ZSL CAMERA TRAP ANALYSIS PACKAGE

RAJAN AMIN, KEVIN DAVEY, TIM WACHER

ZSL CAMERA TRAPPING

• BIODIVERSITY SURVEY AND MONITORING

• RESEARCH IN ANALYTICAL METHODS

• TRAINING IN FIELD IMPLEMENTATION

• ANALYTICAL PROCESSING TOOLS

• RANGE OF SPECIES, HABITATS & CONSERVATION OBJECTIVES

• ALGERIA

• KENYA

• TANZANIA

• LIBERIA

• GUINEA

• NIGER

• SAUDI ARABIA

ZSL CAMERA TRAPPING

• MONGOLIA

• NEPAL

• THAILAND

• INDONESIA

• RUSSIA

• Et al.

KENYA: ADERS’ DUIKER

COASTAL FOREST

• Critically endangered species • Poor knowledge of wildlife in the area

MONGOLIA: GOBI BEAR

DESERT • Highly threatened flagship species • Very little known about it

NEPAL: TIGER

• National level surveys, highly threatened flagship species

GRASSLAND AND FORESTS

SAUDI ARABIA: ARABIAN GAZELLE

• Highly threatened species • Monitoring reintroduction efforts

ZSL CAMERA TRAP ANALYSIS PACKAGE

OCCUPANCY

ACTIVITY

SPECIES RICHNESS

TRAPPING RATE & LOCATION

Why is an analysis tool needed?

WA Large-spotted Genet

0

1

2

3

4

5

6

7

0 2 4 6 8 10 12 14 16 18 20 22

Hr.

Even

ts

Bourlon's Genet

0

1

2

3

4

5

6

7

8

0 2 4 6 8 10 12 14 16 18 20 22

Hr.

Even

ts

0

5

10

15

20

25

30

0 10 20 30 40 50 60

Days of Camera trapping

N S

pe

cie

s

Observed Discovery Rate

Minus 1 sd

Plus 1 sd

Diversity estimate (Jacknife 1)

MANUAL PROCESSING: MULTI-SPECIES STUDIES

45 cameras x 150days x c.30sp

MANUAL PROCESSING: MULTI-SPECIES STUDIES

80 Camera sites x 100 days x c.30sp

Amin, R., Andanje, S., Ogwonka, B., Ali A. H., Bowkett, A., Omar, M. & Wacher, T. 2014 The northern coast forests of Kenya are nationally and globally important for the conservation of Aders’ duiker Cephalophus adersi and other antelope species. Biodivers. Conserv. DOI 10.1007/s10531-014-0842-z

CAMERA TRAP ANALYSIS PACKAGE

• A DATA MANAGEMENT AND ANALYSIS SYSTEM FOR CAMERA TRAP ARRAYS

Starting Point: Camera arrays: Guinea 2008 & Kenya 2010

Why is it needed?

• Camera arrays – Create very large data sets

• Multiple species

• Multiple data manipulations required

• Lack of central data management system

• High potential for errors in manual data handling

• Files tend to proliferate during manual analysis

• Lack of standardisation in manual analysis

• Very slow, loss of data, incomplete analyses/reports

• No equivalent package available (when project started..)

What does it do? Phase 1

• Targeted at processing data from camera arrays

• Manages multiple surveys within a single database

• Provides standardised data model for comparison and monitoring biodiversity over the longer term

• Country species templates

• Enables data filtering, image checking, processing and correction

• All tables and graphs produced can be customised and exported in different formats.

What does it do? Phase 1 Outputs:

– Survey effort reports

– Species list (taxonomically ordered with information on habitat, habit, tropic level, adult body weight, IUCN Red List threat status) with number of images, number of events and number of camera stations detected

– Rarefaction curves and species richness estimates

– Species spatio-temporal plots

– Species trapping rates with standard errors (overall and daily / seasonal)

– Species occupancy modelling (with sites covariates)

– Distribution plots of trapping rates and occupancy (in Google Earth, QGIS and ArcGIS)

– Activity patterns

ZSL– CAMERA TRAP DATA PROCESS

ZSL Camera Trap Tool

Field variables

Ana

Note: The tool requires appropriate ‘R’ packages pre-loaded (but no manipulation of ‘R’ necessary) and computer date/time format harmonised – See manual

Back up

Analysis package

Crowd sourcing?

