like bipartite::plotweb, e.g., try

data(Safariland)
plotweb(Safariland, high.lablength=3, low.lablength=0, arrow="down")

get rid of node and tip labels

How do we access the node and tip labels to change their size, font, or to remove them?

retrieve ggphylo from Cran repository

Hi, I would like to use ggphylo to run a R tutorial but I could not find the package in the Cran repository archive in order to download the binary file. Is there a way to get ggphylo in R 3.3.3?
thanks a lot