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cf9bb89..9153378 100644 --- a/docs/404.html +++ b/docs/404.html @@ -78,12 +78,12 @@

  • 3 Hidden Markov models
  • II. Transitions
  • Introduction
    • -
  • 4 Survival
    • -
  • 5 Movements between sites, and states
    • +
  • 4 Live and dead
    • +
  • 5 Sites and states
  • III. Case studies
  • Introduction
  • 6 Life history
    • -
  • 7 Covariates
    • +
  • 7 Covariates
  • 8 Miscelleanous
  • 9 Lack of fit
  • IV. Conclusions
    • diff --git a/docs/about-the-author.html b/docs/about-the-author.html index 6895aa2..e9d7c18 100644 --- a/docs/about-the-author.html +++ b/docs/about-the-author.html @@ -78,12 +78,12 @@

  • 3 Hidden Markov models
  • II. Transitions
  • Introduction
    • -
  • 4 Survival
    • -
  • 5 Movements between sites, and states
    • +
  • 4 Live and dead
    • +
  • 5 Sites and states
  • III. Case studies
  • Introduction
  • 6 Life history
    • -
  • 7 Covariates
    • +
  • 7 Covariates
  • 8 Miscelleanous
  • 9 Lack of fit
  • IV. Conclusions
    • diff --git a/docs/covariates.html b/docs/covariates.html index 71418bc..d1294d2 100644 --- a/docs/covariates.html +++ b/docs/covariates.html @@ -79,7 +79,7 @@

  • II. Transitions
  • Introduction
  • 4 Survival
    • -
  • 5 Movements between sites, and states
    • +
  • 5 Of sites and states
  • III. Case studies
  • Introduction
  • 6 Life history
    • diff --git a/docs/covariateschapter.html b/docs/covariateschapter.html new file mode 100644 index 0000000..81c7a66 --- /dev/null +++ b/docs/covariateschapter.html @@ -0,0 +1,218 @@ + + + + + + +Chapter 7 Covariates | Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models + + + + + + + + + + + + + + + + + + + + +
    +
    +
    Skip to main content + +
    +

    + Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models: + Theory and Case Studies in R +

    + +
    + + +
    +

    +7 Covariates +

    +
    +

    +7.1 Missing values +

    +

    NAs reprise du papier de Bonner, ou modèle de croissance poisson, ou rien hein…

    +

    Work on missing values by Bonner et al. (2006) and Langrock and King (2013) and Worthington et al. (2015).

    +
    +
    +

    +7.2 Nonlinearities +

    +

    splines à la main et avec jagam, ex snow petrels

    +
    +
    +

    +7.3 Covariate selection +

    +

    rjmcmc on turdus merila, papier Evolution Gimenez. Exemple cigognes, papier Gimenez WinBUGS.

    +
    +
    +

    +7.4 Sex uncertainty +

    +

    Pradel et al. (2008) and Genovart, Pradel, and Oro (2012)

    +
    +
    +

    +7.5 Actuarial senescence +

    +

    Choquet et al. (2011), Péron et al. (2016), Marzolin on dipper in Ecology.

    +
    + +
    +

    +7.7 Uncertainty in age +

    +

    Papier Vincenzo et d’autre papiers.

    + +
    +
    +
    + + +
    + +
    + +
    +
    + + + + diff --git a/docs/crashcourse.html b/docs/crashcourse.html index efc0d18..b1d44ba 100644 --- a/docs/crashcourse.html +++ b/docs/crashcourse.html @@ -78,12 +78,12 @@

  • 3 Hidden Markov models
  • II. Transitions
  • Introduction
    • -
  • 4 Survival
    • -
  • 5 Movements between sites, and states
    • +
  • 4 Live and dead
    • +
  • 5 Sites and states
  • III. Case studies
  • Introduction
  • 6 Life history
    • -
  • 7 Covariates
    • +
  • 7 Covariates
  • 8 Miscelleanous
  • 9 Lack of fit
  • IV. Conclusions
    • @@ -260,7 +260,7 @@ 

     sample_from_posterior <- rbeta(1000, 20, 39) # draw 1000 values from posterior survival beta(20,39)
 mean(sample_from_posterior) # compute mean with Monte Carlo integration
-## [1] 0.3443
    +## [1] 0.3365

    You may check that the mean we have just calculated matches closely the expectation of a beta distribution10:

