URL updates

DESCRIPTION

@@ -7,7 +7,7 @@ Authors@R: c(
     role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0587-9355")),
     person("James", "Manton", role = c("aut"), comment = c(ORCID = "0000-0001-9260-3156"))
     )
-URL: https://github.com/natverse/nat, https://natverse.github.io
+URL: https://github.com/natverse/nat, http://natverse.org/
 BugReports: https://github.com/natverse/nat/issues
 Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
     biological image data, especially traced neurons. Reads and writes 3D images
@@ -85,6 +85,6 @@ Collate:
     'xformimage.R'
     'xformpoints.R'
     'zzz.R'
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.1
 Encoding: UTF-8
 VignetteBuilder: knitr

R/amiralandmarks-io.R

@@ -62,7 +62,7 @@ write.landmarks.amira<-function(x, file){
 #'   
 #'   \item CMTK
 #'   
-#'   \item Fiji (see \url{http://fiji.sc/Name_Landmarks_and_Register}) }
+#'   \item Fiji (see \url{https://imagej.net/Name_Landmarks_and_Register}) }
 #'   
 #'   See examples section for how to produce a listing of all currently 
 #'   available formats with \code{fileformats}.

R/neuron-io-fiji.R

@@ -39,8 +39,8 @@ read.fijixml<-function(f, ..., Verbose=FALSE){
 #' @param Verbose Whether to print status messages during parsing.
 #' @details This is an XML based format so parsing it depends on installation of
 #'   the suggested XML package.
-#' @references \url{http://fiji.sc/Simple_Neurite_Tracer} 
-#'   \url{http://fiji.sc/Simple_Neurite_Tracer:_.traces_File_Format}
+#' @references \url{https://imagej.net/Simple_Neurite_Tracer} 
+#'   \url{https://imagej.net/Simple_Neurite_Tracer:_.traces_File_Format}
 #' @export
 read.neuron.fiji<-function(f, ..., simplify=TRUE, Verbose=FALSE){
   l=read.fijixml(f, ..., Verbose=Verbose)

R/neuron-io.R

@@ -15,7 +15,7 @@
 #'   \item \bold{neuroml} See \code{\link{read.neuron.neuroml}}
 #'   
 #'   \item \bold{fijitraces} See \code{\link{read.neuron.fiji}}. The file format
-#'   used by the \href{http://fiji.sc/Simple_Neurite_Tracer}{Simple Neurite 
+#'   used by the \href{https://imagej.net/Simple_Neurite_Tracerr}{Simple Neurite 
 #'   Tracer} plugin of Fiji/ImageJ.
 #'   
 #'   \item \bold{hxlineset,hxskel} Two distinct fileformats used by Amira. 
@@ -490,7 +490,7 @@ getformatwriter<-function(format=NULL, file=NULL, ext=NULL, class=NULL){
 #'   These functions would normally be called from \code{read.neuron(s)} rather 
 #'   than used directly.
 #' @section SWC Format: According to 
-#'   \url{http://research.mssm.edu/cnic/swc.html} SWC file format has a
+#'   \url{http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html} SWC file format has a
 #'   radius not a diameter specification
 #' @param f path to file
 #' @param ... Additional arguments. \code{read.neuron.swc} passes theseto 

README.md

@@ -3,12 +3,12 @@
 [![Release Version](https://img.shields.io/github/release/natverse/nat.svg)](https://github.com/natverse/nat/releases/latest) 
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/nat)](https://cran.r-project.org/package=nat) 
 [![Build Status](https://img.shields.io/travis/natverse/nat.svg)](https://travis-ci.org/natverse/nat) 
-[![Coverage Status](https://coveralls.io/repos/natverse/nat/badge.svg?branch=master)](https://coveralls.io/r/natverse/nat?branch=master)
+[![Coverage Status](https://coveralls.io/repos/natverse/nat/badge.svg?branch=master)](https://coveralls.io/github/natverse/nat)
 [![Docs](https://img.shields.io/badge/docs-100%25-brightgreen.svg)](http://natverse.github.io/nat/reference/)
 
 
 An R package for the (3D) visualisation and analysis of biological image data, especially tracings of
-single neurons. See [nat.examples](https://github.com/jefferis/nat.examples) and [frulhns](https://github.com/jefferis/frulhns) for sample code.
+single neurons. See [nat.examples](https://github.com/natverse/nat.examples) and [frulhns](https://github.com/jefferis/frulhns) for sample code.
 
