Introduction | Obtaining and loading the data. | Exploring the data | Finding data for for a particular species | Accessing the matrices | Filtering/subsetting the database based on metadata | Potential issues with MPMs | Calculations from matrices | References

Introduction | Preliminaries | Introduction to piping | Piping with Rcompadre | The mutate function | Using mutate with Rcompadre functions that return vectors | Vectorizing within mutate with the apply functions | Vectorizing over multiple arguments | The group_by and summarize functions | Obtaining a single representative of each species | Using CompadreDB objects with ggplot

Introduction | Preliminaries | Introduction to vectorisation | Manual approach | Loop approach | Vectorised approach | Vectorising custom functions | Accessor functions and vectorisation | Using cdb_unnest() to avoid accessors | Other apply functions | When functions fail | 1. Remove or skip problem elements | 2. Modify the function

Introduction | Aims | Preparation | 1. Functional forms of mortality and reproduction | 2. Trajectories of mortality and reproductive output, and production of life tables | 3. From life table to MPM | 4. Producing sets of MPMs based on defined model characteristics | Conclusion

Introduction | Aims | Preparation | 1. Life cycle archetypes and generating an MPM | 2. Generate a random Lefkovitch MPM based on an archetype | 3. Generate sets of Lefkovitch matrices | 4. Constraining the output matrices | Conclusion

Introduction | Aims | Estimate 95% Confidence Intervals | Sample sizes that vary across the MPM | Exploring the impact of sample size | Conclusion | Addendum

Overview | Recap: Assumed knowledge | R.1. Basic anatomy of life cycles and MPMs | R.2. Projecting population change | R.3. Analysis of population equilibrium (eigenanalysis) | Representing and loading MPMs in Rage | Families of Rage functions for life history analysis | 1. Standardized vital rates | 2. Deriving life tables from MPMs for age-from-stage analyses | 3. Perturbation analyses | 4. Deriving life history traits | 5. Transforming MPMs | References

The CompadreDB object | The matrices | The stage information | The metadata | Version information | Data preparation | A simple example | Including stage descriptions and version information | References

Introduction | Loading MPMs and basic anatomy | Survival and lifespan traits | Reproduction and maturation traits | Life table component traits | Shape of mortality and fecundity | References

Introduction | Preliminaries | Age-from-stage methods with a single matrix population model | Extending to many matrix population models | References

Introduction | Preliminaries: Constructing an MPM from lower-level vital rates | Deriving vital rates of survival | Deriving vital rates conditional on survival | Summarizing vital rates within stages | Growth, shrinkage, stasis, and dormancy | Fecundity | Summarizing vital rates across stages | Simple average across stage classes | Weighted average across stage classes | Distinguishing between possible and impossible transitions | References

Introduction | Types of issue | Missing data | Excessive zeros | Excessive survival | Excessive mortality | Irreducibility and ergodicity | Singularity of the U matrix | Matrix split errors | Function requirement summaries | Other issues | Finally... | References