So good afternoon everyone. So far we've done some, we've seen some excellent science, we've seen phylogenetics, we've seen antimicrobial resistance. That's sorts of fantastic things. And now for something completely different. We're going to look at some pretty pictures, well hopefully pretty pictures. Think about trees, think about geography, think about time, and see how we can put these things together. We don't have any sort of automatic present-to-advanced-to thing, eh? Okay, alright. So what are we trying to accomplish here? It's a fairly profound question, but the idea behind the module is that we want to be able to generate appropriate data sets, right? So what's an appropriate data set? What's an inappropriate data set? We want to be able to take our data sets and manipulate them in various different types of applications. The ones that you'll be seeing in the tutorial are going to be phylo-canvas, micro-react and Genghis, giving you a bit more of an overview later on. And then once you've shot things into those programs, interpreting the results, analyzing and interpreting the results of a phylogeographic analysis, right? I got my map, I got my tree, I got my pretty colors, it wasn't me. So these are important questions. And we are going to start in 1797. So, as one does. So how many of you are familiar with the whole John Snow cholera water pump story? Zero. Okay, some in the back. Excellent. I think it was Gary. Gary or Ed alluded to it yesterday. So the John Snow story is basically, oh, look at all the people of cholera. Oh, look, there's a cluster of people of cholera here. Oh, look, there's a water pump that's giving people cholera. That's pretty cool. But this comes over 50 years before that. And this was a fellow named Valentine Seaman, who was a medical doctor, I think it's what they're called, in New York City, and published an article in 1797, Medical Repository, looking at something similar. The focus of his investigation was yellow fever. So this is a dock in New York City, or a series of docks in New York City. That's Front Street, that's Allegable Street, that's Fly Market, that's Pine Street. And the idea is that in 1797 or slightly before, there were outbreaks of yellow fever that happened. And as one might imagine, a dock in 1797 in New York was not the cleanest environment known to humanity. It was pretty foul.  Dumping the build, ballast water, you name it. And people started getting sick from yellow fever. And so it's cool in some sense, because what Dr. Seaman did was took a map of this immediate neighborhood in one other spot in New York as well, and said, is there any information that we can glean from the geographic locations of these sequences? And so it can be a bit difficult to make out, and actually this is an enhanced version of the original, which has aged reasonably well, all things considered. And this is the map. And if you could see the little dots there, those are individual cases of yellow fever that were identified. And so as you can immediately see, the little bitty dots are kind of concentrated in one particular spot. You may not be able to see them, but there are other dots that are numbered, and those correspond to cases where individuals contracted and then died from yellow fever. So here's an overlay with the actual names of the individuals who passed away. And then these sort of inferred regions of high concentration, which you refer to as miasmas, potential sources, and just considering different hypotheses. And I don't have the image, but one interesting thing that people have done with this is if you look at the dates, it actually kind of stands out, you can draw these sort of temporal contours to see the cases expanding over time, which is pretty interesting. This website, which I discovered while I was preparing this material, is amazing. It's like a historical cartographer of epidemiology and the examples that he has, absolutely stunning. So we haven't talked about consumption in the last couple of hours, so let's get back to it. This is another map. This is the state of Massachusetts. And this is a study by Henry E. Yersol Babich in 1862, considering potential causes of consumption tuberculosis in New England, specifically the state of Massachusetts. And so what he did was he took every county in Massachusetts and encoded it according to the incidence of tuberculosis. And so it's completely illegible, sort of done in this 1860s cursive that no one could ever read. But the idea is that you have some of this is like in the towns, in the towns on the countryside, particularly in the towns and so on and so forth. And so that's why we have the blue, red border with blue centers across the St. George and all that. Those all refer to different degrees and types of incidence. And then he constructed these rather remarkable tables where you have all of the different incidences of consumption in different counties and then considering different environmental factors, in particular soil humidity, soil moisture, trying to build a link. In the end, the strongest link was soil humidity versus the increased incidence of consumption. Okay, so this is a nice visualization. This is actually the original, which is in the collections of the University of Colorado. It's kind of humbling in a way to look at what people were capable of 150, 200, 300 years ago. All right, so what's biologiography? Well, the term was coined by John Avice in 1787. He had a long and prosperous life. 1987, which some of us might remember, a field of study concerned with the principles and processes governing the geographic distributions of genealogical lineages, especially those within and among closely related species. Not that bacterial species actually exist, but we can pretend they do. So the idea being that for any particular collection of microorganisms, we can look at their phylogenetic relationships and we can look at their spatial distributions and try to infer something from the intersection of those. So there's a nice example here. And this is from the next string.org website, which has several different examples of temporal phylogenographic tracking of different recent outbreaks. So this is the Ebola example. And immediately, hopefully even just without me explaining it, you can grab a couple of key pieces of information about the distribution and possibly the spread of the Ebola virus throughout the three countries there. So what do we see? What are your first impressions? What's going on here? Sorry? Three points of entry. Three points of entry? Okay. To the three different countries? Yeah. Okay. So what are you basing that on? The clusters and the map. So we have clusters in the tree and you can see that they're distinguishable colors and often we see these clusters of the same color, which correspond to clades. So phylogenetically cohesive groups of isolates that are from the same country. So here's a big pile of green, which corresponds to guinea. And then there's a lot of blue right here on the on. And you can see that, you know, there's sort of implied transmission events here. So for example, this blue area, probably most of the stuff going on here was in Sierra Leone. But then as we track this through, we can see several cases where we get green dots emerging. And those might very well correspond to transmission across international boundaries. And so looking a bit more closely at this, you can't really see it from where you are. But each of these locations corresponds to an appropriate level division. Not canty, but different countries have different divisions. And localities, circles, the size of the circle indicates the number of cases. And then there are actually arrows connecting circles, which indicate implied transmission events or even rates of transmission between different localities. So there's a lot of information there. And it's amazing what you can accomplish with a tree and a very simple coloring scheme. So why phylogyography? Well, we want to know about the relationship, space, time and environmental factors. Some questions that we might ask are, what are the most likely points of origin, introduction into a region? So we already saw that with the Ebola example. When and where did an outbreak most likely originate? Can we infer that from some of these data sets? Are there specific settings that are at greater risk? I would have changed this last one if I had the opportunity to. Because settings is like command line arguments. But settings actually is referring to environmental parameters. Heavy rainfall, locations with heavy rainfall, for example. So if you can do the phylogyographic visualization and the modeling, you might be able to get at some of these questions. So what do we need? Well, obviously we want phylogyography. We want some sort of coordinate information at some level of resolution. And those of you who've worked with these types of data, will know that often the data are not presented at the most fine-grained level of resolution. A lot of the data sets that we've obtained from our collaborators are fuzzed either by mapping them up to some sort of higher level like postal code rather than house. Or even just have had some random noise added to them. Which you'll see in an example where a lot of cases end up in the Wanda Fuca Strait. Temporal data, right? So if you want to have some sort of temporal context of the outbreak, then you want that information. Contextual information. So this is settings, right? So location attributes, information about the patients, right? So you might want to know which isolates came from an assisted care facility. Which ones came from a school, right? Which ones came from the taco food truck outside? Which I don't actually want to know. And then for phylogyography, obviously you need a phylogenetic tree. Some sort of description of the inferred relationships amongst your isolates. So this is a fairly redundant representation because the workflow is take the stuff I just said, do analysis, and get results. So there we go. We don't need to dwell on that slide, I don't think. So let's take a closer look at what I said. Okay, so this is geofylogy, right? So this is the Haiti cholera data, which I believe you were working with last night. This is kind of a superset of what you were working with, I believe, right? Is that, yeah, okay. So this is obviously more than the data sets that we're looking at because this would be kind of intractable in the context of a two-day workshop. But immediately you can see the same sort of patterns, right? We have a phylogenetic tree relating cholera isolates. And because one of the key questions here was about the origin of the Haitian outbreak, there are a lot of sample Haitian isolates, right? That's all the red ones up there, which do actually almost but not quite constitute a claim because they are interrupted or intermingled with the Nipahal 4 data set right at the top. You can see green indicates other Nepalese clades in the tree, and then we have purple for Bangladesh and then various other country isolates, just not highlighted with any particular color. And so what can we see from this? Well, it's very instructive that we see this clay that has only Nepalese and Haitian isolates. Immediately that suggests a pretty strong connection between the two. This is not to say it could very well be that there are unobserved isolates from the third country, and so we do need to be careful about that. But there is a strong suggestion here that there is a very close connection, especially so Gary's not here. I can't tease him about phylogenetics. Do you remember yesterday Gary talking about the difference between a cladogram and a phylogram? So what's this? And what's useful about a phylogram in this context? Yes, those branches up there are really, really short. They're like this basically zero. So it's pretty much the same thing sampled again and again and again and again. And so the fact that not only is there this close phylogenetic relationship, but we can also look at the branch lengths and say, you know, there's almost no sequence change here to speak of, gives us further support for the idea of this strong connection between Nepal and Haiti. So this is interesting. The tree that we're looking at here was actually built using maximum personally, which is perhaps a bit surprising. But then they use