fix urls

Author: cboettig

.Rbuildignore

@@ -12,3 +12,4 @@ cran-comments.md
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.github$
+^CRAN-SUBMISSION$

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.1.5
+Date: 2024-02-16 04:38:55 UTC
+SHA: 35168a0399bc6376c2f4f03b902c42a0c6d0fc5b

DESCRIPTION

@@ -11,8 +11,8 @@ Description: Interface to the API for 'TreeBASE' <http://treebase.org>
     them.
 License: CC0
 Encoding: UTF-8
-URL: https://docs.ropensci.org/treebase, https://github.com/ropensci/treebase
-BugReports: http://www.github.com/ropensci/treebase/issues
+URL: https://docs.ropensci.org/treebase/, https://github.com/ropensci/treebase
+BugReports: https://github.com/ropensci/treebase/issues
 Depends:
     R (>= 2.15),
     ape

README.md

@@ -1,15 +1,10 @@
 treebase
 ========
 
-[![Build Status](https://api.travis-ci.org/ropensci/treeBASE.png)](https://travis-ci.org/ropensci/treeBASE)
-[![Build status](https://ci.appveyor.com/api/projects/status/d74vw3cpwh0kdg3e/branch/master)](https://ci.appveyor.com/project/sckott/treebase/branch/master)
-
 _An R package for discovery, access and manipulation of online phylogenies_
 
-- [Publication in Methods in Ecology and Evolution](http://dx.doi.org/10.1111/j.2041-210X.2012.00247.x)
-- [Development version source code on github](https://github.com/ropensci/treebase)
-- [HTML package documentation](http://ropensci.github.com/treeBASE/)
-- [Report issues, bugs or feature requests](https://github.com/ropensci/treebase/issues)
+- [Publication in Methods in Ecology and Evolution doi:10.1111/j.2041-210X.2012.00247.x
+
 
 
 Installation
@@ -34,11 +29,8 @@ Phylogenies_from_Huelsenbeck <- search_treebase("Huelsenbeck", "author")
 
 More interesting examples will take advantage of `R` to loop over large amounts of treebase data that would be to tiresome to search for, download and analyze by hand. Welcome to the era of big data phylogenetics.  
 
-- Browse the examples in the [documentation](http://ropensci.github.com/treeBASE/)
-- We are preparing a short manuscript to introduce the motivation, functions, and use-cases for the `treebase` package.  Meanwhile, a [preprint is available](https://github.com/ropensci/treeBASE/blob/master/inst/doc/treebase/treebase_github.md) as a dynamic document, where all of the examples shown are produced by the code shown using `knitr`. [See source code](https://github.com/ropensci/treeBASE/blob/master/inst/doc/treebase/treebase.Rmd).  
-
 
-- treebase is part of the [rOpenSci Project](http://ropensci.github.com)
+- treebase is part of the [rOpenSci Project](https://ropensci.org/)
 
 References
 ----------

vignettes/vignette.Rmd

@@ -12,7 +12,7 @@ vignette: >
 
 
 Here are a few introductory examples to illustrate some of the functionality of the package. Thanks in part to new data deposition requirements at journals such as Evolution, Am Nat, and Sys Bio, and
-data management plan requirements from NSF, I hope the package will become increasingly useful for teaching by replicating results and for meta-analyses that can be automatically updated as the repository grows. Additional information and bug-reports welcome via the [treebase page](http://github.com/ropensci/treebase/issues).
+data management plan requirements from NSF, I hope the package will become increasingly useful for teaching by replicating results and for meta-analyses that can be automatically updated as the repository grows. Additional information and bug-reports welcome via the [treebase page](https://github.com/ropensci/treebase/issues).
 
 Basic tree and metadata queries
 ==========
@@ -132,4 +132,4 @@ all <- search_treebase("Consensus", "type.tree", branch_lengths=TRUE)
 tt <- drop_errors(sapply(all, timetree))
 is_yule <- sapply(tt, pick_branching_model)
 table(is_yule)
-```
+```