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RUB User`s Manual

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2. 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 21 RU Bangarang 1 0 Users Manual Keen 2013 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Sighting number 35 Subevent 36 Subsubevent blank in this case 37 Comment WIW BHV BTH MIS CAN OTH With Whales Behavior Breath subsubevents Subevent Key BTH Log a breath of an individual or group At the click of this button timestamps and gpsstamps are given to the breath for the designated individual in the group MIS Log that a breath was missed so that not all is lost in breath interval analyses down the road CAN Log that a breath was mistakenly logged it will be canceled later on OTH Log a behavior other than breaths See Abbreviation appendix Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Sighting number 35 Subevent 36 Subsubevent 37 Group Individual 38 Other Behavior BAB GEN PRY Bait Ball General Entry or Prey Entry Bait Ball Bonanza K D gt ee Lan GOWNS Long w OWN 210 Bearing 1 2 Reticle MTI__F observed By CELOK Prey Comment Taxon Depth oop H BF E Add Species AWESOME m Echosounder on Images and IDs em o me mi ae ee n Access Home Screen gt Other Events gt Bait Ball This form was designed to be a quick and easy way of entering spastic data during a baitball encounter Clicking on the Predator buttons will open the appro
3. 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Sighting Number 35 Bearing 36 Reticle 37 Observer options determined by what has been entered in SURvey form 38 Position WIW POS With Whales Position Update Le With Whales Sighting 1 Position Update Behavior Group Ind G H Reticle Missed BTH BTH Bearing Lat N Breath Cancel BTH BTH i Est Distance m Long W a L TH Observed By z Store Other Bhvr Images and IDs O Images Taken Camera wi H Local Name Feature Fe Individual G E DFO ID e Comment Fluke Dive KJ KICL T Access Home Screen gt Sightings gt Select Sighting gt With Whales button When the With Whales form is opened the effort is changed automatically to 4 or With Whales When the form is closed however effort is not changed You must manually go to the effort page and change effort However if your effort is With Whales and you end a sighting ANY sighting your effort defaults to Casual 5 So if you are with a whale and you leave the With Whales form to end a distant sighting effort will be momentarily switched to casual until you re open the With Whales form Columns 1 Event 20 RU Bangarang 1 0 Users Manual Keen 2013 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Sighting number 35 Subevent 36 Subsubevent b
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5. Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix OBS Update Observer Positions D RU Bangarang 1 0 Users Manual Keen 2013 Observer Positions 0 x LatN COMNo Longw COMNo Observer Position Mi H mo H Roc pom g ps Comment im ma em fe Access Home Screen gt Other Events gt Observer Positions You can also double click the left of the observers status bar on the Home Screen The observers on offer here are determined by what is entered into the SURvey form Here you can only change their positions Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers ECO BEG END Echosounder Recording Begin and End Va ive Acoustics TANN Eng W Begin he Do LC eecorating L F occasion oT Filename Comments O Memorable ratN __ ktongw E ORAS z Access Home Screen gt Effort allows you to quickly denote the beginning and end of recording This does NOT end the recording You must do that manually on the echosounder computer This only notes that it has ended Home Screen gt Other Events gt Active Acoustics allows you to input more information and update an ongoing recording This screen can be modified then closed and the modifications will be saved however if the Back button is used modifications will not be saved Columns 1 Event 2 Date 3 Time 10 RU Bangaran
6. Engine oil level 35 Coolant level 36 Fuel level 37 House volts 38 RPM 39 Oil gauge 40 Temp gauge 41 Block temperature measured using infrared thermometer 42 Gearbox temperature 43 Heat exchanger temperature END End of RU Bangarang session This line is output automatically at the shutdown of the program Columns RU Bangarang 1 0 Users Manual Keen 2013 Event Date Time Latitude Longitude Filepath Total number of sightings for RUB session to this will make it easy to total the season sighting number NAIOP WN KH Effort Events EFF Change of Effort KA EEL L Access Home Screen gt Effort This effort code is saved to a public variable each time it is updated Most other forms save the current values for these effort variables visual passive acoustic and active acoustic in their outputs The effort form disables and enables buttons according to what the current effort is For example if the effort variable is currently 1 meaning On Transect the button to begin a transect is disabled This helps the user avoid mistakes In the above figure effort is currently at Casual and there are no acoustic recordings going on To Begin at a station you must first select the station number The Begin button will then become enabled When the program begins the default effort status is Casual 5 Effort status is displayed on the Home Page Columns 1 Event 2