statistical measures and we're going to get into those in more depth when you're on to try and infer times of most recent common ancestors. So you have statistical models. And part of it is if you have, and we often deal with this, for trying to build large phylogenies based on things sampled roughly at the same time, then you don't really have a time context. It's like all of these things were isolated this year, so we don't really have some estimate of how much things change through time. In this case, we do. We actually have isolates collected between sequences here where, Phil, were you on this paper? Yes. So what was the, was it 2006 was the first sequence or something like that? Yeah, about 2006. So, you know, we have several years here, and that could serve as a useful calibration to say, ah, we have some idea of how the rate at which things change. Obviously, that's not always going to be the case, but we can calibrate it and say, based on certain assumptions of the relationship between time and sequence change, we can infer times of most recent common ancestry. And so in this case, clay A, which is our very, very non-divergent AT-plus-NECOM play, it was referred to be just over a year before 2010 that the common ancestor of that clay existed. Now, as is very common with Bayesian analysis in particular, we're all comfortable with the idea of confidence intervals as the measure of dispersion around an estimate. It's standard deviation. So we get these mean estimates here, and you would hope to sort of increase your confidence in the precision of the result and the accuracy of the result, too, that you would have very small confidence intervals. It's like, you know, it's about one year, but my confidence interval says 0.9 years to 1.1 years. Well, with Bayesian analysis, often it's no such luck, and here we have between 0.46 years and 1.93 years. So we need to take these things in context. But you can walk back through the tree and use the same sort of assumptions, molecular clock assumptions, right, that the rate of change is consistent through time, or using what's called a relaxed molecular clock. The rate of change is sort of consistent through time, right, which is about as technical as I'm going to get about that. But we can continue to make these assumptions and try to map back earlier and earlier common ancestors to different clades. What happens if there is no constant sequence of clock?  So the... Sorry. So there's... What was that about editing the presentation, Sam? So the... At one extreme end, we have perfectly predictable molecular clock, right? Oh, it's Saturday. Time to mutate. So that allows you... Saturday night, right? You've got nothing better to do. I'm going to exchange this A for a G. So in that case, you get very precise estimates, right? Often what people use is called the relaxed molecular clock, where instead of enforcing the same strict rate of substitution on a branch, you say, alright, branches can change, but there's going to be some sampling where if the previous branch, the ancestral branch, has a rate of X, then I'm going to let the descendant branch change, but it's going to be somewhere centered around X, the probability. So you can have this sort of retention of roughly, like sort of an approximate retention of the molecular clock idea by strictly enforcing it. And then, right, you can increase the amount of dispersion around that, and at some point, you know, you throw up the clock assumption entirely, and then you can't really make any temporal inferences at all. The best you can say is, here's the sequence substitutions, so you can't really say much about time. Alright, so I've already talked about this. So this is not a Bayesian tree. It's a Bayesian inference of times. It's a differently inferred tree. And the other thing I should have pointed out, Gary mentioned bootstrap support values yesterday, right? So the idea behind the bootstrap is you've got your real alignment, and you build a tree, and then you take your real alignment, you shake it 100 times, sample with replacement, and you build 100 trees. And bootstrap support on a bifurcation event is high if many of those 100 trees contain that thing as well. So if all of your 100 trees contain that same bifurcation, the same split, then its bootstrap support is going to be 100. And so this is all to say, in a rather inefficient way, that where you see many branches emerging from the same vertical line, the phylogenetic package said something more. It said, here's the complete branching history, but a lot of the bootstrap values stunk, so we're actually going to collapse those relationships and say, we don't know. A lot of cases we don't care, right? It doesn't matter whether ZX8586 is slightly more closely related to this one than the bad one. It doesn't really affect our inference at all, and by doing this it's good because we're not stating more about the data than we should, at least not as much more. The other nice thing about this is that by using a molecular clock or a relaxed molecular clock, it's the title of that paper that was first introduced. It's called Relaxed Phylogeny and Dating with Confidence, which is a pretty good title. So you can infer the position of the root and the time of the root, right? The common ancestor of everything in the tree. Okay, so tutorial, right? Three components. I'm going to introduce you to PhiloCanvas, and here's a question. How many of you have done development in JavaScript? For those of you who haven't done it, I can't recommend it because full disclosure, and I'm going to say this again in the tutorial, PhiloCanvas is a JavaScript library. It's very cool, but in trying to wrap appropriate JavaScript to create an interface in HTML, my brain almost exploded. So MicroReact takes PhiloCanvas and does awesome phylogenographic things. So we're going to take a couple of examples in that, and then we're going to try out the Ganga software that's been developed in my lab, which is not... So the first two are web-based. Mine is not, but it does offer additional options like data manipulation and visualization. Honest data manipulation. So like I said, PhiloCanvas is a JavaScript library. You can draw trees right in your browser, you can drag them, you can zoom, you can make things blue, whatever you like. And so you invoke it from HTML, embed it on a web page, and one of the great things is that it's got an API, so you can develop your own software that plugs into the basics and extends the functionality, which is a very, very useful thing. That's how MicroReact sits on top of that. And so just one example.  So here's an example. Excuse me. Motivate or terrify you. The basic idea here is that we've loaded a simple tree, ABCD, right? Fortaxon tree, classic. And we want to make this one look strange. And so all we do is say, okay, this is one of our leaves, this, and we're going to set the discipline. Color is going to be red, shapes is circle, right? So there's the red branch, blah, blah, blah, just setting the attributes, right? It's pretty, you know, if you look at the actual names there, label color black, I guess what the letter A is black. So the control statements can be a bit weird, but the actual setting of different parameters is pretty straightforward. All right. And then we move on to microreact. Pretty good today. It's going to look better than the tutorial, I swear. And the basic idea behind microreact is that you have three pens, three different views of your data. Space, space, tree, time. And you can interact with each of these three panels in various ways. What you do in one panel can impact on what happens in the other panels. For example, if you have your geographic view of things, there's a little button here you can click to draw a polygon or round the samples you really care about. Space, polygon, polygon, polygon. That will be reflected in the tree that gets updated and in the timeline. So when you want to run Zika virus, the motion picture, it will be focused on points that you selected. So microreact is beautiful in its simplicity. What do you need to do in microreact? You need a comma-separated file. What do you need in the comma-separated file? You need unique identifiers, which in general you need, and some georeferences, right? Latitude, longitude, that's it. Now there's not much you can do with that, but it's a start. You can add arbitrary columns after that. You can say facility, right? Assistant care facility, school, so on and so forth. What's the color associated with that? So you can populate your data in whatever way you like, which is a very useful thing. The tree is optional, so if you just want to visualize stuff on the map, go for it. It also has a certain date convention, so if you want to actually have your time references, you just put that in the appropriate column formats in that comma-separated file. Okay, so that's it. Comma-separated file, optional tree. Your maps just come from the open street map layer, so it's like Google Maps but not the same oppressive degree of copyright. And then File of Canvas allows you to go kind of mess around with the tree a bit. You get these time animations. One of the greatest things about this is that the projects you create in MicroReact, you get a link, you share the link, other people can immediately go and see that project as well. I'll mention right now and I'll mention again in the tutorial, MicroReact, you can actually create projects without logging in, so you don't need an account to create a project. The problem with that is that once you create a project without being logged in, you can't do anything with it afterwards.  I want to delete it. No, can't do it. So I strongly recommend you create an account, and then you create your, they're actually just called, so a project within MicroReact is called MicroReact, so create a MicroReact within your login session, and then you can manipulate it and delete it afterwards. It's pretty straightforward. And then finally, Genghis. So this is some software that's been under development for several years in my lab, and the objectives are in some ways very similar to the objectives of MicroReact, but Genghis is a standalone application rather than a web app, and that creates some unique advantages and some unique disadvantages. So we're going to look a bit into the contrasts between the two. The data that you feed to both of them is very, very, very simple. Phil had created a file as input. Hi, Phil. We're all digested into mapping. Although to be fair, I think Phil was checking email. What's this? It's upside down Genghis. I like it. Southern Hemisphere Genghis. So what's that? I'm sorry, Gary's not here. I have to tease somebody. So now I've forgotten what I was saying. I was talking about the input files, and so the main difference between MicroReact input file and Genghis input file is that your unique identifier for MicroReact is called ID. The unique identifier for Genghis is called Site ID. So we have two redundant columns in your project assignment file, and that's why. Okay, so just to give a bit more information about Genghis, how it's put together. And so the data, I've already pretty much covered this. So map data, so raster and vector formats are supported. So raster is simply like a bitmap image or some sort of pixel-based description of the data. A vector is simply like a line-based description of contours. Either is fine. You can have one raster and overlay several vectors if you want. So samples, right, so different locations in a comma-separate file. And one thing that's a little different between Genghis and MicroReact is that for each location, what we call it, confusingly a sample, you can actually have several things at that location. And you'll see this with the cholera example. We have our locations, which should have changed that area. So that's the location. Samples that give us locations. With the Haiti data set, we have several de Patemann, Haiti, right, Al-Tibannit, and so on and so forth. And so the problem there is that we have multiple isolates from Al-Tibannit. And so this file, the first CSV, will have georeferences for each of those sites. We call a sequence file. We'll have multiple isolates for each of those sites. And that lets us do with more of the data. Newic-formatted tree. You're familiar with the Newic format? It's a bunch