Files in jbrzusto/motus-R-package
Operate a server to process data for http://motus.org

.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/Copse.R R/RL.R R/TS.R R/archiveMessage.R R/archivePath.R R/as.list.motusMap.R R/authenticate_user.R R/claimJob.R R/cleanTagRegistrations.R R/cleanup.R R/closeRecvSrc.R R/commitMetadataHistory.R R/createFilterTagsDB.R R/createRecvTagDB.R R/dataServer.R R/dateStem.R R/dbHumanizeTimestamps.R R/dbInsertOrReplace.R R/deleteFromMotus.R R/deleteTestBatches.R R/digestFile.R R/dirSortedBy.R R/dropBatchesFromTransfer.R R/email.R R/embroilHuman.R R/enqueue.R R/enqueueCommand.R R/ensureMonoBN.R R/ensureMotusTransferTables.R R/ensureParamOverridesTable.R R/ensureRecvDBTables.R R/ensureServerDB.R R/ensureServerDirs.R R/ensureTagProjDB.R R/error_from_app.R R/exportGlobalTags.R R/fixDOSfilenames.R R/getDownloadURL.R R/getFeeder.R R/getFileAsBZ2.R R/getFileAsText.R R/getGlobalTagsView.R R/getMap.R R/getMotusDeviceID.R R/getMotusMetaDB.R R/getPGID.R R/getParamOverrides.R R/getProjDir.R R/getProjectTags.R R/getRecvDBPath.R R/getRecvModel.R R/getRecvSrc.R R/getRecvType.R R/getTagProjSrc.R R/getYearProjSite.R R/guessTagModel.R R/hackError.R R/handleExportData.R R/handleExportPulses.R R/handleFullRecvRerun.R R/handleLogs.R R/handleLtFiles.R R/handleLtFindtags.R R/handleNewFiles.R R/handlePlotData.R R/handleQueueArchives.R R/handleRegisterTags.R R/handleRerunReceiver.R R/handleSGfiles.R R/handleSGfindtags.R R/handleSanityCheck.R R/handleServerFiles.R R/handleSyncReceiver.R R/handleUnknownFiles.R R/handleUnpackArchive.R R/handleUploadFile.R R/handleUploadProcessed.R R/isTopJob.R R/isTopJobDone.R R/jobFail.R R/jobHasFolder.R R/jobLog.R R/jobPath.R R/jobProduced.R R/lightWeightCopy.R R/loadJobs.R R/lockSymbol.R R/loggingTry.R R/ltDTAregex.R R/ltDefaultFindTagsParams.R R/ltFindTags.R R/ltGetCodeset.R R/ltMergeFiles.R R/ltSyncDBtoRepo.R R/makeQueuePath.R R/makeReceiverPlot.R R/makeTagProjDB.R R/matchTags.R R/motusAuthenticateUser.R R/motusConstants.R R/motusDeployTag.R R/motusListProjects.R R/motusListSensorDeps.R R/motusListSensors.R R/motusListSpecies.R R/motusLoadSecrets.R R/motusLog.R R/motusQuery.R R/motusQuickRegTag.R R/motusRegisterReceiver.R R/motusRegisterTag.R R/motusReserveKeys.R R/motusSaveSecrets.R R/motusSearchTags.R R/moveDirContents.R R/moveFiles.R R/moveFilesUniquely.R R/moveJob.R R/newJob.R R/newSubJob.R R/openMotusDB.R R/parseFilenames.R R/plotTagTimeline.R R/postInstall.R R/predictTagLifespan.R R/processServer.R R/productsDir.R R/purgeFromMotus.R R/pushToMotus.R R/queueJob.R R/queueKnownFiles.R R/queueUnfinishedSubjobs.R R/readDTA.R R/realFile.R R/refreshMotusMetaDBCache.R R/regexPieces.R R/registerProducts.R R/repackageRecoverdSGdata.R R/reparentJob.R R/rerunUploadJob.R R/retryJob.R R/return_file_from_app.R R/return_from_app.R R/runningCount.R R/safeFileRename.R R/safeSQL.R R/safeSQLiteConnect.R R/safeSrcSQLite.R R/safeSys.R R/safe_arg.R R/serverCommon.R R/serverError.R R/sgDefaultFindTagsParams.R R/sgFilenameRegex.R R/sgFindTags.R R/sgMergeFiles.R R/sgRawDataRegex.R R/sgStreamToFile.R R/sgSyncDBtoRepo.R R/sgTimeAtBoot.R R/splitToDF.R R/sqliteToRDS.R R/statusServer.R R/statusServer2.R R/subjobsInQueue.R R/syncDBtoRepo.R R/syncServer.R R/tagview.R R/testFile.R R/textFileContents.R R/toInbox.R R/toTrash.R R/topJob.R R/trimCommonPath.R R/updateMetadataForTags.R R/updateTagDeployments.R R/uploadServer.R R/validateMotusTagDB.R R/validate_request.R R/wavFindTags.R R/z%or%.R R/z.onLoad.R README.md data/speciesTagModel.R
