A wrapper around Renjin to provide a convenient way to load the contents of file saved in R's RData format in Clojure.
One might want to do this because they have found an interesting dataset that has been published in this format.
We have not yet released to clojars, so the recommended installation is with deps.edn:
For deps.edn users:
appliedsciencestudio/rdata {:git/url "https://github.com/appliedsciencestudio/rdata/"
:sha "151e6dead06b38995f1f30b09d954a060f7a2a9c"}Because of a deps.edn issue with transitive dependencies which
depend on non-standard repositories, you must have the key/value pair
"bedatadriven" {:url "https://nexus.bedatadriven.com/content/groups/public/" in the
:mvn/repos of your deps.edn file. For instance:
:mvn/repos {"central" {:url "https://repo1.maven.org/maven2/"}
"clojars" {:url "https://clojars.org/repo"}
"bedatadriven" {:url "https://nexus.bedatadriven.com/content/groups/public/"}}Run the tests:
clj -A:test:runner
You can also build a deployable jar of this library:
$ clojure -A:jar
then install it locally:
$ clojure -A:install
This library exports a single useful function, read-rdata, which --
somewhat predictably -- reads a file saved in the RData format used by
R.
The file contents are returned as nested maps (RData files can contain
arbitrarily nested data). The top-most level of the returned structure
is a key/value mapping from name to dataset, while the leaf nodes will
always be vectors of some primitive type (int, double, inst,
and so on).
The R attributes stored with each value are attached to the Clojure
translation of that value as Clojure metadata.
(def mers
(read-rdata "test/data/mers_korea_2015.RData" {:key-fn keyword}))
(keys mers)
;;=> (:mers_korea_2015)
(-> mers :mers_korea_2015 keys)
;;=> (:linelist :contacts)
(-> mers :mers_korea_2015 :linelist keys)
;;=> (:id :age :age_class :sex :place_infect :reporting_ctry :loc_hosp :dt_onset :dt_report :week_report :dt_start_exp :dt_end_exp :dt_diag :outcome :dt_death)
(-> mers :mers_korea_2015 :linelist :place_infect)
[1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2]
;; hm, place 1 or place 2? Maybe the metadata can tell us what this means...
(-> mers :mers_korea_2015 :linelist :place_infect meta)
;;=> {:class ["factor"], :levels ["Middle East" "Outside Middle East"]}
;; Ah, it's a two value factor (note that R values start from 1, so one
;; must decrement the factor's index to look it up in the vector held in
;; the meta.Copyright © 2020 Applied Science
Distributed under the MIT License.
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