7. GEN PRY NEW UPD END POS IMG COM BHV BHV BHV BHV BTH MIS FLK OTH Users Manual Keen 2013 Description New Output file Survey status Conditions Comment Comment flagging output for revision Engine status report End of output file Effort Update on Observer Positions Echosounder Begin recording Echosounder End recording Passive acoustics Begin recordings Passive acoustics End recording Passive acoustics New detection Passive acoustics Update on detection Passive acoustics End of detection CTD cast Zooplankton tow Secchi disk cast Debris sighting Bait Ball encounter general info Bait Ball encounter prey data Salmon sighting Vessel sighting Bird sighting Marine Mammal sighting Whale sighting new Whale sighting update Whale sighting end Encounter between vessel and whale With Whales position update With Whales Image and ID data With Whales comment With Whales behavior breath With whales behavior missed breath With whales behavior fluke With whales behavior other behavior 2 DATE is given in the format yyymmdd 3 TIME is Pacific Daylight Time taken from the computer system time given in the format hhmmss 4 RU Bangarang 1 0 Users Manual Keen 2013 4 5 GPS Coordinates are given in the format e g 5326543 12912897 This format is an expedient way to enter GPS data manually if the antenna fails I have written functions in R that translate th
8. gt Sightings gt Whale Users Manual Whale Sighting New or Update Whale Sighting E F If directional bearing of course EA WERS Lan COMNo Long W COMNo Keen 2013 To update a sighting select the open sighting on the main Sightings page and click the Update button below Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 OO 36 oO 38 99 40 41 42 43 44 45 46 Sighting number Subevent NEW UPD Bearing maximum length is 3 characters Reticle maximum length is 3 characters Observer options determined by what has been entered in SURvey form Blank previously Position Group size minimum Group size maximum Group size best Species 1 see abbreviation list Percent composition of total group size default is 100 Species 2 Percent composition 19 RU Bangarang 1 0 Users Manual 47 Behavior see abbreviation list default is BL blow 48 Direction of travel 49 Depth 50 General location SIW END End a Whale Sighting Keen 2013 A sighting is ended by selecting it on the Main Sightings page filling in the lat long and observer information on the bottom right of the form and clicking the End Sighting button If your effort is With Whales 4 when you end a sighting your effort automatically defaults to Casual 5 Columns 1 Event 2 Date
9. muak Buttons on the left allow you to enter specific types of sightings The central window displays any whale sightings that are still open A maximum of 5 can be open at any one time A dialog box will alert you when sightings must be closed in order to enter a new one DEB Debris or Plankton Sighting COMNo RckWd Field Extent Birds interacting a Withi gt Patch Within Strip o but on the line ROO ee see Access Home Screen gt Sightings gt Debris Plankton Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Type 35 Extent 36 In strip Boolean TRUE if clearly in the strip FALSE if not Default is TRUE 37 But on the Line Boolean TRUE if on the line of the strip FALSE if not Default is FALSE 38 Birds associating rafting Boolean TRUE if birds are associating with the debris FALSE if not Default is FALSE YUM Salmon Sighting 15 D RU Bangarang 1 0 Users Manual Keen 2013 LatN COMNo Number of jumps a Within Strip a but on the line Observer EMK Comments emo omu B O l Access Home Screen gt Sightings gt Salmon Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers determined by what has been entered in SURvey form 34 Jumps 35 Within Strip Boolean TRUE if clearly within the strip width F
10. ALSE if not Default is TRUE 36 But on the line Boolean TRUE if on the line of the strip FALSE if not Default is FALSE 37 Observer 38 Comment VES Vessel Sighting Vessel Sighting b42 Bearing Type CRZ__ H Name Zuiderdam ks Reticle Behavior TR H Company Holland America Observed By MTI If directional bearing of course INW Lat COMNo rongwEoMNo Comment Ce im ic 6 m e 8 sz Access Home Screen gt Sightings gt Vessel Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Bearing maximum length 1s 3 characters 16 RU Bangarang 1 0 Users Manual Keen 2013 35 Reticle maximum length is 3 characters 36 Observer options determined by what has been entered in SURvey form 37 Blank column previously Position 38 Vessel type 39 Name 40 Company 41 Direction of travel 42 Comment SIB Seabird Sighting Bird Sighting 0 x Alcid PF re Raptor Behavior Direction of travel Observer Storm Petrel Cormorant m Within Strip 4 but on line 2 EMK FLYN NE Phalaropes et al Waterfowl a Kittiwake MarbMurr Breed Group Size Lat N COMNo Shearwater Long W COMNo o Juvenile Brant Grebe Update Add species Jaegers Comp S me o omona O M Access Home Screen gt Sightings gt Bird This form is designed for rapid entry of a large amount of observations Wh