data/tagLifespanPars.rda
inst/doc/2018-May_issues.md
inst/doc/Makefile
inst/doc/beeper_product_format.md
inst/doc/data_flow.dot
inst/doc/data_flow.pdf
inst/doc/data_flow.svg
inst/doc/lotekTagLifespanByBatteryAndBI.csv
inst/doc/maintenance.md inst/doc/modelLotekTagLifeSpan.Rmd inst/doc/modelLotekTagLifeSpan.pdf
inst/doc/modelLotekTagLifeSpan.rda
inst/doc/motus_administrator_guide.md inst/doc/motus_data_overview.md inst/doc/motus_data_overview.pdf inst/doc/motus_processing_overview.md inst/doc/networked_receivers.md inst/doc/rds_format.md
inst/doc/rds_format.txt
inst/doc/requirePrograms.md
inst/doc/sensorgnome_data_flow.dot
inst/doc/sensorgnome_data_flow.pdf
inst/doc/sensorgnome_data_flow.svg
inst/doc/servers.md inst/doc/slow_queries.md inst/doc/status_api.md inst/doc/status_of_transition_to_new_server.md inst/doc/tag_detection_imprecision.md
inst/doc/tags_view_graph.dot
inst/doc/tags_view_graph.pdf inst/doc/uploads.md
inst/motusMetadataSchema.sql
inst/motusTransferTableSchema.sql
inst/receiverToMasterKeyMapSchema.sql
inst/root_overlay.md
inst/root_overlay/etc/apache2/sites-available/001-sgdata-ssl.conf
inst/root_overlay/etc/apache2/sites-available/002-sgdata-nossl.conf
inst/root_overlay/etc/apache2/sites-available/live-sensorgnome
inst/root_overlay/etc/cron.d/monthly_trash_dump
inst/root_overlay/etc/cron.d/refreshMotusMetaDB
inst/root_overlay/etc/cron.d/sqlite_daily_backup
inst/root_overlay/etc/rc.local
inst/root_overlay/etc/sysctl.d/local.conf
inst/scripts/backup_sqlite_db.sh
inst/scripts/boot_time_tasks.sh
inst/scripts/chown_sg_www-data.sh
inst/scripts/create_live_sqlite_database.sqlite
inst/scripts/debug.php
inst/scripts/decryptLotekDB.R inst/scripts/hackError.R
inst/scripts/killAllMotusServers.sh
inst/scripts/killMotusDataServer.sh
inst/scripts/killMotusProcessServers.sh
inst/scripts/killMotusStatusServer.sh
inst/scripts/killMotusStatusServer2.sh
inst/scripts/killMotusSyncServer.sh
inst/scripts/lastError.R
inst/scripts/maintenance/README.TXT
inst/scripts/maintenance/buildFileRepo.R
inst/scripts/maintenance/checkSyncDBtoRepo.sh
inst/scripts/maintenance/clearTransferTables.R inst/scripts/maintenance/ensureAllFiles.R
inst/scripts/maintenance/ensureAllFiles.sh
inst/scripts/maintenance/generate_projAmbig.R inst/scripts/maintenance/humanize.R inst/scripts/maintenance/makeDailyHierarchy.R inst/scripts/maintenance/populate_products_table.R
inst/scripts/maintenance/post_install.sh
inst/scripts/maintenance/re-push-metadata_hash.R inst/scripts/maintenance/register_failed_uploads.R inst/scripts/maintenance/syncDBtoFiles.R inst/scripts/maintenance/syncDBtoRepo.R inst/scripts/maintenance/update_batchRuns_tagDepProjectID.R inst/scripts/maintenance/update_hits_tagDepProjectID.R
inst/scripts/monthly_trash_dump.sh
inst/scripts/refreshMotusMetaDB.R
inst/scripts/rerunMotusServers.sh
inst/scripts/rerunReceiver.R inst/scripts/rerunUploadJob.R inst/scripts/retryJob.R
inst/scripts/rpack
inst/scripts/runAllMotusServers.sh
inst/scripts/runMotusDataServer.sh
inst/scripts/runMotusProcessServer.sh
inst/scripts/runMotusStatusServer.sh
inst/scripts/runMotusStatusServer2.sh
inst/scripts/runMotusSyncServer.sh
inst/scripts/runNewFiles.R
inst/scripts/sqlite_daily_backup.sh
inst/scripts/updateAllProjectGlobalFiles.R
