Main Package of the EMU Speech Database Management System

Provides the next iteration of the EMU Speech Database Management System (EMU-SDMS) with database management, data extraction, data preparation and data visualization facilities.


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The emuR package provides the next iteration of the EMU Speech Database Management System (EMU-SDMS) with database management, data extraction, data preparation and data visualization facilities. It also contains a server that is intended to host databases in the emuDB format (see vignette('emuDB_intro')) to the EMU-webApp (http://ips-lmu.github.io/EMU-webApp/). The querying of annotations is performed using EMU's own EQL2 (EMU Query Language Version 2).

This package is part of the next iteration of the EMU Speech Database Management System which aims to be as close to an all-in-one solution for generating, manipulating, querying, analyzing and managing speech databases as possible. For an overview of the system please see http://ips-lmu.github.io/EMU.html and/or https://www.sciencedirect.com/science/article/pii/S0885230816302601 .

Installation

install.packages("emuR")

As this also installs all of the dependencies (incl. the wrassp package) this is the only installation step necessary to install the EMU-SDMS on your system. The only other requirement of the EMU-SDMS is a modern web browser (Chrome (recommended!) / Firefox / ...) which most people should already have on their systems.

Quick start

For more information see the The EMU-SDMS Manual

For Developers / Beta-Testers

Installation (two alternative methods)

  • either download & extract the package from GitHub. Then install it with the following command:
install.packages("path/to/emuR", repos = NULL, type="source")
  • or install the latest development version from GitHub (preferred method):
library(devtools)
install_github("IPS-LMU/emuR", build_vignettes = TRUE)

News

emuR 1.1.2

new features / performance tweaks / improvements

  • rewrite of list_files() that leads to massive speed bump
  • implemented convert_wideToLong() function to convert trackdata tibble objects to their long form representation (useful for spectral analysis)
  • query() sub-function now sets perl = TRUE arguments in regexp call when using sessionPattern and bundlePattern (useful for e.g. for negative look-around bundlePattern = "^((?!msajc003).)*$")
  • implemented export_seglistToTxtCollection()
  • normalize length now also using list() with do.call(rbind, res_list)
  • implemted new runMINNI boolean parameter in runBASwebservice_all()

bug fixes

  • https default on serve()
  • fixed problems of calcFreqs = T in convert_wideToLong() (possibly caused by newer version of dplyr?)

emuR 1.1.1

new features / performance tweaks / improvements

bug fixes

  • fixed bad column init. in normalize_length() column
  • removed detritus LaTex files (e.g. .log, .aux) from vignette/pics directory (as requested by CRAN maintainer)

emuR 1.1.0

new features / performance tweaks / improvements

  • URL encoding of bundle and session names to allow for URL string reserved characters in bundle and session names
  • error message of get_trackdata() now contains seglist row index if "Can not extract following"
  • normalize_length() now allows for additional non-numeric columns
  • changed stop() to warning() in get_trackdata() when samplerates are inconsistent (closes #190)
  • better error message when there is a naming mismatch of _emuDB dir _DBconfig.json
  • using sub() instead of tools::file_path_sans_ext() to handle _ in file extensions
  • query(), requery_seq() and requery_hier() now supports the resultType "tibble" (and get_trackdata(), requery_seq(), requery_hier() and serve() support them as input)
  • serve() function now uses seglist$start and seglist$end instead of seglist$sample_start and seglist$sample_end
  • implemented first version of update_itemsInLevel() (only label updates for now)
  • now setting the sample_start and sample_end values in query results when EVENT levels are queried (previously only start was set)
  • implemented first versions of create_links() (currently not checking for anything), create_itemsInLevel() (only EVENTs and ITEMs) and update_itemsInLevel() (only labels) and delete_itemsInLevel()
  • list_bundles() outside of loop for performance bump in get_trackdata()
  • better error message in add_files() if no files are found
  • consistentOutputType of get_trackdata() is not set to TRUE and is reset to T if resultType is "emuRtrackdata" or "tibble" (fixes #203)
  • avoiding negative times_rel and times_norm values in create_emuRtrackdata() by setting them to 0 (caused by string to numeric conversion precision errors)
  • requery_seq() now inserts NA values for the out of bounds rows instead of dropping them.
  • implemented list_sampleRates() function
  • get_trackdata() is now iteratively appending to a list() instead of into a SQLite temp table. This is a fairly large performance boost and also fixes #206.
  • added deprecation warnings to vignettes (added links to manual chapters)

