00:43:17 Amy Myrbo (she/her) - Amiable Consulting: And please put your questions in the chat, or raise your hand (sometimes that's harder for us to see), if you have questions! We will try to pause every once in a while to solicit qs. 00:45:39 Amy Myrbo (she/her) - Amiable Consulting: The GSA Events Code of Conduct is here: https://www.geosociety.org/GSA/Events/EventConductCode/GSA/Events/Conduct.aspx 00:46:06 Nicole Lapeyrouse: I get Null 00:48:30 Amy Myrbo (she/her) - Amiable Consulting: Nicole, did you solve your issue or is it still happening? 00:49:01 Nicole Lapeyrouse: I am re running these packages to see if it fixes library(clam) clam() library(rbacon) Bacon() 00:51:11 Amy Myrbo (she/her) - Amiable Consulting: For anyone just joining, Maarten is currently addressing questions from the post-course survey, and will then move on to today's session! 00:52:21 Michelle Nelson: Is it normal for R Studio to cut off the values, this is what I get when I type in dnorm(cc[,2],130,20) "[ reached getOption("max.print") -- omitted 8501 entries ]" sorry if I missed this 00:53:14 Amy Myrbo (she/her) - Amiable Consulting: I'll save this for the next q session Michelle. Thanks. 00:54:06 Amy Myrbo (she/her) - Amiable Consulting: This is the hardest but most important figure to understand. 00:55:21 Amy Myrbo (she/her) - Amiable Consulting: If you don't quite understand this, I would recommend looking at the animation in the session 1 materials. Stare at it until you understand! 00:56:27 Dan Gavin: If there is time can you quickly cover when it is appropriate to smooth the calibration curve before calibrating? 00:56:57 Michelle Nelson: Thank you! 00:58:39 Dan Gavin: Got it. Thanks. 00:59:53 Amy Myrbo (she/her) - Amiable Consulting: The animation is in the slides from last week (not the GitHub site), and there is another useful set of animations here: https://chrono.qub.ac.uk/blaauw/wiggles/calibrate.html 01:03:37 Amy Myrbo (she/her) - Amiable Consulting: Sorry, here's the link for today's session code etc (with a download link for the slides): https://maarten14c.github.io/GSA_agemodeling/session_2a.html 01:08:17 nkehrwald: I know that we are using the hiatus at 470 as an example, but in "real life" when would we be justified for assuming a hiatus at a certain time? 01:08:28 Amy Myrbo (she/her) - Amiable Consulting: Ooh good question 01:09:26 Laura Barnett: #requ 01:09:26 Amy Myrbo (she/her) - Amiable Consulting: A couple things: first, sedimentology. You may have evidence of a hiatus such as an abrupt change in lithology. 01:10:16 David Grimley: another could be a paleosol 01:10:24 Amy Myrbo (she/her) - Amiable Consulting: Second, the age-depth model may look a lot more likely if you put in a hiatus. But I think Maarten is talking about this! 01:10:55 Amy Myrbo (she/her) - Amiable Consulting: Paleosol, absolutely. Or sand or another type of winnowed or desiccation surface. 01:11:46 Natalia Szymańska: Santa! 01:11:47 Chantel Saban: Santa 01:11:47 Christina Tenison: santa claus? 01:13:04 lisa boush: Great analogy—— 01:14:09 Amy Myrbo (she/her) - Amiable Consulting: We <3 uncertainty 01:15:10 Amy Myrbo (she/her) - Amiable Consulting: And of course those blue symbols are the probability distribution functions of each calibrated date. 01:16:08 Amy Myrbo (she/her) - Amiable Consulting: Instead of just a dot with error bars, we have the actual entire probability distribution. 01:16:54 Amy Myrbo (she/her) - Amiable Consulting: Whoa 01:17:47 Amy Myrbo (she/her) - Amiable Consulting: We will pause for questions in a moment 01:18:18 Amy Myrbo (she/her) - Amiable Consulting: Bacon, BChron, and OxCal 01:18:19 Michelle Nelson - USU Luminescence Lab: reminds me of a braided river 01:19:45 Chris Conwell: Are the probability densities of each data point determined using the clam method shown in the last session of this course? 01:20:17 Amy Myrbo (she/her) - Amiable Consulting: Great question. You can do that calibration with CALIB. But Bacon does it for you as part of the age-depth modeling process! 01:20:21 Amy Myrbo (she/her) - Amiable Consulting: (@Chris) 01:20:32 Chris Conwell: Thanks Amy 01:21:25 Edward Duarte Martinez: Those are the iterations generated by Monte Carlo Simulations? 