tonight we're going to take team of presentation called tax incremental financing 101 we're going to give a little bit of a background about TIF districts some definitions some information and then dive into the current districts and the financials related to that so the city has retained elders associates to help us look at the districts and make some recommendations moving forward on their financial stability and or closure of those districts so we'll go through some of that in detail so to start out with what is a TIF a TIF is a mechanism for funding development and infrastructure related to redevelopment and or development it allows all taxing jurisdictions benefiting from the development to share in its costs we interchangeably use the word TIF in TID so a TIF is the actual financing option that allows a municipality a town village or city to fund infrastructure and other improvements through property tax revenue on a new developed property and a TID is the actual boundary or the district of the area identified by the municipality for the certain type of development so a little bit about the TID law background the TIF law was adopted by legislation at the state in 1975 to eliminate blighted areas and urban neighborhoods before the TIF law was enacted a mean us if a municipality wanted to expand its local tax-based municipality alone would have to pay the cost but the overlapping taxing jurisdictions would also benefit from the growth the legislator saw this as a situation as unfair and viewed TIF as a way to help remedy the problem and encourage cooperation between local governments and the city of shabuigan's case the other taxing jurisdictions is the shabuigan county the school district shabuigan area school district and Lakeshore technical college so there's a number of tids or tips tids blight elimination was an early one and that was replaced sometime later by a rehabilitation district this district is technically is typically open for 27 years an industrial TID is used to fund industrial and business parks and it's open for 20 years a mixed-use district is mixed-use development so it could be residential and or commercial that is open for 20 years and then an environmental district is used to fund environmental cleanup so how does TIF work and we've had a lot of discussions about this but upon creation the value of the TID is frozen for the property for property tax distribution purposes so basically whatever the value of that property within that district is at the time of certification by the Department of Revenue that's basically held stagnant and that's the value that the in our case the city would get in the taxing jurisdictions would get from a value going into the general fund any new value created in the district above that then goes into the district and used to pay down expenditures within the district so that's kind of and then when the district closes all taxing entities start to realize the benefits of the new value so the the purpose of this is really economic development tool and to revitalize in our case old areas that are vacant or blighted or underutilized bring some new value in and then when the district closes that goes back on the tax rolls and everybody sees a benefit so there's a number of ways that TIF projects can be funded it can be done through bonding of a upfront funding where the city would go out and borrow the money and give it basically a grant if you will to the developer another one is a city led pays you go so that's the one that we typically use so that's where the developer has to capital outlay the monies and then based on the income from future tax generation they get paid back over time as well as the developer led pays you go I guess those could be kind of interchangeably basically that they're for their paying for the improvements in their financing package and then as they perform over time we would pay them back so there's a number of ways that you can amend districts for reasons to amend a different district would be to modify the project plan to add or subtract property within the TID to extend the maximum life or to donate tax increments to other districts TIF amendments boundaries may be changed up to four times there's no limit on the project plan amendments one expenditure period amendment if it's not cash flowing and then both the TID amendments and project plan change plane project plan changes need to be approved by the joint review board so what is the joint review board in our case it's a representative from the Sheboygan area school district one from the technical college one from Sheboygan County a representative from the city and a public member and then there's the opportunity for an affordable housing extension so this was added to TIF in 2009 and it allows a city that has a district that has retired its debt or other obligations to extend the life of the district for one year and if the city adopts a resolution extending the district for one year and disclose it how it intends to improve its housing stock you can take these funds and use them for other purposes so the Department of Revenue grants approval on these extensions 75% of the tax increments need to benefit affordable housing anywhere