     20/(20+39) # expectation of beta(20,39)
@@ -269,7 +269,7 @@ 
    
 
     quantile(sample_from_posterior, probs = c(2.5/100, 97.5/100))
 ##   2.5%  97.5% 
-## 0.2253 0.4602
    
+## 0.2266 0.4695

    diff --git a/docs/dispersal.html b/docs/dispersal.html index 6c566af..fd77578 100644 --- a/docs/dispersal.html +++ b/docs/dispersal.html @@ -4,16 +4,16 @@ -Chapter 5 Movements between sites, and states | Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models +Chapter 5 Sites and states | Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models - + - + @@ -78,12 +78,12 @@

  • 3 Hidden Markov models
  • II. Transitions
  • Introduction
    • -
  • 4 Survival
    • -
  • 5 Movements between sites, and states
    • +
  • 4 Live and dead
    • +
  • 5 Sites and states
  • III. Case studies
  • Introduction
  • 6 Life history
    • -
  • 7 Covariates
    • +
  • 7 Covariates
  • 8 Miscelleanous
  • 9 Lack of fit
  • IV. Conclusions
    • @@ -99,7 +99,7 @@

    -5 Movements between sites, and states +5 Sites and states

    WORK IN PROGRESS. I’m missing a section on gof w/ R2ucare and posterior predictive checks/Bayesian p-values.

    @@ -35066,12 +35066,12 @@

    - +

    -
    ## Time difference of 19.07 secs
    +
    ## Time difference of 19.01 secs

    We can have a look to numerical summaries:

     MCMCsummary(mcmc.output, round = 2)
@@ -5627,7 +5627,7 @@ 
    
 ## |-------------------------------------------------------|
 end_time <- Sys.time()
 end_time - start_time
-## Time difference of 17.68 secs
    +## Time difference of 17.84 secs

    The numerical summaries are similar to those we obtained with the complete likelihood, and effective samples sizes are larger denoting better mixing:

     MCMCsummary(mcmc.output, round = 2)
@@ -5763,7 +5763,7 @@ 
    
 ## |-------------------------------------------------------|
 end_time <- Sys.time()
 end_time - start_time
-## Time difference of 17.81 secs
+## Time difference of 17.63 secs
 MCMCsummary(mcmc.output, round = 2)
 ##     mean   sd 2.5%  50% 97.5% Rhat n.eff
 ## p   0.61 0.06 0.49 0.61  0.72    1  1453
diff --git a/docs/index.html b/docs/index.html
index dd90a1e..016b818 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -78,12 +78,12 @@ 
    
 
  • 3 Hidden Markov models
    • 
 
  • II. Transitions
    • 
 
  • Introduction
    • 
-
  • 4 Survival
    • 
-
  • 5 Movements between sites, and states
    • 
+
  • 4 Live and dead
    • 
+
  • 5 Sites and states
    • 
 
  • III. Case studies
    • 
 
  • Introduction
    • 
 
  • 6 Life history
    • 
-
  • 7 Covariates
    • 
+
  • 7 Covariates
    • 
 
  • 8 Miscelleanous
    • 
 
  • 9 Lack of fit
    • 
 
  • IV. Conclusions
    • 
diff --git a/docs/introduction-4.html b/docs/introduction-4.html
index de7f0c9..04f8e2f 100644
--- a/docs/introduction-4.html
+++ b/docs/introduction-4.html
@@ -78,12 +78,12 @@ 
    
 
  • 3 Hidden Markov models
    • 
 
  • II. Transitions
    • 
 
  • Introduction
    • 
-
  • 4 Survival
    • 
-
  • 5 Movements between sites, and states
    • 
+
  • 4 Live and dead
    • 
+
  • 5 Sites and states
    • 
 
  • III. Case studies
    • 
 
  • Introduction
    • 
 
  • 6 Life history
    • 
-
  • 7 Covariates
    • 
+
  • 7 Covariates
    • 
 
  • 8 Miscelleanous
    • 
 
  • 9 Lack of fit
    • 
 
  • IV. Conclusions
    • 
@@ -104,7 +104,7 @@ 
    Introduction
   
    
 
-
+
 
    
     
    
   
    
-
+
 
 
    
     
    
   
    
 
    
-4 Survival
+4 Live and dead
 
    
 
    
 
    
@@ -9892,11 +9892,11 @@ 
    
 
    
   
    
 
-
+
 
    
     
    
   
    
 
-
+