of parentheses, lots of colons, semi-colon at the end. Easy. Core application is in C plus, carriage return plus. This was done on Windows. And then we have the open geographical environment. And then we have various ways to interact. So we have a scripting interface. So if you want to throw some Python code at it, we use the RPI2 libraries if you want to embed our code inside Python. And then we have the graphical user interface, which is how people normally interact with games. This is WexPython. And then by virtue of having the Python interface, it makes it actually really easy. So like Filocanvas, there are certain defined ways to interact with Gengis and say, Dear Gengis, please give me the following information. Dear Gengis, take the following information and draw some bars on the map or something like that. Developing stuff like that is relatively straightforward. So you can do data retrieval, data analysis, and then output, you can have images. You can save an image if you want to do that. You can also save and restore sessions. So you make your beautiful, beautiful canvas. You're like, I have to go do this other thing now, so you can come back and restore your session. All right, so first view of Gengis. Not a genomic epidemiology example. We have the Hawaiian Islands. So this is a digital elevation model, which is why we have these pointy mountain things. The color gradient didn't work out so well in the transition. Anyway, no worries. Different islands. And then we have different locations from each island, which is reflected in the dots on the map, colored by island, right? So green is the big island. I've never been to Hawaii, so I can't really name the other ones. And then you see the three-dimensional tree overlaid onto the map. So you can say, all right, here's some green stuff. And one nice thing about Gengis is that you can color it such that an internal edge has a color if all of the leaves under it have that color. So here's an internal edge. It's green. And that's because all of the things under it are green. Here's an internal edge. And we've set that to white because there are different colors underneath. So it's relatively easy to visualize places where you have nice cohesion of your data. In this case, it's geography. But again, it could be facility. It could be some patient attribute. So it makes it a little bit easier to interpret the trees. Now, 3D trees can be pretty, but they can also be a bit annoying because you're trying to map information in three dimensions projected onto a two-dimensional field into your three-dimensional brain, which doesn't always work out so well. So my former PhD student, Donovan Parks, came up with an algorithm to do this. Come on. There we go. To do two-dimensional trees instead. Now, normally you might think that a two-dimensional tree is easier than a three-dimensional tree, but that's not the case. A 3D tree, all you have to do is draw branches that go to the various points and then merge them above. For a 2D tree, you want to take this a step further. And so you may recall yesterday, Gary mentioning that in a phylogenetic tree, if this... Yeah, why not? If this is a phylogenetic tree, you can actually take any internal node and rotate it. I'm not going to demonstrate that. Rotate it. Someone call it androids. And not change the meaning of the tree. So it's kind of like we have the tree pointing this way, A with B, C with D. Well, if we spin things around so that it's C with D and A with B, we haven't changed the meaning of anything. So what Donovan's algorithm does is it takes your tree and rotates the internal edges until it reaches a point where the alignment of those edges with the geographic points is optimal. One way to visualize this is to say, here's the tree, right? So the tree leaves mapped to this dash line, the geographic axis. The geographic points are mapped in order to this line here. So this parallel line is tree leaves, and this one is geographic axis. Basically what Genghis is trying to do is, if you connect the appropriate leaf with the appropriate site, it's trying to minimize the crossings. Because a crossing indicates a place where the geography and the phylogeny cannot be reconciled. So what does it mean for this example? It means that in general, and this is one of the reasons why bonds of Cadi-Dids are like the classic first year biology textbook case, there's actually a really, really nice gradient along the axis of the Hawaiian Islands where in general Cadi-Did samples from adjacent islands tend to be more closely related to each other. So that's what we're seeing here. Now over in this case though, we cannot actually reconcile the geography with the phylogeny for a couple of the islands here, which is why we get these crosses. So it may not be... You can use this to sort of examine and actually test because there's a statistical test for this, the relationship between the linear geography and the phylogeny, and that's perfectly fine, but in general, particularly in a genomic epidemiology context, your outbreak is probably not going to follow a straight line. If anybody has any counter examples, I would love to hear about them. But at the very least, even if it's not useful from a scientific point of view, from a visualization point of view, it does make the job somewhat easier. All right, and we'll play with a few of the customizations later on, but the point of Genghis is that it's infinitely or near infinitely customizable. So you have your 3D trees. You can change your tree colorings. You can change your line thicknesses. You can do weird stuff. There's cladogram, right? So everything maps to the same point in the axis. So branch lengths are not meaningful. Phylogram, branch lengths are meaningful. So there's different parameters you can play with, and we're going to explore this in the tutorial. So key features. I already talked about the optimal leaf ordering of your trees. Edge coloring, collapsing internal nodes, and I'll show you some neat examples of that. You can also split some trees, right?  Apart from that, I'll be showing a cartogram example. If you're not familiar with the term, you're certainly familiar with the concept. You'll see that later. And then some of these plugins that we've implemented. So here's an example. This is MRSA. The colors are showing up fantastically well. But hopefully you can see the country outlines in the back. You might recognize your favorite countries. And we have the different locations mapped, right? And so each color corresponds to a different country, and then these are mapped back to a two-dimensional tree. And you can see in some cases, we have many, many samples from... I think it's Sumatran. All falling into a clade. And so all I've done here is just collapse that clade.  We just have one big triangle that maps nicely up to Sumatran. So the idea here is that you have very fine control over the visualization to really emphasize the patterns you want to emphasize. So cartograms, again, back to the Haiti color example. So we have a tree. We have a map. We have colors. What more could you ask for? Interpretability. Yes, from this, I can tell that most of our samples are from Haiti and Nepal. Submit to nature. No, we need to take this a step further. So we can see the filogram that's very nice. And here's that very flat line of stuff. And here, just to clarify, if necessary, the coloring is basically... Haiti is divided into its divisions. There are five, I believe, represented here. And then Haiti, sort of, Nepal, five divisions. And then Haiti into its various... it helped them off, Sudeth, Sudvest, Sudmit, and so on. And so that's what those colors refer to. It's still kind of the big mess. And then everything else is kind of in the background, kind of switched everything else off-degree. So you get the context, but you really want the focus there. So what do we do about this? What can we do? What's that? You could zoom in, absolutely. So that's one possibility. If you want to, you can just zoom right in on Haiti and look at the filogenetics, the filogenetic relationships there. So that's kind of like focus. Now, the downside of that is that you lose the global context. And so that's certainly something you can do. What my recently graduated master's student, Alex Kedi, did was implemented cartograms. How many of you know what cartograms are? Okay, well, this is what cartograms are, right? So you can take regions of high density of points, and you can actually distort the map to emphasize them. So the idea here is that we have very dense sampling in Haiti and Nepal, and by expanding those regions, we can get a more detailed view of those regions without losing the global context. So now the five locations in Nepal are readily distinguishable, the locations in Haiti are distinguishable, and we can select a claim here that actually has three Nepalese samples, instead of trans-liberal. But we have Haitian samples, and so now we can start to see which parts of Haiti are most closely connected with which parts of Nepal. And it's configurable, and you can take this as far as you want to. There's a couple of extreme examples we can do with this. You can keep going until basically the map is nothing but, excuse me, Haiti and Nepal, and everything else is squished off to the corner. Now one of the limitations here, of course, is that unlike with, you know, Google Maps sort of zooming-based procedure, you're limited to the resolution of your basement, which is why Haiti is turned into a green fog. You can still see coloring with the locations, but the background country, you know, you don't have the resolution to show that particularly well. So this is a relatively easy example of phylogyographic visualizer. Sorry, a fisheye zoom. But you're still limited by the basic resolution of the map, right, if you're expanding an area, and you're still, you're kind of, you're not able to interpolate really either way, I think, right? Because it's, you know, it's a very different procedure, you're connected with the same thing, right? An expansion of one part of the map. And so, you know, if there's not a lot of fine-grained detail there, then you're kind of ending up in the same place, I think. Did you just use a higher-res map? Sure, yep. Is this available? So the situation for digital maps has actually gotten worse over the last few years. There's one resource that we use a lot which is called Natural Earth, which has some beauty, and that's referenced in the tutorial document, which has some beautiful, beautiful maps that have been very carefully designed and curated, raster maps, vector maps, and so on. But the other data source we used to use, which is still, you know, which still exists, is the NASA 30-meter shuttle radar topography mission, right, so remotely sensed, fairly high-resolution elevation data. And there used to be this beautiful web mapping service where you could go to the Oak Ridge National Lab, you hit the map, and you're like, I'm going to draw a rectangle, and then you click the button that says, download my rectangle. That's our resolution. It doesn't exist anymore. So there are various places. Like the situation in Canada is pretty good. We have a lot of publicly available cartographic data, digital elevation models, a very fine resolution. The problem there is certainly a manageable one because you get the map data in defined blocks, sort of geographic ranges, and so you need to use a library to stitch them together and sub-sample them as appropriate. So the short answer is yes, but it can sometimes be difficult to find the right, you know, the perfect map, which is why we often default to the natural Earth because it's convenient. It's a pretty decent resolution. It's manageable. Are there any other questions? I saw a couple of hands up, although I think maybe the other hands were just pointing at Anna. Okay. So that one's kind of messy, but it's nothing compared to this. So this is the dataset that was kind of provided to me by Patrick Tang, and it is about, if I recall correctly, about 400 neural virus samples from kind of Vancouver and surrounding areas. And I'll tell you right now, what did the million ways? There's no geographic structure here whatsoever, right? And there's just this huge wall, like a massive wall on the points around Vancouver. So this is pretty hideous. I'm