Borrowing strength | The matrix | Ignore the problem | Fill in including constraints on transitions | Fill in using uninformative priors on fertility | Effects of informative priors | Interactive Exploration | Obtaining credible intervals on vital rates and $\lambda$ | References

Part I: Obtaining the projection matrix | Step 1: Load and munge the single population data for L. elto | Step 2: Obtain starting number of individuals per stage | Part 2: Using priors to incorporate rare transitions | Use uninformative priors | Transition matrix | Fertility matrix | Other options for argument returnType | Incorporate informative priors | Part 3: Obtain Credible Intervals | Obtain CI for indvidual matrix entries | Credible intervals on $\lambda$

Snail kites | Background | Study design and data sources | Survival values | Why a Beta distribution? | Moment matching: from mean and SD to $\alpha$ and $\beta$ | Interpreting the effective sample size | Comparing Beta and normal priors | Reproductive rates | Components of reproduction | Nest success as a Beta variable | Young per successful nest | Comparing prior sources | Interpretation | Building the matrices | Propagating uncertainty to $\lambda$ | Connection to raretrans | Literature cited

Overview | Biased estimates from small samples | The example population: Chamaedorea elegans | Providing the stage-population vector N | Part 1: Observed matrix and its limitations | Part 2: Adding priors with fill_transitions() | Uniform (non-informative) prior | Informative (expert) prior | Adjusting prior weight | Part 3: Adding priors for fecundity with fill_fertility() | Combined posterior matrix | Part 4: Other return types | Augmented fate matrix (TN) | Full projection matrix A | Alpha and beta vectors (fertility) | Part 5: Simulating matrices and credible intervals on $\lambda$ | Part 6: Credible intervals on individual transition probabilities | Computing credible intervals with transition_CrI() | Visualising credible intervals with plot_transition_CrI() | Visualising the full posterior density with plot_transition_density() | Summary | References

What this vignette shows | The data | Build the input matrices | Compute credible intervals | Visualise | Including the dead fate | Excluding the dead fate | Next steps | Reference

Introduction | The Cypripedium calceolus transition matrix (matU) | Computing credible intervals | Visualising with plot_transition_CrI() | Including the dead fate (default) | Excluding the dead fate | Effect of prior weight | Visualising full posterior densities | With uninformative prior | Effect of prior weight on densities | Summary | References