01:21:36 Christina Tenison: how many samples do you need for age depth modelling? (ideally) 01:21:59 Edward Duarte Martinez: Thanks! 01:22:54 Amy Myrbo (she/her) - Amiable Consulting: Blaauw, M., Christen, J.A., Bennett, K.D. and Reimer, P.J., 2018. Double the dates and go for Bayes—Impacts of model choice, dating density and quality on chronologies. Quaternary Science Reviews, 188, pp.58-66. 01:23:33 Christina Tenison: thanks! 01:26:01 Amy Myrbo (she/her) - Amiable Consulting: And CALIB is still a wonderful and useful tool for calibrating single dates. Nice clean output for publications as well. Recommended! http://calib.org/calib/ 01:26:40 Amy Myrbo (she/her) - Amiable Consulting: Simpler to use for single dates than OxCal or Bcal imo 01:27:55 Nancy Bigelow: I find Oxcal hard to run. Calib and Bacon are easier (to me, anyway). 01:30:22 Amy Myrbo (she/her) - Amiable Consulting: Wow, that person started a revolution. 01:32:55 lisa boush: Bayes was a Cambridge man, BTW— 01:36:16 Nancy Bigelow: 50% 01:36:17 Edward Duarte Martinez: 50 01:36:17 Christina Tenison: 50% 01:36:18 Natalia Szymańska: 50% 01:36:38 Amy Myrbo (she/her) - Amiable Consulting: Only happens in the Twilight Zone 01:36:59 Dan Gavin: 0 01:37:01 Troy Michael Ferland: 15% 01:37:09 lisa boush: %30 01:37:13 lisa boush: $30? 01:37:25 Cale Gushulak: Can't be known 01:37:33 lisa boush: Unless you have big pockets—— 01:37:33 Jill Coleman Wasik: Are you the kind of person to carry cash? 01:37:42 Christina Tenison: do you carry cash at home? 01:38:12 Christina Tenison: 100% rainy here :) 01:48:07 Amy Myrbo (she/her) - Amiable Consulting: So if you have questions please feel free to pop them in the chat, or raise your hand and I'll call on you! Thanks. I will ask Maarten about how to decide when and where to insert hiatuses 01:49:52 Chris Conwell: Hi Marten, the PDFs for each calibration point in the bayesian age-depth framework shown in your examples are presumably based on analytical uncertainty of 14C measurements. Can we still use a bayesian approach if instead our calibration points are based in biostratigraphy, i.e. stratirgaphic position of biozone boundaries? Paleozoic carbonate stratigrapher asking :) 01:50:07 Laura Caitlin Streib: BChron, OxCal, and Bacon are for radiocarbon dates? Is there a Bayesian based package that could be used for older records with lots of dating methods, like luminescence, magnetic reversal, and tephra dates in addition to radiocarbon? 01:50:34 Chris Conwell: Maarten*, sorry for misspelling 01:51:07 Chris Conwell: My question is closely related to Laura's 01:51:53 Amy Myrbo (she/her) - Amiable Consulting: @Laura, Bacon can be used with all of these kinds of dates in addition to or instead of radiocarbon. 01:52:30 Amy Myrbo (she/her) - Amiable Consulting: You would just choose to not run those dates through the radiocarbon calibration. We will cover that! Thanks for the question! 01:52:33 Chris Conwell: Great to hear, thanks Maarten 01:53:11 Amy Myrbo (she/her) - Amiable Consulting: And it can't be plus or minus zero :D 01:55:35 Amy Myrbo (she/her) - Amiable Consulting: Sometimes you only go back and see the lithologic evidence after you have the age-depth model! 01:58:17 Amy Myrbo (she/her) - Amiable Consulting: I will put in a couple Bayes resources here in the chat. They are nothing you need to get distracted by now, but they will be here in the chat for your reference. 01:58:23 Amy Myrbo (she/her) - Amiable Consulting: https://www.countbayesie.com/blog/2015/2/18/bayes-theorem-with-lego 01:58:31 Amy Myrbo (she/her) - Amiable Consulting: Bayes Theorem with Legos 02:00:39 Amy Myrbo (she/her) - Amiable Consulting: A book Maarten recommended in a course a few years ago; I have found it useful: https://g.co/kgs/v2adtA 02:01:05 Amy Myrbo (she/her) - Amiable Consulting: Howson and Urbach, Scientific Reasoning: The Bayesian Approach 02:05:05 Amy Myrbo (she/her) - Amiable Consulting: And finally https://yalebooks.yale.edu/book/9780300188226/theory-would-not-die 02:05:27 Amy Myrbo (she/her) - Amiable Consulting: The Theory That Would Not Die: How Bayes' Rule Cracked the Enigma Code, Hunted Down Russian Submarines, and Emerged Triumphant from Two Centuries of Controversy Sharon Bertsch McGrayne 02:10:15 lisa boush: My apologies—Bayes went to the University of Edinburgh! So sorry— 02:17:40 Jason Price: So should the gray lines and green graphs match on an RBacon run? 02:17:43 Nancy Bigelow: So if the green lines on the prior and memory graphs don't match the model, that is bad? And we should adjust the settings? 