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naryn

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

Installation

install.packages("naryn")

Or for the latest development version:

remotes::install_github("tanaylab/naryn")

Usage

See the vignette for more details.

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Version

Install

install.packages('naryn')

Monthly Downloads

126

Version

2.6.30

License

MIT + file LICENSE

Maintainer

Aviezer Lifshitz

Last Published

September 27th, 2024

Functions in naryn (2.6.30)

emr_entries.get

emr_download_example_data

Download example database

emr_filter.create

Creates a new named filter

Unload all tracks from naryn database

emr_entries.reload

Reload entries from disk

Remove an entry

emr_entries.rm_all

Remove all entries

emr_filter.create_from_name

Create a filter from an automatically generated name

emr_db.subset.info

Returns information about the current subset

emr_filter.info

Returns the definition of a named filter

emr_filter.exists

Checks whether the named filter exists

emr_entries.get_all

Get all entries

emr_filter.clear

Clear all filters from the current environment

emr_filter.name

Generate a default name for a naryn filter

Finds Id-Time points that match track expression

emr_entries.set

Returns a list of named filters

emr_db.subset.ids

Returns the ids that constitute the current ids subset

emr_monthly_iterator

Create an iterator that goes every year/month

Convert time periods to internal time format

emr_ids_coverage

Returns ids coverage per track

emr_filter.attr.src

Get or set attributes of a named filter

emr_ids_vals_coverage

Returns ids coverage per value track

Returns evaluated track expression

Convert EMR time to POSIXct

Calculates summary statistics of track expression

Convert time to character format

emr_track.import

Imports a track from a file or data-frame

emr_track.unique

Returns track values

Returns track ids

Convert from internal time to year, month, day, hour

Deletes a named filter

emr_track.var.get

Returns value of a track variable

emr_filters.info

Returns the filter definition of named filters given a filter expression

emr_track.attr.set

Assigns a value to the track attribute

emr_track.logical.rm

Deletes a logical track

Converts time from internal format to a year

Returns a list of track names

emr_track.create

Creates a track from a track expression

emr_vtrack.info

Returns the definition of a virtual track

emr_time2dayofmonth

Converts time from internal format to a day of month

emr_track.attr.get

Returns the value of the track attribute

emr_track.attr.rm

Deletes a track attribute

Returns a list of virtual track names

emr_vtrack.create

Creates a new virtual track

Create a syntactically valid variable name from a string

emr_vtrack.clear

Clear all virtual tracks from the current environment

Decode a variable created by string_to_var

emr_track.logical.exists

Is a track logical

emr_vtrack.name

Generate a default name for a virtual track

Deletes a virtual track

emr_track.logical.info

Returns information about a logical track

emr_track.var.rm

Deletes a track variable

Calculates quantiles of a track expression

emr_track.var.ls

Returns a list of track variables for a track

emr_track.addto

Adds new records to a track

Toolkit for medical records data analysis

emr_track.readonly

Gets or sets "read-only" property of a track

emr_track.logical.create

Creates a logical track

emr_track.attr.export

Returns attributes values of tracks

Returns information about the track.

emr_vtrack.create_from_name

Create a virtual track from an automatically generated name

Deletes a track

Converts time from internal format to an hour

emr_vtrack.exists

Checks whether the virtual track exists

Converts time from internal format to a month

emr_track.exists

Checks whether the track exists

Returns a vector of db ids which have a version of the track

Moves (renames) a track

emr_track.percentile

Returns track percentile of the values

emr_track.var.set

Assigns value to a track variable

emr_vtrack.attr.src

Get or set attributes of a virtual track

.create_logical_track_filter

Create a filter for logical track

Initializes connection with Naryn Database

Get a vector of variables inside an expression

Reloads database

An environment for storing the package global variables

Calculates distribution of track expressions

.emr_vtrack.get

Get virtual track parameters given a string

Annotates id-time points table

Parse an R filter string

Converts date and hour to internal time format

Defines an ids subset

Calculates correlation statistics for pairs of track expressions