11. HELM HELM HELM HELM HELM HELM HELM HELM HELM HELM HELM HELM HELM HELM HELM MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MTI MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL STAR STAR STAR STAR STAR STAR STAR STAR STAR STAR STAR STAR STAR STAR STAR STAR STAR MIDL MIDL STAR STAR STAR ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC ROC PORT PORT PORT PORT PORT PORT PORT PORT PORT PORT PORT PORT PORT PORT MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL MIDL PORT PORT MIDL MIDL MIDL 25 Sophie whale pt hartley BEG 20130921_225640_1 TRN END 20130921_225640__1 WIW True Awesome BEG WIF 20130921 225704 1 TOW 100 NEW WIF 20130921 225704 1 Sweet 1 HW FEED 3 1 3 UPD WIF_20130921 225704 1 this is REALLY awesome 1 HW FEED 2 3 3 END WIF_20130921 225704 _ 1 1 HW 225709 WIF_20130921 225704 1 STP WIF_20130921 225704 1 TOW 100 False this was an awesome recor
12. No 230715 COM No 230721 COM No 230725 COM No 230734 COM No 230744 COM No 225811 COM No 225811 COM No 230754 COM No 230925 COM No 231002 COM No 231005 COM COM COM COM COM COM COM COM COM COM COM COM COM COM COM COM COM COM COM COM storm COM COM COM COM COM COM COM COM COM COM COM COM COM COM COM COM COM Oo OOOOOOGOOOGOOOCOOOOCOhHOO ot z gt H o lt s ooo0oo0o0o000000 00 0N0O0 000000 00rPEPEBPO oooo0oooocoocoocoocoocoococoe0co OoOrrA RA AHH HB HE oo Ss 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM EMK 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM 01 CAM FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL f FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL FULL lo l H amp PRPPRPPRPPRPRPRPRPRPRPRPRPEP
13. RU Bangarang 1 0 Users Manual Keen 2013 Research Underway Bangarang Data Entry Program Users Manual Developed by Eric Keen Scripps Institution of Oceanography Summer 20138 ekeen ucsd edu CONTENTS Diodot a2 ccuncontaseucsesctarentececacdeceaancuee 1 Where to Download cccc cece ceceneeeeeceees 1 Get Started os fenigasesanisacsnivsscseneiuneeremmess 1 Output OVELVIEW ccccccc cece eeeeceeseeeees 3 Output Standard Fields c ccc cece eee ees 4 Output Event Details cece eee cece cece eee 5 Appendix 1 Example output cc ccc eceeeeee 24 Appendix 2 RUB Abbreviations 05 25 INTRODUCTION RU Bangarang RUB is a data entry program designed specifically for my dissertation work in the northern Great Bear Fjordland It is designed to be an easily viewed intuitive button based way of entering observations while letting the computer take care of associating each entry with the necessary but intensive logistical data time gps coordinates current conditions observers on board effort status etc The forms are designed to be navigated by using the mouse using the tab key or using the touch screen It is also designed to output these data in a single file that can serve as both a raw record of the day s work and a single source from which to draw certain types of data e g locations of hydrophone recordings and the locations of sighted whales These at least were my i
14. SO ee ee m Home Screen gt Comment Sightings Main gt Comment There are also shortcuts to the comment form on various sightings forms COM is just a non revisionary comment entry The comment string is unlimited length The Comment window is not maximized so that windows underneath can be referenced for the comment Some forms have a column entry of their own which is appended to the end of their line In later versions the comment system in this program may be streamlined Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers RU Bangarang 1 0 Users Manual Keen 2013 34 Comment REV Revise recent code REV flags the code for review and editing by the PI later This output is achieved by checking the checkbox underneath the comment box that reads Flag recent code for review It has the same column names as COM ENG Engine status and performance Morning Temp gauge Coolant Levels e Temperature Engine Block Temperature Gearbox House Volts y Temperature Heat Exchanger fe Research Volts fe m o mam eee ee Access Home Screen gt Vessel Report fuel levels operating temperature and other maintenance related conditions of the engine This form is purely for the record keeping of the skipper Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34
