Removed non-API calls to Rf_GetOption in the C++
code.
naryn 2.6.30
Removed non-API calls to R in the C++ code.
naryn 2.6.29
Fixed noRemap additional issue by adding Rf_
prefix in the c++ code.
naryn 2.6.28
Fix: emr_track.mv did not move track attributes.
“exists” virtual track function without parameters now checks for
existence of any value.
naryn 2.6.27
Fix: do not truncate expression names in emr_extract
when tidy=TRUE.
naryn 2.6.26
Fixed compilation warnings on M1 Mac.
Added emr_time2posix, emr_posix2time,
emr_time2char and emr_char2time
functions.
naryn 2.6.25
Fixed clang warnings.
Fix: filter name to include operator when name is automatically
generated
naryn 2.6.24
Allow filters names with a dot when creating an automatic virtual
track name.
Fixed an error when multiple processes are calling
emr_track.var.set on the same track.
naryn 2.6.23
Fixed memory misalignment errors.
naryn 2.6.22
Added emr_filters.info that returns filters information
given a filter expression (e.g. f1 | f2).
Bug fix: vtrack on logical track to categorical track with no
parameters returned an wrong results.
Fixed clang-UBSAN error when creating an empty track.
Added “modification_time” to emr_track.info.
naryn 2.6.21
Removed C++11 specification from Makevars.
naryn 2.6.20
fixed some CRAN warnings.
naryn 2.6.19
fix: emr_vtrack.create with func="exists"
returned NA instead of 0 when the track didn’t have any value at the
iterator interval.
naryn 2.6.18
Fix: deal with complex filters in emr_vtrack.name and
emr_vtrack.create_from_name.
naryn 2.6.17
New functions: emr_vtrack.name and
emr_vtrack.create_from_name allow creating virtual tracks
with standard names.
naryn 2.6.16
Added some examples to the documentation.
Fix: crash when calling emr_track.create with
expr=''
naryn 2.6.15
Added entries - a key/value store for storing simple strings and
numbers in a naryn database. See
emr_entries.ls, emr_entries.get,
emr_entries.set, emr_entries.rm and
emr_entries.reload.
Added string_to_var and var_to_string
functions to generate valid variable names from strings.
emr_track.rm can now accept multiple tracks as
input.
Do not allow importing patients that do not appear at
patients.dob.
Fixed issue #83
Fix: emr_track.rm returned an error when given
character(0).
naryn 2.6.14
Added include in order to compile with gcc13
naryn 2.6.13
Fixed c++ clang-UBSAN and gcc-UBSAN errors.
Fixed rchk warnings.
naryn 2.6.12
Fixed: hang when all iterator intervals were outside of
stime and etime.
naryn 2.6.11
Fixed an additional clang warning.
naryn 2.6.10
removed emr_traceback function
Fixed C++ compilation warnings and possible memory leaks.
naryn 2.6.9
Removed global variables from the package - EMR_ROOTS, EMR_GROOT,
EMR_UROOT, EMR_FILTERS and EMR_VTRACKS are now a part of a dedicated
environment called .naryn. You can access them using
.naryn::EMR_ROOTS etc.
naryn 2.6.8
Optimized the performance of the emr_track.exists
function.
naryn 2.6.7
Check that attributes are in ASCII format.
naryn 2.6.6
Allow duplicated tracks when running emr_track.attr.set
in batch mode.
naryn 2.6.5
Added batch mode for emr_track.attr.set and
emr_track.attr.rm.
Added include_missing parameter
emr_track.attr.export allowing missing tracks and
attributes.
naryn 2.6.4
Added support for filters which are based on virtual tracks.
naryn 2.6.3
Added support for operator based filtering, see ‘operator’ argument
in emr_filter.create
Added support for track attributes to logical tracks.
Bug fix: dbs order was changed to lexicographical order on
emr_db.connect.
Bug fix: stray logical tracks on non-global dbs were shown.
Bug fix: emr_time functions failed when there was an
NA in an integer vector.
Bug fix: emr_track.attr.get returned attribute name
instead of value.
emr_track.var.get now returns NULL when
variable doesn’t exist.
Make sure logical tracks cannot be created on non-global db.
Added db_id parameter to emr_track.ls
Removed cpp11 package dependency
naryn 2.6.2
Added support for multiple databases.
New functions: emr_filter.name and
emr_filter.create_from_name allow creating filters with
standard names.
Bug fix: allow calling emr_track.logical.create when
values are a list of length 1.
Bug fix: wrong results when creating virtual track where the source
is a logical track without parameters.
naryn 2.6.1
Added support for logical tracks.
emr_filter.create and emr_vtrack.create
now return silently the name of the filter/vtrack.
