Problem set 3: Structured population models Easton R. White Foundations of Quantitative Reasoning

Matrix population models1 Caswell 2001. Matrix Population Models. Sunderland, MA: Sinauer Associates Inc. is the best reference on all things matrix models. are widely used to study plant and animal populations.

Assignment

In teams of two, address the following questions:

  1. What species (and location if available) did you choose? Why did you choose the species?
  2. What question do you want to answer about this population (e.g. population status, best management strategies)?
  3. Calculate eigenvalue, stable age distribution, elasticity, and sensitivity. What does this tell you about the population?
  4. Using the calculations in part (c), or additional calculations, address the question you proposed in part (b).

Submit your writeup as an R markdown file on Github. This can be a private or public repository. I expect to see commits to the repository from each partner.

Data

There are two databases of matrix models you can investigate: COMPADRE (plant-focused) and COMADRE (animal-focused). They are both available online https://www.compadre-db.org/Data. The data is downloaded as an .Rdata file. Each file is then organized as follows:

compadre/comadre +-- metadata {dataframe with ca 60 columns and one row one for each set of matrices (mat A, matU, matF, matC)
         |
         +-- matrixClass {list with one entry for each set of matrices. Each entry is a data frame with 3 columns: MatrixClassOrganized, MatrixClassAuthor, MatrixClassNumber.}
         |
         |-- mat {list with one entry for each row of metadata}
         |     |
         |     +-- matA {matrix}
         |     +-- matU {matrix}
         |     +-- matF {matrix}
         |     \-- matC {matrix}
         |
          \-- version {a vector with version information}

Therefore, as an example, to access the list of common names, you would enter comadre$metadata$CommonName. To find the matrix model of the 901st population in the database, you would enter comadre$mat[901][[1]]. More information on the databases is available online: https://github.com/jonesor/compadreDB