Читать книгу Statistical Approaches for Hidden Variables in Ecology - Nathalie Peyrard - Страница 4

1 Chapter 1Figure 1.1. The map at the top shows the tracking data for a male Cape dolphin (...Figure 1.2. Figure extracted from Figure 4 in Lopez et al. (2015). The black lin...Figure 1.3. Graphical model. For a color version of this figure, see www.iste.co...Figure 1.4. Illustration of the quantities present in equations [1.5]–[1.8]. Pt ...Figure 1.5. Masked Booby (Sula dactylatra) Photo: Sophie Bertrand. For a color v...Figure 1.6. Area of study (shown in red on the map) and three trajectories obtai...Figure 1.7. Result of Kalman smoothing on part of the booby trajectories. Smooth...Figure 1.8. Representation of states along trajectories estimated using two diff...Figure 1.9. Distribution of our chosen metrics for the states estimated using ou...Figure 1.10. Contingencies of estimated states for our two models. For a color v...Figure 1.11. Evolution of the probability of being in state 1 or state 2 over ti...Figure 1.12. Evolution of estimated transition probabilities as a function of di...Figure 1.13. Study zone (red dot on the map) and three trajectories of three dif...

2 Chapter 2Figure 2.1. Illustration of van Noordwijk and de Jong’s (1986) “Y” model. Exampl...Figure 2.2. Directed acyclic graph of the model. The squares represent observabl...Figure 2.3. A posteriori distributions of parameters in the latent model (logari...Figure 2.4. Comparison of observed and simulated ring width from 1989 to 2015 an...Figure 2.5. Boxplot of resource (net primary productivity, in gC.m−2.year−1) sim...Figure 2.6. Illustration of the developed Bayesian model, with process and data ...Figure 2.7. Correlation between sinks and probabilities. a) Correlation density ...

3 Chapter 3Figure 3.1. Schematic illustration of a hidden Markov modelFigure 3.2. Two-state capture–recapture model expressed in HMM formFigure 3.3. Multi-state capture–recapture model expressed in HMM formFigure 3.4. Diagram of a dynamic occupancy model expressed as an HMMFigure 3.5. Identification of local minima in the deviance of an HMM. Numerica...Figure 3.6. Visualization of heterogeneity: map of the heterogeneity class to wh...

4 Chapter 4Figure 4.1. Expectation of the total number of cases associated with the posteri...Figure 4.2. Joint posterior distributions of couples (α, κ), (t0, α) and (t0, κ)...Figure 4.3. Map of wolf detections in southeastern France (black dots) and the a...Figure 4.4. Estimated response curves. Estimated relations between individual de...Figure 4.5. Predicted occupation probability map for 2016, obtained using the mo...Figure 4.6. Proportion of plants susceptible to WMV across the area of study. Fo...Figure 4.7. Proportions of classic and invasive variants in a landscape: data an...

5 Chapter 5Figure 5.1. Illustration of dependency relationships in an MHMM-DF. Case of two ...Figure 5.2. Layout of the 10 fields and 90 patches in the experimental farm at E...

6 Chapter 6Figure 6.1. The Chilean network: 1,362 trophic interactions observed in the inte...Figure 6.2. Adjacency matrix and corresponding representation of the non-directe...Figure 6.3. Incidence matrix and corresponding representation of the bipartite b...Figure 6.4. Simulation of a modular network for the parameters shown on the left...Figure 6.5. Simulation of a food web for the parameters shown on the left. A rea...Figure 6.6. Simulation of a nested bipartite network for the parameters shown on...Figure 6.7. Simulation of a bipartite network with a modular and nested structur...Figure 6.8. Schematic representation (based on Picard et al. 2009) of the estima...Figure 6.9. Classic representation obtained using the R bipartite package. Diffe...

7 Chapter 7Figure 7.1. The three factors that determine the actual distribution of a specie...Figure 7.2. Localization and names of the 18 gradients of ORCHAMP. For a color v...Figure 7.3. Effective sample size (ESS, top panels) and potential scale reductio...Figure 7.4. Distribution of TSS and RMSE score across species for in-sample pred...Figure 7.5. Posterior support values for species regression coefficients. Red if...Figure 7.6. The residual correlation matrix. Only significant values (i.e. 95% c...Figure 7.7. Model-based ordination analysis. The two latent variables can be see...Figure 7.8. Model-based ordination analysis, as above, but when we include the h...Figure 7.9. Cross-validation predicted probability of (a) presence and (b) cross...

8 Chapter 8Figure 8.1. Illustration of dependency in the PLN model. Random variables are ci...Figure 8.2. PLN: geometric view of the model for two species. A) Positions in th...Figure 8.3. Poisson log-normal model with the “site” covariate. Representation o...Figure 8.4. Poisson log-normal model with the “period” covariate. Representation...Figure 8.5. Dimension reduction for (left to right): a model without covariates;...Figure 8.6. Representation of samples on the AEI islet in the first principal pl...Figure 8.7. Effect of parameter λ on edge density (left) and model fitting (righ...Figure 8.8. Stability of edges selected for the model including the effects of t...Figure 8.9. The selected interaction network: visualization using the PLNmodels ...Figure 8.10. The selected interaction network: visualization of the partial corr...Figure 8.11. Interactions between two sea urchin species: red (STRFRAAD, Strongy...

9 Chapter 9Figure 9.1. Polar representation of VPI (equation 9.3) by values of ℓ for four c...Figure 9.2. Geometric mean of the square mean quadratic prediction errors over r...Figure 9.3. Circles of correlations resulting from the first three components. F...Figure 9.4. Spatial representation of the first three components. For a color ve...Figure 9.5. Geometric mean of the square roots of the mean quadratic prediction ...Figure 9.6. Geometric mean of the RMSE as a function of the number of components...Figure 9.7. Factorial planes (1,2), (1,3) and (2,3) obtained using mixed-SCGLR o...Figure 9.8. Observed and predicted abundance maps for the species with the highe...

10 Chapter 10Figure 10.1. Conventions used in representing an SEM. Latent variables are shown...Figure 10.2. SEM defined a priori for our case study. The exogenous latent varia...Figure 10.3. Main steps in SEM analysis. The diagrams follow the SEM presentatio...Figure 10.4. Estimators of the parameters of the SEM in Figure 10.2. Section A: ...Figure 10.5. SEM resulting from correction of the model shown in Figure 10.2, af...Figure 10.6. Divergences between the correlation matrices of the latent variable...Figure 10.7. SEM resulting from correction of the model in Figure 10.5, limiting...Figure 10.8. Estimated relationships within the relational model of the SEM from...Figure 10.9. Test of causal relations in the relational model shown in Figure 10...