Allow addition of entries with the same id/time/values to
emr_track.addto.
emr_dist and emr_cor now have a
dataframe parameter that returns the results in a tidy
format.
Bug fix: wrong results in emr_dist when
right=FALSE and values were a fraction.
Added convenience time functions (emr_time, year, months etc).
Support periodic iterators: emr_monthly_iterator,
emr_yearly_iterator
Use the devtools ecosystem: roxygen
documentation and testthat for tests.
Added a NEWS.md file to track changes to the
package.
naryn 2.6.0
New concept: track attributes
New functions: emr_track.attr.get, emr_track.attr.set,
emr_track.attr.rm, emr_track.attr.export.
Support filtering by track attributes in: emr_track.ls,
emr_track.global.ls, emr_track.user.ls.
naryn 2.5.10
Fixed an occasional crash in functions receiving a track
expression.
Redirect all messages and progress to stderr instead of stdout.
naryn 2.5.9
Fixed a resource leak effecting nearly all functions but manifesting
mainly in emr_ids_coverage and emr_ids_vals_coverage by “protection
stack overflow” error.
naryn 2.5.8
Bug fix in emr_track.mv: track variables are not moved.
naryn 2.5.7
Bug fix in emr_track.mv: error when moving a file between different
file systems.
naryn 2.5.6
New function: emr_track.mv
naryn 2.5.5
Bug fix: occasional memory corruption in track expressions using OR
operator in the filter.
naryn 2.5.4
Bug fix: occasional crash in emr_track.rm.
Bug fix: Ctrl+C doesn’t stop emr_track.import.
naryn 2.5.3
Bug fix: sub-second creation/deletion/modification of tracks in
concurrent sessions might corrupt the database.
naryn 2.5.2
emr_track.import, emr_track.addto: run-time and memory consumption
improvements.
naryn 2.5.1
Allow creation of empty tracks.
naryn 2.5.0
Support concurrent sessions adding / deleting / modifying tracks. As
long as the tracks files are not manipulated outside of naryn, sessions
should always resync the changes at the beginning of a new transaction
and hence access up-to-date version of tracks and up-to-date list of
existing tracks. Manipulating track files outside of naryn requires
emr_db.reload.
emr_db.init: split load.on.demand parameter to
global.load.on.demand and user.load.on.demand.
emr_db.init: new ‘do.reload’ parameter.
Run-time improvement in emr_db.init when
load.on.demand==FALSE: previously - rebuild list of tracks. Currently -
read track list from ‘.tracks’.
Major run-time and memory consumption improvement in
emr_db.reload: previously - rebuild list of tracks and
reload all tracks into memory. Currently - rebuild list of tracks
and reload outdated tracks (if load.on.demand==FALSE) or kick
them out of memory (if load.on.demand==TRUE).
emr_db.reload: while rebuilding the list DB gets
locked, concurrent transactions will need to wait till the task
completes.
Currently - each transaction starts with fetching a track list from
‘.tracks’, if ‘.tracks’ had been modified between the transactions.
Outdated tracks are unloaded from the memory (if load.on.demand==TRUE)
or reloaded (if load.on.demand==FALSE).
Previously - new transaction continues using old track list and outdated
tracks up until emr_db.reload is called.
Bug fix: ‘.ids’ file is reloaded in each transaction even if the
updated version of it is already in the memory.
emr_time2hour, emr_time2dayofmonth, emr_time2month, emr_time2year,
emr_date2time do not require anymore to open a database.
naryn 2.4.4
Removed MINID/MAXID constants from global environment.
IDs for Beat iterator and Time Interval take their ids from ‘dob’
track.
Bug fix in emr_track.import, emr_track.addto: crash when source data
frame has ‘ref’ but no ‘value’ column.
Bug fix in Time Intervals iterator: in some cases ids outside of
subset might be produced.
DB cache file format has changed. The file is now called ‘.tracks’.
The first call to emr_db.init will recreate this file after a full DB
reload.
naryn 2.4.3
Removed MINTIME/MAXTIME constants from global environment.
All functions receiving stime/etime parameters and an iterator:
defaults can no longer be used for stime/etime when the iterator type is
Ids, Beat or Extended Beat.
DB cache file format has changed, the first call to emr_db.init will
recreate this file after a full DB reload.
naryn 2.4.2
Bug fix in emr_track.info: returned path is NULL.
naryn 2.4.1
More robust handling of .naryn-cache file when several users
simultaneously add / delete tracks. Might resolve various glitches when
emr_db.reload() is needed.
naryn 2.4.0
emr_vtrack.create / emr_vtrack.attr.src: allow ‘src’ to be a data
frame. Syntax: src=list(data.frame, T/F), where T/F indicates whether
the data is treated as categorical (otherwise: quantitative).