going to show you some of the things we can try to do, again in Genghis, to try and tease out some patterns or at least focus in on attractables part of the dataset. Because hopefully by looking at this and this awful example, you get some ideas about how to improve the visualizations of non-terrible datasets. Just to complete spoiler, none of these actually works very in a very satisfactory way. One thing about visualization, sometimes the best you could say is, it's complicated, right? And we've all seen these, right? There was that paper a few years ago about the hair ball graph. We took, it doesn't matter what kind of data, right? We took data that has entities and relationships, right? So the graph, nodes and edges. And we built a giant hair ball. Here it is. You're like, I cannot get anything from this apart from there's lots of nodes and they're somewhat connected. So if that's the message you're trying to send, well, you know, mission accomplished. Who's ready for coffee now? So one thing you can do. Just pretend the tree isn't there for a second. It is a tree. But you can remove some of the noisy background stuff, right? Maybe you don't actually need those pretty shadings and so on. Just really kind of focus on the data. Okay, that's a 3D tree. We can go and do a 2D tree. And now you really appreciate just how many leaves there are in this pretty tree and how there's really no clear relationship between any sort of linear gradient and the geographic ordering of the points. These, by the way, are now colored by site, or sorry, by location type. So again, it's a care facility, school, restaurant, and so on and so forth. Okay, we haven't really improved things very much. Maybe we just want to discard a map. Discard a map. And so this is getting into that sort of microreact frame of mind where we have the map over here and we have the tree over here and we're not explicitly trying to link the two because it's hopeless. So, what can we read from this tree? It's complicated, right? But it's actually, I mean, you know, part of it is, are there clear clusterings of specific locations? No. And there are actually statistical measures you can use to try and characterize this to basically say that there's Fitch's algorithm, which basically says, I have a bunch of different types of characters in the tree. Care facility, school, whatever. If I walk through the tree, how often do I need to change? If that makes sense.  Imagine yourself walking along the branches of the tree. Very rarely do you encounter a transition between blue and yellow. If you're walking along this tree, you're going to have to encounter frequent transitions because there's no cohesion here. Does that make sense? It's like the weirdest explanation. Hopefully it's okay. And so, again, you know, is there a really strong clustering? Well, certainly not readily apparent at this scale. What else can we do? Well, we can bring the time axis to bear, and we can hope that the, ooh, that looks promising. And so if we have temporal information, we can run a movie of... Let's try that again. Okay, 3, 2, 1, go. So you can see points appearing through time, and, you know, the sort of intensity reflects the recency. So you can see certain clades expanding over time. There's not so much. Okay, so at least... But at least you can kind of focus on specific aspects of the data at specific points in time. And this comes up again in the micro-react framework, where you can play movie forward within certain time limitations. Well, what else can we do? Okay, well, let's change the color. Okay, because people have classified neurovirus into various genotypes, and this is kind of interesting. So we can look at the tree, and the root is down here, and you can see that most of the things at the end of the root are this genotype 2, variant 12. So when you see that, there's sort of lots of stuff at the base of the tree, then that suggests that that's the ancestral genotype. The root of the tree is probably group 2, variant 12. And then you can see different types emerging from within that. So here's a specific root, and here's a specific clade as well. So we've collapsed any clade where everything in that clade is the same genotype. Now, hopefully, if we collapse things that are of the same genotype, then we get a lot of stuff collapsed, because if the genotypes are not cohesive, what does that say about your tree? It says that one of those is wrong. So what else we got? So that's a big tree. We can also extract subsets of interest. Again, so we've stopped trying to link the tree leaves directly to them. But you can still see these colored genotypes and you can say, well, here's this orange genotype, where they're there and there. So this is a case where we've sub-selected part of the tree and then are just focusing on those relationships. Okay. I was worried whether this top was going to go an hour. Now I'm worried if this top is going to go an hour. Any questions? Deep breath. Sure. This might be because I'm not familiar with the field, but when you're calculating the time to mutation, basically, do you ever use that in a forward predictive manner or is it always looking back to determine the origin? Oh, so you're saying you're trying to use molecular clock information to predict the future in some sense. Yeah. Like, would you be basing vaccine development if it's mutating so fast? And what's the point in trying to build a vaccine that's contained for whatever? Like, do you make any decisions on that kind of information? Um, I think the answer is kind of yes. I mean, you think about the way influenza evolves, where each season it's like, I diversify, diversify. There's zillion versions of me, and then like one or two will survive to the next season. So in those cases, I mean, that population structure certainly influences the strategy for development of vaccines, right? And so is that the same as the rate of evolution? Well, it's kind of influenced by it, right? So it's not really directly losing it, but certainly the properties. That's a big part of it. Anybody else have any other good examples? So the question was if we have molecular clock information, is that ever used in a forward sense, you know, to try and justify certain decisions, whether it's vaccine development, other types of strategies? I'm up here and not thinking very well, so if anybody else has any ideas, it'd be great. Hearing none, your reward is to get hit with Bayesian phylogeny. So, um, I see that I have theoretically five minutes left. What should I do? Okay, so, Bayesian approaches. What's great about them? Gary touched on them briefly yesterday, and the key to Bayesian approaches, sorry, take a step back. Maximum likelihood, maximum likelihood of trees. I have sequence alignment, and I have model. What's the model? The model is the tree, the shape of the tree, the branch lengths. Find me the best tree. Long story short, maximum likelihood. Bayesian approaches do not say that. Bayesian approaches say sample from a set of pretty good trees and build me sort of a general representation of that. I don't want a single answer. I want good answers with plausible confidence intervals around me. What's great about Bayesian approaches, in particular the ones that have been developed, is that you can parameterize it as much as you want. You can have parameters for everything, right? So the tree branch lengths are obvious, but on top of that, you know, substitution rates kind of fall into that. Um, collage, well that's the tree shape, position of the root, population sizes, geographic diffusion. These can all be parameters in your model. One of the problems with Bayesian analysis is that it takes for freaking ever if you have a lot of parameters, but that's your problem. So you do have to choose somewhat carefully which things you want to parameterize and which things you want to say, I'm okay with that. Remember what Gary said about rooting yesterday, when you can and when you cannot. When can you actually infer the position root? What information do you need? Okay, time is the big one. So you need an out-group, right? Confident out-group, or you need temporal information, or you need to make some assumption that, like, the midpoint of the tree is the root, which is not necessarily the root. And so with the Bayesian stuff, again, you can sort of infer this molecular clock and then try and get information, infer stuff about the position of the root. Beast is the most widely used application by far for the sort of Bayesian population inference. Mr. Bayes is another widely used package, but that's really, I think, still focused on phylogeny. Beast offers a much more rich parameterization. And so this is great because then, specific questions that you might have, like the reproduction rate, right? Or temporal information. The frequency with which an outbreak jumps from location to location. All of this stuff can be represented as parameters in your Bayesian analysis. So here's an example. This is from 2014, and this is looking for, looking at alien influenza H5 and more. So I probably shouldn't dwell too much on this. But the basic idea here is that we have a tree, which is inferred from, in this case, the Himaludan sequence from all these different isolates. Here we have the time, and it's sort of the same package of stuff, trying to infer times of recent common ancestry. And in this particular case, also trying to get posterior probabilities of different candidate geographic locations of the root. And so here's the legend, right? Here's the color guide. And basically you can see that most of these sites have basically no associated probability. It's the probability of common ancestor being in Novosibirsk. Nothing, essentially. What are the two locations with the highest posterior mass? Well, Hong Kong and Hong Kong. So you can immediately get a sense of that from doing this type of analysis. I'm not going to go into details about the parameters of the sampling strategy and so on, but that's the idea. And so people are very interested in saying, well, where do these things come from? So this is a goose sample from Hong Kong that is seen as kind of the ancestor of a lot of this. So was it originally from Hong Kong? Well, we can put probabilities on that. Using the same data set, the authors try to infer rates of migration. So I believe it was 19 different geographic locations they were looking at, and essentially they said, well, we want to have a model that has sort of the probability or the frequency of migration between each pair of sites. However, trying to fit a model with all possible pairings of 19 sites is not a good idea, because if you're familiar with this sort of... over-define this sort of way more parameters than you have data, this just leads nowhere. And so what you can do is you can actually say, well, I expect most of the rates to be pretty close to zero. So we're going to assume that a lot of them are close to zero, and then only really represent the ones that are somewhat dissimilar. And so this is looking at both the Wuton and Neurodimidase, Neurodimidase, not proteins, and trying to see whether those actually imply different or sort of similar patterns and rates of cognitive uncertainty. So it's interesting that they show this degree of agreement in spite of the fact that they actually have somewhat different phylogenetic histories. I only showed you HA, but in the paper they show HA and NA, and there are some substantial differences there. And if you're familiar with processes like the process of reassortment and influenza evolution, then that's one of the big reasons why. So, again, I think Gary talked about priors. He talked about priors. So you're kind of, you know, basically what you're trying to do is infer a model, and a prior is basically saying, before we even run the data, I have the following expectations. So I'm going to put prior probabilities on that. In many cases, we kind of feel a bit squeaky about trying to put some sort of informative prior on things. Let's say flat prior, right? One of the problems of doing this is that, you know, in general, I mean it makes sense, right? You want to be agnostic, you don't want to impose something on it. However, sometimes what you think is a flat prior is not actually a flat prior. And this is particularly true of phylogenetic trees. If you say each tree has an equal prior probability of being the true tree, that's not saying that each relationship in the tree has an equal probability of being correct. So there's a bit of messiness there. Bayesian methods can take forever. As anybody who's trying to build a Mr. Bayes tree with 50 leaves in it would know. And then this, you know, it's a mixed blessing. Deciding on model complexity.  