Package: naryn 2.6.30

Aviezer Lifshitz

naryn: Native Access Medical Record Retriever for High Yield Analytics

A toolkit for medical records data analysis. The 'naryn' package implements an efficient data structure for storing medical records, and provides a set of functions for data extraction, manipulation and analysis.

Authors:Misha Hoichman [aut], Aviezer Lifshitz [aut, cre], Ben Gilat [aut], Netta Mendelson-Cohen [ctb], Rami Jaschek [ctb], Weizmann Institute of Science [cph]

naryn_2.6.30.tar.gz

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naryn.pdf |naryn.html✨
naryn/json (API)
NEWS

# Install 'naryn' in R:
install.packages('naryn', repos = c('https://tanaylab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/tanaylab/naryn/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

data-analysismedical-records

5.48 score 3 stars 4 scripts 199 downloads 115 exports 22 dependencies

Last updated 1 months agofrom:8141ff3939. Checks:OK: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-linux-x86_64OKOct 29 2024
R-4.4-mac-x86_64OKOct 29 2024
R-4.4-mac-aarch64OKOct 29 2024
R-4.3-mac-x86_64OKOct 29 2024
R-4.3-mac-aarch64OKOct 29 2024

Exports:.create_logical_track_filter.emr_expr_vars.emr_filter.emr_vtrack.get.naryn%>%daydaysemr_annotateemr_char2timeemr_coremr_date2timeemr_db.connectemr_db.initemr_db.init_examplesemr_db.lsemr_db.reloademr_db.subsetemr_db.subset.idsemr_db.subset.infoemr_db.unloademr_distemr_download_example_dataemr_entries.getemr_entries.get_allemr_entries.lsemr_entries.reloademr_entries.rmemr_entries.rm_allemr_entries.setemr_extractemr_filter.attr.expirationemr_filter.attr.keeprefemr_filter.attr.srcemr_filter.attr.time.shiftemr_filter.attr.valemr_filter.clearemr_filter.createemr_filter.create_from_nameemr_filter.existsemr_filter.infoemr_filter.lsemr_filter.nameemr_filter.rmemr_filters.infoemr_ids_coverageemr_ids_vals_coverageemr_monthly_iteratoremr_posix2timeemr_quantilesemr_screenemr_summaryemr_timeemr_time2charemr_time2dateemr_time2dayofmonthemr_time2houremr_time2monthemr_time2posixemr_time2yearemr_track.addtoemr_track.attr.exportemr_track.attr.getemr_track.attr.rmemr_track.attr.setemr_track.createemr_track.current_dbemr_track.dbsemr_track.existsemr_track.global.lsemr_track.idsemr_track.importemr_track.infoemr_track.logical.createemr_track.logical.existsemr_track.logical.infoemr_track.logical.lsemr_track.logical.rmemr_track.lsemr_track.mvemr_track.percentileemr_track.readonlyemr_track.rmemr_track.uniqueemr_track.user.lsemr_track.var.getemr_track.var.lsemr_track.var.rmemr_track.var.setemr_vtrack.attr.filteremr_vtrack.attr.funcemr_vtrack.attr.id.mapemr_vtrack.attr.keeprefemr_vtrack.attr.paramsemr_vtrack.attr.srcemr_vtrack.attr.time.shiftemr_vtrack.clearemr_vtrack.createemr_vtrack.create_from_nameemr_vtrack.existsemr_vtrack.infoemr_vtrack.lsemr_vtrack.nameemr_vtrack.rmemr_yearly_iteratorhourhoursmonthmonthsstring_to_varvar_to_stringweekweeksyearyears

Dependencies:clicpp11dplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithryaml

advanced naryn

Rendered fromadvanced.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2022-11-21
Started: 2022-10-03