Bug fix in emr_filter.attr.src: error when ‘src’ is a data
frame
naryn 2.3.12
Bug fix: various functions may suddenly return an empty data
frame
naryn 2.3.11
Bug fix: crash if the period of beat / extended beat iterator is set
to 0
naryn 2.3.10
Bug fix: crash in certain scenarios while using ‘filter’ parameter.
For example: filter=“(track1 & track2) & (track3 &
track4)”
naryn 2.3.9
Bug fix in emr_filter.attr.src: error if ‘src’ is ID-Time table
naryn 2.3.8
Bug fix in emr_filter.create: named filters become inconsistent if
src of the existing filter is changed from global track to user track or
vice versa
Bug fix in emr_vtrack.create: virtual tracks become inconsistent if
src of the existing filter is changed from global track to user track or
vice versa
Bug fix in emr_filter.ls: if filters exist with src based on user
space tracks, only these filters are returned
Bug fix in emr_vtrack.ls: if virtual tracks exist with src based on
user space tracks, only these virtual tracks are returned
Run time optimizations in emr_filter.create and
emr_vtrack.create
naryn 2.3.7
Bug fix in emr_db.subset: error if src==NULL
Bug fix in virtual track, func=“stddev”: crash when stddev is
computed over a single value
naryn 2.3.6
Bug fix in emr_track.percentile: lower bound is returned even if
lower=FALSE
naryn 2.3.5
Bug fix: MINTIME/MAXTIME may be wrongly set. As a result performance
might be compromised and invalid results might be produced when defaults
are used for stime,etime. Please call emr_db.reload() to set the correct
values!
naryn 2.3.4
Replaced “categorial” with “categorical” in all the parameters and
documentation
naryn 2.3.3
Bug fix: “child process ended unexpectedly” errors, crashes and hang
ups whilst multitasking when running out of memory
naryn 2.3.2
New iterator type: “Id-Time” Intervals (dataframe with ‘id’,
‘stime’, ‘etime’ columns)
New filter type: “Id-Time” Intervals
naryn 2.3.1
Set/retrieve a single attribute of a virtual track via:
emr_vtrack.attr.src, emr_vtrack.attr.func, emr_vtrack.attr.params,
emr_vtrack.attr.keepref, emr_vtrack.attr.time.shift,
emr_vtrack.attr.id.map, emr_vtrack.attr.filter
Set/retrieve a single attribute of a named filter via:
emr_filter.attr.src, emr_filter.attr.keepref,
emr_filter.attr.time.shift, emr_filter.attr.val,
emr_filter.attr.expiration
naryn 2.3.0
Filters can be applied now to the virtual tracks
emr_vtrack.create: new ‘filter’ parameter
naryn 2.2.11
emr_vtrack.create: new “sample.time” function
naryn 2.2.10
Switched from custom random seed control (options(grnd.seed=…)) to
R’s standard (set.seed)
emr_db.subset: ‘seed’ parameter removed
New function: emr_db.subset.info
naryn 2.2.9
Issue a warning if beat / extended beat iterator is used without a
filter and it produces more than options(emr_warning.itr.no.filter.size
= …) points (default: 100000). To suppress this type of warning use
options(emr_warning.itr.no.filter.size = -1)
naryn 2.2.8
emr_dist, emr_cor: new “right” parameter (similar to “cut”
function)
naryn 2.2.7
emr_vtrack.create: new “sample” function
naryn 2.2.6
Bug in multitasking: buffer overflow and possible memory corruption
when the child process generates an error
naryn 2.2.5
emr_vtrack.create: time.shift column can now be used within ‘id.map’
data frame uniquely remapping times and not only ids
naryn 2.2.4
Multitasking stability issues
naryn 2.2.3
Bug fix in emr_screen: in multitasking mode returns wrong
results
Bug fix: multitasking + debug mode might lead to hanging
naryn 2.2.2
Bug fix in track expression evaluation engine: virtual track with
func=“size” returns NaN instead of 0 when no values fall into the
iterator interval
naryn 2.2.1
New function: emr_annotate
naryn 2.2.0
New functions: emr_track.var.get, emr_track.var.set,
emr_track.var.rm, emr_track.var.ls
emr_track.import, emr_track.create: introduce restrictions for track
naming
naryn 2.1.11
Bug fix in track expression evaluation engine: if two or more
virtual tracks differ only by values (supplied in params) and are used
in one track expression, the value of the first one is used for the
rest
naryn 2.1.10
Bug fix: in certain circumstances an error “Database was not loaded.
