Woohoo- I am officially done with my lab work for the population genetics study on the two biological control agents (*Neochetina bruchi* and *N. eichhorniae*) of the invasive water hyacinth. I will post a blog updating you on the how-to’s and my results soon! Finally – I am done driving back and forth to the Bay Area- and currently just working on data analysis and writing up everything here in LA. Stay tuned!

**In the mean time…**

As I promised, here is the Part II to my recent blog: How-To: Stage-Structured Matrix Models.

In this last blog, I discussed the importance of stage-structured matrix models in calculating the intrinsic rate of increase of organisms with developmental stages (such as the weevils!) and detailed how to construct a stage-structured matrix models in excel. Again here is that file: Julies_tutorial_example_matrix_for_popbio

**So now that you have your matrix.. what do you do next?**

**1st: Convert your matrix into a csv file such as the one I created below** based on the excel file above. Just remember- don’t include the headers or row names. I am unable to upload, so I am pasting a picture of the matrix in excel below.

**2nd: Save this file as a csv to your working directory that you use in the R statistical program.** If you haven’t used R before, then go to the R website to download the program, and refer to the below links on how to set up R, your working directory, and how to import files:

1) http://sphweb.bumc.bu.edu/otlt/MPH-Modules/BS/R/R1_GettingStarted/R1_GettingStarted8.html

2) http://www.r-tutor.com/r-introduction/data-frame/data-import

*Also I highly recommend downloading R studio before you start as well -makes everything a lot easier- download R studio here*

**3rd: Install the ‘popbio’ package. You can read about this package here.**

**4th**:** Run the below code!**

#below tutorial on getting a matrix model into R and analyzing with pop bio

library(popbio)

library(popdemo)

help(popbio) #this provides more information on this package

tutorial.mm=read.table(file=”tutorial_matrix_pop_bio.csv”, sep=”,”, header=FALSE)

tutorial.mm

tutorial.L=lambda(tutorial.mm)

tutorial.L

intrinsic=log(tutorial.L)

intrinsic

#You should obtain an intrinsic rate of increase of 0.0217994

**5th: If you want to analyze the stable stages, reproductive values, net reproductive rate , generation time,and conduct an eigen analysis…. Then you will also need to do the following: **

#below to get more information:

###############NEED TO FIRST LIST STAGES

stages<-c(“egg”,”1st_2nd_larvae”,”3rd_larvae”, “pupae”,”pre_rep”, “adult”)

colnames(tutorial.mm)<-stages

rownames(tutorial.mm)<-stages

tutorial.matrix=as.matrix(tutorial.mm)

tutorial.matrix

stable.stage(tutorial.matrix)

reproductive.value(tutorial.matrix)

eigen.analysis(tutorial.matrix)

fundamental.matrix(tutorial.matrix)

net.reproductive.rate(tutorial.matrix)

generation.time(tutorial.matrix)

#Congratulations! You did it!