class: center, middle, title-slide .title[ # Known knowns, unknown knowns and unknowns: Uncertainty in state assignment ] .date[ ### last updated: 2023-07-01 ] --- ## Uncertainty in state assignment Multievent models extend multistate models with uncertainty in state assignment ??? + In this module, we're going to talk about multievent models. + Multievent models extend multistate models with uncertainty in state assignment. + Let's see some examples to fix ideas. + These examples are from published papers which used multievent models. -- + Breeding status in female roe deer is ascertained based on fawn detection -- + Sex status is ascertained based on morphological criteria in Audouin's gulls -- + Disease status in house finches is ascertained based on birds' eyes examination -- + Hybrid status in wolves is ascertained based on genetics -- + Dominance status in wolves is ascertained based on heterogeneity in detection -- We need to explicitly consider state assignment in a model ??? + The common thing to all these examples is that. + We need to explicitly consider state assignment in a model. -- HMMs to the rescue! ??? + And to do that, we'll use HMMs again! --- ## Examples <br> + Testing life-history trade-offs while accounting for uncertainty in breeding status + Quantifying disease dynamics while accounting for uncertainty in disease status + Estimating survival while accounting for individual heterogeneity in detection ??? + In this module, I'll go through 3 examples. + Testing life-history trade-offs while accounting for uncertainty in breeding status. + Quantifying disease dynamics while accounting for uncertainty in disease status. + Estimating survival while accounting for individual heterogeneity in detection. --- ## Examples <br> + **Testing life-history trade-offs while accounting for uncertainty in breeding status** + Quantifying disease dynamics while accounting for uncertainty in disease status + Estimating survival while accounting for individual heterogeneity in detection --- background-image: url("img/sooty.jpg") background-size: cover ### <span style="color: white;">Sooty shearwater (David Boyle)</span> --- # Uncertainty in breeding status + 3 states + breeding (B) + non-breeding (NB) + dead (D) + 4 observations + not encountered (0) + found, ascertained as breeder (1) + found, ascertained as non-breeder (2) + found, status unknown (3) ??? + We still have 3 states, breeding, non-breeding and dead. + With regard to observations, a bird may be not encountered. + It may also be encountered, but in contrast with multistate CR data, we don't know its state for sure. + It may be found and ascertained or classified as breeder. + It may be found and ascertained or classified as non-breeder. + It may be found be we are unable to determine whether it's breeding or non-breeding. --- class: middle ### How states generate observations .center.nogap[ <!-- --> ] ??? + Now how do the states generate the observations? --- class: middle ### How states generate observations .center.nogap[ <!-- --> ] --- class: middle ### How states generate observations .center.nogap[ <!-- --> ] --- class: middle ### How states generate observations .center.nogap[ <!-- --> ] --- class: middle ### How states generate observations .center.nogap[ <!