Package: TKCat 1.2.2

TKCat: Tailored Knowledge Catalog

Facilitate the management of data from knowledge resources that are frequently used alone or together in research environments. In 'TKCat', knowledge resources are manipulated as modeled database (MDB) objects. These objects provide access to the data tables along with a general description of the resource and a detailed data model documenting the tables, their fields and their relationships. These MDBs are then gathered in catalogs that can be easily explored and shared. Finally, 'TKCat' provides tools to easily subset, filter and combine MDBs and create new catalogs suited for specific needs.

Authors:Patrice Godard [aut, cre, cph]

TKCat_1.2.2.tar.gz
TKCat_1.2.2.zip(r-4.7)TKCat_1.2.2.zip(r-4.6)TKCat_1.2.2.zip(r-4.5)
TKCat_1.2.2.tgz(r-4.6-any)TKCat_1.2.2.tgz(r-4.5-any)
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TKCat_1.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
TKCat/json (API)

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

Bug tracker:https://github.com/patzaw/tkcat/issues

Pkgdown/docs site:https://patzaw.github.io

On CRAN:

Conda:

6.30 score 5 stars 67 scripts 526 downloads 126 exports 110 dependencies

Last updated from:65e11b3fcd. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK212
source / vignettesOK295
linux-release-x86_64OK221
macos-release-arm64OK179
macos-oldrel-arm64OK198
windows-develOK169
windows-releaseOK139
windows-oldrelOK130
wasm-releaseOK141

Exports:add_chMDB_useradd_chTKCat_collectionadd_collection_memberadd_feature_defadd_helpersadd_km_featureadd_km_specadd_km_tableadd_property_valuesadd_table_defadd_table_featuresadd_unit_defarchive_chMDBas_chMDBas_fileMDBas_KMRas_memoMDBch_insertch_join_querych_union_querychange_chTKCat_passwordcheck_chTKCatchMDBchTKCatcollection_memberscollection_members<-compare_MDBcount_recordscreate_chMDBcreate_chTKCat_usercreate_KMRcreate_POKdata_file_sizedata_filesdata_modeldata_tablesdb_disconnectdb_infodb_info<-db_reconnectdb_tablesdecode_bindimsdrop_chMDBdrop_chMDB_projectionsdrop_chTKCat_userempty_chMDBencode_binexplore_MDBsfileMDBfilter_mdb_matrixfilter_with_tablesget_chMDB_metadataget_chMDB_timestampsget_chTKCat_collectionget_collection_mapperget_confrontation_reportget_hostsget_km_specget_KMRget_local_collectionget_MDBget_POKget_queryget_R_helpersget_shared_collectionshas_km_specheadsimport_collection_mapperimport_local_collectioninit_chTKCatis_chMDB_publicis_current_chMDBis.chMDBis.chTKCatis.fileMDBis.KMRis.MDBis.memoMDBis.metaMDBis.POKis.TKCatjoin_mdb_tableslist_chMDB_timestampslist_chMDB_userslist_chTKCat_collectionslist_chTKCat_userslist_feature_propertieslist_local_collectionslist_MDBslist_measurement_unitslist_measurementslist_POKslist_property_valueslist_table_featureslist_table_typeslist_tablesmanage_chTKCat_usersmap_collection_membersmaterialize_chMDB_projectionsMDBsmemoMDBmergeTree_from_RelTableModelmergeTrees_from_RelDataModelmetaMDBparse_R_helpersread_collection_membersread_fileMDBread_KMRrelational_tablesremove_chMDB_userremove_chTKCat_collectionrm_km_featurerm_km_tablescan_fileMDBssearch_MDB_fieldssearch_MDB_tablesset_chMDB_accessset_chMDB_timestampshow_collection_defTKCatunarchive_chMDBupdate_chMDB_grantsupdate_chTKCat_userwrite_collection_memberswrite_MergeTree

