For the analysis summary of Roz’s health paper, I prepared a knitr document. This simply allows you to easily weave text and dynamic R code. We were able to iterate over plots, content, and analyses very easily as this can be shared and published online. I’ll make another one for this analysis here, and we can iterate through results and portions of the text for the main body of the paper.

The big questions for this paper are:

For the first round of this document, I’ll start with the plots we talked about last week. These are:

  1. Health of some # of individuals with annotation depicting how we’ll quantify & tabulate health during entanglement periods
  2. The boxplot of overall health during entanglment windows (i.e. not just the last 6 months) by severity & gear status
  3. Showing the health of animals with a box plot for the last 6 months of the entanglement window - facted by entanglement type and severity
  4. Showing two slope graphs of health decline and recovery by severity and gear status
  5. Recovery after gear is cleared, colour-coded by severity
  6. Showing the same 6-month boxplot, but only for reproductively active females

Since it’s relatively easy for me to show #4 and #5 for females. So I’ll structure the results to show 3, 4, & 5 for all animals, and then again for just reproductively active females.

Also, note that the slope graphs have a labeling issue that I adjust in Adobe Illustrator. I’ll do that at the last step, as I have to do that manually. For now, I know the labels can overplot, but don’t worry, they will get changed.

Ok, for the health plot of individuals, I’ll show one here, but will plot all of them in a separate pdf. You can browse through them to see if there is one you like/want to depict in the paper. You sent me a list of females, which contains:

 efems <- c(1140, 1158, 1163, 1266, 1430, 1601, 1608, 1705, 1815, 2029, 2040, 2240, 2301, 2645)

Here I’ll plot 1163 as an example, but I’ve made a PDF containing all of these for your perusal.

plot of chunk plothealth

Interestingly, to me, all of the whales that are presumed dead (1163, 1430, 1601, 1815, 2240), are all estimated to be dead in the model. That is nice to see that consistency, and marks a thing to explore for the survival paper as well as the report card paper.

Ok, next we’ll plot the overview boxplot that shows health during the last 6 months of the entanglement window, as a function of injury severity and gear-carrying status:

plot of chunk boxStatus

Now we’ll refine this by looking at the boxplot of health within the last 6 months - by month.

plot of chunk boxStatusLast6

Next let’s look at the slope graphs of health decline/recovery during two periods: 1) start of entanglement window to end of entanglement window; and 2) end of entanglement window to 12 months afterwards (n.b. that if the animal is carrying gear, this is 12 months after the last date with gear). First, during the entanglement window:

plot of chunk slopeAllBA

Next, for the 12 months following entanglement:

plot of chunk slopeAllAR

And then we can look at the recovery of animals over that 12-month period as a line by severity status.

plot of chunk rcovAns

Now we’ll show the same results as above, but only for reproductively active females. First the boxplot:

plot of chunk entFemalesBoxPlot

Then the recovery lines.

plot of chunk entFemalesRecovery

Finally the slope plots. During Entanglement first:

plot of chunk entFemalesSlopeBA

And then recovery following entanglement:

plot of chunk entFemalesSlopeAR