within the city not just specific to that district and affordable housing is defined by the law as housing costing norm no more than 30% of the households gross monthly income so this is a listing of the current tids within the city of Sheboygan so TIF 6 is south pier and the lakefront out to the marina that's our oldest district tid 10 is the water street area primarily down here along the river the kingsbury apartments and some of those garden toy apartments were included in that tid 12 is a street office building so that is the Nemsha what used to be the Nemsha for Herman Miller office building where roadie dales is today and the grand stay hotel so it's a small district kind of on that corner the land tid 13 is landmark condo so this is the landmark building that had burnt in 2007 and was rebuilt that includes that property as well as the founders club or the old Sheboygan senior community tid 14 it was originally created for festival foods development and has since expanded to include the Meyer foods tid 15 is the pick and save property and some residential property on the south side of Sheboygan tid 16 is downtown a street basically it's a street from the river up to the Weill center and then expands out to include the Wells Fargo property to the east tid 17 is Indiana Avenue so it's basically from the lake out to 14 Street and then down south 7th Street to just shy of King Park so the old Oppenberg property is kind of the southern limit tid 18 is the south point enterprise campus our new business center on the south side tid 19 is the River Bend neighborhood this is primarily around the Dolmese decor where the Water Street hotel is being watershed hotel is being developed the old glass coffee shop and then the LT Lakeshore Technical College campus across the road so it's a small district kind of on the kind of bend in the river and then the last one tid 20 is the former van der Waart where Oscar apartments and quick trip are being built so we're going to dive into the district's a little bit more detail so the tiff 6 tid 6 the south pier you can see the map on the screen it is a fairly large district it was created in 1992 the expenditure period so anything after that date of 1231 2017 we're unable to make any further expenditures in that district and it's slated to close in 2023 it had been amended a number of times it has gone through a number of years of changing of tiff loss so that's 33 years is the expansion time that's not really never seen but there was some challenges with issues related to the south pier development and blue harbor that the legislature took some additional action to extend that district the estimated close date is this year it was originally created as a blight elimination district it has currently is generating around 1.5 million in increments so that's the new tax value on top of basically the revenue that the district is creating and as I mentioned this one would be eligible for an affordable housing tax credit in 2022 and close in 2022 so we'll talk about what that looks like and what those numbers look like near the end of the slides but I would the next one I would turn it over to fill the talk about the financials great thank you Chad good evening everyone Phil cost about dollars nice to be with you we these are all going to look very similar these are our our materials and we're numbers people so bear with me what you'll see here is that in the orange heading is where we're showing the anticipated revenues for a tax increment district here we have the tax increment the revenue that's actually the increase in valuation and the taxes generated on that there's exempt computer aid and many of these that are kind of held constant by the Department of Revenue here you have a ground lease fee that is revenue that's coming back into this district some loan receivables and to a total revenue number so if you've taken that revenue number minus your obligations what we're trying to drive down to is is the district healthy enough at this point to actually close out partly why we've got involved was to make sure that we're looking at each of the districts with the intent to see whether or not a district can be closed if there could be a revenue sharing should it be amended we kind of went through all those criteria for each of the districts under the expenditures there are some remaining debt payments a transfer and some small administrative costs and as Chad indicated in 2022 we would expect to generate enough revenue to be able close out this district with the ability to again if at your it's a policy decision to keep these districts open but you would be able to collect a million 442 of revenue in 2023 to for affordable housing so we'll touch on each of these and a little bit and get more into the affordable housing discussion later on so the next district is tid 10 the water street it's set up the same way there's a map kind of showing the boundaries along the Sheboygan River this was a blight elimination district created in 1997 would close could close in 2024 or earlier it generates about 390 $2400 in tiff increment revenue it is eligible for the affordable housing extension as well and to close in 2022 so I will let Phil talk