inst/scripts/www/data_server_unavailable.php
inst/scripts/www/fake_authenticate_user.php
inst/scripts/www/index.html
inst/scripts/www/index.php
inst/scripts/www/jquery-ui-1.12.1/AUTHORS.txt
inst/scripts/www/jquery-ui-1.12.1/LICENSE.txt
inst/scripts/www/jquery-ui-1.12.1/external/jquery/jquery.js
inst/scripts/www/jquery-ui-1.12.1/images/ui-icons_444444_256x240.png
inst/scripts/www/jquery-ui-1.12.1/images/ui-icons_555555_256x240.png
inst/scripts/www/jquery-ui-1.12.1/images/ui-icons_777620_256x240.png
inst/scripts/www/jquery-ui-1.12.1/images/ui-icons_777777_256x240.png
inst/scripts/www/jquery-ui-1.12.1/images/ui-icons_cc0000_256x240.png
inst/scripts/www/jquery-ui-1.12.1/images/ui-icons_ffffff_256x240.png
inst/scripts/www/jquery-ui-1.12.1/index.html
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.css
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.js
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.min.css
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.min.js
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.structure.css
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.structure.min.css
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.theme.css
inst/scripts/www/jquery-ui-1.12.1/jquery-ui.theme.min.css
inst/scripts/www/jquery-ui-1.12.1/package.json
inst/scripts/www/jquery.mustache.min.js
inst/scripts/www/login.php
inst/scripts/www/mustache.min.js
inst/scripts/www/obsolete/status2.php
inst/scripts/www/robots.txt
inst/scripts/www/status.php
inst/scripts/www/status2.css
inst/scripts/www/status2.html
inst/scripts/www/status2.js
inst/scripts/www/status_message.html
man/Copse.Rd man/MOTUS_API_ENTRY_POINTS.Rd man/RL.Rd man/Reval.Rd man/TS.Rd man/addToOrder.Rd man/api_info.Rd man/archiveMessage.Rd man/archivePath.Rd man/authenticate_user.Rd man/batches_for_all.Rd man/batches_for_receiver.Rd man/batches_for_tag_project.Rd man/beginsWith.Rd man/cash-.motusMap.Rd man/cash-.safeSQL.Rd man/cash-set-.motusMap.Rd man/childrenWhere.Copse.Rd man/claimJob.Rd man/cleanTagRegistrations.Rd man/cleanup.Rd man/closeRecvSrc.Rd man/commitMetadataHistory.Rd man/compressedFileDone.Rd man/createFilterTagsDB.Rd man/createRecvTagDB.Rd man/dataServer.Rd man/dateStem.Rd man/dbHumanizeTimestamps.Rd man/dbInsertOrReplace.Rd man/deleteFromMotus.Rd man/deleteTestBatches.Rd man/deviceID_for_receiver.Rd man/digestFile.Rd man/dirSortedBy.Rd man/dropBatchesFromTransfer.Rd man/dumpJobDetails.Rd man/email.Rd man/embroilHuman.Rd man/enqueue.Rd man/enqueueCommand.Rd man/ensureMonoBN.Rd man/ensureMotusTransferTables.Rd man/ensureParamOverridesTable.Rd man/ensureRecvDBTables.Rd man/ensureServerDB.Rd man/ensureServerDirs.Rd man/ensureTagProjDB.Rd man/error_from_app.Rd man/exportGlobalTags.Rd man/files_from_recv_DB.Rd man/files_from_repo.Rd man/fixDOSfilenames.Rd man/getDownloadURL.Rd man/getFeeder.Rd man/getFileAsBZ2.Rd man/getFileAsText.Rd man/getGlobalTagsView.Rd man/getMap.Rd man/getMotusDeviceID.Rd man/getMotusMetaDB.Rd man/getPGID.Rd man/getParamOverrides.Rd man/getProjDir.Rd man/getProjectTags.Rd man/getRecvDBPath.Rd man/getRecvModel.Rd man/getRecvSrc.Rd man/getRecvType.Rd man/getTagProjSrc.Rd man/getYearProjSite.Rd man/get_job_stackdump.Rd man/get_receiver_info.Rd man/gps_for_receiver.Rd man/gps_for_tag_project.Rd man/grapes-or-grapes.Rd man/guessTagModel.Rd man/hackError.Rd man/handleExportData.Rd man/handleExportPulses.Rd man/handleFullRecvRerun.Rd