But the more parameters you add, the longer it takes to fit that model, and the more likely you're going to get very unstable estimates of your parameters. So you do have to be fairly careful with that. And one of the ways the authors here deal with that is by saying, yes, we're going to have a lot of parameters. Excuse me, but we're going to set a prior that most of those parameter values are going to be zero. So it's kind of deflating a lot of them and saying, let's have lots of opportunities, but let's throw out most of the implausible ones. Okay, almost there. So this was a paper that was published actually about three or four weeks ago, maybe five or six weeks ago now. Again, looking at Ebald. And so this was a collection of 1600 and 10 publicly available genomes from the really intense part of the outbreak between 2014 and 2015. And actually, if, you know, we haven't really talked a lot about sort of data munging. That's a lot of the presentations you've heard in the last couple of days are like, how to deal with your data. I haven't really talked about that. However, if you want a sense of sort of nastiness that can come up in biological data analysis, look at the supplementary methods of this paper, because there's some sort of standard data cleaning stuff they did.  It's like Ebola specific and really kind of mind blowing.  You also want to know something about the specific system you're looking at. Are there specific nucleotide biases? I didn't know this, but apparently Ebola is kind of wacky this way. Are there repeat regions? Are there other things that you really need to think about before just, you know, pushing the big red button, turning the crank? Relax molecular clock. I already talked about that. Markov chains. So this is actually one of the ways in which we can get posterior probabilities, basically by saying, well, how good is it if this parameter is this value, this parameter is this value, right? So it's like one realization along, right? If this is the tree and this is the transmission rates and if this and if this and this, how good is it? Get that information, put it over here. Walk to another possibility. Okay, well, what if the tree is like this, right? And this parameter is like that. Markov chain is where you're walking from model to model and getting a sense of which ones are good and which ones are not so good. So this is one of the most common ways of getting these Bayesian posterior probabilities. So what do they find? Well, through various methods, they actually modeled the, they didn't, I can't remember the number of locations. It was about 46 or something like that. And so they wanted to know transmission rates. But as you saw before, you don't really want to fit a parameter for each pair of those 46. What they did instead was they looked at various descriptors. So for even pair of sites, how distant are they? And then instead of saying, well, what's the rate of transmission from here to here, you just say in general, if two sites are 50 kilometers apart, what's the expected rate of transmission? Does that make sense? Still awake, which is good. Kind of sleepy after lunch. Maybe you had healthier options than I did. So what's interesting is that they considered 25 different potential influential factors driving the rate of transmission. And this is table S1, I think, if you want to look at all of them. Some of them are pretty interesting. I wrote them down, but Ben, my book's over there. So they looked at all these different candidates, and then they had ways to kind of filter them and say, well, these ones don't really stand out against statistical noise. So we're going to set them aside. Out of their 25, they found five important factors. One was barely above the margin of interest. I'm not even showing you that one. One is that not surprisingly, sites within countries tend to have higher transmission rates than sites between countries. OK, the system works. Distances between regions is important independently of the national versus international population size at source and destination. OK, these things all make sense. And then if they share an international border. So in general, the disperse of the transmission rates between sites in different countries is relatively low, unless they're sharing the work with each other. So this all makes sense. And it's nice to be able to consider a bunch of different model parameters and discard the ones that have no evidence.  So we live in an amazing age. And this is something that Andrew touched on a lot in his presentation, but also his tutorial, where people are now starting to realize that if bioinformatics is a scientific pursuit, then it should be repeatable. Because that's kind of one of the fundamental things about testing hypotheses and doing research. So we are seeing more movement towards things like galaxy workflows. If you submit to microbial genomics, the journal, you need to have a lot of diligence in terms of people being able to repeat the analyses you did. Your data need to be made available. Your contextual data need to be made available. The reason I mention this here is because this is an animation that is tied with the paper that I was just showing you. Running through, again, it's a temporal simulation. It's a pretty heavy bowl, basically, in the geographic context. And it shows over time incident rates, incidence rates, and transmission, inferred transmission events. And what's really cool about this is all of the code that was used to do this is available through GitHub. Right, through the author's GitHub site. So, I wish I made this. I didn't make this, but I wish I did. Maybe I should just lie and claim that I did make it through the tree, gradually emerging there. Think of it all the different visual cues that they're using. They're using size, they're using color, they're using this temporal information, curvature to distinguish from other types of information. And you can see, right, here's the end of the outbreak. The end. Go get some coffee. We'll see you in 25 minutes.


Hi everyone, Joe for jasmiescasebrakes.com with another pack break of a Prison Basketball Retail Edition, this is break number 10, and with two last dance mixer spots being given away at the end. But let's do the break itself first, big thanks, and good luck to these folks here, and the randomizer for the spot, the mixer spot should be at the end of the break, different dice roll. For the break itself, three and a one, four times for each list, one, two, three, four, and got Ryan down two, Zack, four times for the teams, and fours and five and a time. Got the T-wolves down two, the Rockets after four, right, so there's the first half of the list right here, Quinton with the Grizzlies, and then Jonathan with the Pelicans, nice. TWC trade window closed, let's print, and let's rip, good luck. Alright, let's see what we've got in this little pack here, any surprises? We've got Kemba Walker, Kevon Looney, we've got Hyped Ben Simmons, and a Jared Culver rookie car, that's not too shabby. Alright, that Jared Culver will go to Ryan Shackleton, he's a top ten pick, you never know. I think he was doing okay before the pause, before the NBA season got a pause. Alright, now the important part of this break, that right there, are last, last dance mixers, let's grab everybody's names, and the top two after five will be in it. One, two, three, four, good luck everybody, fifth and final time. Appreciate everybody getting in and trying, top two is going to be Ryan and Zach. Congrats to both of you, Zach S, Ryan S, we'll see you for that mixer tomorrow, jaspyscasebreaks.com, bye bye.


So we're taking up S1, S something today. I think it's age 133. It's 133. Bill that has to do with a little procedure during a hearings. Eric will happily go through the bill with us. So if you would Eric, if you could lead us along. Yes, I'd be happy to. It has to do I. It has. I'm sorry. I'm going to give you the, the action. I think we should do a little bit more of that. So I would like to add to this. I would like to add to this. I would like to add to that relating to a emergency relief from abuse, orders, and relinquishment of firearms. Yes. Thank you. Senator Sears. Eric, it's Patrick with the. Office of legislative council here to walk the committee through. The bill that center Sears just mentioned age. One 33 and act relating to. Emergency relief from abuse orders. And relinquishment of firearms. As it passed the house. that it's dealt with relief from abuse orders, which are known as RFA's, quite a bit off and on over the years, but I think it might help to just refresh the committee's recollection for a moment and as to what they are and how they come about. An RFA, a relief from abuse order is an order that the court can issue to protect a family or household member from abuse by another family or household member. That's kind of it in a nutshell. The way it's obtained is that a family or household member can go into court and they file a complaint to have an affidavit attached to it. And if the court finds based on the affidavit and other evidence by a preponderance of the evidence, so it's a preponderance of the evidence standard more likely than not. If the court finds by that preponderance standard that the plaintiff, though the family or household member has been abused by the other family or household member in the past and that there's a danger of future abuse, so it's got to make those two findings, abuse in the past, danger of future abuse, by a preponderance of the evidence. If it makes those findings, then it can issue the RFA, the relief from abuse order in order to protect the plaintiff from further abuse in the future and that order can contain a variety of things. We'll look at the language in a moment, but it could say that the person can't have any contact with the plaintiff. They have to remain a certain distance from the plaintiff. Maybe they can't have any contact with the plaintiff's children. They have to move out of the house. There's a variety of things that could be in the order. But the point is that it restricts the ability, what the defendant can do with respect to the plaintiff. That's the big picture of what it does. And the couple of things I think that will be helpful for the committee to keep in mind as we look at the language of the bill, is that there's two types of RFA, two types of relief from abuse orders. There's a final order and there's an emergency order. And the structure actually may seem familiar to the committee, not only from looking at RFA's in the past, but the ERPO orders, the emergency relief protection orders that the committee drafted several years ago were based on this exact same structure. There's a final order and an emergency order. And the way the final order works is that the defendant has to, the court has to hold a hearing and the defendant has to be present at the hearing. So they have to get notice of the hearing, they have to be present there at the hearing. And the court can only issue a final order after having had that hearing with the defendant present. And the order can remain in effect for any period specified by the court. In other words, there's no maximum period for the effectiveness of this final relief from abuse order. It's common for them to be a year, but it could be more, some are longer. On the other hand, the emergency relief from abuse order can be issued ex parte. Remember that means that the defendant does not have to be present. It can be only the plaintiff who is present when the motion is filed and when the order is issued. Now, the reason for that, as you can guess from the title of it, is it's called an emergency relief from abuse order. Remember, I mentioned that generally the standard is that there has to be the court has to find a danger of future abuse. For an emergency order to issue, there has to be an immediate danger of future abuse. So it's a different, it's a different standard, has to be immediate. And