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urol-e5 / timeseries

Data generated from e5 time series sampling in Moorea
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Add Ik and Ic calculations to PI curve code #51

Closed AHuffmyer closed 10 months ago

AHuffmyer commented 10 months ago

Add code to calculate Ik and Ic to PI curve code.

AHuffmyer commented 10 months ago

Hey @ferdi-p! I have a question about this. We want to add calculations for Ik (light saturation point) and Ic (light compensation point) to our PI curve calculations. We used an nls curve fit to generate Am, AQY, and Rd values. Ik is calculated as Am / AQY. I believe that Ic (which is essentially the x intercept) can be calculated as Rd / AQY. Have you calculated these metrics before? Does this sound correct? I'm digging through the literature but the math is tough for me to decode :)

ferdi-p commented 10 months ago

Hi Ariana! Hmm I forgot the functional form / the parameter names. Can you remind me where to find the equations (or just the paper draft)?

On Thu, Aug 10, 2023 at 4:00 PM Ariana S Huffmyer @.***> wrote:

Hey @ferdi-p https://github.com/ferdi-p! I have a question about this. We want to add calculations for Ik (light saturation point) and Ic (light compensation point) to our PI curve calculations. We used an nls curve fit to generate Am, AQY, and Rd values. Ik is calculated as Am / AQY. I believe that Ic (which is essentially the x intercept) can be calculated as Rd / AQY. Have you calculated these metrics before? Does this sound correct? I'm digging through the literature but the math is tough for me to decode :)

— Reply to this email directly, view it on GitHub https://github.com/urol-e5/timeseries/issues/51#issuecomment-1674029707, or unsubscribe https://github.com/notifications/unsubscribe-auth/AN2ISI3VSAHDWWV55DXJPZ3XUVRZTANCNFSM6AAAAAA3LYCUKI . You are receiving this because you were mentioned.Message ID: @.***>

AHuffmyer commented 10 months ago

I found some definitions in this paper here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8722371/

Our script for calculating curves and parameters is here: https://github.com/urol-e5/timeseries/blob/master/timepoint_1/scripts/pi_curves_nls_step2.Rmd

ferdi-p commented 10 months ago

ok yea that looks good. I sent you a Slack to be sure I remember the function for the fits right.

On Thu, Aug 10, 2023 at 4:13 PM Ariana S Huffmyer @.***> wrote:

I found some definitions in this paper here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8722371/

Our script for calculating curves and parameters is here: https://github.com/urol-e5/timeseries/blob/master/timepoint_1/scripts/pi_curves_nls_step2.Rmd

— Reply to this email directly, view it on GitHub https://github.com/urol-e5/timeseries/issues/51#issuecomment-1674038664, or unsubscribe https://github.com/notifications/unsubscribe-auth/AN2ISI4NFRXYVHTMQYNJXKTXUVTJRANCNFSM6AAAAAA3LYCUKI . You are receiving this because you were mentioned.Message ID: @.***>

AHuffmyer commented 10 months ago

Ferdi derived equations for our quadratic equation. Updated in each time point nls step 2 scripts.