man/handleLogs.Rd man/handleLtFiles.Rd man/handleLtFindtags.Rd man/handleNewFiles.Rd man/handlePlotData.Rd man/handleQueueArchives.Rd man/handleRegisterTags.Rd man/handleRerunReceiver.Rd man/handleSGfiles.Rd man/handleSGfindtags.Rd man/handleSanityCheck.Rd man/handleServerFiles.Rd man/handleSyncReceiver.Rd man/handleUnknownFiles.Rd man/handleUnpackArchive.Rd man/handleUploadFile.Rd man/handleUploadProcessed.Rd man/hits_for_receiver.Rd man/hits_for_tag_project.Rd man/infimum.Rd man/isTopJob.Rd man/isTopJobDone.Rd man/jobFail.Rd man/jobHasFolder.Rd man/jobLog.Rd man/jobPath.Rd man/jobProduced.Rd man/lightWeightCopy.Rd man/list_jobs.Rd man/list_receiver_files.Rd man/loadJobs.Rd man/lockSymbol.Rd man/loggingTry.Rd man/ltDTAregex.Rd man/ltDefaultFindTagsParams.Rd man/ltFindTags.Rd man/ltGetCodeset.Rd man/ltMergeFiles.Rd man/ltSyncDBtoRepo.Rd man/makeQueuePath.Rd man/makeReceiverPlot.Rd man/makeTagProjDB.Rd man/makeWhere.Rd man/matchTags.Rd man/maybeRetireJob.Rd man/metadata_for_receivers.Rd man/metadata_for_tags.Rd man/motusAuthenticateUser.Rd man/motusDeployTag.Rd man/motusListProjects.Rd man/motusListSensorDeps.Rd man/motusListSensors.Rd man/motusListSpecies.Rd man/motusLoadSecrets.Rd man/motusLog.Rd man/motusQuery.Rd man/motusQuickRegTag.Rd man/motusRegisterReceiver.Rd man/motusRegisterTag.Rd man/motusReserveKeys.Rd man/motusSaveSecrets.Rd man/motusSearchTags.Rd man/moveDirContents.Rd man/moveFiles.Rd man/moveFilesUniquely.Rd man/moveJob.Rd man/names.motusMap.Rd man/newJob.Rd man/newSubJob.Rd man/openMotusDB.Rd man/parseFilenames.Rd man/plotTagTimeline.Rd man/postInstall.Rd man/predictTagLifespan.Rd man/print.safeSQL.Rd man/processServer.Rd man/productsDir.Rd man/project_ambiguities_for_tag_project.Rd man/pulse_counts_for_receiver.Rd man/purgeFromMotus.Rd man/pushToMotus.Rd man/queueJob.Rd man/queueKnownFiles.Rd man/queueUnfinishedSubjobs.Rd man/readDTA.Rd man/realFile.Rd man/receivers_for_project.Rd man/refreshMotusMetaDBCache.Rd man/regexPieces.Rd man/registerProducts.Rd man/repackageRecoveredSGdata.Rd man/reparentJob.Rd man/rerunUploadJob.Rd man/retryJob.Rd man/return_from_app.Rd man/runningCount.Rd man/runs_for_receiver.Rd man/runs_for_tag_project.Rd man/safeFileRename.Rd man/safeSQL.Rd man/safeSQLiteConnect.Rd man/safeSrcSQLite.Rd man/safeSys.Rd man/safe_arg.Rd man/serializeNoHeader.Rd man/serno_collision_rules.Rd man/serverCommon.Rd man/serverError.Rd man/setParent.Copse.Rd man/sgDefaultFindTagsParams.Rd man/sgFilenameRegex.Rd man/sgFindTags.Rd man/sgMergeFiles.Rd man/sgRawDataRegex.Rd man/sgStreamToFile.Rd man/sgSyncDBtoRepo.Rd man/sgTimeAtBoot.Rd man/size_of_update_for_receiver.Rd man/size_of_update_for_tag_project.Rd man/splitToDF.Rd man/sqliteCloneIntoDB.Rd man/sqliteToRDS.Rd man/statusServer.Rd man/statusServer2.Rd man/status_api_info.Rd man/sub-sub-.motusMap.Rd man/sub-subset-.motusMap.Rd man/subjobsInQueue.Rd man/subset-.Copse.Rd man/syncDBtoRepo.Rd man/syncServer.Rd man/tags_for_ambiguities.Rd man/tagview.Rd man/testFile.Rd man/textFileContents.Rd man/toInbox.Rd man/toTrash.Rd man/topJob.Rd man/trimCommonPath.Rd man/uncompressedSize.Rd man/updateMetadataForTags.Rd man/updateTagDeployments.Rd man/uploadServer.Rd man/validateMotusTagDB.Rd man/validate_request.Rd man/wavFindTags.Rd
src/Makefile
src/Sqlite_Compression_Extension.c
tests/testthat.R
jbrzusto/motus-R-package documentation built on Dec. 5, 2018, 6:55 a.m.