the emergency order can only be in effect for 14 days. So you've got those distinctions there. Yes, that can be issued ex parte, in other words, without the defendant's presence, but it can only be last for a maximum of 14 days. And within that 14 day period, the court has to schedule a hearing. And the way it ordinarily works is that at that hearing, either the plaintiff will then file for the final order, because for the final order situation, the defendant has to be there. So they can file for a final relief from abuse order, which can be for a longer period than 14 days. Sometimes they agree, there are times when it goes away within that 14 day period for whatever reason. But if they want it to, if the plaintiff wants it to be in effect any longer, they have to come to that hearing, the defendant has to be there. And then if the court makes that preponderance finding that there's still a danger of future abuse, then they can issue a final order for a longer period of time. So- But they can do that right now, correct? Yes, yeah, exactly. That's, I'm just- The court can do this. And you get, how's this process different than the extremist protection order? Yeah. Well, one of the differences is that the extremist protection order can only be sought by, I believe it's a law enforcement officer or the state's attorney. Whereas in this case, it's a family or household member who typically brings it. I'm looking at the S5. Which is the particularly, in light of what just happened in Indianapolis for mass shooting there, the young man with a history of mental health problems. And for some reason they did not, the extremist protection order wasn't, they took a shotgun, I think, but he was able to go out and buy other salt style weapons. And then, so I'm just wondering, if we wouldn't be better to consider that bill, not obviously not S5, but the process there and consider letting under S5 a person, a healthcare provider, reason of believes the patient poses an extreme risk causing harm to them or herself or another person by purchasing or possessing firearms, blah, blah, blah, would be able to file for a petition. So what you would do here would be add healthcare provider and would be family member. Senator Sears, I thought we did, I thought we did that in a couple of years ago when we were talking about the responsibility of a healthcare provider to report an immediate danger from a patient and maybe- Eric can explain that, we didn't go that far. Oh, okay. Plus, I don't think it passed, did it? It didn't pass. The past was allowing somebody to go to law enforcement, family member can go to law enforcement, accept that and ask for an extreme risk protection order as S5 would allow the healthcare provider to avoid being a hyper violation if they were to- No, this wasn't around extreme risk orders. This was around the Kulagowski decision and the required healthcare providers if there was an immediate risk, it required them to notify. Yeah, but that wasn't just firearms though. No, that's true. Okay, all right. I think that was everything. Okay. If you remember that case, he had assaulted the performer with a wrench. It was the danger, it was the danger part of it. Yeah, the dangerous part of it. Okay. So I'm just looking at that process and this process. I think there are policy decisions for the committee, but just the one distinction to keep in mind under current law is that these relief from abuse orders can be filed by family or household members while family or household members cannot file for an ERPO. Those are law enforcement officers only. I understand. So, but you can certainly make whatever adjustments to either one of those that as a policy matter, you think it's good policy. But I'm trying to understand why we need this bill as it stands, if they can already do it. That's what I'm having a hard time with. Right. Judges can already do this, right? I believe you'll hear from Judge Greerson that it is, and I don't want to put words in his mouth, but that the general practice is that for emergency relief from abuse orders, that some of the forms do include references for firearms, relinquishment by the defendant, and that it is common practice for relinquishment to be ordered in connection with these, but that it's not uniform and that it would be helpful to have it in statute. So I think that's their perspective on that, but I'll let him test it. That's unusual. Usually they don't want us to take away some of their independence. Well, that actually would say maybe right into the language, if you want to take a look at it, Senator Sears, real quick. And I think- Unless the committee has other questions about my questions. I just, I have a question. Is an ERPO order? Is it only able to be filed by a family member or can the neighbor next door file it? Remember, Senator Nitko, we're not talking about ERPOs. Did you mean to be asking about ERPOs right then or the order in this bill? I'm asking about the current one in place with where someone can file for an emergency order. You have- This is an RFA. This is a relief from disorder, not an ERPO. And that's what we're looking at in the bill in front of us. And it's only a family or household member can file for it. Okay, so the neighbor can't. Correct. Okay. Okay, thanks. Yep, sure. And family or household member is defined in the statute. So actually, I'm going to pull up the, unless there are other questions, sorry. Eric, how long ago was it we made changes to the statute to enable that to happen? To enable which part? For the judge to be able to remove on the request of a family member, I'm trying to remember, I know Philip wasn't on the committee at the time. Autumn Water Song and Kara Cookson were involved in the conversations and I went around the building trying to get universal approval from everybody based on the fact that we injected due process into the system. And I'm trying to remember COVID has me totally stumped on how long ago that was. Well, I don't think that one, if you're thinking of the emergency relief from abuse order piece, which a couple of years ago was in a house built that never did pass the legislature. So the current practice of permitting relinquishment or ordering relinquishment of firearms in connection with these emergency relief from abuse orders is based on the courts inherent authority in an emergency situation. It's not based on the statutory language itself. So I think Judge Gerrison again can talk about that in more detail, but it's based on the inherent authority of the court to protect litigants during emergency situations. As opposed to anything express in statute. But I remember the center bang the same language you're talking about, but that ultimately didn't pass. So looking at the language itself, the I'll pull that up real quick, just to sort of ground the committee and where we are. And in fact, the first thing I will pull up is the existing statute, just so you can see what we're talking about here. So this is the relief from abuse statute currently in title 15 domestic relations section, chapter 21, abuse prevention. So as you were asking Senator Nitka as to who can bring one of these actions, it's just a family or household member. And you see in the definitions right there, definition number two, household member is defined. So that obviously family member means someone who's related, but it could also be a household member, but as you say, it's defined as a person. It had either they've been roommates, shared an occupancy or dwelling or had a dating or sexual relationship would qualify a person as a household member. Now, section 1103, this is the final order section that I was talking about. So this is the final relief from abuse order that could be in effect for whatever period of time that the court sets specifically in the order. Again, you see in subsection A, it's a family or household member who may seek relief from abuse by filing the complaint. And then you'll see under subsection B, this is the final order court can grant relief only after notice to the defendant in a hearing. So again, this final order requires that the defendant be present for a hearing. Plain if has the burden of proving of abuse by a preponderance of the evidence. Now you see under subsection C there, no, this is the, sorry, the preponderance of the evidence standard is also in subsection B. But under C one, that introductory language, the court shall make such borders as it deems necessary to protect the plaintiff or the children or both if it finds, and then there's the findings that it has to make. The defendant has abused the plaintiff and either there's a danger of further abuse, in other words, in the future, or that the defendant is currently incarcerated for one of those listed offenses. Now that language that I, that very, that first sentence, that first clause of C one, court shall make such orders as it deems necessary to protect the plaintiff or the children. They're actually, that's very broad. You see that, that is essentially giving the court to make any order that it deems necessary to protect the plaintiff or the children. That language was interpreted in a Vermont Supreme Court case to include the ability to order relinquishment of firearms. So, but this is only in the final order situation, right? So with respect to the final order, that language has been interpreted to permit ordering firearms relinquishment, but that same language is not in the emergency order statute. And I think that's another reason to respond to your question center series as to why it's viewed as necessary to put something in statute specifically, because that language is in the final order statute, but not in the emergency order statute. This is the final order language, again, goes on to list some of the things that may be included in the order. Again, there's broad discretion that I just mentioned any order to protect safety, but could include, you know, an order that the defendant refrained from abusing plaintiffs or the plaintiff's children in the future, B, vacate the household, C, temporarily award parental rights and responsibilities, D, the parent-child contact can also be in the order. There's a number of different things. And so I'm gonna move then now, so this is all final order down to the next section, which is 1104, you see emergency release. So this is the statute related to the emergency relief from abuse order. And again, under this one, you'll see that it says in subsection A that in this case, contrary to what we just saw, that the order may be issued, this is the second line down under A, may be issued ex parte without notice to the defendant. So in other words, as I said, in this emergency situation, the order can be issued with the plaintiff present, but not the defendant. And this is where I hear some complaints from people when their clothes have been taken, everything is taken out of the apartment that they're most sharing, for example. Am I correct here? I think so, Senator Sears, yeah. So it's not just firearms here. You mean in the bill or what could happen? What can happen? Yeah, I think that's right, yeah. But the difference, Eric, as I understand it with the bill is in the final relief from abuse hearing, there is due process because the defendant has received notice, there's been a hearing, if there's one that was requested and the judge has made, I shouldn't have said it requested, there will be a final hearing, whether the defendant shows up or not is irrelevant, but the defendant does get notice in the difference with what this bill is calling for is to enable that property to be removed in the emergency situation where there is no due process for the defendant because they don't even know necessarily that there's something happening at court. Would that be a fair way to synthesize it? Well, I would agree with you, Senator Benning, to the extent that you're right, that it permits the relinquishment of the firearm without notice to the defendant and without a hearing. But I think that under the due process precedence that there are circumstances under which short-term brief denials of property can be done what's known as pre-hearing. In other words, it's a pre-hearing deprivation of property and they have to be short brief and the defendant has to have a reasonable opportunity to be able to contest that out of hearing