bug fixes

  • propper fix for "now ordering by items_idx not by start_start_seq_idx which led to bad label sequences (fixes #140)"
  • fixed bad indexing in normalize_length() when sl_rowIdx values are not a c(1, 2, 3, 4, ...) sequence
  • fixed staticContours SSFF tracks not being sent to EMU-webApp (fixes #195)
  • fixed bug with completely empty levels that caused a bad resort of levels in _annot.jsons in rewrite_allAnnots()
  • fixed bug in add_files() that was using the wrong variable (fixes #196)
  • added error message when querying levels without time-bearing sub-levels (closes #150)
  • fixed bug in create_emuRtrackdata() with handling trackdata object of class spectral
  • correct recalculation of ITEM IDs of missing levels in .hlb files (== only present in ESPS files) in convert_legacyEmuDB()
  • fixed handling of completely empty levels in .hlb files
  • normalize_length() now handles various additional column types (not just "numeric")

emuR 1.0.0

new features / performance tweaks / improvements

  • implemented new consistentOutputType parameter for get_trackdata() to always return a trackdata or emuRtrackdata object independent of what the cut and npoints arguments are set to
  • now removing levelCanvasOrder entry in remove_levelDefinition() (fixes #156)
  • serve() method now uses GET to deliver media files to the EMU-webApp. This avoids the base64 conversion overhead and is a quite significant load time improvement
  • explicit error message in convert_legacyEmuDB() when invalid redundant links are found
  • better error message in BPF parser
  • convert_legacyEmuDB() automatically converts .ssd media files to .wav and normalizes the annotations to start at 0 (only if attr(ssd,'startTime') is not 0).
  • added sort() S3 method for emuRsegs objects
  • checking for badly sorted emuRsegs in requery_hier() and requery_seq() functions
  • create_emuRtrackdata() returns a simple data.frame object not a data.table object
  • emuRtrackdata object now contains a times_norm (normalized time values between 0 and 1 for each segment) column by default
  • added note to print.emuRsegs() to give the user a hint about missing columns
  • implemented print.emuRtrackdata() to avoid overly verbose output
  • implemented normalize_length() function as S3 function to normalize the lenght of each segment in an emuRtrackdata object
  • added absolute_file_path column to output of list_files()
  • query engine does not rely on label index in label array any more (updated convert_queryResultToEmuRsegs() to use resultAttrDef instead of labelIdx). Closes #164.
  • added browser argument to serve() function which is passed on to utils::browseURL() function
  • requery_seq() now uses start_item_seq_idx and end_item_seq_idx of seglist instead of start_item_id and start_item_id to simplify function
  • implemented check_emuDBhandle() function that is used on every exported function that takes a emuDBhandle as an argument to check if the handle is still valid (closes #176)
  • implemented "tibble" as resultType option in get_trackdata(). This will probably replace the "emuRtrackdata" option in future (it contains exactly the same data/columns).
  • prechecking if attribute definition is already defined (closes #182)
  • get_trackdata() now uses temporary SQL tables to store the intermediate results (massive performance gains!). Removed nrOfAllocationRows parameter as this is no longer needed as no matrix is used to store the intermediate results. (also closes #125)
  • convert_TextGridCollectio() using dir.exists() instead of file.exists() to check dirs
  • all read operations now use the readr package (avoids encoding problems like #187)
  • list_attributeDefinitions() now allows for a name vector to be passed in
  • rewrite of rewrite_allAnnots() functions for faster rewrites of _annot.json files to disk
  • improved cleanup in testing DBconfig functions
  • now ordering by items_idx not by start_start_seq_idx which led to bad label sequences (fixes #140)

bug fixes

  • fixed problem of updating cache. Didn't handle data.frame object that was thought to be a vector correctly!
  • fixed a bug in the BPF export function, which meant that WAVE files were only copied into one session
  • added missing $ in pattern arguments in list.files call in list_files (fixes #170)
  • not adding ssffTrackDefinition to DBconfig if user input is no (closes #171)
  • fixed bad seq_start_seq_idx and seq_seq_idx returned by requery_seq() (fixes #183)
  • fixed bad seq_start_seq_idx returned by internal query_databaseHier() function
  • fixed bad sorting of requery_seq()/requery_hier() when calcTimes = F (still sorted by start_sample instead of the correct seq_idx)
  • added readr::parse_character() to data received in serve() as this is recoded in windows (fixes #188).

