knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
Unfortunately, the BacDive Web Service does not allow SQL-like queries for the content of specific fields within the strain's datasets. If you find the functionality explained in BacDive-ing in too limited, please try the following, semi-automatic approach to using BacDiveR.
Copy the URL of the results page from your browser's address bar. Alternatively, copy it from the "Download list of BacDive Ids" link to the top right of the "hits" list.
Paste the copied URL into a call to the data <- bd_retrieve_by_search("…")
function.
Enjoy the list of downloaded datasets, just as you would after using
data <- bd_retrieve_data(searchTerm = ..., searchType = ...)
.
bd_retrieve_data(searchTerm = …, searchType = "taxon")
can be used to download all
datasets for the genus or a specific species given in …
. Broader searches are
possible through the advanced search, for example for all Archaea:
Archaea_data <- bd_retrieve_by_search("https://bacdive.dsmz.de/advsearch?advsearch=search&site=advsearch&searchparams%5B70%5D%5Bcontenttype%5D=text&searchparams%5B70%5D%5Btypecontent%5D=contains&searchparams%5B70%5D%5Bsearchterm%5D=archaea")
Please note the messages about estimated download times for such large downloads.
This is not a BacDiveR feature, but base
R's saveRDS()
is particularly useful
for offline-storage of lots of search results, because re-downloading them would
take rather long. Continuing the Archaea example, the following code writes the
dataset to a file, loads it again, and verifies the data integrity:
saveRDS(Archaea_data, "Archaea.rds", version = 3) Archaea_data_stored <- readRDS("Archaea.rds") identical(Archaea_data, Archaea_data_stored)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.