about this one all right thank you Chad and again if you look at the same setup as the last one not going to walk through each of the numbers here but again in the in the orange heading or all the revenues and the expenditures are all in the in the green you do have a development and set up with Van Horn development a group here that will be fully paid off in 2023 there's some general fund advances that are going to be reimbursed back to the general fund as part of this district and again what we're projecting in the balance columns in 2022 you would have the ability to get in to close this district out with the possibility again of retaining one years of revenue for affordable housing. The next district is Tid 12 the East Street office building and grand state and then some of the wild center black pig and some of the parking lots so this district like the other ones is a rehabilitation district created in 2000 would close could close in 2027 this is a donor district to Tid 17 so this is sharing revenues from this district to Tid 17 which was Indiana Avenue. However that may not be needed in the future because Tid 17 is doing better than anticipated. So this district generates around 191,776 in revenues and like the other districts is eligible for the affordable housing. Yeah again much smaller district much smaller revenue amounts here one of the things we discovered quickly as we got into to number 17 was that we really didn't need to share additional revenue with 17 which then freed up the ability for Tid number 12 to close out in 2022 as well as Chad indicated to 17 is healthy enough at this point is but enough development for the support itself without revenue coming from another district. So this district will be looked to be close will be looking to close out in 2022 as well. The next one Tid 13 landmark condos as I said before it's primarily the landmark condos and the founders club or the should wagon the old should wagon senior community. A very small district really generated to facilitate the development of the condo project so was created in 2005 expenditure period runs to 27 20 27 and it has an end date of 2032. It is a donor district like Tid 12 with Tid 17 generates around 442,000 and would be eligible for the affordable housing tax credit. I've been around so long I created this district back in 2005 so I'm back so this district again was created back as Chad indicated. This is a a blight district meaning it could stay open for a lot longer period of time. But again decision at least at the staff level at this point is to close this district out since revenue doesn't need to be shared with 17 as well so this will be able to be closed out and again possibly up to about $400,000 available for affordable housing also. Tid 14 the Taylor Heights Festival Foods and Myers so you can see the district that this covers primarily the area around Taylor and Erie Avenue and some of the on and off ramps and then the old the sunny ridge and some of that redevelopment area to the northeast I guess you could say so this was created in 2011 could close in 2031 it was created as a mixed use district which would give it a maximum life of 20 years. It generates about 1.5 million a year in revenues and like the other ones is eligible for the housing affordable housing extension. Yes, I was involved in this district creation as well. And really this this really was the old Menards building that was in turn into festival foods Walmart sorry Walmart building. It has been a while thank you back back a while so again similar to the other districts we expect this district to be able to pay off all its obligations with the cumulative balance that remains and again 2022 bill close out this district. Tid 15 the pick and save. So this was used for the redevelopment of the what used to be the came out into the pick and save that unfortunately sets vacant however there is a lease that they're they're paying that the same rate as if they were in the building so the developer really has no interest in going out and finding a tenant but the tax value has to our benefits stayed at that high level as if the building is occupied. So this was created in 2011 as well would could have a closure of 2031 as a mixed use district for 20 years. Revenue is about 230,000 and is eligible for the housing extension in 2024 and could close in 2024 because there's some obligations that still need to be met. Yeah, very similar story here. There are obligations here that run through 2024. There's a cumulative balance that's been built up in that in that did fun and again enough in 22 are ready to close out this district. This is one you could you could probably keep open for other purposes in that neighborhood but with all another prospect it makes sense to close this out at this time. Tid 16 the downtown Sheboygan a street as I said basically runs from the visitor center property all the way up to Wisconsin Avenue and then that little leg that goes to the East is the wall Wells Fargo and some property that they own West of North 6th Street. I think that is so anyway that district was created in 2015. It was created to provide development incentives to develop the high point apartments and the encore