IMAGE PROCESSING

CONVERTS THIS…

TO MANAGED DATA SYSTEM: IMAGE CHECKING, SORTING & EDITING

SUMMARY REPORTS: CAMERA OPERATION

CAMERAS STATION SAMPLING HISTORY : IBEX RESERVE, SAUDI ARABIA

SUMMARY REPORTS: SAMPLE EFFORT

No. CAMERAS WORKING ON EACH DAY OF SURVEY : BONI FOREST, KENYA

15/0

6/2

010

13/0

6/2

010

11/0

6/2

010

09/0

6/2

010

07/0

6/2

010

05/0

6/2

010

03/0

6/2

010

01/0

6/2

010

30/0

5/2

010

28/0

5/2

010

26/0

5/2

010

24/0

5/2

010

22/0

5/2

010

20/0

5/2

010

18/0

5/2

010

16/0

5/2

010

14/0

5/2

010

12/0

5/2

010

10/0

5/2

010

08/0

5/2

010

06/0

5/2

010

04/0

5/2

010

02/0

5/2

010

30/0

4/2

010

28/0

4/2

010

26/0

4/2

010

24/0

4/2

010

22/0

4/2

010

20/0

4/2

010

18/0

4/2

010

16/0

4/2

010

14/0

4/2

010

12/0

4/2

010

10/0

4/2

010

08/0

4/2

010

06/0

4/2

010

04/0

4/2

010

02/0

4/2

010

31/0

3/2

010

29/0

3/2

010

27/0

3/2

010

25/0

3/2

010

23/0

3/2

010

21/0

3/2

010

19/0

3/2

010

17/0

3/2

010

Num

ber

of

Sam

plin

g C

am

era

Sta

tions

20

19

18

17

16

15

14

13

12

11

10

9

8

7

6

5

4

3

2

1

0

SUMMARY REPORTS: CAMERA PERFORMANCE

CAMERA PERFORMANCE : BONI FOREST, KENYA

SUMMARY REPORTS: CAMERA LOCATION & PERFORMANCE

CAMERA LOCATIONS AND PERFORMANCE ON GOOGLE EARTH : BONI FOREST, KENYA

Camera Station Latitude Longitude

Ca

me

ra

reco

ve

ry

Ca

me

ra s

etu

p

Oth

er

- b

lan

k

Oth

er

-

ca

me

ra m

ou

nt

mo

ve

me

nt

Oth

er

- in

se

ct

Wild

life

Wild

life

-

un

ide

nti

fia

ble

Wild

life

-

un

ide

nti

fie

d

TOTAL

C1_BN-01-01 001° 39' 11.82" S 041° 16' 25.51" E 26 15 69 6 0 942 0 0 1058

C2_BN-01-02 001° 38' 20.88" S 041° 16' 02.30" E 48 18 57 0 3 945 0 0 1071

C3_BN-01-03 001° 37' 29.87" S 041° 15' 16.32" E 6 12 21 0 0 2358 0 0 2397

C4_BN-01-04 001° 36' 34.56" S 041° 14' 35.83" E 51 15 228 0 0 1332 0 0 1626

C5_BN-01-05 001° 35' 33.80" S 041° 14' 02.13" E 42 12 33 0 0 1227 0 0 1314

C6_BN-01-06 001° 34' 45.37" S 041° 13' 31.94" E 18 18 51 0 0 111 0 0 198

C7_BN-01-07 001° 33' 49.56" S 041° 12' 55.63" E 0 24 30 0 0 672 15 0 741

L1_BN-01-08 001° 39' 49.14" S 041° 15' 34.58" E 24 15 33 0 0 573 24 0 669

L2_BN-01-09 001° 38' 53.46" S 041° 15' 05.06" E 90 12 39 0 0 669 27 0 837

L3_BN-01-10 001° 37' 58.37" S 041° 14' 28.23" E 23 6 24 0 0 462 0 0 515

L4_BN-01-11 001° 37' 09.01" S 041° 13' 49.49" E 34 9 12 0 0 1149 0 0 1204

L5_BN-01-12 001° 36' 14.99" S 041° 13' 15.60" E 25 15 123 0 0 669 39 0 871

L6_BN-01-13 001° 35' 19.15" S 041° 12' 40.04" E 10 5 60 0 0 2685 42 0 2802

R1_BN-01-14 001° 33' 49.53" S 041° 12' 55.59" E 32 24 30 0 0 546 21 0 653

R2_BN-01-15 001° 38' 37.09" S 041° 17' 29.86" E 0 12 15 0 0 390 24 0 441

R3_BN-01-16 001° 37' 47.82" S 041° 16' 51.96" E 0 0 0 0 0 0 0 0 0

R4_BN-01-17 001° 36' 49.29" S 041° 16' 08.53" E 42 12 18 0 0 888 9 0 969

R5_BN-01-18 001° 36' 00.77" S 041° 15' 35.49" E 24 12 189 0 0 5283 54 0 5562

R6_BN-01-19 001° 35' 00.47" S 041° 15' 03.60" E 26 12 36 0 0 1137 9 0 1220

R7_BN-01-20 001° 34' 08.37" S 041° 14' 27.62" E 51 12 21 0 0 1029 9 3 1125