15. Season Status data are displayed on the Home Page The observers selected here determine which observer initials are available in the Observed By fields of the sightings forms Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Other observers 35 Sail from 36 Sail to SEA Sea State and Sighting Conditions Conditions Vessel Spd GPS Heading RPM ee fe eo a O E swell m 0 1 cloudCover 65 Precip CER Visipitty amy E H Glare Bearing Current Flowing to the Left pho Right ho Strength Moat F mE J Wind Avg Spd km hr Out of the Air Temp C Barometric RU Bangarang 1 0 Access Users Manual Keen 2013 Home Screen gt Conditions You can also double click on the top left of the Conditions status screen on the Home Screen The data filled out in this form are displayed in the updated Master Conditions string See the section regarding it above for units and an index of columns Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers COM Access Comment Comment Lat N COM No Long W COM No Research Sightings None But 0 so far Longw comno PAM Off O Flag recent code for review i Store Acoustic Detections None Tows None out Current flowing Wind mph from the Echosounder Off Baro millibars Season P
16. avigation position at the helm MIDL The midships position PORT The bow position looking on the port side of the vessel STAR The bow position looking on the starboard side of the vessel 34 onward Event Details OUTPUT Event Details Following these standard data the output line then provides event specific data at the end of the line These Event Details are formatted uniquely for each event Some events are more information rich than others e g whale sightings while some are straightforward e g position and effort updates Below I outline the output 5 RU Bangarang 1 0 Users Manual Keen 2013 of each event code and the mechanics of the associated form s for logging it Logistics Events NEW New RUB Session has begun This line is output automatically at the opening of the RUB program No prefix conditions or observers are reported here Columns Event Date Time Latitude Longitude filepath moor w Ne SUR Survey Status Access This form automatically pops up at the openinge of the program It can also be accessed from the home screen See figure of form in Getting Started The default observers are changed according to who is on board at the time EMK is always a default observer This current version of RUB does not save the survey status info from the previously opened session Most of the details in this event are saved publicly and displayed in the outputs of other forms All
17. ding EMK HELM MTI STAR ROC MIDL this is awesome correction this is REALLY awesome STA 2 1 106100407 20130921 295929 csv mixing zone here True STA 2 100 VERTI EMK 9 34 MTI 9 23 ROC 8 97 A 20130921 2308 01 CAMA 342151 456756 230908 COM No COM No 250 275 that was awesome 89 23 123 45 EMK YAT Yacht s Up n a NE this yacht was awesome Wood Small Single True True True 1 True True EMK that salmon was awesome False True 75 FLYN MarbMurr Breed 20 Herring gull 20 Red necked phalarope 20 Surf scoter 123 45 In Strip But on the line EMK TR NW 0003 0003 0004 DP 25 PW 25 HS 50 1 BEG 123 45 EMK dig 25 2 HW 050 FW 50 BL N A 450 redfern point 1 UPD 123 45 EMK 7 1 2 2 HW 050 FW 50 TR S z 250 1 POS 45 123EMK 125 G 1 IMG True FL WILL G CSY0037 Claude 1 BHV BTH A 1 BHV MIS A 1 BHV CAN A 1 BHV FLK A 1 BHV OTH A BCH 1 COM this is awesome 1 END 123 45 EMK PRY ZOOP SURF GEN 341 13 EMK WBW True True 225858 123 45 EMK HELM SFV TR E Taken WIF it just happened all of a sudden like 3 4 x fall p fell 13 4 1500 60 160 178 120 139 RU Bangarang 1 0 Users Manual Keen 2013 APPENDIX 2 RUB Abbreviations Index Block CAM Caamano Sound CMP Campania Sound EST Estevan Sound SQS Squally Channel South SQN Squally Chann
18. el North WHA Whale Channel WRI Wright Sound VER Verney Passage and north Ursula MCK McKay Reach and south Ursula Whales HW Humpback FW Fin KW Killer BW Baleen generic Small Marine Mammals MarMams DP Dalls Porpoise PW Pacific White sided Dolphin SS Stellar s Sea Lion CS California Sea Lion HS Harbor Seal ES Northern Elephant Seal SO Sea Otter RO River Otter Occasion STA Station WIW With Whales HOC Ad Hoc unplanned OTH Other Image Feature FTR FL Fluke LD Left Dorsal RD Right Dorsal OT Other Species Vessel Types SAL Sailing vessel REC Recreational sports fishing vessel YAT Yacht pleasure cruiser CFV Commercial Fishing Vessel Seiner GIT Gitga at boat CRZ Cruise ship TKR Tanker BRG Barge and tug Tug Tug Vessel Company WCR West Coast Resorts NKL North King Lodge HNJ Hermann and Janie GIT Gitga at Spirit Guardian OTH Other Behavior With Whales Marine Mammsls Birds MIL Milling BL Blow STAT Stationary SLP Sleeping MI Milling FLYN Flying BCH Breach FE Feeding FLOC Flocking PEC Pectoral Slap SL Sleeping FLUS Flushed FAC Face Slap HO Hauled Out FEED Feeding TAL Tail Slap BR Breach RAFT Rafting on debris TON Tonal Blow PS Pec Slap BALL Bait Ball SPY Spy Hop OT Other FOLO Following a boat FED Deep Foraging Dive FEL Lunge Feed at surface Vessels Acoustic FEB Bubble Net Feed TR Travel MOAN Moan TRN Traveling North n o re WSTL Whistle TRE TR East ishing FEED Feed