Readme and manuals

Help Manual

Help pageTopics
Toolkit for medical records data analysisnaryn-package naryn
Annotates id-time points tableemr_annotate
Calculates correlation statistics for pairs of track expressionsemr_cor
Converts date and hour to internal time formatemr_date2time
Initializes connection with Naryn Databaseemr_db.connect emr_db.init emr_db.init_examples emr_db.ls
Reloads databaseemr_db.reload
Defines an ids subsetemr_db.subset
Returns the ids that constitute the current ids subsetemr_db.subset.ids
Returns information about the current subsetemr_db.subset.info
Unload all tracks from naryn databaseemr_db.unload
Calculates distribution of track expressionsemr_dist
Download example databaseemr_download_example_data
Get an entryemr_entries.get
Get all entriesemr_entries.get_all
List entriesemr_entries.ls
Reload entries from diskemr_entries.reload
Remove an entryemr_entries.rm
Remove all entriesemr_entries.rm_all
Set an entryemr_entries.set
Returns evaluated track expressionemr_extract
Get or set attributes of a named filteremr_filter.attr.expiration emr_filter.attr.keepref emr_filter.attr.src emr_filter.attr.time.shift emr_filter.attr.val
Clear all filters from the current environmentemr_filter.clear
Creates a new named filteremr_filter.create
Create a filter from an automatically generated nameemr_filter.create_from_name
Checks whether the named filter existsemr_filter.exists
Returns the definition of a named filteremr_filter.info
Returns a list of named filtersemr_filter.ls
Generate a default name for a naryn filteremr_filter.name
Deletes a named filteremr_filter.rm
Returns the filter definition of named filters given a filter expressionemr_filters.info
Returns ids coverage per trackemr_ids_coverage
Returns ids coverage per value trackemr_ids_vals_coverage
Create an iterator that goes every year/monthemr_monthly_iterator emr_yearly_iterator
Calculates quantiles of a track expressionemr_quantiles
Finds Id-Time points that match track expressionemr_screen
Calculates summary statistics of track expressionemr_summary
Convert time periods to internal time formatday days emr_time hour hours month months week weeks year years
Convert time to character formatemr_char2time emr_time2char
Convert from internal time to year, month, day, houremr_time2date
Converts time from internal format to a day of monthemr_time2dayofmonth
Converts time from internal format to an houremr_time2hour
Converts time from internal format to a monthemr_time2month
Convert EMR time to POSIXctemr_posix2time emr_time2posix
Converts time from internal format to a yearemr_time2year
Adds new records to a trackemr_track.addto
Returns attributes values of tracksemr_track.attr.export
Returns the value of the track attributeemr_track.attr.get
Deletes a track attributeemr_track.attr.rm
Assigns a value to the track attributeemr_track.attr.set
Creates a track from a track expressionemr_track.create
Returns a vector of db ids which have a version of the trackemr_track.current_db emr_track.dbs
Checks whether the track existsemr_track.exists
Returns track idsemr_track.ids
Imports a track from a file or data-frameemr_track.import
Returns information about the track.emr_track.info
Creates a logical trackemr_track.logical.create
Is a track logicalemr_track.logical.exists
Returns information about a logical trackemr_track.logical.info
Deletes a logical trackemr_track.logical.rm
Returns a list of track namesemr_track.global.ls emr_track.logical.ls emr_track.ls emr_track.user.ls
Moves (renames) a trackemr_track.mv
Returns track percentile of the valuesemr_track.percentile
Gets or sets "read-only" property of a trackemr_track.readonly
Deletes a trackemr_track.rm
Returns track valuesemr_track.unique
Returns value of a track variableemr_track.var.get
Returns a list of track variables for a trackemr_track.var.ls
Deletes a track variableemr_track.var.rm
Assigns value to a track variableemr_track.var.set
Get or set attributes of a virtual trackemr_vtrack.attr.filter emr_vtrack.attr.func emr_vtrack.attr.id.map emr_vtrack.attr.keepref emr_vtrack.attr.params emr_vtrack.attr.src emr_vtrack.attr.time.shift
Clear all virtual tracks from the current environmentemr_vtrack.clear
Creates a new virtual trackemr_vtrack.create
Create a virtual track from an automatically generated nameemr_vtrack.create_from_name
Checks whether the virtual track existsemr_vtrack.exists
Returns the definition of a virtual trackemr_vtrack.info
Returns a list of virtual track namesemr_vtrack.ls
Generate a default name for a virtual trackemr_vtrack.name
Deletes a virtual trackemr_vtrack.rm
Create a syntactically valid variable name from a stringstring_to_var
Decode a variable created by string_to_varvar_to_string