apartments. It's a 20 year district. It runs through 2035 its annual income is around 587,000. So there's a little bit more to tell here. Yeah, so if you spend a little bit of time looking at this cash flow and you look at the last columns on the right where it says annual and cumulative you'll see that for the time being this district is in the red. Not unusual for newer districts to be in the red until development really picks up. There's projected shortfalls for the next couple of years. Until a lot of the debt and the incentives fall off. We fully expect that will be fully reimbursed back. And in 2032 this district will be in the black and will have the ability to close out at that time, which will still be 5 years earlier than the maximum life. So it's just taking a little time to to work its way through. But from all project our projections at this point will be a healthy district in the future. So this is a real example of how what if it's set up for is to take on a lot of debt in the beginning and then pay it off over time as the increment comes in. There had there was some there's been a number of capital projects that have been funded against this district like the updates to the street lighting to LED conversion along a street. So that's an ongoing expense that has been built into this as well. So to 17 is the Indiana district was created in 2018. So it's relatively new. It's a 27 year district. It could run through 2042. It sees increment revenue of about 800,000 per year. And the indications are that it will be it'll do fine. It'll be cat. It'll be positive cash flow moving forward. It was really created to facilitate some of the redevelopment along Indiana Avenue, the former pentaire property and then the opt and bird property to the south. So you can see that it's a relatively large district. It has seen some successful projects with the Badger state lofts and the condo development that occurred along the Sheboygan River and then should the development on the former Kepsil move forward that will only help it out a lot more. So it right now is a recipient of tids 12 and 13. But going forward it has plenty of cash flow that it doesn't necessarily need that. Yeah. If you look at the the revenue projections and you look at the projected revenue, you'll see that we do show in the third and fourth, fourth and fifth columns from the left. The revenues that have come in from 12 and 13. And then the third column from the right is that cumulative balance. So there is a healthy fund balance in this tax increment district. In part, I think through from revenues from to 12 13, a little bit of bomb proceeds, some land sale as well. We expect this district. If you look at the cumulative column to stay in the black through the life and again close out well early 11 years earlier than the allowed life of the district at this point be a very successful district for the city. So the next few districts are pretty new and there's some opportunity. So there is you won't see a ellers comparison on these because we're because of the age, frankly. So I'm just going to go through some of the details and then there won't be any additional slides on the performance. But the tit 18 south point enterprise campus created in 2018, the expenditure period through 2035, the end date was 2038 has now been approved by the Department of Revenue to 2040. And that's based on an update of the lack basically to try to get us through the pandemic because we haven't had a lot of development out there as was originally anticipated. So we had worked with ellers to extend this to 2040 to cover some cash flow issues going forward. And we believe that it will make it's got about 15 to 18 million or so of outstanding debt. But we believe in the end, it'll ultimately make it. It'll cash flow itself. Right now, it's generating around 900,000 in revenue is what we budgeted. And that's primarily from the FedEx project. That's also in this district and some improvements that torgonals making in our current business center. Tid 19 River Bend neighborhood. So this was also created in 2018. It will close in 2038. It's a mixed use district. You can see where this is. The this is a fluid situation. We've got a number of developments happening. We may need to extend this to include the former may line and the adjacent redevelopment authority property, JP Marine along commerce street to facilitate some redevelopment and some street construction upgrades in that area going forward. And then the last one is the Tid 20, which is the former Vanderbilt. This was a 27 year district created in 2020 closes in 2047 as a rehabilitation district and could basically has minimal debt against it other than some street lights on Georgia Avenue and potentially some trail improvements. So this could be a future donor district with other rehabilitation districts if needed or close early. This has to pay a fairly large tip incentive, almost $7.5 million to the roughly $47 million Oscar apartment deal. Well, here's the good news, folks. It's it's really a situation where you have a lot of activity in districts, districts that have been around for quite some time. And you're at a point where you have the ability to close out six of the