Please call emr_db.init.” is printed
naryn 2.1.9
Bug fix in emr_filter.create: warning is issued when ID-Time table
is used as source
Bug fix in emr_ids_coverage: when src is an ID-Time table and the
filter is used “..emr_tmp_filter does not exist (9)” error is
generated
Bug fix in emr_ids_vals_coverage: when src is an ID-Time table
“..emr_tmp_filter does not exist (9)” error is generated
naryn 2.1.8
New function: emr_track.percentile
emr_summary: renamed two members of the result member from “Total
intervals”/“NaN intervals” to “Total values”/“NaN values”
naryn 2.1.7
New functions: emr_track.exists, emr_vtrack.exists,
emr_filter.exists
emr_ids_coverage - new additional parameters: stime, etime,
filter
emr_ids_vals_coverage - run-time optimizations
naryn 2.1.5
emr_filter.create: support vector of values for “val” parameter
naryn 2.1.4
Redesigned emr_track.import function - supports data frame, does not
allow anymore to add records to the existing track
New function: emr_track.addto
New “space” argument to emr_track.create function
naryn 2.1.3
New filter on values for all virtual track functions applied to
categorical tracks. The filter is given via “param” in
emr_vtrack.create
Bug fix: virtual track function “exists” might not work on
non-integer values where double(val) != float(val)
naryn 2.1.2
Bug fix: various functions might hang when emr_debug and
emr_multitasking options are both TRUE
naryn 2.1.1
New virtual track functions for simple linear regression model:
lm.slope, lm.intercept
naryn 2.1.0
Bug fix: occasional defunc processes AND/OR hanging in multitasking
mode
naryn 2.0.6
Mild run-time optimizations due to switching to C++11
naryn 2.0.5
Bug fix: MAXTIME and MAXID might be incorrectly set which might have
grave effect on iterators, multitasking, etc. Please call
emr_db.reload() on all your trackdbs
New option: emr_debug=T/F
naryn 2.0.4
Bug fix in multitasking mode: child process does not die after
generating an error
naryn 2.0.3
Run-time optimization in a filter when NOT is applied to a list of
time intervals
naryn 2.0.2
Run-time optimization in a filter when NOT is applied to a list of
ids
naryn 2.0.1
emr_db.init: new “load.on.demand” parameter
emr_db.init: very fast run-time when “load.on.demand” parameter is
used
naryn 2.0.0
Multitasking for all functions that use track expression evaluation
engine
emr_extract and emr_screen: new “sort” parameter
New R options controlling multitasking behavior: emr_multitasking,
emr_min.processes, emr_max.processes
Run-time optimizations in track expression evaluation engine in
single-task mode
Bug-fix: wrong iteration on dense tracks when subsets are used
naryn 1.4.7
Bug-fix: in certain cases incorrect results when NOT is used in the
filter
Run-time optimization when NOT is used in the filter
naryn 1.4.6
emr_extract: receive track expressions as a vector
emr_extract: new “tidy” parameter
emr_extract: “colnames” parameter renamed to “names”
Run-time optimizations
naryn 1.4.5
Run-time optimization on long filters
Run-time optimization when NOT operator is used in a filter
naryn 1.4.4
Bug fix in filters: incorrect result when OR and NOT are used
together
naryn 1.4.3
Bug fix in filters: expiration and val produce incorrect results
when used together
Bug fix in emr_db.init: occasional crash due to too many files
open
naryn 1.4.2
New functions: emr_ids_coverage and emr_ids_vals_coverage
Bug fix: MINTIME, MAXTIME, MINID, MAXID constants are not updated
after emr_track.create, emr_track.import and emr_track.rm are
called
naryn 1.4.1
New function: emr_cor. Returns correlation statistics for each pair
of a track expression vector
naryn 1.4.0
New concept: subsets. Use subsets to define train / test sets.
Please refer user manual for further details
New functions: emr_db.subset, emr_db.subset.ids
New option: emr_rnd.seed. Currently used by emr_quantiles
naryn 1.3.3
New global EMR_TIME variable that stores the times of the current
iterator
Return an empty data frame instead of NULL in emr_extract and
emr_screen when result set is empty
Added user manual (still incomplete but covers already tracks,
virtual tracks, track expressions and iterators).
naryn 1.3.2
Run-time optimizations
naryn 1.3.1
New iterator type: beat iterator aligned to the time that appears
in a data frame or a track (aka birthday). Syntax:
iterator=list(period, data.frame(id=…, time=…))
iterator=list(period, trackname)
Note: each id must appear only once in the data frame /
track.
naryn 1.3.0
New concept: global tracks and user tracks. emr_track.import creates
tracks in global tracks directory, emr_track.create does it in user
tracks directory.
