Generate production plots for herring about csas-latex HOT 8 CLOSED

•The variable it is now the second column in the matrix d3_survey_data and its been transposed and pit in V1 = it_hat in V2
•The variable obs_ct is now called dCatchData , and it's been transposed in the last column of this matrix
•The variable M_tot is now called M.- YES
•The variable ut2 is now called ut , and it's a matrix where column sums are equal to ut2 . -YES both are equal to 1-exp(-colsum(ft))

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have you managed to get Rob's code to run?

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For the WP, I think it would be easiest to reproduce the SAR figs, for AM1 and AM2, all 5 stocks

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No, I haven't managed to run it yet -- I think it's looking for some data files that aren't in the DropBox folder. The data files will have new names now too. I haven't spent much time on this yet though; I was going to work on it today. It looks like panels (a) and (b) are repeats from the storyboard. What do you think about adding panels (c) and (d) from this figure to the storyboard? This would avoid duplication, which could be good in this already lengthy document.

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Got it to run! On V1 data..

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Panels (a) and (b) show the entire time series, but panels (c) and (d) show the Dive period only -- just confirming that's what you want.

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yes, this is what I want :)

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Roger.
Data for these plots comes from *.rep files. I'm unfamiliar with the contents, and some of the object names seem to have changed. Are the following assumptions correct?

• The variable it is now called it_hat.
• The variable obs_ct is now called dCatchData, and it's been transposed.
• The variable M_tot is now called M.
• The variable ut2 is now called ut, and it's a matrix where column sums are equal to ut2.

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