19. en the page opens the box listing possible species seen is blank Click on one of the seabird group buttons and the box fills with possible species within that group The appropriate species is then selected and other information is filled in If more than one species is seen in the group you can add species to the sighting upon clicking Add Species the species listbox will empty and you must press another Taxon button to select from its species list A maximum of 5 species can be included in a single sighting After the fifth species is added the Add Species button is disabled Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 In Strip Boolean TRUE if clearly in the strip FALSE if not Default is TRUE 35 But on the Line 36 Group size 37 Behavior Codes 4 character strings STAT stationary swimming FLYN in flight FLOC flocking 17 RU 38 99 40 41 42 43 44 45 46 4 48 49 50 ol 52 SIM Bangarang 1 0 Users Manual Keen 2013 FLUS flushed by our vessel FEED foraging feeding RAFT rafting on debris BALL bait ball bonanza FOLO following our vessel Species 1 Species 1 percent composition of overall group size default is 100 Species 2 Gif present Species 2 percent composition Species 3 1f present Species 3 perc comp Species 4 if present Species 4 perc comp Species 5 if prese
20. g 1 0 Users Manual Keen 2013 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Subevent 35 Filename Filename is currently coded as yyyyMMdd_hhmmesstt_ of the day 2 characters if less than 10 recordings the first character is an underscore For example 20130603_093212pm_1 The file extension for Syqwest Hydrobox echosounder output is odc 36 Occasion Occasion codes 3 character strings are similar to those in CTD TRN Along transect STA station POI point count WIW with whales DVM daily vertical migration ADH Ad hoc impromptu unplanned 37 A blank column previously Station number 38 Memorable Boolean TRUE is yes it is memorable FALSE if not 38 Comment unlimited length PAM BEG STP NEW UPD END Passive Acoustic Monitoring recording Passive Acoustics LatN COMNo Longw COMNo unit New Detection Comments EN Long End Recording KA E a ree Subevents BEG Denotes the beginning of a recording STP Denotes the end of a recording NEW A new acoustic detection during a recording UPD An update of a previously detected noise END And of an acoustic detection Access Home Screen gt Effort allows you to quickly denote the beginning and end of recording This does NOT end the recording You must do that manually on the echosounder computer This only notes that it has ended Home Screen gt Other Events gt Passive Acous
21. ing call TRS TR South AN Anchor TBLO Tonal blow TRW TR West WW With Whales SOCL Social call OT Other ECHO Echolocation click SONG Song OTHR Other 26
22. is string of numbers into a format that can be mapped in the R package PBSmapping from the DFO Pacific Biological Station In certain events the GPS stamp in this first section of output corresponds to only the beginning of the event If the GPS readings begin misbehaving there is a GPS Repair button on the Other Events form that usually fixes the problem 6 11 EVENT PREFIX This section of the output line consists of multiple columns 6 Effort status 0 0ff Effort 1 On Transect 2 Point Count no longer used 3 At station 4 With Whales 5 Casual Effort 7 PAM Recording status 1 for recording 0 for not recording 8 Echosounder status 1 for recording 0 for not recording 9 Study circuit 10 Block CAM Caamano Sound CMP Campania Sound EST Estevan Sound SQS Squally South SQN Squally North WHA Whale Channel WRI Wright Sound MCK McKay Reach South Ursula VER Verney Passage North Ursula 11 Mode Full Lite or Zero 12 27 MASTER CONDITIONS Beaufort Swell height Cloud cover Visibility Precipitation Glare bearing left glare bearing right water current strength current direction flowing to the GPS speed knots vessel heading engine RPM wind average speed mph wind direction coming out of the air temperature Celsius barometric pressure kPa 28 33 OBSERVERS Observers reported as their 8 initials Positions are 4 letter descriptors HELM The data entry n
23. lank in this case 37 Bearing maximum length is 3 characters 38 Reticle maximum length is 3 characters 39 Observer options determined by what has been entered in SURvey form 40 Estimated distance a convenient replacement to reticles when you are close to the whale 41 Group Individual This allows you to differentiate between following the group and following an individual within the group If you are following an individual arbitrarily assign it a letter e g A and make a comment about why this individual is trackable and distinguishable from the others WIW IMG With Whales A good photo ID image is taken This entry is a convenient way of matching photographs to sightings when processing images in PhotoMechanic at the end of a day It is especially convenient if you are tracking certain individuals in a group worth making notes on e g mothers and calves Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Sighting number 35 Subevent 36 Subsubevent blank in this case 37 Images Taken True or False 38 Feature FL RD LF Other 39 Camera 40 Group Individual designation 41 DFO ID if recognized 42 Local name if known WIW COM Comment logged while with a whale There is a convenient comment field on the With Whales page The second you store a comment the field clears and is ready to accept the next comment Columns