-- --> ] ??? + To wrap up each live state can generate 3 observations. + The only deterministic link is that between the dead state and the observation non-encountered. + Cause if you're dead, you cannot be detected for sure. --- ### HMM model for breeding states with uncertainty Vector of initial state probabilities $$ `\begin{matrix} & \\ \mathbf{\delta} = \left ( \vphantom{ \begin{matrix} 12 \end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} z_t=B & z_t=NB & z_t=D \\ \hdashline \pi_B & 1 - \pi_{B} & 0\\ \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \end{matrix} } \right ) \begin{matrix} \end{matrix} \end{matrix}` $$ + `\(\pi_B\)` is the probability that a newly encountered individual is a breeder + `\(\pi_{NB} = 1 - \pi_B\)` is the probability that a newly encountered individual is a non-breeder ??? + OK now let’s specify the model. + First thing we need, and it’s a big difference with multistate models, we need initial state probabilities cause we cannot assign states to individuals w/ certainty. + Let's define pi_B the prob that a newly encountered individual is a breeding individual. + We write down the prob for each state at first encounter. We have pi_B, then the prob of being a NB is the complementary. And the prob of being dead at first encounter is 0 of course. --- ### HMM model for breeding states with uncertainty Transition matrix $$ `\begin{matrix} & \\ \mathbf{\Gamma} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} z_t=B & z_t=NB & z_t=D \\ \hdashline \phi_B (1-\psi_{BNB}) & \phi_B \psi_{BNB} & 1 - \phi_B\\ \phi_{NB} \psi_{NBB} & \phi_{NB} (1-\psi_{NBB}) & 1 - \phi_{NB}\\ 0 & 0 & 1 \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right ) \begin{matrix} z_{t-1}=B \\ z_{t-1}=NB \\ z_{t-1}=D \end{matrix} \end{matrix}` $$ + `\(\phi_B\)` is breeder survival, `\(\phi_{NB}\)` that of non-breeders. + `\(\psi_{BNB}\)` is the probability for an individual breeding a year to be a non-breeder the next year. + `\(\psi_{NBB}\)` is the probability for an non-breeder individual to breeder the next year. ??? + The transition parameters are in a matrix similar to the one we used for multistate models. --- ### HMM model for breeding states with uncertainty Observation matrix $$ `\begin{matrix} & \\ \mathbf{\Omega} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12\end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} y_t=0 & y_t=1 & y_t=2 & y_t=3\\ \hdashline 1 - p_B & p_B \beta_B & 0 & p_B (1-\beta_B) \\ 1-p_{NB} & 0 & p_{NB} \beta_{NB} & p_{NB} (1-\beta_{NB})\\ 1 & 0 & 0 & 0 \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12\end{matrix} } \right ) \begin{matrix} z_{t}=B \\ z_{t}=NB \\ z_{t}=D \end{matrix} \end{matrix}` $$ + `\(\beta_B\)` is the probability to assign an individual in state B to state B. + `\(\beta_{NB}\)` is the probability to assign an individual in state NB to state NB. + `\(p_B\)` is the detection probability of breeders, `\(p_{NB}\)` that of non-breeders. ??? + The main difference between multistate and multievent models is here, in the observation parameters. + We introduce two new parameters. + deltaB: prob. to correctly assign an indiv. that is in state B to state B + deltaNB: prob. to correctly assign an indiv. that is in state NB to state NB + We put everything in a matrix, as usual. The observation matrix. + In rows we have the states, breeding, non-breeding and dead. + In columns, at the same occasion, we have the observation, detected and ascertained B, detected and ascertained NB, detected and state unknown, and not detected. + For example, the prob of being detected and assigned to the state B, given that you’re in state B is the product of the detection prob in B and delta the prob of correctly assigning a B individual to state B. --- ### HMM model for breeding states with uncertainty Because animals are all captured, `\(p_B = p_{NB} = 1\)` at first encounter: $$ `\begin{matrix} & \\ \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12\end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} y_t=0 & y_t=1 & y_t=2 & y_t=3\\ \hdashline 0 & \beta_B & 0 & (1-\beta_B)\\ 0 & 0 & \beta_{NB} & (1-\beta_{NB})\\ 1 & 0 & 0 & 0 \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12\end{matrix} } \right ) \begin{matrix} z_{t}=B \\ z_{t}=NB \\ z_{t}=D \end{matrix} \end{matrix}` $$ Note: Breeding assessment is unaffected. ??? + Then at first encounter, what happens is that step 1 of encounter is degenerate because individuals are all captured. Just set all the p’s to 1 in the encounter matrix. + The breeding assessment matrix remains unchanged. --- ### Our model `\((\phi_B, \phi_{NB}, \psi_{BNB}, \psi_{NBB}, p_B, p_{NB}, \beta_B, \beta_{NB}, \pi)\)` .tiny-font[ ```r multievent <- nimbleCode({ # ------------------------------------------------- # Parameters: # phiB: survival probability state B # phiNB: survival probability state NB # psiBNB: transition probability from B to NB # psiNBB: transition probability from NB to B # pB: recapture probability B # pNB: recapture probability NB # piB prob. of being in initial state breeder # betaNB prob to ascertain the breeding status of an individual encountered as non-breeder # betaB prob to ascertain the breeding status of an individual encountered as breeder # ------------------------------------------------- # States (z): # 1 alive B # 2 alive NB # 3 dead # Observations (y): # 1 = non-detected # 2 = seen and ascertained as breeder # 3 = seen and ascertained as non-breeder # 4 = not ascertained # ------------------------------------------------- ... ``` ] --- ### Our model `\((\phi_B, \phi_{NB}, \psi_{BNB}, \psi_{NBB}, p_B, p_{NB}, \beta_B, \beta_{NB}, \pi)\)` .small-font[ ```r multievent <- nimbleCode({ ... # Priors phiB ~ dunif(0, 1) phiNB ~ dunif(0, 1) psiBNB ~ dunif(0, 1) psiNBB ~ dunif(0, 1) pB ~ dunif(0, 1) pNB ~ dunif(0, 1) piB ~ dunif(0, 1) betaNB ~ dunif(0, 1) betaB ~ dunif(0, 1) ... ``` ] --- ### Our model `\((\phi_B, \phi_{NB}, \psi_{BNB}, \psi_{NBB}, p_B, p_{NB}, \beta_B, \beta_{NB}, \pi)\)` .small-font[ ```r multievent <- nimbleCode({ ... # vector of initial stats probs delta[1] <- piB # prob. of being in initial state B delta[2] <- 1 - piB # prob. of being in initial state NB delta[3] <- 0 # prob. of being in initial state dead ... ``` ] --- ### Our model `\((\phi_B, \phi_{NB}, \psi_{BNB}, \psi_{NBB}, p_B, p_{NB}, \beta_B, \beta_{NB}, \pi)\)` .small-font[ ```r multievent <- nimbleCode({ ... # probabilities of state z(t+1) given z(t) gamma[1,1] <- phiB * (1 - psiBNB) gamma[1,2] <- phiB * psiBNB gamma[1,3] <- 1 - phiB gamma[2,1] <- phiNB * psiNBB gamma[2,2] <- phiNB * (1 - psiNBB) gamma[2,3] <- 1 - phiNB gamma[3,1] <- 0 gamma[3,2] <- 0 gamma[3,3] <- 1 ... ``` ] --- ### Our model `\((\phi_B, \phi_{NB}, \psi_{BNB}, \psi_{NBB}, p_B, p_{NB}, \beta_B, \beta_{NB}, \pi)\)` .small-font[ ```r multievent <- nimbleCode({ ... # probabilities of y(t) given z(t) omega[1,1] <- 1 - pB # Pr(alive B t -> non-detected t) omega[1,2] <- pB * betaB # Pr(alive B t -> detected B t) omega[1,3] <- 0 # Pr(alive B t -> detected NB t) omega[1,4] <- pB * (1 - betaB) # Pr(alive B t -> detected U t) omega[2,1] <- 1 - pNB # Pr(alive NB t -> non-detected t) omega[2,2] <- 0 # Pr(alive NB t -> detected B t) omega[2,3] <- pNB * betaNB # Pr(alive NB t -> detected NB t) omega[2,4] <- pNB * (1 - betaNB) # Pr(alive NB t -> detected U t) omega[3,1] <- 1 # Pr(dead t -> non-detected t) omega[3,2] <- 0 # Pr(dead t -> detected N t) omega[3,3] <- 0 # Pr(dead t -> detected NB t) omega[3,4] <- 0 # Pr(dead t -> detected U t) ... ``` ] --- ### Our model `\((\phi_B, \phi_{NB}, \psi_{BNB}, \psi_{NBB}, p_B, p_{NB}, \beta_B, \beta_{NB}, \pi)\)` .small-font[ ```r multievent <- nimbleCode({ ... # probabilities of y(first) given z(first) omega.init[1,1] <- 0 # Pr(alive B t = 1 -> non-detected t = 1) omega.init[1,2] <- betaB # Pr(alive