Dependencies:arrowaskpassassertthatbase64encbitbit64brewbslibcachemcallrcliClickHouseHTTPcliprcodetoolscolourpickercommonmarkcpp11crayoncrosstalkcurldata.tableDBIdescdigestdplyrDTevaluatefarverfastmapfontawesomefsfuturegenericsggplot2globalsgluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttr2isobandjquerylibjsonlitejsonvalidateknitrlabelinglaterlatticelazyevallifecyclelistenvlitedownmagrittrmarkdownMatrixmemoisemimeminiUIopensslotelparallellypillarpkgbuildpkgconfigpkgloadprettyunitsprocessxprogresspromisespspurrrR6rappdirsRColorBrewerRcppreadrReDaMoRrintrojsrlangrmarkdownroxygen2rprojrootrstudioapiS7sassscalesshinyshinydashboardshinyjssourcetoolssystibbletidyselecttinytextzdbutf8uuidV8vctrsviridisLitevisNetworkvroomwithrxfunxml2xtableyaml

Introduction to TKCat
Introduction | Create an MDB: a minimal example | Loading example data | Creating a data model with ReDaMoR | Binding the model to the data in an MDB object | Adding information about an MDB | Documenting collection members | Writing an MDB in files | Leveraging MDB | HPO | ClinVar | CHEMBL | MDB implementations | Exploring information | Pulling, subsetting and combining | Filtering and joining | Merging MDBs with collections | Collections and collection members | Shared collections and merging | Merging without collection | A centralized catalog of MDB in ClickHouse (chTKCat) | Local TKCat | chTKCat | Pushing an MDB in a chTKCat instance | Specific operations on chMDB objects | Data organization in ClickHouse | Defining and using Requirements for Knowledge Management (KMR) | Appendices | chTKCat operations | Instantiating the ClickHouse database | Install ClickHouse, initialize and configure the TKCat instance | Cleaning and removing a TKCat instance | User management | Creation | Update | Drop | chMDB management | chMDB Creation | Populating chMDB | Deleting a chMDB | Collection management | Implementation | Data models | Default database | Modeled databases | TKCat collections | Creating a collection | Documenting collection members | Collection mapper functions | Remarks about supported data format and data types | Matrices of values | Documents stored as base64 values | References
Rendered fromTKCat.Rmdusingknitr::rmarkdown

Last update: 2026-05-19
Started: 2024-04-30

Defining and using Requirements for Knowledge Management (KMR) in TKCat
Defining KMR | KMR organization | Define requirements | Table and mandatory features | Optional features | Possible values for feature properties | Measurements | KM specifications | Exploring requirements | Documenting MDB specifications | Simple example | Piece Of Knowledge (POK) | Helpers | KMR helpers | MDB helpers | POK objects
Rendered fromTKCat-KMR-POK.Rmdusingknitr::rmarkdown