24. lename in which the session s data has been stored The program will then close vez The Back Button Almost every form in RUB displays the Bangarang whale tail icon shown above Clicking this icon will close the current form without saving any information to the text file and return you to the home screen RU Bangarang 1 0 Users Manual Keen 2013 OUTPUT Overview RU Bangarang RUB saves logged data into a single txt file in a dedicated folder on the C drive C Bangarang Text files are cross platform open source and highly stable They can be read in as csv s in R The text file output also provides a raw unfiltered narrative of the day s research effort A downside is that it is barely legible to the untrained eye However the text file can then be fed to an R script that breaks the single file into highly organized dataframes WITHOUT risking the corruption of the original data Every line in the output text file corresponds to a certain event For instance all the information given during a seabird sighting is reported as a single line in the output In each line the data is comma separated into columns Each line regardless of event follows the same format for the first many columns Almost all entries will have the following packages of data for each line to make post processing easier Format of a typical output line Event Code Date Time GPS Event Prefix Master Conditions Observers Subevent Code Event De
25. nt Species 5 perc comp Direction of travel Observer options determined by what has been entered in SURvey form Observer position Time of position update GPS of position update Juvenile Boolean TRUE if yes the bird added is a juvenile Marine Mammal non whale Sighting i Marine Mammal Sighting m In Strip Initial behavior O But on the line Observed By If directional bearing of course Min ERI Best Groupsize i J 2 JE Composition o i Lan COMNo Longw COMNo bs Species 1 eae a L T species3 Emon 0m omia a is m Access Home Screen gt Sightings gt MarMam Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers OA OO 36 O7 38 99 40 41 Bearing maximum length is 3 characters Reticle maximum length is 8 characters Observer options determined by what has been entered in SURvey form Behavior Direction Group size minimum estimate Group size maximum estimate Group size best guess 18 RU 42 43 44 45 46 4 SIW NEW amp UPD Bangarang 1 0 Species 1 see Abbreviation index Spp1 percent comp default is 100 Spp2 Spp2 percent comp Spp3 Spp3 percent comp Sighting 176 Bearing 23 Reticle Min x Depth m Location Middle ofCasanave Composition Hw Fl Species1 fo O species KA ENKOLI LN I TTTTTTTCCSC CtisCia Access Home Screen
26. ntentions The program was written in Visual Basic 2010 Express and published as a stand alone executable file exe for Windows The program outputs text files to a folder it creates on the C directory of your computer In addition to making this program available to others I have provided the project files for the program as well as my R scripts for analyzing the output text files on my website They could be tailored to specific research needs or provide examples to those who start from scratch A warning Iam by no means a programmer and the scripts are scrappy to say the least Do not expect eloquent or efficient code WHERE TO DOWNLOAD RUB can be used only on Windows platforms XP 7 or 8 that have the free VB NET framework installed The program can be downloaded for free either as a stand alone exe or as a Visual Basic project able to be edited It can be accessed here on Eric s website Navigate to Research gt Dissertation Work gt Reports amp Software GETTING STARTED When the program starts up the user is presented with a start up window whose Visual Basic code contains most of the running mechanics of the program saving master variables and updating the GPS location This window can be minimized but it cannot be closed It will only be closed when the Home Screen is closed and the user confirms that she is sure she wants to quit RU Bangarang 1 0 ers Manual Keen 2013 Bangarang Master BANGARANG Data Ent