B t = 1 -> detected B t = 1) omega.init[1,3] <- 0 # Pr(alive B t = 1 -> detected NB t = 1) omega.init[1,4] <- 1 - betaB # Pr(alive B t = 1 -> detected U t = 1) omega.init[2,1] <- 0 # Pr(alive NB t = 1 -> non-detected t = 1) omega.init[2,2] <- 0 # Pr(alive NB t = 1 -> detected B t = 1) omega.init[2,3] <- betaNB # Pr(alive NB t = 1 -> detected NB t = 1) omega.init[2,4] <- 1 - betaNB # Pr(alive NB t = 1 -> detected U t = 1) omega.init[3,1] <- 1 # Pr(dead t = 1 -> non-detected t = 1) omega.init[3,2] <- 0 # Pr(dead t = 1 -> detected N t = 1) omega.init[3,3] <- 0 # Pr(dead t = 1 -> detected NB t = 1) omega.init[3,4] <- 0 # Pr(dead t = 1 -> detected U t = 1) ... ``` ] --- ### Our model `\((\phi_B, \phi_{NB}, \psi_{BNB}, \psi_{NBB}, p_B, p_{NB}, \beta_B, \beta_{NB}, \pi)\)` .small-font[ ```r multievent <- nimbleCode({ ... # likelihood for (i in 1:N){ # latent state at first capture z[i,first[i]] ~ dcat(delta[1:3]) y[i,first[i]] ~ dcat(omega.init[z[i,first[i]],1:4]) for (t in (first[i]+1):K){ # z(t) given z(t-1) z[i,t] ~ dcat(gamma[z[i,t-1],1:3]) # y(t) given z(t) y[i,t] ~ dcat(omega[z[i,t],1:4]) } } }) ``` ] --- ## Results .center[ ``` mean sd 2.5% 50% 97.5% Rhat n.eff betaB 0.19 0.01 0.16 0.19 0.21 1.01 332 betaNB 0.76 0.05 0.66 0.76 0.86 1.01 65 pB 0.56 0.03 0.51 0.56 0.62 1.06 229 pNB 0.60 0.04 0.53 0.60 0.67 1.03 142 phiB 0.81 0.02 0.78 0.81 0.85 1.01 312 phiNB 0.84 0.02 0.80 0.84 0.87 1.00 354 piB 0.71 0.03 0.66 0.71 0.76 1.02 115 psiBNB 0.23 0.02 0.18 0.22 0.27 1.00 214 psiNBB 0.25 0.04 0.17 0.25 0.34 1.00 95 ``` ] + Breeders are difficult to assigned to the correct state. + Non-breeders are relatively well classified as non-breeders. + No cost of breeding, neither on survival, nor on future reproduction. --- .center.nogap[ <!-- --> ] --- background-color: #234f66 ## <span style="color:white">Live demo</span> .center[  ] --- ## Examples <br> + Testing life-history trade-offs while accounting for uncertainty in breeding status + **Quantifying disease dynamics while accounting for uncertainty in disease status** + Estimating survival while accounting for individual heterogeneity in detection ??? + Let's have a look to another example. + Very similar to the previous example. --- ## Animal epidemiology with uncertain disease states + We consider a system of an emerging pathogen *Mycoplasma gallisepticum* Edward and Kanarek and its host the house finch, *Carpodacus mexicanus* Müller. --- background-image: url("img/infectedhousefinch.jpg") background-size: cover ### <span style="color: white;">A house finch with a heavy infection (Jim Mondok).</span> --- ## Animal epidemiology with uncertain disease states + We consider a system of an emerging pathogen *Mycoplasma gallisepticum* Edward and Kanarek and its host the house finch, *Carpodacus mexicanus* Müller. + [Faustino et al. (2004)](https://besjournals.onlinelibrary.wiley.com/doi/10.1111/j.0021-8790.2004.00840.x) and [Conn & Cooch (2009)](https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2664.2008.01597.x) studied impact of pathogen on host demographic rates. + Problem is true disease state for some encountered individuals is ambiguous because seen at distance. + In this context, how to study the dynamics of the disease? --- # States and observations + 3 states + healthy (H) + ill (I) + dead (D) + 4 observations + not seen (0) + captured healthy (1) + captured ill (2) + health status unknown, i.e. seen at distance (3) --- class: middle ### How states generate observations. .center.nogap[ <!-- --> ] --- class: middle ### How states generate observations. .center.nogap[ <!-- --> ] --- class: middle ### How states generate observations. .center.nogap[ <!