within a reasonable time afterward. So the only... But the initial filing to get there is limited to law enforcement or the state's attorney? In this case, no, it could be, it still could be the family member or the household member. I want to make... I'm trying to understand this and you completely confused me, Joe. Are you talking about firearms or let's say that the individual has tools and things that he or she needs in order to perform their job, their infrastructure? Yeah, I'm only talking about firearms, Dick. Okay, Bob, I'm talking about everything. Is there any, can they take everything? No, I don't think so, Senator Sears. So if you look at what can be in this final order, it's listed very specifically in subdivision one there. Excuse me, A through B. And that proposal, in fact, in H-133 is to add an E to that. It now says A, B, C, D. That's what can be in this final... Sorry, this emergency relief from abuse order. So currently it's... You can see A, it can either include an order that the defendant refrained from abusing the plaintiff or children or their animals. In other words, don't commit any more abuse in the future. B, refrain from interfering with the plaintiff's personal liberty or the personal liberty of the children. C, refrain from coming into a fixed... Coming within, sorry, a fixed distance of the plaintiff or the plaintiff's children, residents, et cetera. So a certain amount of space that they can't go within in terms of the plaintiff. Or D, D is the no contact order that I mentioned earlier. Can also have a no contact order that can't contact the plaintiff's children, et cetera. So I don't see anything other than these. In other words, there's no general language in this emergency statute, like what we saw. I'm just gonna spin up real quick just so we can compare it to what was in the final order. Remember the final order included right there in the middle of the page, C1. The court shall make such orders as it deems necessary to protect the plaintiff or the children or both. So that's very broad in the final order. But we're only talking about the emergency order situation in which there is not similarly broad language. And that may well be, I don't know. It's been on the books for a while. It may be that that's because it's more narrowly... But it sounds like if they already can take the firearm, they're already interpreting in 11.04, the things that are in the above that you just described, and am I missing something? My understanding is that the taking of the firearm in this situation, the real inquisition under 11.04 is not on the basis of that language that we just saw in 11.03. It's on the basis of the court's constitutional inherent authority to respond to emergency situations. That there's not that parallel language in 11.04 for emergency orders that there is in 11.03 for final orders. So who takes the firearms under this plan? Well, they're relinquished, the order... Yeah, but relinquished at home, that's my question. Yes, that could be, and this will track us to its interesting statute that this committee has worked on a few years ago. You remember, there is a statute on the books in Title 20 that has to do with how firearms are relinquished. So it could be to a law enforcement officer. It could be to a federally licensed firearms dealer. It could be to a family or household member if the court approves that. You remember that process that was written? So that whole process is set up specifically for firearms that are relinquished pursuant to relief from abuse orders. So that's how it could be done. So has the person been charged with a crime? No. Well, I should say not necessarily. They could have been, but not necessarily. Well, how did it get to court? Because the plaintiff came in and filed for the relief from abuse order. They filed a motion. Now would be probably a good time to look at the new language because you see ABCD and what I just went through. So in... Oh, sorry. In age 133, here we are. So you'll see, this is the language we just looked at. That's existing law 1104, the emergency situation. Ex parte, no notice required as Senator Benning mentioned. And so can be done without the defendant being present. We just looked at this as the existing ABCD. And then the bill proposes to add an E that the order may include in addition to what we just described, the no contact, don't abuse in the future, et cetera, could also include a provision that the defendant immediately relinquish until the expiration of the order, which remember is 14 days maximum. All firearms that are in the defendant's possession, ownership or control, and to refrain from acquiring or possessing any firearms while the order is in effect. Again, that maximum 14 day period that the order would be in effect. And then if the circumstances warranted and the plaintiff wanted to do so, they could try and get the final order at the hearing. Which could include firearms relinquishment as well. But as I mentioned, that's already covered under the existing final order statute. And how does the order work to prevent the person from acquiring any firearms while the order is in effect? And this question goes back to Indianapolis. Yeah, I think it's a legal obligation on the part of the defendant, and then if the person- But the seller would have no idea that this person is not on any, you know, if the seller, the person walks into a gun shop, decides to buy a firearm, the seller would have no idea that this person is on a list, wouldn't they? That's a good question, Senator Sears. And I would wanna follow up with Jeff Wallin on that. And it might be a good question for Judge Gerrison as well as to whether when the court issues these orders, do they submit the names to the NCIC or the NICS database that would put someone on that list? I'm not- I don't think there's time, my understanding. It takes quite a bit of time to, I'd love to hear from the witnesses how they prevent somebody from acquiring a firearm during the period of this temporary order. May I also ask the question? Sure. So does the court make a decision here about all of these things? So somebody comes in with an emergency relief from abuse order asking for it and asks that all the firearms be removed and all the rest of it. Does the court actually just grant it or do they? I guess my question is how much discretion do they have in terms of ordering this if they suspect that there may be some, that it isn't a legitimate complaint or it's, I'm not exactly sure how to phrase this, but if it isn't, does the court have any discretion in saying, you know, you're right, we need to do this right away or you've been here 20 times before and then you keep dropping it. Does the court have any discretion here? I think the answer to that is yes, Senator White. And I think I understand the point you're making. It's that as you see in lines, well, and there's subdivision one there, the order may be granted. So my understanding is that based on the facts and circumstances, the court's gonna decide whether or not there's been a sufficient showing that there's danger or that these weapons exist or that something supports the order. It's not just the pro forma, in other words. Okay, thanks. That was my question, much better said by you. Well, thank you. Well, I'd love to hear anything else, Eric, that you wanted to cover. No, I don't think so. I think that gives kind of the committee the sense of what the proposal is. And then, you know, I'm sure witnesses so we'll have helpful testimony as well. Yeah, I know a lot of times, you know, we certainly want to keep the victims of domestic violence safe as possible. But I think there's a lot of questions here about how this would actually work in real time and how they would prevent somebody from wiring. Senator Nica. Nice question. I think Eric, you said something about the plaintiff could request the final hearing at the same time when they come in for the emergency order. And what's the situation with that? I think actually the typically the emergency order sets the date right in it for the date of the final order. So when they issue the emergency order, it'll say right in the order, here's when the final order is. But my understanding, I think the practitioners will know this better is that there are times when the parties just don't show up for the final order or they drop, sorry, for the final hearing or the case is resolved or somehow reached, there's an agreement reached so that the final hearing doesn't always necessarily happen, but that the date for it is set right in the emergency order. So as long as the defendant gets notice, then what doesn't show up, then the whole thing can go forward without the person being there, is that correct? Which would be the final hearing. As long as they've received actual notice, yes. Yes, they have to, as long as they've been notified of the hearing, they can choose not to attend certainly. And this does not require any crime having been committed or any charge being levied against the defendant, correct? That's correct. This is based on the finding of... It's a whole different matter. Had nothing to do with somebody being arrested and charged with domestic violence or abuse. Right, this is the process we have in law that's separate from that, yes. Well, Eric, correct me if I'm wrong, but the judge has to find on the basis of the evidence that there has been abuse. Yes, not a crime necessarily. Not a crime, right, yeah. No, but this is all based on a finding, at least a temporary finding that there has been abuse. Yes, correct. And there's likely to be immediate abuse again. Right, both of those are required for this emergency order. You have past abuse, there was abuse in the past and there's an immediate danger of further abuse. But that is all based on the word of the person. I think it's, yes, I think you're right. A lot of that is based on the affidavit and the testimony of the plaintiff that the judicial officer asked them questions, that sort of thing. But it may never get to the criminal courts. Yeah, that's certainly possible, yeah. So when I hear the opponents of this talk about due process, that's part of what the issue is, correct? That's all of what the issue is. What I'm trying to get at, Joe, is that they could take other things beyond firearms. Well, what they can do right now is limited to what you saw in the emergency order language. I mean, this edition is E, if you take A through D, that's what can be done. Those provisions are all basically designed to protect the individual, but they don't require loss of liberty or loss of property. But E brings in loss of property to the equation. But my product, here's the problem. If they can already do E, why do we need E? And what is to prevent them from taking other items? Eric, if I misspeak here, correct me, my understanding from your walkthrough is they can't do E now during the emergency order, but they can do it during the final order. Well, I think my understanding is that they are doing E. And when I say they, I'm referring to the court putting it in an order, and that they're doing it not pursuant to any express language in the statute, which is what they are doing with respect to the final order. It's pursuant to that language in the final order that provides broad discretion. So that's what you meant about the distinction between the inherent authority of the court versus the statutory authority. Exactly, exactly. Okay, got it. So you were correct, and Dick, my mistake. Yeah, they're already doing it. And people are, I mean, in order to prevent it, you would have to say you can't do it. If the opponents of this bill don't want this done, then you would need to switch the language to say you can't do it. But this bill means that it's just codifying what is current practice as far as I can understand. Yeah, I think that's right, Senator Sears. I think that's one of the ways that it was described in the House. It's codifying current practice. So if you're opposed to this, you would want language that would prevent the court from doing, from E. Well, and I think also if you're opposed to it, you might say having E in there would suggest to a judge going down this path as opposed to, you know, if it's not there, but it's theoretically in their ability. So maybe this would make it more common so I could see that objection to it as well. Yeah, but to best of my knowledge, nobody has challenged the courts authority to do this. But should we codify just because it's current practice? Good question. From an individual standpoint, an individual can argue that the judge has basically crossed a line and then forced the issue to get their weapons back. Here you're saying, no, the legislature has actually endorsed this, which makes that argument all the more difficult. Yeah, I mean, I think we're right on target here. But I'm still focused on how they can control somebody from acquiring. I realize they'd be violating court order, but other than that, what can they do? So those are a lot of questions, Judge. Well, and Senator Sears, if I could just point that question in 2015, we passed legislation that required reporting to the NICS database. And I'm wondering if that piece of legislation covered this situation. I don't know, but doesn't it take a couple of weeks to get into the database? Yeah, I'm sure. And then it takes a period of time to get out.  