TOTAL: 572 260 1089 6 3 23067 273 3 25273

SUMMARY REPORTS: PHOTO TYPE TOTALS

Camera recovery 4.9 %

Camera setup 3.68 %

Other - blank 4.59 %

Other - camera mount movement 0 %

Other - insect 0 %

Wildlife 83.61 %

Wildlife - unidentif iable 3.22 %

Wildlife - unidentif ied 0 %

Camera Station: R1_BN-01-14

Camera recovery 2.26 %

Camera setup 1.03 %

Other - blank 4.31 %

Other - camera mount movement 0.02 %

Other - insect 0.01 %

Wildlife 91.27 %

Wildlife - unidentif iable 1.08 %

Wildlife - unidentif ied 0.01 %

Camera Station: <All>

BONI FOREST – COASTAL KENYA 2010

COMPILED SPECIES LISTS

SAPO NATIONAL PARK - LIBERIA

Order Family or Subfamily Scientific Name Local NameIUCN

StatusHabitat Habit Trophic Level

Avg.

Adult

Weight

(kg)

Avg.

Home

Range

(km²)

No. of

Images

No. of

Events

No. of

Stations

Detected

in

Mammalia

Carnivora Felidae Caracal aurata African golden cat VU Forest T Carnivore 10 6 3 2

Carnivora Felidae Panthera pardus Leopard NT Mixed T Carnivore 40 6 2 2

Carnivora Herpestidae Atilax paludinosus Marsh mongoose LC Wetland SA Carnivore 3 216 59 16

Carnivora Herpestidae Crossarchus obscurus Common cusimanse LC Forest T Carnivore 1 15 5 4

Carnivora Herpestidae Liberiictis kuhni Liberian mongoose VU Forest T Carnivore 2.3 3 1 1

Carnivora Mustelidae Mellivora capensis Honey badger LC Mixed T Carnivore 10 6 1 1

Carnivora Viverridae Civettictis civetta African civet LC Mixed T Carnivore 11.5 60 9 6

Carnivora Viverridae Genetta bourloni Bourlon's genet NT Forest T Carnivore 1.5 30 10 5

Carnivora Viverridae Genetta pardina Pardine genet LC Forest T Carnivore 1.5 24 4 4

Carnivora Viverridae Genetta sp. Genet sp. Mixed T Carnivore 0 24 8 7

Cetartiodactyla Cephalophinae Cephalophus dorsalis Bay duiker LC Forest T Herbivore 20 63 16 8

Cetartiodactyla Cephalophinae Cephalophus jentinki Jentink's duiker EN Forest T Herbivore 68 30 7 5

Cetartiodactyla Cephalophinae Cephalophus niger Black duiker LC Forest T Herbivore 22 33 10 6

Cetartiodactyla Cephalophinae Cephalophus ogilbyi Ogilby's duiker LC Forest T Herbivore 17 276 71 20

Cetartiodactyla Cephalophinae Cephalophus sp. Duiker sp. Forest T Herbivore 0 84 26 13

Cetartiodactyla Cephalophinae Cephalophus zebra Zebra duiker NT Forest T Herbivore 14 195 51 14

Cetartiodactyla Cephalophinae Philantomba maxwelli Maxwell's duiker LC Woodland T Herbivore 3 339 84 19

Cetartiodactyla Suidae Potamochoerus porcus Red River Hog LC Mixed T Omnivore 53 36 3 2

Cetartiodactyla Tragulidae Hyemoschus aquaticus Water Chevrotain LC Forest SA Herbivore 11 24 7 2

Pholidota Manidae Phataginus tricuspis White-bellied pangolin VU Forest T Insectivore 2.5 9 3 3

Pholidota Manidae Smutsia gigantea Giant pangolin VU Forest T Insectivore 32 15 3 3

Primates Cercopithecidae Cercocebus atys Sooty Mangabey VU Forest G Frugivore 8 944 158 25

Primates Cercopithecidae Cercopithecus campbelli Campbell's monkey LC Woodland Ar Herbivore 3.5 12 4 2

Primates Cercopithecidae Cercopithecus diana Diana monkey VU Forest Ar Herbivore 4.5 3 1 1