27. ount Conducted during a point count for birds OTH Other conducted for some other reason WIW With Whales conducted because we are doing a focal follow of whales 35 Station number 36 Replicate refers to the first second or third cast at that site in case there are several The default entry is 1 37 CastAway filename Using the system time the probably filename of the CTD cast is recorded in the same format as it will be save in the CTD itself This will aid in matching casts to the RUB output 38 Comments on surface features debris eddies observed water column characteristics etc ZOO A zooplankton tow 13 RU Bangarang 1 0 Users Manual Keen 2013 Zooplankton Tow Occasion Pay out depth m 250 Localdepth m 275 _ Flowmeter before 25342 Begin Tow Identification 20131002 1117 01 CAM2 Elapsed time of 50m payout 86 43 GPS driftspeed 6 from 25m mark to 75m tn om Flowmeter after 396754 Long W RSC ee ree Access Home Screen gt Other Events gt CTD The buttons are programmed to be enabled and disabled only when the critical information has been entered For example you can press the BEGIN tow button unless the flowmeter number has been entered first Correspondingly you can t store the code unless the flowmeter number has been stored afterward Because tows usually happen in succession 1 e along block transects or when With Whales the values from
28. priate sighting page without closing the BaitBall form Columns 22 RU Bangarang 1 0 Users Manual Keen 2013 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Subevent GEN or PREY 35 Gen Bearing Pry prey 36 Gen Reticle Pry depth 37 Observer options determined by what has been entered in SURvey form 38 Blank column Previously Position 39 Camera used if any 40 Images Taken Boolean TRUE if images were taken FALSE if not Default is FALSE 41 Echosounder Boolean TRUE if the echosounder is recording during the encounter FALSE if not Default is FALSE 42 Timestamp of when form is stored and baitball is left ENC Encounter between Vessel and Whale Vessel Encounter Bearing to Incident Reticle Observed By Position Whale Vessel Sighting svi 1 HW 2 111942 Type Behavior TR H Direction SE Image Series 4 Taken Camera wF H Description VERY close call NOT awesome _ _ LatN COMNo Longw omno E m o 0 muam a eee Access Home Screen gt Other Events gt Vessel Encounter Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Sighting number 35 Bearing maximum length 1s 3 characters 36 Reticle maximum length is 3 characters 37 Observer options determined by what has been entered in SURvey form 38 Ve
29. ry Program RU Bangarang 1 0 Summer 2013 Eric Keen S itution Blew ae Note the high contrast display need for viewing outdoors This is a property of the laptop and not the program The user is then asked to enter basic survey information about the day see SUR info below for details Survey Circuit o2 H Sightings so far o0 H Block au H Mode FULL J Observer 1 Observer 2 Observer 3 Other Observers EA E 6 a LT The Home Screen The user interacts with RUB starting at the Home Screen This screen both displays the status of all ongoing research efforts and provides menus for entering new observations 09 13 13 Circuit 02 Mode FULL Lat N COM No 17 50 00 Block SQU Effort Casual Long W COM No Observers EMK HELM MTI MIDL ROC PORT Conditions Research GPS Spd 4 8 RPM 1500 Sightings None But 0 so far BFT 0 Swell 0 1 RU Bangarang Home Screen Sightings PAM Off Conditions Cloud 65 Precip CLR Acoustic Detections None Vis lt Inf Glare no no Other Events Current Modrt flowing NE Wind 3 2mph from the SW Echosounder Off Baro 1023 2millibars Season EA ENKOLI ILI ld Tows None out Exiting To exit RUB you must close the Home Screen A dialog box will appear making sure you wish to quit If you did not mean to quit press No and nothing will close If you press Yes a dialog box will appear telling you the fi
30. ssel type 39 Behavior of Vessel 40 Direction of travel 41 Images taken true or false 42 Camera used 23 RU Bangarang 1 0 Users Manual Keen 2013 43 Description unlimited string length APPENDIX 1 EXAMPLE OUTPUT Below is an example of every possible output in the program 24 Keen 2013 Users Manual Bangarang 1 0 RU NEW SUR SEA EFF ECO ECO PAM PAM PAM PAM PAM OBS COM REV CTD SEK ZOO VES DEB YUM SIB SIM SIW SIW WIW WIW WIW WIW WIW WIW WIW WIW SIW BAB BAB ENC ENG POS END 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20130921 20 225452 225458 COM No 225531 COM No 225624 COM No 225640 COM No 225653 COM No 225704 COM No 225709 COM No 225736 COM No 225753 COM No 225805 COM No 230026 COM No 225904 COM No 225911 COM No 225929 COM No 225953 COM No 230852 COM No 230046 COM No 230148 COM No 230208 COM No 230225 COM No Fork tailed 230349 COM No 230441 COM No 230538 COM No 230626 COM No 230656 COM No 230710 COM No 230713 COM