New functions: emr_track.create, emr_track.rm, emr_track.global.ls,
emr_track.user.ls
emr_db.init: new user.dir parameter
emr_db.init: renamed root parameter to global.dir
emr_track.info: added file path to the output.
emr_track.import: removed reload_db parameter. Imported track will
automatically be efficiently reloaded.
naryn 1.2.1
emr_filter.create: new “val” parameter (slicing)
emr_filter.create: new “expiration” parameter. Please refer
reference manual for usage.
Run-time optimizations
naryn 1.2.0
New concept: named filters. No more parameters (time shift, keepref)
are allowed in track expression filters. Please use named filters
instead.
New functions: emr_filter.create, emr_filter.rm, emr_filter.ls,
emr_filter.info
New virtual track functions: earliest.time, latest.time,
closest.earlier.time, closest.later.time
emr_time2…: return NaN if the time is NaN
emr_time2…: return numeric instead of integer
4+5 = ability to use emr_time2… in track expressions
Bug fix in emr_track.import: do not allow creation of a track if
identically named virtual track already exists
naryn 1.1.8
emr_vtrack.create: new id.map parameter
emr_vtrack.create: renamed time_shift parameter to time.shift
naryn 1.1.7
emr_dist: allow implicit breaks (use breaks=NULL) if the track
expression constitutes of a categorical track or a virtual track that is
based on a categorical track
naryn 1.1.6
Run-time optimizations when track expression equals to a track or a
virtual track
naryn 1.1.5
New logical parameter in emr_track.import: “categorical”
Track format had been changed
New function: emr_track.unique - returns sorted unique values of a
track. Hint: use this functions to set breaks when categorical track is
used
emr_vtrack.create: “val” parameter had been removed
emr_vtrack.create: new functions “value”, “size”, “frequent”,
“exists”
emr_vtrack.create: functions “earliest”, “latest” and “closest”
return -1 in case of ambiguity for categorical tracks
Interpret data frame with id, time columns as patient-time even if
ref column is missing
Bug fix: emr_db.init continues failing after it failed once (for
example: due to invalid track format)
naryn 1.1.4
New functions: emr_track.info, emr_summary
Enable patient ids to be used as iterators
Enable patient ids to be used in filters
Patient ids format for 2 & 3: data frame with the first column
named “id”
Enable time intervals to be used as iterators
Enable time intervals to be used in filters
Time intervals format for 5 & 6: data frame with the first
columns named “stime” and “etime”
Run-time optimization when OR is used in iterator filter
Report error id-time list used for iterator / filter contains two
records that differ only by reference when keepref == FALSE
Bug fix in filter when time after shift precedes the epoch
Bug fix in beat iterator: invalid progress report
naryn 1.1.3
Enable beat iterator (iterator=integer) produce references if
keepref=T
Support filters when beat iterator is used
1+2 means that one can now run complex iterators. For example
iterator=track1 | track2, keepref = R can be simulated with help of a
beat iterator and a filter as: iterator=1, keepref=R, filter=“track1(R)
| track2(R)”
Support filters when patient-time list is used as an iterator
Enable patient-time lists to be used in the filter. The syntax is
identical to tracks, e.g.: filter=“mylist1(F, c(10,20)) | track &
!mylist2”
Prefetch track files into shared memory: initial emr_db.init is
expected to be slower, however subsequent access to the tracks is
faster
naryn 1.1.2
Use shared memory to store tracks in RAM
naryn 1.1.1
Added regression tests
Bug fix in emr_date2time: crash if year is out of range
Bug fix in emr_vtrack.create: functions percentile.upper.min,
percentile.lower.min, percentile.upper.max, percentile.lower.max
generate an error
Bug fix: track format changes depending on the OS.
naryn 1.0.5
New function: emr_dist
naryn 1.0.4
Increase the maximal number of simultaneously used virtual tracks to
10K
naryn 1.0.3
Add “val” parameter to emr_vtrack.create
naryn 1.0.2
Allow addition of data into the existing tracks emr_track.import
(use “add” parameter)
naryn 1.0.1
New functions: emr_quantiles, emr_track.import
Support new functions in virtual tracks: percentile.upper,
percentile.lower, percentile.max.upper, percentile.max.lower,
percentile.min.upper, percentile.min.lower
Track format changed, old track format is not supported anymore