Primates Hominidae Pan troglodytes verus Western Chimpanzee EN Forest T Insectivore 50 18 5 5

Proboscidea Elephantidae Loxodonta africana cyclotis African forest elephant VU Forest T Herbivore 1000 51 3 3

SPECIES ACCUMULATION AND RICHNESS CURVES

AUTOMATICALLY LAUNCHES ‘R’ TO RUN CALCULATION Or export processed data e.g to EstimateS - Colwell 2013

SPATIO-TEMPORAL PLOTS

FOUR-TOED SENGI : ARABUKO-SOKOKE FOREST, KENYA

Mean number of independent photographic events per trap-day times 100

Ara

bia

n b

abble

r

Ara

bia

n g

azelle

Ara

bia

n s

pin

y m

ouse

Bat sp.

Bla

cksta

rt

Bushy-t

aile

d ji

rd

Cam

el

Cape h

are

Com

mon k

estr

el

Desert

eagle

ow

l

Desert

hedgehog

Desert

lark

Dom

estic

cat

Donkey

Eura

sia

n c

olla

red d

ove

Fox s

p.

Gre

y m

onito

r

Gre

y w

olf

Hoopoe

Laughin

g d

ove

Murid s

p.

Nubia

n ib

ex

Red fox

Rock h

yra

x

Sand p

art

ridge

Shoat

Spanis

h s

parr

ow

Str

ioalte

d b

untin

g

Unid

entif

ied b

ird

Unid

entif

ied c

at

White

-cro

wned w

heate

ar

White

-specta

cle

d b

ulb

ul

3.8

3.6

3.4

3.2

3

2.8

2.6

2.4

2.2

2

1.8

1.6

1.4

1.2

1

0.8

0.6

0.4

0.2

0

TRAPPING RATES

WADI NUKHAYLAN : IBEX RESERVE, SAUDI ARABIA

DATA EXPLORATION: TEMPORAL SEQUENCES

Species: Camel

08/0

6/2

013

01/0

6/2

013

25/0

5/2

013

18/0

5/2

013

11/0

5/2

013

04/0

5/2

013

27/0

4/2

013

20/0

4/2

013

13/0

4/2

013

06/0

4/2

013

30/0

3/2

013

23/0

3/2

013

16/0

3/2

013

09/0

3/2

013

02/0

3/2

013

23/0

2/2

013

16/0

2/2

013

09/0

2/2

013

02/0

2/2

013

26/0

1/2

013

19/0

1/2

013

12/0

1/2

013

05/0

1/2

013

29/1

2/2

012

22/1

2/2

012

15/1

2/2

012

08/1

2/2

012

01/1

2/2

012

24/1

1/2

012

17/1

1/2

012

Num

ber

of In

dependent P

hoto

gra

phic

Events

9

8.5

8

7.5

7

6.5

6

5.5

5

4.5

4

3.5

3

2.5

2

1.5

1

0.5

0

CAMELS Nov.12 to Jun 13

EVENT FREQUENCY BY DATE

TERMIT - NIGER Nov.12 to Jun 13

Species: Golden jackal

08/0

6/2

013

01/0

6/2

013

25/0

5/2

013

18/0

5/2

013

11/0

5/2

013

04/0

5/2

013

27/0

4/2

013

20/0

4/2

013

13/0

4/2

013

06/0

4/2

013

30/0

3/2

013

23/0

3/2

013

16/0

3/2

013

09/0

3/2

013

02/0

3/2

013

23/0

2/2

013

16/0

2/2

013

09/0

2/2

013

02/0

2/2

013

26/0

1/2

013

19/0

1/2

013

12/0

1/2

013

05/0

1/2

013

29/1

2/2

012

22/1

2/2

012

15/1

2/2

012

08/1

2/2

012

01/1

2/2

012

24/1

1/2

012

17/1

1/2

012

Num

ber

of In

dependent P

hoto

gra

phic

Events

4.5

4

3.5

3

2.5

2

1.5

1

0.5

0

Species: Dorcas gazelle

08/0

6/2

013

01/0

6/2

013

25/0

5/2

013

18/0

5/2

013

11/0

5/2

013

04/0

5/2

013

27/0

4/2

013

20/0

4/2

013

13/0

4/2

013

06/0

4/2

013

30/0

3/2

013

23/0

3/2

013

16/0

3/2

013

09/0

3/2

013

02/0

3/2

013

23/0

2/2

013

16/0

2/2

013

09/0

2/2

013

02/0

2/2

013

26/0

1/2

013

19/0

1/2

013

12/0

1/2

013

05/0

1/2

013

29/1

2/2

012

22/1

2/2

012

15/1

2/2

012

08/1

2/2

012

01/1

2/2

012

24/1

1/2

012

17/1

1/2

012

Num

ber

of In

dependent P

hoto

gra

phic

Events

4.5

4