-- --> ] --- class: middle ### How states generate observations. .center.nogap[ <!-- --> ] --- class: middle ### How states generate observations. .center.nogap[ <!-- --> ] --- ### HMM model for disease states with uncertainty Vector of initial state probabilities $$ `\begin{matrix} & \\ \mathbf{\delta} = \left ( \vphantom{ \begin{matrix} 12 \end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} z_t=H & z_t=I & z_t=D \\ \hdashline \pi_H & 1 - \pi_{H} & 0\\ \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \end{matrix} } \right ) \begin{matrix} \end{matrix} \end{matrix}` $$ + `\(\pi_H\)` is the probability that a newly encountered individual is healthy. + `\(\pi_{I} = 1 - \pi_H\)` is the probability that a newly encountered individual is ill. --- ### HMM model for disease states with uncertainty Transition matrix $$ `\begin{matrix} & \\ \mathbf{\Gamma} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} z_t=H & z_t=I & z_t=D \\ \hdashline \phi_H (1-\psi_{HI}) & \phi_H \psi_{HI} & 1 - \phi_H\\ \phi_{I} \psi_{IH} & \phi_{I} (1-\psi_{IH}) & 1 - \phi_{I}\\ 0 & 0 & 1 \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right ) \begin{matrix} z_{t-1}=H \\ z_{t-1}=I \\ z_{t-1}=D \end{matrix} \end{matrix}` $$ + `\(\phi_H\)` is the survival probability of healthy individuals, `\(\phi_I\)` that of ill individuals. + `\(\psi_{HI}\)` is the probability of getting sick, `\(\psi_{IH}\)` that of recovering from the disease. --- ### HMM model for disease states with uncertainty Transition matrix, incurable disease $$ `\begin{matrix} & \\ \mathbf{\Gamma} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} z_t=H & z_t=I & z_t=D \\ \hdashline \phi_H (1-\psi_{HI}) & \phi_H \psi_{HI} & 1 - \phi_H\\ 0 & \phi_{I} & 1 - \phi_{I}\\ 0 & 0 & 1 \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right ) \begin{matrix} z_{t-1}=H \\ z_{t-1}=I \\ z_{t-1}=D \end{matrix} \end{matrix}` $$ + No possibility of recovering from the disease, that is `\(\psi_{IH} = 0\)`. Once you get sick, you remain sick `\(\psi_{II} = 1 - \psi_{IH} = 1\)`. + For analysing the house finch data, we allow recovering from the disease, and we will use transition matrix from previous slide. --- ### HMM model for disease states with uncertainty Observation matrix $$ `\begin{matrix} & \\ \mathbf{\Omega} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12\end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} y_t=0 & y_t=1 & y_t=2 & y_t=3\\ \hdashline 1-p_H & p_H \beta_H & 0 & p_H (1-\beta_H)\\ 1-p_I & 0 & p_{I} \beta_{I} & p_{I} (1-\beta_{I})\\ 1 & 0 & 0 & 0 \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12\end{matrix} } \right ) \begin{matrix} z_{t}=H \\ z_{t}=I \\ z_{t}=D \end{matrix} \end{matrix}` $$ + `\(\beta_H\)` is the probability to assign a healthy individual to state H. + `\(\beta_{I}\)` is the probability to assign a sick individual to state I. + `\(p_H\)` is the detection probability of healthy individuals, `\(p_I\)` that of sick individuals. --- ### Results .center[ ``` mean sd 2.5% 50% 97.5% Rhat n.eff betaH 0.99 0.01 0.97 0.99 1.00 1.01 1421 betaI 0.05 0.01 0.03 0.05 0.08 1.00 6477 pH 0.17 0.02 0.13 0.17 0.22 1.01 331 pI 0.58 0.10 0.41 0.57 0.80 1.04 220 phiH 0.88 0.02 0.84 0.88 0.92 1.01 360 phiI 0.99 0.01 0.96 0.99 1.00 1.00 1004 pi 0.96 0.01 0.93 0.96 0.98 1.00 4190 psiHI 0.22 0.04 0.16 0.22 0.32 1.02 311 psiIH 0.46 0.08 0.32 0.45 0.63 1.02 392 ``` ] + Healthy individuals are correctly assigned, while infected individuals are difficult to ascertain. + Sounds like being infected has an effect on detection and survival. Run models without effects and compare with WAIC for formal testing. + Infection rate is 22%, recovery rate is 46%. --- .center.nogap[ <!