31. tails Many of these packages comprise several columns Most standard output entries follow the following column index 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 6 Effort 7 PAM Status 8 Echosounder Status 9 Circuit 10 Block 11 Survey Mode 12 27 Conditions 12 Beaufort sea state 13 Swell height m 14 Percent cloud cover 15 Visibility 16 Precipitation status 17 Glare left bearing 18 Glare right bearing 19 Current strength 20 Curren direction setting 21 Vessel GPS speed 22 Vessel Heading 23 Vessel speed over water 24 Wind speed Averaged mph 25 Wind direction out of the 26 Air temperature 27 Barometer 28 33 Observers 28 Observer 1 29 Observer 1 position helm midship bow port bow starboard 30 Observer 2 31 Observer 2 position 32 Observer 3 33 Observer 3 position RU Bangarang 1 0 Event Details 34 OUTPUT Standard Fields 1 EVENT CODE A three character acronym that describes the event being reported see Output Index below For instance an output line describing a Slghting of a seaBird begins with the event code SIB Event Subevent Col 1 Where applicable Logistics Effort NEW SUR SEA COM REV ENG END EFF OBS ECO ECO PAM PAM PAM PAM PAM Stations CTD ZOO SEK DEB Sightings BAB BAB YUM VES SIB SIM SIW SIW SIW ENC WIW WIW WIW WIW WIW WIW WIW BEG END BEG STP NEW UPD END
32. the last entered tow during the program s session are displayed when a new Tow form is opened The values however are still editable Columns 1 Event 2 Date 3 Time this is when the tow began 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Occasion automatically supplied if effort is already At Station 35 Tow Identification Number TIN Format without spaces in reality yryyMMddhhmmtt CIRCUIT BLOCK Station Code For example In Caamano Sound South on Circuit 2 on June 22 at 08 43am at station 02 the TIN will be 201306220843am1CSS02 36 Flowmeter begin 6 digits 37 Flowmeter end 6 digits 38 End timestamp 39 End Latitude should be automatically logged by the software unless the GPS has failed 40 End Longitude should be automatically logged 41 Payout m The default pay out depth is 250m the total length of the zooplankton line but it can and SHOULD be changed according to local depth 41 Local depth m 42 Comment Sightings Events To enter a sighting go to the Sightings button on the Home Screen You will be brought to this new window 14 RU Bangarang 1 0 Users Manual Keen 2013 LP Sighting MASTER ag x New Sighting Open Whale Sightings Sit Spp Grp Location Whale Bird WET Ee ME Salmon End Coordinates 2 ee e CIO Debris Enc p Plankton Update Sighting ong W n ye With Whale Bearing __ Observer Reticle L L TH Cm o 6
33. tics allows you to input more information and update an ongoing recording Note that there is no back button on this page To get away from the page without storing changes the form must be X d out on the top right of the screen Once a recording is logged as having begun acoustic detections can be logged updated and ended The Open Detections box lists any ongoing detections Users can select a detection from this box and update or end it Only 5 detections can be open at a time Columns 11 RU Bangarang 1 0 Users Manual Keen 2013 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Subevent 35 Filename formatted automatically as it will likely appear in the output from Raven on the PAM Mac 36 Unit which hydrophone is used Default is the TOWed array 37 Payout Default payout is the full length of the Bangarang array 100m 38 Memorable Boolean TRUE means the recording is memorable and FALSE means it is not Default is FALSE 39 Comment unlimited string length 40 Detection number tally kept automatically by computer 41 Spp See abbreviations index 42 Behavior See abbreviations index 43 Signal to noise ratio 0 silent to 5 distorted 44 Vessel noise 0 silent to 5 distorted 45 Background noise 0 silence to 5 loud Station Events SEK Secchi Cast Secchi Cast LatN COMNo Longw COMNo Occasion sta T If Station
34. which 2 H Cloud e5 Secchi depth m 87 EKT 6 a ma ca o Viewerbox Used Store Drop Angle VERTI m o mu A Access Home Screen gt Other Events gt Secchi Cast Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Viewbox used Viewbox Boolean TRUE if used FALSE if not used 35 Occasion see CTD output 36 Station If your effort has already been changed to At Station the station number will automatically be filled in on this form 37 Cloud cover 12 RU Bangarang 1 0 Users Manual Keen 20138 38 Angle 39 Observer 1 filled in automatically from what was entered in the SURvey page Same for other obs 40 Observer 1 depth m 41 Observer 2 42 Observer 2 depth 43 Observer 3 44 Observer 3 depth CTD A CTD cast CTD Cast Lat CONN Long w Commo Occasion sa Y H Station Replicate Filename 10G100407_20131002_181613 csv Comment fThisisAwesome A Store PSC ee ree Access Home Screen gt Other Events gt CTD Columns 1 Event 2 Date 3 Time 4 Latitude 5 Longitude 6 11 Prefix 12 27 Conditions 28 33 Observers 34 Occasion STA Station at a Study Station within a block DVM Dawn and evening diel vertical migration observations HOC Ad Hoc unplanned conducted due to interesting features encountered or just plain feel like it POI Point C

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