emuR 0.2.3

new features / performance tweaks / improvements

  • tweaked runBASwebservice_maus(); improved performance for presegmented bundles
  • performance bump for fapply() by preallocating result matrix
  • performance bump for trapply() by preallocating result matrix
  • performance bump for mel.spectral() by preallocating result matrix
  • performance bump for bark.spectral() by preallocating result matrix
  • updated DBI calls to comply with the latest best practices (using DBI::dbExecute() instead of DBI::dbGetQuery() for non-SELECT queries)
  • BPF collection exporter documented and now public

bug fixes

  • export_TextGridCollection() now handles partial includes of bundle and session names correctly (issue #147)
  • added missing check if anagestConfig is defined to rename_attributeDefinition()
  • setting useBytes to T to avoid reencoding under windows
  • fixed bug in add_ssffTrackDefinition() that was trying to access fp which was renamed in a refactor to filesDf
  • fixed export to autodetect S3 methods (cbind & rbind for trackdata)

emuR 0.2.2

new features / performance tweaks / improvements

  • some changes to the parameter names in the BAS webservice functions
  • convert_txtCollection and convert_BPFCollection now name topmost item "bundle"
  • added functions to set and get level descriptions in DBconfig
  • BAS webservice functions now perform a cache update prior to departure
  • added multiple perspectives to ae demo database
  • choosing explicit paths with intersecting hierarchies now possible
  • remove levelDef & linkDef now implement force parameters
  • new function convert_txtCollection converts plain text collections into single-node emuDB
  • new functions runBASwebservice_* that call various BAS webservices from inside emuR
  • NULLing out empty DFs on list_level/linkDefs for more consistent API
  • newLinkDefType argument implemented in autobuild_linkFromTimes() to generate linkDefinition if so desired
  • automatically removing superlevel from levelCanvasOrder if convertSuperlevel is set to TRUE in autobuild_linkFromTimes()

bug fixes

  • wrapped readChars in enc2utf8 to avoid encodings issues on windows
  • updating label table correctly on add_attributeDefinition() (#138)
  • runBASwebservice_maus / minni / all now no longer ignore unlinked items (idx -1) but treat them as linkless segments
  • commented out cat() in train() function be be less verbose
  • BAS webservice calls now get their own temp directories (UUID based). This avoids race conditions when several scripts are running in parallel.
  • convert_txtCollection now treats perspectives as array (as it should)

emuR 0.2.1

new features / performance tweaks / improvements

  • added new EMUwebAppConfig -> perspectives -> signalCanvases -> minMaxValLims config option to emuDB vignette
  • requery_hier + requery_seq now implement the same timeRefSegmentLevel parameter as query (#135)

bug fixes

  • fixed requery_hier() bug of requery on same attribute definition
  • fixed requery_hier() bug of requery on same level but different attribute definition

emuR 0.2.0

new features / performance tweaks / improvements

  • rewrite of query engine to not require links_ext table any more (== redundant links)
  • calcTimes parameter added to query() / requery_seq() / requery_hier() to make calculating times optional (extreme performance boost if no times have to be calculated)
  • rewrite of annotJSONcharToBundleAnnotDFs() for faster loads emuDBs containing large annotJSONs
  • replaced tidyjson as annot.json parser with own solution at tidyjson didn't scale well on larger annotation files
  • added verbose parameter to export_TextGridCollection()
  • improved pre-check of dir exists in export_TextGridCollection()
  • added new replace_itemLabels function
  • improved export_TextGridCollection() doc
  • improved replace_itemLables() speed
  • implemented rename_emuDB() (#116)
  • implemented duplicate_level() (#113)
  • implemented linkDuplicates parameter in duplicate_level()
  • autobuild_linkFromTimes() speed improvements
  • FUNCQ queries (start(),end(), medial()) now additionally support TRUE & FALSE and T & F values (vs. 0 & 1)
  • added attrDefNames column to list_levelDefinitions() output
  • can now deal with read only emuDBs by copying the cache to tempdir() and making it writable for the user
  • added start_item_seq_idx and end_item_seq_idx to emuRsegs object
  • added start_item_seq_idx and end_item_seq_idx type values to all intermediate result tables
  • added optional function to reduce hierarchical query results to left and right most children only (large performance gain on calcTimes = T)
  • rewriting annot.json files now updates MD5 sums as well (avoids unnecessary reload on next load_emuDB)
  • rewriting annot.json files now writes all (including empty / missing) attributeDef. labels

bug fixes

  • fixed bad DBconfig gen. on add_perspective
  • fixed list_linkDefinitions() returning strings as factors
  • fixed bad error message when passing in ITEM levels to autobuild_linkFromTimes()
  • fixed incorrect handling of DBconfig when writeToFS was set to FALSE (writeToFS is now called rewriteAllAnnots)