districts this year. And there's some financial impacts to that there's there's really three impacts. One is that the city like most other communities in the state of Wisconsin are are trying to figure out workforce and affordable housing. This will be one avenue to deal with that. So what we projected if you close out in 22 these six districts that if you look at where it says anticipated amount for affordable housing, the projection is about $3.9 million that would go into a fund that Chad talked about earlier that there's some some some you have to kind of work through the process of how the funds can be used. But it's really your mark for affordable housing. So it'll be a really good start to a fund in the city of Sheboygan that will allow the city to be more active and working towards workforce and affordable housing issues. Second, when we look at tax impact of anticipated borrowings and and in your operating lobby, one of the benefits of closing out districts is you get a big bump in valuation where you're spreading the overall operations and debt over a larger tax base. Closing out these districts about $190 million of value will come back online. That will help absorb again future increases in both operating and debt service and kind of hopefully level out the tax levy as well. And then finally the third is that I mentioned earlier in tip number 10. There's a general fund reimbursement above 419,000 I'll go back to the general fund so you get a bump in valuation which helps when it comes budget time. That'll really take effect in budget year 2024. You have about $3.9 million that'll go into an affordable housing fund and a little bit of money coming back to the general fund as well. So wrapping this up so the last couple slides here are just some information that we hear all the time. How many tids can the city have? Obviously, if we close six districts will be creating additional opportunity should the need arise. But the state statute requires that the equalized value of taxable property in all districts does not exceed 12%. With the most recent creation of TID 20, the city's total equalized value of existing tids was around 190 million and we could go up to a maximum of 350 million. So we prior to that if we didn't close any districts would have still plenty of value to do that. But with closing districts obviously that total number will go down. Couple advantages of tids. It can increase property values, spur private development, create a stronger, broader tax base, stimulates the investment outside the district typically and benefits the underlying taxing districts at the end of the TIF as we just discussed. Some disadvantages of the district doesn't materialize as planned. The city may have to find other sources to fund it and that's kind of where some of those advances from the general fund have happened over the years. Tids may be used in areas where development would have not normally occurred and it can increase the administrative burden of managing these local districts. So that's it in a nutshell. If there's any questions, we would be happy to answer them. All right. Thanks Chitinville for that very informative and engaging conversation. Any questions from Alders? Alder Flicky Pineski. Thank you. For an example, TID 13 right now, if we close it, we get about 200,000 of revenue. If we keep it open, if I read the charts correctly, if we keep it open, we get a million dollars in a couple more years. Is that accurate? Yeah, I think it's 300,000 is the revenue, the increment that's generated. So either that would keep going into building up a fund balance or in this case could be shared with the donor district, which was TID 17. I don't know where the 1.5 million, what it came from. Okay, I guess more generally my question is when I looked at the charts, closing them out now gives us a certain dollar amount. If we wait another year, we get a higher increment. Is that accurate? You want to answer that? Yeah. Mr. Cossin. I just wanted to pull this up, sir. It was TID 13 that I was looking at. Yeah, so there's a couple of things. There are one, once you have, the state statute is very clear that once you have... I don't know why this is different, but it's not advancing the slides. Sorry. Okay. Well, I'll just answer it generally. So the statutes are very clear that once you have met all the obligations that you're required statutorily to close out the district. You can't just keep it open to build a fund balance in a tax increment district. So to keep it open, in the case of TID 13, you would have to undertake additional capital expenditures to keep it open. If there aren't expenditures that be made in TID 13, then statutorily you're required to close out the district. I think the decision by staff has been, at this point, there are no future capital expenditures in that area. Therefore, we don't need to share the revenue with TID number 17 anymore. Let's close out the district. Okay. That answered my question. Thank you. Any other follow-ups? Older Flicky Paneski? No. Any additional questions from elders? All right. Thank you, Chad. Thank you, Phil. Thank you, Illars, for all your work and keeping the TIFFs rolling and in pretty good health. Thank you.