Last update: 2026-05-19
Started: 2024-05-07

Readme and manuals

Help Manual

Help pageTopics
Format bytes numbers in human readable values.format_bytes
An MDB (Modeled DataBase) based on files: fileMDB$.chMDB $.fileMDB as.list.fileMDB fileMDB names<-.fileMDB rename.fileMDB [.fileMDB [[.fileMDB
Add a user to an MDB of a chTKCat objectadd_chMDB_user
Import a collection in a chTKCat databaseadd_chTKCat_collection
Add a collection member to an MDBadd_collection_member
Add a feature definition to Knowledge Management Requirements (KMR)add_feature_def
Add a set of helper functions to a compatible objectadd_helpers add_helpers.KMR add_helpers.MDB
Add KM feature specifications to an MDB objectadd_km_feature
Add empty KM specification tables to an MDB objectadd_km_spec
Add KM table specifications to an MDB objectadd_km_table
Add possible values to an integer or a character feature property in KMRadd_property_values
Add a table definition to Knowledge Management Requirements (KMR)add_table_def
Add possible features to table type in KMRadd_table_features
Add a unit definition to Knowledge Management Requirements (KMR)add_unit_def
Archive a chMDB in a chTKCatarchive_chMDB
Push an MDB object in a ClickHouse databaseas_chMDB
Write an MDB objectas_fileMDB as_fileMDB.chMDB as_fileMDB.fileMDB as_fileMDB.memoMDB as_fileMDB.metaMDB
Convert in a KMR object when possibleas_KMR
Convert any MDB object in a memoMDB objectas_memoMDB
Insert records by batches in a Clickhouse tablech_insert
Build a ClickHouse 'JOIN' query from two sub-queriesch_join_query
Build a ClickHouse 'UNION' query from several sub-queriesch_union_query
Change chTKCat passwordchange_chTKCat_password
Check a chTKCat objectcheck_chTKCat
An MDB (Modeled DataBase) relying on ClickHouse: chMDBas.list.chMDB chMDB names<-.chMDB rename.chMDB [.chMDB [[.chMDB
Connect to a ClickHouse TKCat instancechTKCat
Collection memberscollection_members collection_members.chMDB collection_members.chTKCat collection_members.fileMDB collection_members.memoMDB collection_members.metaMDB collection_members.TKCat collection_members<- collection_members<-.chMDB collection_members<-.fileMDB collection_members<-.memoMDB
Compare two MDB objectscompare_MDB
Count the number of recordscount_records count_records.MDB
Create a database in a chTKCatcreate_chMDB
Create a chTKCat usercreate_chTKCat_user
Create an MDB object with Knowledge Management Requirements (KMR)create_KMR KMR
Create a piece of knowledge (POK) from an MDB and a KMRobjectcreate_POK POK
Get the size of data files from a fileMDB objectdata_file_size
Get the data files from a fileMDB objectdata_files
Get object data modeldata_model data_model.chMDB data_model.fileMDB data_model.memoMDB data_model.metaMDB
Get object data tablesdata_tables data_tables.chMDB data_tables.fileMDB data_tables.memoMDB data_tables.metaMDB
Disconnect an object from a databasedb_disconnect db_disconnect.chMDB db_disconnect.chTKCat db_disconnect.metaMDB
DB informationdb_info db_info.chMDB db_info.fileMDB db_info.memoMDB db_info.metaMDB db_info<- db_info<-.chMDB db_info<-.fileMDB db_info<-.memoMDB db_info<-.metaMDB
Reconnect an object to a databasedb_reconnect db_reconnect.chMDB db_reconnect.chTKCat db_reconnect.metaMDB db_reconnect.POK
Get the DB tables from a chMDB or metaMDB objectdb_tables
Decode base64 stringdecode_bin
Detailed information about the format of the tablesdims dims.chMDB dims.fileMDB dims.memoMDB dims.metaMDB
Drop a database from a chTKCatdrop_chMDB
Drop in ClickHouse any projection documented in the data modeldrop_chMDB_projections
Drop a user from a chTKCat objectdrop_chTKCat_user
Empty a chMDB in a chTKCatempty_chMDB
Encode a binary file in a base64 stringencode_bin
Explore available MDB in a shiny web interfaceexplore_MDBs explore_MDBs.chTKCat explore_MDBs.TKCat
Filter a matrix stored in an MDBfilter_mdb_matrix filter_mdb_matrix.chMDB filter_mdb_matrix.fileMDB filter_mdb_matrix.memoMDB filter_mdb_matrix.metaMDB
Filter an MDB object according to provided tablesfilter_with_tables filter_with_tables.chMDB filter_with_tables.fileMDB filter_with_tables.memoMDB filter_with_tables.metaMDB
Filter a chMDB object and return a memoMDBfilter.chMDB
Filter a fileMDB object and return a memoMDBfilter.fileMDB
Filter a memoMDB objectfilter.memoMDB
Filter a metaMDB objectfilter.metaMDB
Format a chTKCat object for printingformat.chTKCat
Get the metadata of an MDB from a chTKCat connectionget_chMDB_metadata
Get instance timestamps of an MDB in chTKCatget_chMDB_timestamps
Get a collection from a chTKCatget_chTKCat_collection
Get the default mapper function for a collectionget_collection_mapper
Get the last generated MDB confrontation reportget_confrontation_report
Get database hostsget_hosts get_hosts.chMDB get_hosts.chTKCat get_hosts.DBIConnection get_hosts.metaMDB