-- --> ] --- background-color: black # <span style="color:white">Live demo</span> <br> <br> .center[  ] --- ## Examples <br> + Testing life-history trade-offs while accounting for uncertainty in breeding status + Quantifying disease dynamics while accounting for uncertainty in disease status + **Estimating survival while accounting for individual heterogeneity in detection** ??? + Our last example is about individual heterogeneity and how to account for it with HMMs. --- ## Individual heterogeneity with finite mixtures. + Gray wolf is a social species with hierarchy in packs which may reflect in species demography. ??? + As an example, we'll work with gray wolves. --- background-image: url("img/wolfdominance.jpg") background-size: cover --- ## Individual heterogeneity with finite mixtures. + Gray wolf is a social species with hierarchy in packs which may reflect in demography. + Shirley Pledger in a series of papers developed heterogeneity models in which individuals are assigned in two or more classes with class-specific survival/detection probabilities. + [Cubaynes et al. (2010)](https://conbio.onlinelibrary.wiley.com/doi/abs/10.1111/j.1523-1739.2009.01431.x) used HMMs to account for heterogeneity in the detection process due to social status, see also [Pradel et al. (2009)](https://link.springer.com/chapter/10.1007%2F978-0-387-78151-8_36). ??? Dominant individuals tend to use path more often than others, and these paths are where we look for scats. --- # Individual heterogeneity + 3 states + alive in class 1 (A1) + alive in class 2 (A2) + dead (D) + 4 observations + not captured (0) + captured (1) --- ### HMM model for individual heterogeneity Vector of initial state probabilities $$ `\begin{matrix} & \\ \mathbf{\delta} = \left ( \vphantom{ \begin{matrix} 12 \end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} z_t=A1 & z_t=A2 & z_t=D \\ \hdashline \pi & 1 - \pi & 0\\ \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \end{matrix} } \right ) \begin{matrix} \end{matrix} \end{matrix}` $$ + `\(\pi\)` is the probability of being alive in class 1. + `\(1 - \pi\)` is the probability of being in class 2. --- ### HMM model for individual heterogeneity Transition matrix $$ `\begin{matrix} & \\ \mathbf{\Gamma} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} z_t=A1 & z_t=A2 & z_t=D \\ \hdashline \phi & 0 & 1 - \phi\\ 0 & \phi & 1 - \phi\\ 0 & 0 & 1 \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right ) \begin{matrix} z_{t-1}=A1 \\ z_{t-1}=A2 \\ z_{t-1}=D \end{matrix} \end{matrix}` $$ + `\(\phi\)` is the survival probability, which could be made heterogeneous. --- ### HMM model for individual heterogeneity Transition matrix, with change in heterogeneity class $$ `\begin{matrix} & \\ \mathbf{\Gamma} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} z_t=A1 & z_t=A2 & z_t=D \\ \hdashline \phi (1-\psi_{12}) & \phi \psi_{12} & 1 - \phi\\ \phi \psi_{21} & \phi (1-\psi_{21}) & 1 - \phi\\ 0 & 0 & 1 \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right ) \begin{matrix} z_{t-1}=A1 \\ z_{t-1}=A2 \\ z_{t-1}=D \end{matrix} \end{matrix}` $$ + `\(\psi_{12}\)` is the probability for an individual to change class of heterogeneity, from 1 to 2. + `\(\psi_{21}\)` is the probability for an individual to change class of heterogeneity, from 2 to 1. --- ### HMM model for individual heterogeneity Observation matrix $$ `\begin{matrix} & \\ \mathbf{\Omega} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12\end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} y_t=0 & y_t=1\\ \hdashline 1 - p_1 & p_1\\ 1 - p_2 & p_2\\ 1 & 0 \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12\end{matrix} } \right ) \begin{matrix} z_{t}=A1 \\ z_{t}=A2 \\ z_{t}=D \end{matrix} \end{matrix}` $$ + `\(p_1\)` is detection for individuals in class 1, and `\(p_2\)` that of individuals in class 2. --- ## Results .center[ ``` mean sd 2.5% 50% 97.5% Rhat n.eff p1 0.38 0.09 0.23 0.38 0.56 1.04 210 p2 0.50 0.12 0.25 0.50 0.73 1.01 229 phi 0.81 0.05 0.71 0.81 0.91 1.04 317 pi 0.62 0.12 0.36 0.63 0.83 1.02 164 ``` ] + We have lowly detectable individuals (class A1 with `\(p_1\)`) in proportion 62%. + And highly (or so) detectable individuals (class A2 with `\(p_2\)`) in proportion 38%. + N ote that interpretation of classes is made a posteriori. + Survival is 81%. --- .center.nogap[ <!-- --> ] --- ### HMM model for individual heterogeneity + You may consider more classes, and select among models, see [Cubaynes et al. (2012)](https://oliviergimenez.github.io/pubs/Cubaynesetal2011MEE.pdf). + You may also go for a non-parametric approach and let the data tell you how many classes you need. This is relatively easy to do in Nimble, see [Turek et al. (2021)](https://arxiv.org/abs/2007.10163). + More about individual heterogeneity in [Gimenez et al. (2018)](https://oliviergimenez.github.io/pubs/GimenezCamGaillard2017Oikos.pdf). --- class: middle, center ## HMMs to analyse capture-recapture data With the same data, ask further questions, just consider different states. --- background-image: url("https://media.giphy.com/media/3o8dFn5CXJlCV9ZEsg/source.gif") background-size: cover --- background-image: url("img/archer.png") background-size: cover --- ### How to make our models remember? + So far, the dynamics of the states are first-order Makovian. + The site where you will be depends only on the site where you are, and not on the sites you were previously. + How to relax this assumption, and go second-order Markovian? + Memory models were initially proposed by [Hestbeck et al. (1991)](https://esajournals.onlinelibrary.wiley.com/doi/abs/10.2307/2937193) and [Brownie et al. (1993)](https://www.jstor.org/stable/2532259?origin=crossref&seq=1#metadata_info_tab_contents), then formulated as HMMs in [Rouan et al. (2009)](https://link.springer.com/article/10.1198/jabes.2009.06108). See also [Cole et al. (2014)](https://onlinelibrary.wiley.com/doi/10.1002/ece3.1037). --- ### Remember HMM model for dispersal between 2 sites Transition matrix $$ `\begin{matrix} & \\ \mathbf{\Gamma} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} z_t=A & z_t=B & z_t=D \\ \hdashline \phi_A (1-\psi_{AB}) & \phi_A \psi_{AB} & 1 - \phi_A\\ \phi_B \psi_{BA} & \phi_B (1-\psi_{BA}) & 1 - \phi_B\\ 0 & 0 & 1 \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right ) \begin{matrix} z_{t-1}=A \\ z_{t-1}=B \\ z_{t-1}=D \end{matrix} \end{matrix}` $$ Observation matrix $$ `\begin{matrix} & \\ \mathbf{\Omega} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} y_t=0 & y_t=1 & y_t=2 \\ \hdashline 1 - p_A & p_A & 0\\ 1 - p_B & 0 & p_B\\ 1 & 0 & 0 \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right ) \begin{matrix} z_{t}=A \\ z_{t}=B \\ z_{t}=D \end{matrix} \end{matrix}` $$ --- ## HMM formulation of the memory model -- + To keep track of the sites previously visited, the trick is to consider states as being pairs of sites occupied -- + States + AA is for alive in site A at `\(t\)` and alive in site A at `\(t-1\)` + AB is for alive in site A at `\(t\)` and alive in site B at `\(t-1\)` + BA is for alive in site B at `\(t\)` and alive in site A at `\(t-1\)` + BB is for alive in site B at `\(t\)` and alive in site B at `\(t-1\)` + D is for dead -- + Observations + 0 not captured + 1 captured at site A + 2 captured at site B --- ## HMM formulation of the memory model Vector of initial state probabilities $$ `\begin{matrix} & \\ \mathbf{\delta} = \left ( \vphantom{ \begin{matrix} 12 \end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} z_t=AA & z_t=AB & z_t=BA & z_t=BB &z_t=D \\ \hdashline \pi_{AA} & \pi_{AB} & \pi_{BA} & \pi_{BB} & 0\\ \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \end{matrix} } \right ) \begin{matrix} \end{matrix} \end{matrix}` $$ + where `\(\pi_{BB} = 1 - (\pi_{AA} + \pi_{AB} + \pi_{BA})\)`, + and `\(\pi_{ij}\)` at site `\(j\)` when first captured at `\(t\)` and site `\(i\)` at `\(t - 1\)`. --- ## HMM formulation of the memory model Transition matrix $$ `\begin{matrix} & \\ \mathbf{\Gamma} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \\ 12 \\ 12\end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} z_t=AA & z_t=AB & z_t=BA & z_t=BB & z_t=D \\ \hdashline \phi_{AAA} & \phi_{AAB} & 0 & 0 & 1 - \phi_{AAA} - \phi_{AAB}\\ 0 & 0 & \phi_{ABA} & \phi_{ABB} & 1 - \phi_{ABA} - \phi_{ABB}\\ \phi_{BAA} & \phi_{BAB} & 0 & 0 & 1 - \phi_{BAA} - \phi_{BAB}\\ 0 & 0 & \phi_{BBA} & \phi_{BBB} & 1 - \phi_{BBA} - \phi_{BBB}\\ 0 & 0 & 0 & 0 & 1 \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \\ 12 \\ 12\end{matrix} } \right ) \begin{matrix} z_t=AA \\ z_t=AB \\ z_t=BA \\ z_t=BB \\ z_t=D \end{matrix} \end{matrix}` $$ + `\(\phi_{ijk}\)` is probability to be in site `\(k\)` at time `\(t + 1\)` for an individual present in site `\(j\)` at `\(t\)` and in site `\(i\)` at `\(t - 1\)` --- ## HMM formulation of the memory model Transition matrix, alternate parameterization $$ `\begin{matrix} & \\ \mathbf{\Gamma} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \\ 12 \\ 12\end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} z_t=AA & z_t=AB & z_t=BA & z_t=BB & z_t=D \\ \hdashline \phi \psi_{AAA} & \phi (1 - \psi_{AAA}) & 0 & 0 & 1 - \phi\\ 0 & 0 & \phi (1 - \psi_{ABB}) & \phi \psi_{ABB} & 1 - \phi\\ \phi \psi_{BAA} & \phi (1 - \psi_{BAA}) & 0 & 0 & 1 - \phi\\ 0 & 0 & \phi (1-\psi_{BBB}) & \phi \psi_{BBB} & 1 - \phi\\ 0 & 0 & 0 & 0 & 1 \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \\ 12 \\ 12\end{matrix} } \right ) \begin{matrix} z_t=AA \\ z_t=AB \\ z_t=BA \\ z_t=BB \\ z_t=D \end{matrix} \end{matrix}` $$ + `\(\phi\)` is the probability of surviving from one occasion to the next. + `\(\psi_{ijj}\)` is the probability an animal stays at the same site `\(j\)` given that it was at site `\(i\)` on the previous occasion. --- ## HMM formulation of the memory model Observation matrix $$ `\begin{matrix} & \\ \mathbf{\Omega} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \\ 12 \\ 12\end{matrix} } \right . \end{matrix}` \hspace{-1.2em} `\begin{matrix} y_t=0 & y_t=1 & y_t=2 \\ \hdashline 1 - p_A & p_A & 0\\ 1 - p_B & 0 & p_B\\ 1 - p_A & p_A & 0\\ 1 - p_B & 0 & p_B\\ 1 & 0 & 0 \end{matrix}` \hspace{-0.2em} `\begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \\ 12 \\ 12\end{matrix} } \right ) \begin{matrix} z_t=AA \\ z_t=AB \\ z_t=BA \\ z_t=BB \\ z_t=D \end{matrix} \end{matrix}` $$ --- ## Further reading + Seminal paper by Pradel (2005) [Multievent: An Extension of Multistate Capture–Recapture Models to Uncertain States](https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1541-0420.2005.00318.x). Biometrics, 61: 442-447. + Dupuis (1995) had a similar idea for the Arnason-Schwarz model: Dupuis, J. (1995) [Bayesian estimation of movement and survival probabilities from capture-recapture data](https://academic.oup.com/biomet/article-abstract/82/4/761/252161). Biometrika. Vol. 82, pp 761-772. + See also for a review Gimenez et al. (2012) [Estimating demographic parameters using hidden process dynamic models](https://oliviergimenez.github.io/pubs/Gimenezetal2012TPB.pdf). Theoretical Population Biology 82: 307-316. --- background-color: #234f66 ## <span style="color:white">Live demo</span> .center[  ]