 **nat** is a cleaned up version of [code](https://github.com/jefferis/AnalysisSuite) that has been used in a number of papers from our group including:
 
@@ -58,8 +58,8 @@ devtools::install_github("natverse/nat")
 ## Help
 If you want some help using **nat**, then please use the following resources
 
-* For installation issues, see the [Installation vignette](http://natverse.github.io/nat/articles/Installation.html)
-* Start with the [overview package documentation](http://natverse.github.io/nat/reference/nat-package.html) (`?nat` in R)
+* For installation issues, see the [Installation vignette](http://natverse.org/nat/articles/Installation.html)
+* Start with the [overview package documentation](http://natverse.org/nat/reference/nat-package.html) (`?nat` in R)
 * Thematically organised [function reference documentation](http://natverse.github.io/nat/reference/)
 * [nat.examples](https://github.com/jefferis/nat.examples) sample code
 * [nat-user](https://groups.google.com/forum/#!forum/nat-user) Google group - 

vignettes/Installation.Rmd

@@ -31,7 +31,7 @@ pre-requisite for most functionality is a recent version of R (>=3.1.0 recommend
 you use RStudio or R from the terminal, you must have a copy of XQuartz, the X11
 window manager, installed. This is no longer a default install since Mac OS X 
 10.8. You need to install XQuartz, before installing the nat package. Logout and login for the installation to take effect. You can get it from 
-https://xquartz.macosforge.org/landing/. This page is also linked from the 
+https://www.xquartz.org/. This page is also linked from the 
 [Download R for (Mac) OS X](https://cran.r-project.org/bin/macosx/) page.
 
 If you want to apply non-rigid registrations calculated by the 

vignettes/neurons-intro.Rmd

@@ -65,7 +65,7 @@ A subset of the original data are distributed as a sample data object with the
 data("Cell07PNs")
 ```
 
-For more information about these data see [Cell07PNs](http://natverse.github.io/nat/reference/Cell07PNs.html).
+For more information about these data see [Cell07PNs](http://natverse.org/nat/reference/Cell07PNs.html).
 
 This `Cell07PNs` object has two classes `neuronlist` and the base class `list`
 
@@ -172,7 +172,7 @@ Note that if you write `?plot` you will get the documentation for the basic
 `plot` function supplied with R.
 
 It is also good idea to look at 
-[nat's function reference page](http://natverse.github.io/nat/reference/index.html)
+[nat's function reference page](http://natverse.org/nat/reference/index.html)
 which groups available functions into categories that often reflect the class
 of object they can work on.
 
@@ -212,7 +212,7 @@ summary(n1)
 summary(n1.lh)
 ```
 
-See [nat's function reference page](http://natverse.github.io/nat/reference/index.html)
+See [nat's function reference page](http://natverse.org/nat/reference/index.html)
 for additional functions for working with neurons.
 
 ## Neuronlists
@@ -404,7 +404,7 @@ plot(Cell07PNs, subset=Glomerulus=="DA1", add=TRUE)
 So far we have only used 2D plots in this document, but especially for 
 interactive analysis and exploration, it is much more helpful to have 
 3D plots that can be rotated, zoomed etc. **nat** provides numerous functions 
-for [3D plots](http://natverse.github.io/nat/reference/index.html#section--d-plotting-of-objects)
+for [3D plots](http://natverse.org/nat/reference/index.html#section--d-plotting-of-objects)
 based on the [rgl package](https://cran.r-project.org/package=rgl). It is 
 actually possible to embed fully interactive 3d figures in [rmarkdown](http://rmarkdown.rstudio.com/) reports
 like this one by setting the [webgl chunk option](https://CRAN.R-project.org/package=rgl/vignettes/WebGL.html).
@@ -503,7 +503,7 @@ with a chance level of about 25% for these 4 classes.
 
 We hope this tutorial will provide you with a good foundation for further use of
 the **nat** and related packages. Please visit the main 
-[nat README](http://natverse.github.io/nat/index.html) for
+[nat README](http://natverse.org/nat/index.html) for
 suggestions of resources to learn more and solve problems. You may also
 find that some time spent reading Hadley Wickham's [Advanced R](http://adv-r.had.co.nz/) 
 is a worthwhile investment. I recommend the first 7 chapters