Get KM specifications from an MDB objectget_km_spec
Get a KMR object from a TKCat or a chTKCat objectget_KMR
Get the json definition of a local collection of conceptsget_local_collection
Get an MDB object from a TKCat related objectget_MDB get_MDB.chTKCat get_MDB.TKCat
Get a POK from a chTKCat connection or a TKCat objectget_POK
Get SQL queryget_query get_query.chMDB get_query.chTKCat
Get a set of helper functions from an objectget_R_helpers get_R_helpers.KMR get_R_helpers.MDB
Get collections shared by 2 objects and return member combinationsget_shared_collections
Check if KM specifications are available in an MDB objecthas_km_spec
Get the first records of each object data tablesheads heads.chMDB heads.fileMDB heads.memoMDB heads.metaMDB
Import a function to map collection membersimport_collection_mapper
Import a the definition of a collection of concepts in the local environmentimport_local_collection
Initialize a chTKCat databaseinit_chTKCat
Is a chMDB publicis_chMDB_public
Check if the chMDB object refers to the current instance of the MDBis_current_chMDB
Check if the object is a chMDB objectis.chMDB
Check the object is a chTKCat objectis.chTKCat
Check if the object is a fileMDB objectis.fileMDB
Check if an object represents Knowledge Management Requirements (KMR)is.KMR
Check if the object is an MDB objectis.MDB
Check if the object is a memoMDB objectis.memoMDB
Check if the object is a metaMDB objectis.metaMDB
Check if the object is a POK objectis.POK
Check the object is a TKCat objectis.TKCat
Join connected tablesjoin_mdb_tables
List instance timestamps of an MDB in chTKCatlist_chMDB_timestamps
List users of an MDB of a chTKCat objectlist_chMDB_users
List collections available in a chTKCatlist_chTKCat_collections
List chTKCat userlist_chTKCat_users
List properties of a featurelist_feature_properties
List local collections of conceptslist_local_collections
List available MDBlist_MDBs list_MDBs.chTKCat list_MDBs.TKCat
List possible units for a type of measurementlist_measurement_units
List supported types of measurementlist_measurements
List available POKlist_POKs
List of supported values for an integer or a character propertylist_property_values
List the features provided by a set of tableslist_table_features
List types of tables defined in a KMR objectlist_table_types
List tables in a clickhouse databaselist_tables list_tables.chTKCat list_tables.DBIConnection
Manage user information in a shiny interfacemanage_chTKCat_users
Map different collection membersmap_collection_members
Materialize in ClickHouse any projection documented in the data modelmaterialize_chMDB_projections
MDBas.list.MDB c.MDB length.MDB lengths.MDB MDB merge.MDB names.MDB pull.MDB select.MDB
Get a list of MDB from metaMDB objectMDBs
An MDB (Modeled DataBase) in memory: memoMDB$.memoMDB memoMDB names<-.memoMDB rename.memoMDB [.memoMDB [[.memoMDB
Create a ClickHouse MergeTree table from a ReDaMoR::RelTableModelmergeTree_from_RelTableModel
Create ClickHouse MergeTree tables from a ReDaMoR::RelDataModelmergeTrees_from_RelDataModel
A metaMDB object$.metaMDB as.list.metaMDB metaMDB names<-.metaMDB rename.metaMDB [.metaMDB [[.metaMDB
Parse source code to get R helpersparse_R_helpers
Read a collection member JSON fileread_collection_members
Read a fileMDB from a pathread_fileMDB
Read KMR from a pathread_KMR
Get a list of relational tablesrelational_tables
Drop a user of an MDB of a chTKCat objectremove_chMDB_user
Remove a collection from a chTKCat databaseremove_chTKCat_collection
Remove KM feature specifications from an MDB objectrm_km_feature
Remove KM table specifications from an MDB objectrm_km_table
Scan a catalog of fileMDBscan_fileMDBs
Search fields in a TKCat related objectsearch_MDB_fields search_MDB_fields.chTKCat search_MDB_fields.TKCat
Search tables in a TKCat related objectsearch_MDB_tables search_MDB_tables.chTKCat search_MDB_tables.TKCat
Set chMDB accessset_chMDB_access
Set timestamp of the current version of an MDB in chTKCatset_chMDB_timestamp
Show the definition of a collectionshow_collection_def
Subset a chMDB object according to row position in one table and return a memoMDBslice.chMDB
Subset a fileMDB object according to row position in one table and return a memoMDBslice.fileMDB
Subset a memoMDB object according to row position in one tableslice.memoMDB
Subset a metaMDB object according to row position in one tableslice.metaMDB
TKCat: a catalog of MDBc.TKCat names<-.TKCat rename.TKCat TKCat [.TKCat
Unarchive a chMDB in a chTKCatunarchive_chMDB
Update grants on tables in an MDB of a chTKCat objectupdate_chMDB_grants
Update a chTKCat user informationupdate_chTKCat_user
Write a collection member JSON filewrite_collection_members
Write a Clickhouse MergeTree tablewrite_MergeTree