Fix broken links in vignettes

vignettes/1_rodents.Rmd

@@ -78,4 +78,4 @@ restez_disconnect()
 
 ## Next up
 
-**[How to search for and fetch sequences](https://ropensci.github.io/restez/articles/2_search_and_fetch.html)**
+**[How to search for and fetch sequences](https://docs.ropensci.org/restez/articles/2_search_and_fetch.html)**

vignettes/2_search_and_fetch.Rmd

@@ -8,7 +8,7 @@ output: rmarkdown::html_vignette
 
 A downside of the `restez` approach is we are unable to then search the local database for sequences of interest as the database cannot possibly contain sufficient metadata (most notably taxonomic information) to perform as rich a search as online via NCBI. As a result we must perform the sequence discovery process independently from `restez`. In this tutorial we will demonstrate how to perform online searches using the `rentrez` package and then use the search results to look up sequences in a `restez` database.
 
-To run all the code in this tutorial you will need to have already set up the rodents database, see [Build a database of all rodents](https://ropensci.github.io/restez/articles/1_rodents.html).
+To run all the code in this tutorial you will need to have already set up the rodents database, see [Build a database of all rodents](https://docs.ropensci.org/restez/articles/1_rodents.html).
 
 ## Search NCBI
 
@@ -117,4 +117,4 @@ smmry <- rentrez::entrez_summary(db = 'nucleotide', id = 'NC_027278')
 -->
 ## Next up
 
-**[Advanced parsing of a GenBank record](https://ropensci.github.io/restez/articles/3_parsing.html)**
+**[Advanced parsing of a GenBank record](https://docs.ropensci.org/restez/articles/3_parsing.html)**

vignettes/3_parsing.Rmd

@@ -223,4 +223,4 @@ restez_disconnect()
 
 ## Next up
 
-**[Running phylotaR with restez](https://ropensci.github.io/restez/articles/4_phylotar.html)**
+**[Running phylotaR with restez](https://docs.ropensci.org/restez/articles/4_phylotar.html)**

vignettes/4_phylotar.Rmd

@@ -18,7 +18,7 @@ devtools::install_github(repo = 'ropensci/phylotaR')
 ```
 
 ## Setup
-Since we will be running the `phylotaR` pipeline for Dipodinae, we can use the rodents database we created [before](https://ropensci.github.io/restez/articles/1_rodents.html). We do not need to set-up the `phylotaR` pipeline any differently with a `restez` database, except to ensure we have set the `restez` path to the rodent database. (Connections to the `restez` database will be made automatically, `restez_connect` or `restez_disconnect` do not need to be run.)
+Since we will be running the `phylotaR` pipeline for Dipodinae, we can use the rodents database we created [before](https://docs.ropensci.org/restez/articles/1_rodents.html). We do not need to set-up the `phylotaR` pipeline any differently with a `restez` database, except to ensure we have set the `restez` path to the rodent database. (Connections to the `restez` database will be made automatically, `restez_connect` or `restez_disconnect` do not need to be run.)
 
 ```r
 library(phylotaR)
@@ -78,4 +78,4 @@ Compared to running without a `restez` database, phylotaR download can run [**2x
 
 ## Next up
 
-**[Tips and tricks](https://ropensci.github.io/restez/articles/5_tips_and_tricks.html)**
+**[Tips and tricks](https://docs.ropensci.org/restez/articles/5_tips_and_tricks.html)**

vignettes/restez.Rmd

@@ -98,7 +98,7 @@ restez_disconnect()
 
 # 2. Query
 
-Once a restez database has been set up we can query the database using the `gb_*_get()` functions. These functions allow us to retrieve specific columns in the SQL-like database: 'sequence', 'definition', 'accession', 'version' and 'organism'. Also, they allow us to get the whole text formatted record and sequence data in fasta format. In this example, we can use `list_db_ids()` to identify accession numbers in the database. We could also use `entrez_search()` provided the database contains sequences of interest to us, see ['search and fetch'](https://ropensci.github.io/restez/articles/2_search_and_fetch.html).
+Once a restez database has been set up we can query the database using the `gb_*_get()` functions. These functions allow us to retrieve specific columns in the SQL-like database: 'sequence', 'definition', 'accession', 'version' and 'organism'. Also, they allow us to get the whole text formatted record and sequence data in fasta format. In this example, we can use `list_db_ids()` to identify accession numbers in the database. We could also use `entrez_search()` provided the database contains sequences of interest to us, see ['search and fetch'](https://docs.ropensci.org/restez/articles/2_search_and_fetch.html).
 
 > Always remember to disconnect after you have finished your querying!
 
@@ -127,7 +127,7 @@ cat(gb_fasta_get(id = c(id, 'notanid')))
 restez_disconnect()
 ```
 
-Additionally, for more flexibility and options for extracting sequence record information see [GenBank record parsing](https://ropensci.github.io/restez/articles/3_parsing.html).
+Additionally, for more flexibility and options for extracting sequence record information see [GenBank record parsing](https://docs.ropensci.org/restez/articles/3_parsing.html).
 
 # 3. Entrez
 
@@ -156,8 +156,8 @@ restez_disconnect()
 
 For more information about `restez` see the other tutorials:
 
-1. [Build a database of all rodents](https://ropensci.github.io/restez/articles/1_rodents.html)
-2. [How to search for and fetch sequences](https://ropensci.github.io/restez/articles/2_search_and_fetch.html)
-3. [Advanced parsing of a GenBank record](https://ropensci.github.io/restez/articles/3_parsing.html)
-4. [Running phylotaR with restez](https://ropensci.github.io/restez/articles/4_phylotar.html)
-5. [Tips and tricks](https://ropensci.github.io/restez/articles/5_tips_and_tricks.html)
+1. [Build a database of all rodents](https://docs.ropensci.org/restez/articles/1_rodents.html)
+2. [How to search for and fetch sequences](https://docs.ropensci.org/restez/articles/2_search_and_fetch.html)
+3. [Advanced parsing of a GenBank record](https://docs.ropensci.org/restez/articles/3_parsing.html)
+4. [Running phylotaR with restez](https://docs.ropensci.org/restez/articles/4_phylotar.html)
+5. [Tips and tricks](https://docs.ropensci.org/restez/articles/5_tips_and_tricks.html)