The order has been lifted. There is no order yet. They can't get them because they're in that system, if that's what they do. I don't know. Hopefully Major Jonas or Jeffrey Wallin can clear that up for us. All right. Should I pull the language down, Senator Sears? Yeah, please. And I think our next witness is, well, it was supposed to be David Sher, but I'm going to jump right to Judge Grierson. Hopefully David will object. Objection. Thank you, David. Good morning, Judge. Morning, Senator. And good morning to the committee. Thank you for inviting me to testify on this bill. I've obviously been listening and I think the committee has been asking all the right questions for the record. Brian Grierson, Chief Superior Judge, testifying on, I believe it's H-133. I think one place to start on understanding this bill or the issues around this bill are to understand that there are really three, at least three different scenarios that a court may be confronted with, all involving similar behavior, but ending up seeking different forms of relief. So take the hypothetical partners, domestic partners, husband and wife, spouses, whatever term you want to use. If there is domestic violence, physical abuse, as we think of that, the individual, the victim, can contact the police, report a crime, the police will investigate it. That would end up in the criminal court, in the adult court. And as a condition of release, perhaps they would order no possession of firearms. The victim, if they're one of the protected family members under an RFA order, could separately pursue a relief from abuse order, separate and apart from the criminal case. And that would be a plaintiff spouse versus defendant spouse, completely civil proceeding. And that's why you have a different standard of proof. But again, as a result of that proceeding, there could be an order of no possession of firearms. That same individual, and I'm referring to the hypothetical victim spouse, could be concerned about their partner's behavior, erratic behavior, mental health issues. And for that reason, seek assistance from law enforcement or state's attorney to obtain what has been referred to as the ERPO order. And that would be, again, be a separate proceeding. It follows a similar format to relief from abuse, but it does not involve a crime of domestic violence. And it does not necessarily involve abuse or a threat of abuse towards the victim. And therefore, that would be a separate proceeding. And that's why the procedures around ERPO orders are different from relief from abuse. There are times, and have been times certainly, since the introduction of an ERPO order, that a person is charged with a crime of domestic violence in adult court, criminal court. The victim spouse seeks a relief from abuse order on their own, and the state's attorney and or law enforcement for their own reasons may seek an ERPO order. So it doesn't happen very often, but there is sometimes these different proceedings all stemming from the same set of facts. But they are separate and distinct procedures. I don't know, Senator Sears, any more about the Indianapolis situation than perhaps anyone else, other than what I had heard was that the prosecutor in that particular case chose not to pursue a final order on the ERPO charge. And that's why there was no order outstanding that prevented this young fellow from obtaining further firearms. But they did cease to be shot. Apparently they sought it. And again, what I had heard the prosecutor say, he was afraid, and I didn't understand this, but he was afraid if he went to court and lost the hearing to issue a final order, if you will, on ERPO, that they would have to return the shotgun. So rather than taking the risk, they didn't do anything. So I don't think they, I don't know if they returned the shotgun. It doesn't sound like they did, but there was nothing of record that would prevent that individual purchasing further firearms. But to go back to, hopefully that explains the difference between the three types of proceedings. The three process, that's helpful, Judge. So with respect to this order, the committee should have in mind that this Sarah Robinson and her organization, I believe were the folks who originated this, or this bill originated in the house with their support and we were asked to testify and offer comment on it. And the form that you now see it in, I will tell you is what I'm talking about. That's my only judge because I was told that you're the one that sought this change and that. No, I was asked to come in and testify for the court's view. This was not a bill that was initiated by the judiciary. I was asked what I thought of it. And I, as you've heard, and I will confirm that I had... No, that's fine. I just wanted you to know why I was smiling because I was told that it was something you saw. No, we support it in this sense. And the committee has indicated this, that I believe, and by far the majority of the judges who have responded to me, and matter of fact, all the judges who have responded to me, believe they currently have the inherent authority to order this relief at the present time. It is not reflected specifically in statute. And so when I was asked to comment on this bill, I did indicate that I believe we have the inherent authority, that this bill certainly in its present form would essentially as I think Senator Benning or others had codified what we now have the authority to do. What I think that codification does, it brings some consistency in terms of the judges knowing that they have the authority to do this by statute, apart from their inherent authority. But it clearly does not mandate that they do it in every case. The bill as it was originally drafted as opposed to the form in which you see it now, I think to a great extent was as a result of my testimony to suggest that you add this as a section E under the current bill. And the reason for that is if you look at the prefatory paragraph to A through E, it's still a discretionary act on the part of the court. All this bill is indicating another form of potential relief if warranted by the facts. And you'll see in paragraph number 1104, small a paragraph one upon a finding that there is an immediate danger of further abuse and order may be granted requiring the defendant. And all those items in the current bill, A through D are potential relief the court can grant, but they're not required to grant them in every case, nor would they be required to grant the relief that is set forth in the proposed section E. It's just a, if you will, a recitation of the potential forms of relief. And so for that reason, I believe that it does clarify authority that we believe we have and the language that's in front of you now, at least in terms of the placement of it and the wording, to a great extent, was recommended by me for clarification. So the temporary is this order is issued, X part A, without notice of the defendant. And there's a finding, or maybe issued, I should say, and there's a finding that the defendant has abused the plaintiff or the plaintiff's children. That's the judge needs to find that. Yes. In order to do anything else, correct? Yes, and the key to the temporary order as opposed to the final order is number one, it's X part A, meaning the defendant doesn't have the opportunity at that time, but two, there has to be a finding by the court that the order is necessary on an X part A basis because there's an immediate threat of further harm. Senator White asked about to what extent are these granted or not granted? And just by way of example, 2020, I have data shows 2,200 temporary orders were granted, 743 were denied. And those numbers are fairly consistent over the years. So no committee members should feel that there's anything automatic about the granting of a temporary order. There are sometimes the orders, they can be denied outright. There's no evidence of abuse or insufficient evidence of abuse. And they're denied, even when we deny them, the plaintiff has the right to request a final hearing. And then there is no order issued, but it is set for final hearing on their request. Sometimes the order will indicate that there is abuse, but there's not sufficient evidence to show an immediate threat. And therefore the order will be denied, not because there isn't abuse, but because there's no evidence of immediate threat. So this, it is discretionary with the court whether these are ordered and the terms of the orders are discretionary. And the relief that's being sought here as I've indicated, essentially is, this would be codifying what we have. When I canvassed the judges on issues, whether it's this one or others, I never hear from all judges. So I always hesitate to say majority or consensus, but I clearly think there's a consensus on this issue, but I did not hear from any judges saying we do not have the inherent authority. So in that sense, I'm satisfied that this is something that we have the authority to do, but at the same time, it would indicate that it is a form of relief that's available along with A through D. All right. Senator Benning. Judge, I have several questions. First, could you repeat those statistics that you had for 2020? Sure, let me, so 2,200, I'll give you round numbers, 2,200 temporary orders granted, a little more than 700 denied. Then you go to the next step, this helps the final order. Now remember, the final order hearings can be based on a temporary order that's been granted or the plaintiff seeking a final order, even if they've been denied. So the numbers may not match up. So the final orders granted, 1,053 are the numbers that I have. So if you go back to the original numbers, there was about 3,000 requests filed, the 700 plus the 2,200, and a final order granted in about a thousand, little more than 1,000 of those. And a final order denied, that means that could mean either after hearing or the plaintiff did not appear. And these numbers don't tell me. Unfortunately, Judge, and I don't know what to do. We have this issue we are trying to balance 37 things at once here. And this is awesome. And I apologize to you in the middle of your testimony. Sorry. We have to go to a joint meeting of the of the house judiciary at 10 a.m. And we've got like two minutes to get over there. Sorry, I can't bring it back. I apologize. And after this hearing, we are taking up the budgets of the judicial system and state attorneys and et cetera. So I'm sure you'd prefer we take that up as well. So we're going to have to delay this testimony till Tuesday morning and lead off with you. That's fine. And continue this. I'm very sorry about this, but it happens. I really, and to all of you, David and Ingrid and all, I apologize for this. But thank you for making the effort to join us. It's been an interesting conversation. And I look forward to continuing the discussion. Thank you. But one question, if we could check out beforehand, either having Jeffrey Wallen here or find out exactly what happens when there is a temporary order issue. I've written to him as I heard the questions. Yeah, I don't have an answer. That's an important question for us. I understand. And I don't have an answer, but I've written to Jeff while we were, while the testimony was going on. I don't have an answer yet, but I'll have one by next Tuesday. Okay, great.