emuR 0.1.9

new features / performance tweaks / improvements

  • also allowing "time = " in TextTiers
  • "levels of type 'EVENT' are not allowed to be super levels (== parents) in a domination relationship" constraint enforced in add_linkDefinition
  • added "MEDIAFILE_SAMPLES" as constant name to access audio samples to get_trackdata() function
  • improved error message to include tgPath in create_DBconfigFromTextGrid function
  • no integer return value returned by create_emuRdemoData() any more! It was implicitly returned from wrassp function call...
  • improved the slow overlap checking function in the BPF parser (is now O(n) instead of O(n^2))
  • fixed col naming problems for new (unreleased) RSQLite version
  • added export_TextGridCollection() function
  • improved doc for get_trackdata
  • constant naming of EMU-SDMS vs EMU_SDMS in various files
  • rewriting all annotation file on add_levelDefinition, remove_levelDefinition

bug fixes

  • fixed problem in conversion to JSON with empty items array (object '{}' vs array '[]')
  • fixed problem of keywords "number" | "time" | "xmin" | ... in labels causing TextGrid parser to fail
  • fixed problem with to lax RegEx in TextGrid parser
  • fixed validation problem with missing levels regarding types

emuR 0.1.8

new features / performance tweaks / improvements

  • get_trackdata with onTheFly calculation now reuses AsspDataObj if the current utterance is the same as the previous (large performance gain especially on long audio files)
  • checking if DBconfig exists for better error message if 'name' field is not set correctly in DBconfig
  • setting PRAGMA temp_store = 2; for SQLite connections
  • not extracting tables to R if no RegEx needed to create filtered_tmp tables (performance gain when querying large emuDBs)
  • convert_BPFCollection can now assigns the same label to more than one item when unifying tiers
  • newline at the end of load_emuDB if no redundant links are built
  • queries using dominates operator '^' don't use linksExt table anymore -> large performances benefits
  • only using _filtered_tmp tables if RegEx patterns are used
  • changed primary key on items table which leads to massive performance gains (deleting _emuDBcache.sqlite required)

bug fixes

  • fixed error handling of create_emuRtrackdata + added @export to roxygen doc
  • invalid annotJSONs generated by import_mediaFiles fixed
  • convert_TextGridCollection can now handle nested folders again
  • invalid UUIDs in DBConfig produced by convert_BPFCollection. Also added additional unit test to detect this.
  • list_bundles uses session argument again
  • fixed "Expression tree is too large (maximum depth 1000)" error in get_trackdata with long emuRsegs lists

emuR 0.1.7

  • R depends version bump to 3.2.0 (as requested by CRAN maintainer)
  • updated testthat::expect_less_than to expect_lt calls (due to deprecated warnings)
  • Using new .keep_all = T parameter of dplyr
  • removed legacy version of EQL vignette (overlooked as inst/doc was in .gitignore)

emuR 0.1.6

  • skipping in-depth thorough tests on CRAN for query and autobuild SQL functions

emuR 0.1.5

  • fixed problem of interm_res_tables already being present with queries that have multiple recursion depth on both sides of either -> or ^ operand (e.g. query (ae , "[[[Phonetic = n -> Phonetic =z] -> Phonetic = S ] ^ [Text = friends -> Text = she]]"))
  • fixed bad URL in README.md
  • added CITATION file

emuR 0.1.3.9000

  • renamed SQL tables & columns from camel case to underscore notation
  • variable SQL backend implementation

emuR 0.1.2.9000

  • multiple check fixes on various platforms

emuR 0.1.1.9000

  • serve problem with internalVars bug fixed
  • file locking problem that caused vignettes to fail under windows problem fixed

emuR 0.1.0.9000

  • massive refactor of all functions that used to refer to an emuDB by name and optionally by its UUID. They now use the new emuDBhandle object that is now returned by the load_emuDB() function.
  • convert_XXX_to_emuDB() functions renamed to convert_XXX()

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("emuR")

2.0.2 by Raphael Winkelmann, a month ago


https://github.com/IPS-LMU/emuR


Report a bug at https://github.com/IPS-LMU/emuR/issues


Browse source code at https://github.com/cran/emuR


Authors: Raphael Winkelmann [aut, cre] , Klaus Jaensch [aut, ctb] , Steve Cassidy [aut, ctb] , Jonathan Harrington [aut, ctb]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports MASS, tools, utils, stats, methods, graphics, grDevices, stringr, uuid, RCurl, base64enc, shiny, wrassp, jsonlite, RSQLite, DBI, httpuv, dplyr, readr, tibble, purrr, compare, tidyr, git2r, mime, rstudioapi, rlang

Suggests ggplot2, testthat, knitr, rmarkdown


See at CRAN