And we're here with a pre-tech and here you have a seven inch device running windows. Hello. Hello. Hi, so who are you? I'm Zora from pre-tech and What is this device? Oh, this is a seven inch like you like There's a yoga like yes yoga style yoga style and then we also call it a pocket yoga Pocket yoga is bigger. They can go in your pocket My pocket is not open. It's not a real pocket, but if you have real pocket big enough Probably can go in the pocket. Yeah, I think my pocket is no problem. Yeah All right, so what's kind of price is this and what's the CPU? Intel Z8 3 00 so no Z8 3 5 0 and This is the specs right here running Windows 10. Yeah, Windows 10 7 inch full HD IPS and The ports on the side. Yeah, put on the side This is type C. You can be power delivery and also data under this USB 3.0 is for data only and this is micro HDMI and This is me. Yeah for evil and this for micro SD card. Nice and The keyboard is good. Yes mouse thingy thing Yeah Like this is the mouse All right, but you could potentially connect Potentially you can connect type C mouse or something else. So I have a mouse externally. Yeah, and the keyboard is okay What kind of price you talking about for this? How many pieces to order 100 1000 1000 moq and you have many laptops around here Really yeah included the pen. Yeah, you can also support the pen Nice. Yeah, you need to activate the pen, right? Is there a button? Yeah, you have to wait If you set it up correctly Yeah, but you cannot put the pen inside No, no, no have this design. All right. Maybe we can add something that around here and then put it here Cool, and then you have many different laptops around here Which which one is most popular about this one? Yeah, this one. You're right. Good choice. It looks nice Yeah, it looks very nice because this is our private shooting private. Yeah, so you have a nice keyboard nice mouse Mm-hmm Private that means nobody else has it.  Yeah, and it's a 14.1 inch and you can see the glass It's a glass cover screen. This is very special and then you can what kind of price 145 145 with Intel z something That is the Intel N 3350 is it the specs is this this So 3 3 5 0 Intel sir on 3 4 5 0 4 2 0 It's more expensive and then you have full HD Narrow bezel. Yes, you can narrow bezel you say 1 4 5 Price 1 4 5 1 4 5 right correct and MOQ 1k also, right? So this is sleek nice and not too heavy All right slim and then this This is a different different color, right? Different color. We can do all colors. It depends on your request This is silver also can do SSD slot here SSD Nice This is different one or same stuff This is the 14 Core i3 and the for this design. We also have a smaller size That is 12.5 inch. I'm sorry. The sample is not here. Okay So how about the price on this one for the core i3? Why three the price is around two hundred and forty nine Great. This is a lot of ports All kinds of stuff type-c micro HDMI USB 3 and another USB 3 Then you do a lot of like Do you want means you can put it together or separate it and It's all window Intel or do you have different CPU windows Intel also? Yeah, Intel Intel. Yes, correct And this is surface like surface like And Also this size It's a little bit heavy, right? Yeah, what's inside a lot of stuff? Oh Jump some PCBA. There's some yeah battery like that Nice big battery Is it is it a public design nothing special Yeah, and the price on this The special is the keyboard you can see the key buttons is a little larger Bigger than this one. This and this is a 11.6 inch Future All right, and so some of the other stuff you do is a smart phones Media tech Octa-core and you can see this is sky-meter


In a previous episode of Code Club, I showed you how we can use FacetWrap to create different plotting windows according to a categorical variable. In today's episode, we'll use FacetWrap again, but we'll also use FacetGrid to show how we can create separate plotting windows by two categorical variables. Hi, I'm Pat Schloss, and this is Code Club. Each episode, we try to apply reproducible research practices to an interesting biological question. Over the past 40 or so episodes, we've been looking at amplicon or exact sequence variants, a way of describing the diversity of 16S RNA gene sequences that's kind of become the rave in microbial ecology circles. So stay tuned, and we'll tell you more about how we use R to answer questions about these interesting entities. In the last episode, we saw that if we took amplicon sequence variants and defined them at a very narrow threshold, so that the diversity among the sequences that are grouped together in an amplicon sequence variant is very narrow, then we run the risk of splitting a single genome into multiple bins, multiple amplicon sequence variants. To me, this doesn't make a lot of sense because there's no ecological basis for treating different parts of the genome different ways. In some cases, if a genome had seven copies of the 16S gene, they could actually have seven different exact or amplicon sequence variants. But to treat those seven differently doesn't make sense to me. The problem, though, is that as we increase the threshold, sure, we decrease the amount of splitting that