3.5

3

2.5

2

1.5

1

0.5

0

GOLDEN JACKAL Nov.12 to Jun 13

DORCAS GAZELLE Nov.12 to Jun 13

OCCUPANCY MODELLING

Note: Presence/absence matrices exportable for separate analysis

SELECTED MAMMALS : BONI FOREST, KENYA

OCCUPANCY MODELLING: GRAPHIC OUTPUT

Automatically launches ‘R’ to run calculations

SELECTED MAMMALS : SAPO NP, LIBERIA

OCCUPANCY MODELLING WITH SITE COVARIATES

BLUE DUIKER : ARABUKO-SOKOKE FOREST, KENYA

BLUE DUIKER : ARABUKO-SOKOKE FOREST, KENYA

OCCUPANCY MODELLING WITH SITE COVARIATES

ACTIVITY PATTERNS

GIANT SENGI BONI FOREST Mar – Jun 2010

FOUR-TOED SENGI BONI FOREST Mar – Jun 2010

Species: Golden-rumped sengi ssp.

Hour of the Day0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

Num

ber

of

Independent

Photo

gra

phic

Events

20

19

18

17

16

15

14

13

12

11

10

9

8

7

6

5

4

3

2

1

0

Species: Four-toed sengi

Hour of the Day0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

Num

ber

of

Independent

Photo

gra

phic

Events

32

30

28

26

24

22

20

18

16

14

12

10

8

6

4

2

0

Species: Rueppell's fox

Hour of the Day0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

Num

ber

of In

dependent P

hoto

gra

phic

Events

8

7.5

7

6.5

6

5.5

5

4.5

4

3.5

3

2.5

2

1.5

1

0.5

0

Species: Golden jackal

Hour of the Day0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

Num

ber

of In

dependent P

hoto

gra

phic

Events

16

15

14

13

12

11

10

9

8

7

6

5

4

3

2

1

0

African ‘golden wolf’

Ruppell’s fox

ACTIVITY PATTERNS

DISTRIBUTION OF RECORDS Google Earth (QGIS & ArcReader)

AUTOMATIC INTERFACE WITH GOOGLE EARTH BARBARY SHEEP – TERMIT

5 DATA INPUTS:

1. CAMERA LOCATION AND SITE COVARIATES

2. CAMERA MAKE & CONFIGURATION DETAILS

3. CAMERA SETUP, SERVICE & RECOVERY DATES

4. IMAGE DATA

5. SITE COVARIATES

(optional)

DATA PREPARATION

1 - IMAGE DATA

META-DATA EXTRACTION

1 - IMAGE DATA

META-DATA EXTRACTION

DATA STANDARDISATION

• STANDARD ‘PHOTO TYPE’ CLASSES

• EXTENSIVE USE OF LOOK-UP TABLES IN THE DATA MODEL (FIXED AND EDITABLE COMPONENTS)

• SPECIES NAMES BASED ON IUCN REDLIST

• SEPARATE ‘COUNTRY TEMPLATES’ FOR SPECIES

1. IMAGE DATA

1) LOAD META DATA FOR EACH CAMERA SEQUENTIALLY : 2) ENTER PHOTO TYPE & SPECIES BY HAND (MUST MATCH LOOK-UP TABLE OPTIONS)

2. CAMERA SITE NAME, POSITION, SITE VARIABLES

3. CAMERA CONFIGURATION

4. SET-UP, SERVICE, RECOVERY & FUNCTIONING HISTORIES

DEMONSTRATION

CAMERA TRAPPING NEEDS

1) PROTOCOLS & BEST PRACTICES

2) TRAINING: SURVEY DESIGN & FIELD SET UP

3) TRAINING : DATA MANAGEMENT & ANALYSIS

4) DATA ANALYSIS AND REPORTING

IMPACT OF TRAINING

STANDARDISING CAMERA POSITION

50% OF CAMERAS BEFORE TRAINING

95% OF CAMERAS AFTER TRAINING

• Image metadata processing tool

• Population density estimates for marked animals (spatially explicit capture-recapture modelling)

• Population density estimates for unmarked animals

• Activity level modelling

• Diversity measures

• Species community structure analyses

• Statistical tests (chi-square, circular statistics etc.)

• Cross survey analyses

• Standardised reports generation in Word and RTF.

VERSION 2 DEVELOPMENT