modelling spatial distribution of fish, by benjamin planque
DESCRIPTION
Key lecture for the EURO-BASIN Training Workshop on Introduction to Statistical Modelling for Habitat Model Development, 26-28 Oct, AZTI-Tecnalia, Pasaia, Spain (www.euro-basin.eu)TRANSCRIPT
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Introduc)on to Sta)s)cal Modelling Tools for Habitat Models Development, 26-‐28th Oct 2011 EURO-‐BASIN, www.euro-‐basin.eu
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
projec1ng spa1al distribu1ons
niche-‐based models
+
predicted spa1al
distribu1on
environment
biolog
ical re
spon
se
climate forecast/scenario
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
Why model the spa1al distribu1on of fish?
Interpolate between observations Project distributions under scenarios Understand processes that control distributions …multiple objectives
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
A general view of the modelling method
adapted from Anderson, 2010
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
uncertain1es in observa1ons
sampling design: sampling intensity, spa1al/temporal scales, aggregated distribu1ons
sampling gear (trawl) or observa1on (acous1cs):
accessibility to observa1on, sensi1vity, bias and precision
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
uncertain1es in conceptual models
spatial distribution
geographical attachment
environmental conditions
density dependent
habitat selection
spatial dependency
demographic structure
Persistence
species interactions
Local density
spatial location
low
medium
high
Proportional Constant Basin
Local density
Habitat suitabili
ty
low
medium
high
low
medium
high
a
b
spatial location
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
uncertainty in numerical formula1on
func1onal rela1onships linear, polynomial, piecewise, etc...
model complexity number of parameters, non-‐linearity
interac1ons addi1ve, mul1plica1ve, other
sta1s1cal distribu1ons Normal, Poisson, Log-‐Normal, Gamma, Binomial,...
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
uncertainty in parameter es1mates and model fiKng
sta1s1cal distribu1on of parameters confidence intervals, sta1s1cal significance
correlated parameters are parameters independent, and how is this handled by the modeling method?
overparametrisa1on and overfiKng number of parameters vs. number of independent observa1ons
autocorrelated observa1ons spa1al/temporal autocorrela1on reduces the true number of independent observa1ons
metric for model fiKng performance variance, deviance, likelihood, AIC, AUC, GCV,...
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
uncertainty in model evalua1on
metric for model predic1ve performance variance, deviance, likelihood, AIC, AUC,...
true independence of the valida1on data are the valida1on data correlated with fiKng data?
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
Addi1onal considera1ons
Spa1al scale is spa1al scale considered? are the scales of observa1on and modelling consistent?
adaptability of living systems complex adap1ve systems, these may modify their behaviour in the future, surprise is to be expected
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
Evalua1ng uncertain1es
Scale(s)
adaptation
future world
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
Conceptual models
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
Null hypothesis / Geography
H0: no control • Random spatial distribution, • Not really plausible, but often use (implicitly) to test other
hypotheses
H1: geography • Spatial distribution is determined by fixed geographical
coordinates (site attachment) • This is usually not used unless no other hypotheses are
available • It can be used as a null hypothesis for habitat control by
other factors
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
H2:environment
• The habitat can be defined as the geographic manifestation of the realized niche
• It may or may not be occupied by the species
Environmental gradient
Spec
ies
abun
danc
e
habitat
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
H3: density-dependent habitat selection
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
H3: density-dependent habitat selection
Local density
spatial location
low
medium
high
Proportional Constant Basin
Local density
Habitat suitabili
ty
low
medium
high
low
medium
high
a
b
spatial location
The basin model
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
H3: density-dependent habitat selection
• Recent evidence from Lake Windermere (UK) show that pike fish moves between two basins as predicted by DDHS
Haugen et al. 2006.
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
H4: Spatial dependency
"… everything is related to everything else, but near things are more related than distant things”
Tobler, 1970
Sea Surface Temperature Chlorophyll Plaice
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
H4: Spatial dependency
• Patterns of spatial distribution are explained by spatial interactions between (groups of) individuals such as attraction or repulsion
• It can be driven by many processes: spawning or feeding aggregations, swimming capabilities, gamete dispersal/retention
• It is often referred to as patchiness
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
H4: Spatial dependency
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
H5: Demographic structure
• Spatial distributions of individuals vary depending on their size, age, sex or other individual traits
Planque et al. (2005)
Circles
diameter show
mean body
size of
anchovy
Females Males
Lesser spotted dogfish Anchovy length distribution
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
H6: species interactions
growth rate
Location in intertidal zone
low high middle
Chthamalus alone
Balanus alone
Balanus fundamental
niche
Chthamalus fundamental niche
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
H7: memory
• The spatial distribution does not solely results from instantaneous conditions but also from the population’s history – Imprinting (e.g. natal homing) – Social learning (tradition) – Individual memory (habit formation)
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
the conceptual models summarised
spatial distribution
geographical attachment
environmental conditions
density dependent
habitat selection
spatial dependency
demographic structure
Persistence
species interactions
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
Environmental gradients, niches and models
Gradients • Resource • Direct • Indirect
Niches • Fundamental • Realised
Models • Mechanistic • Statistical • Mixed
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
Observa1ons, data, distribu1ons?
Observation process, scale & support • How is the data collected?
• Trawl samples • Sub-sampling • Hydroacoustics
• Sampling design • Random, stratified, transects,…
• Observation scale • Distance between observations
• Observation support • Volume/area sampled
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
Observa1ons, data, distribu1ons?
Observation process, scale & support What statistical distribution to choose? • Continuous:
• Normal • Log-Normal • Gamma
• Discrete: • Binomial, multinomial • Poisson • Negative binomial
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
Count observa1ons versus latent density distribu1on
Survey area Sampling unit
Trawl haul Number of fish in haul=
draw from a binomial distribution with mu= underlying density at the scale of the sampling unit and ‘size’= underlying dispersion at the scale of the sampling unit
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
An example: TrawlCatchModels.R
Context and data • 9y of trawl sampling. Stratified random sampling. Bottom
trawl. Same location each year. 30’ at 3 knots. 25 x 5m opening. Number of individual fish.
• Additional data on temperature and chlorophyll (surface) and bottom topography
Hypotheses • Fish spatial distribution is controlled by 1) temperature, 2)
chla, 3) bathymetry, 4) past distribution, or any combination of the above
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
An example: TrawlCatchModels.R
Analysis • Plot your data: spatial & statistical distributions,
scatterplots • Explore your data: spatial structures, temporal structures,
appropriate statistical distributions, sampling effects • Model the spatial distributions: write model equations for
various hypotheses, fit models on a subset of the data and predict the other
Interpretation • Which models fit best? predict best? Which predictor
should be retained? How complex should the model be? Projections • Projections of future spatial distribution of fish density • Projections of future survey results
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EuroBasin training workshop – 26-28 October 2011 - Modelling the spatial distribution of fish: some key concepts and an application.
What you need to run the exercise
• R (2.13.2) • Librairies:
• fields (6.6.1) • mgcv (1.7-8) • spatial (7.3-3) • gstat (1.0-6) • gamlss (4.1-0) • gamlss.dist (4.0-5) • gamlss.mx (4.0-4) • plotrix (3.2-6)
• Data files: • TrawlCatches_9199.txt • depth.Rdata
• R code
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Introduc)on to Sta)s)cal Modelling Tools for Habitat Models Development, 26-‐28th Oct 2011 EURO-‐BASIN, www.euro-‐basin.eu