Rerender docs

sherrillmix · Jun 23, 2022 · 4595253 · 4595253
1 parent 8c752f1
commit 4595253
Show file tree

Hide file tree

Showing 22 changed files with 58 additions and 26 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -10,7 +10,7 @@ Authors@R: c(person("Scott", "Sherrill-Mix", role = c("aut", "cre"),
 BugReports: https://github.com/sherrillmix/taxonomizr/issues
 Description: Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment.
 Version: 0.9.2
-Date: 2022-06-22
+Date: 2022-06-23
 Suggests:
     testthat,
     knitr,

diff --git a/docs/articles/usage.html b/docs/articles/usage.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.3
 pkgdown_sha: ~
 articles:
   usage: usage.html
-last_built: 2022-06-22T15:26Z
+last_built: 2022-06-23T14:10Z
 
diff --git a/docs/reference/accessionToTaxa.html b/docs/reference/accessionToTaxa.html
diff --git a/docs/reference/getAccession2taxid.html b/docs/reference/getAccession2taxid.html
diff --git a/docs/reference/getNamesAndNodes.html b/docs/reference/getNamesAndNodes.html
diff --git a/docs/reference/read.accession2taxid.html b/docs/reference/read.accession2taxid.html
diff --git a/docs/reference/read.names.html b/docs/reference/read.names.html
diff --git a/docs/reference/read.names.sql.html b/docs/reference/read.names.sql.html
diff --git a/docs/reference/read.nodes.html b/docs/reference/read.nodes.html
diff --git a/docs/reference/read.nodes.sql.html b/docs/reference/read.nodes.sql.html
diff --git a/docs/reference/streamingRead.html b/docs/reference/streamingRead.html
diff --git a/man/accessionToTaxa.Rd b/man/accessionToTaxa.Rd
diff --git a/man/getAccession2taxid.Rd b/man/getAccession2taxid.Rd
diff --git a/man/getNamesAndNodes.Rd b/man/getNamesAndNodes.Rd
diff --git a/man/read.accession2taxid.Rd b/man/read.accession2taxid.Rd
diff --git a/man/read.names.Rd b/man/read.names.Rd
diff --git a/man/read.names.sql.Rd b/man/read.names.sql.Rd
diff --git a/man/read.nodes.Rd b/man/read.nodes.Rd
diff --git a/man/read.nodes.sql.Rd b/man/read.nodes.sql.Rd
diff --git a/vignettes/usage.Rmd b/vignettes/usage.Rmd
@@ -463,6 +463,12 @@ Note that taxa may be the most specific taxon for a given taxa in the taxonomy m
 
 
 ## Changelog
+### v0.9.2
+  * Allow factors as input to accessionToTaxa
+  * Document sqlite pragmas for `read.accession2taxid`
+  * Inherit ... argument documentation for `prepareDatabase`
+  * Catch input/output error while processing large files
+  * Update various user-facing links from ftp to https for easier access
 
 ### v0.8.4
   * Add quote option to `makeNewick`
@@ -511,7 +517,7 @@ In order to avoid constant internet access and slow APIs, the first step in usin
 **Note:** It is not necessary to manually check for the presence of these files since the functions automatically check to see if their output is present and if so skip downloading/processing. Delete the local files if you would like to redownload or reprocess them.
 
 ### Download names and nodes
-First, download the necessary names and nodes files from [NCBI](ftp://ftp.ncbi.nih.gov/pub/taxonomy/):
+First, download the necessary names and nodes files from [NCBI](https://ftp.ncbi.nih.gov/pub/taxonomy/):
 ```{r,eval=FALSE}
 getNamesAndNodes()
 ```
@@ -522,7 +528,7 @@ getNamesAndNodes()
 
 ### Download accession to taxa files
 
-Then download accession to taxa id conversion files from [NCBI](ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/). **Note:** this is a pretty _big_ download (several gigabytes):
+Then download accession to taxa id conversion files from [NCBI](https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/). **Note:** this is a pretty _big_ download (several gigabytes):
 ```{r,eval=FALSE}
 #this is a big download
 getAccession2taxid()