02:24:25 Amy Myrbo (she/her) - Amiable Consulting: So sorry! My Zoom melted down again and the chat and my mic button froze! 02:24:51 Amy Myrbo (she/her) - Amiable Consulting: Guess I shouldn't have updated to the latest version 🙄 02:26:07 Amy Myrbo (she/her) - Amiable Consulting: The default accumulation rate in Bacon was actually changed based on an analysis Simon Goring and others did with a whole bunch of data in Neotoma! 02:27:30 Elizabeth J Davis: Did someone have a hand raised? 02:28:06 Chris Conwell: I think that was me—hit a button by accident? Thanks 02:28:57 Amy Myrbo (she/her) - Amiable Consulting: Don't date it if you think it's a reworked piece of wood :D 02:31:19 Maryann Malinconico: Amy, What is your definition of “reworked wood”? 02:32:20 Chris Conwell: Maarten, when that paper gets published, it'd be great if you/Amy posted an update to the email roster for this course 02:35:11 Chris Conwell: Need to leave early but looking forward to watching the rest of the recording. Thanks Maarten and Amy—this is a fantastic course 02:35:22 Amy Myrbo (she/her) - Amiable Consulting: (And I don't mean to be flippant - I know it's difficult to identify reworked material, and very difficult to resist dating it, especially if you don't have much dateable material!) 02:36:32 Amy Myrbo (she/her) - Amiable Consulting: @Maryann - for example wood (or any material) that has been eroded from shallower water sediments and redeposited in deeper water 02:37:19 Amy Myrbo (she/her) - Amiable Consulting: Or that has been sitting around on the landscape for a long time before being washed into the lake 02:39:12 Amy Myrbo (she/her) - Amiable Consulting: I will ask Maarten to describe in more detail how to set, and to see, the priors. 02:39:31 Nancy Bigelow: This is great Maarten, Thanks! 02:39:47 Nancy Bigelow: I have to go to another zoom :( 02:40:11 Amy Myrbo (she/her) - Amiable Consulting: The code for doing all these things is in the https://maarten14c.github.io/GSA_agemodeling/session_2b.html 02:40:51 Amy Myrbo (she/her) - Amiable Consulting: We will also talk about this folder structure and the files and naming convention! 02:41:01 Amy Myrbo (she/her) - Amiable Consulting: A simple but powerful sticking point 02:41:46 Maryann Malinconico: Amy, Thanks for that. In coal and organic petrology we get into similar concepts but many use “recycled” for the eroded version, but may ignore the “sitting around” concept. 02:42:19 Amy Myrbo (she/her) - Amiable Consulting: Yes, and "sitting around" is probably more properly called "landscape latency" or something! 02:43:18 Monika Ruwaimana: Hi Amy, where we can get the example core radiocarbon data that Maarten used for input to running that code? 02:43:38 Amy Myrbo (she/her) - Amiable Consulting: And there is a way in Bacon to look up which calibration curve is which number. 02:44:02 Monika Ruwaimana: is the example core data include in the package? 02:44:11 Amy Myrbo (she/her) - Amiable Consulting: Yes. In today 02:44:15 Amy Myrbo (she/her) - Amiable Consulting: oops 02:44:37 Amy Myrbo (she/her) - Amiable Consulting: In today's session page (https://maarten14c.github.io/GSA_agemodeling/session_2b.html) run the code below the "Bacon" heading 02:45:20 Amy Myrbo (she/her) - Amiable Consulting: We will unpack all of this more in the followup!!! 02:46:47 Jill Coleman Wasik: The ppt linked on session 2b page is missing a couple slides between RLGH3 data file slide and post run analysis slides. 02:47:11 Amy Myrbo (she/her) - Amiable Consulting: Thank you! I know he's changed them recently. I will flag this. 02:47:21 Monika Ruwaimana: Thank you! got it 02:53:37 Christina Tenison: great thanks! 02:54:08 Maryann Malinconico: I really liked the Bayesian and Monte Carlo parts! 02:54:23 Jill Coleman Wasik: Thank you!! 02:54:32 Joshua Barna: Thank you! This was great!