happens, but we also increase the amount of lumping that happens. That as we increase the threshold to allow more diversity within an amplicon sequence variant, we run the risk of pulling together different species of bacteria. So there's this trade-off between lumping and splitting. Those of you that are familiar with taxonomy will know that this is a constant battle in the field of taxonomy. I think this is a little bit different because even if you're a hardcore splitter, I don't think you would ever really be a proponent of splitting different parts of a genome into different bacterial species or strains. It just doesn't make sense to me. Also we constantly try to remind people that the 16S gene really doesn't have enough resolution to differentiate at the species level. If you want to differentiate at the species level, you really need a full genome sequence and perhaps use a metric like ANI to differentiate between different bins of species or genomes that belong to those species. So in today's episode, what we're going to do is we're going to use facet wrap and facet grid to see how we can directly compare the level of splitting and lumping for a threshold as well as for four different regions in the 16S gene. Even if you don't know what a 16S RNA gene is, perhaps you're not sure what bacteria even are or why you should care about genomics, stay tuned. You'll learn a lot about how I think through problems, how I break it down from kind of a conceptual logic written in words into our code, how we integrate that with make and version control to make our whole analysis more reproducible. Of course I'd love for you to subscribe to the Rifomonas channel and click that bell icon so you know when the next episode is released. We're really going to be building up our story here over the next few weeks, hopefully leading to some type of manuscript that I'll show you how we will then submit to a journal. I don't want you to miss any of that, so go ahead and click that bell icon. For today's episode, we're going to work on issue 36, which I've already filled in on our issue tracker here on our GitHub repository. We want to know how often is the same EASV found in multiple species, so that's a measure of lumping and what fraction of species have multiple EASVs. That's a measure of splitting and then we want to plot this using different combinations of variables and we'll do that using facet wrap, which we've talked about previously, as well as facet grid, which will be something new for us to talk about today. Also we want to use one genome per species and we want to look at this for each of the regions that we've been tracking in our analysis. Moving over to GitHub, I've already created a branch. You'll see that it is red because I have already created a template file for our lumping and splitting analysis for today, so I will fire up our studio and we will see that we are in our working directory. If I go to files, down at the bottom is my RMD file that I've already created. I basically copied it over from the last episode to this episode, changed the title, changed the date, and we're in good shape. As a refresher of what we did last time in this kind of preamble material, you'll recall that we're largely using the tidyverse and we want to set a seed. This is my birth date, 1976, June 20th. Remember that because I want birthday presents. That's okay. Don't worry about it. Just watch the video, like and subscribe and that'll be enough of a present every day of the year. Anyway, so we're going to read in our metadata. You'll notice in here that we have the code to group by our genome ID and species and then return one genome per species and we're using a slice sample that allows us to randomly pick that one genome. And if we use the same seed, we should get the same genomes. If we wanted, we could run this 100 times and then pull all the results together. I'm not so interested in doing that at this point because I'm still trying to feel out the analysis. And if it's something that I like, then maybe we will do it 100 times so that we can then get an average over all those iterations. But for now we're in good shape. We also are reading in our exact and Amplicon sequence variants file. And then we join those together. Those two data frames together and we are changing the ESV values in that threshold column to be zero because those are really Amplicon sequence variants where the diameter of that bin is zero where there's no difference allowed between the fragments. All right, and then we convert that to a number from character to number, which will allow us to plot threshold on the x-axis without too many problems. So I will go ahead and run this code junk and we will be in good shape. All right. So again, I copied in the information from the issue tracker and I then spent some time going through and outlining what I want to do. So I wrote this all without writing any code, honest, and this really helps me to think about the logic that I want to implement with the code. Right. And as you've seen in previous episodes, when I've done this, my outline isn't always perfect. Sometimes I move things around. Sometimes I add information of things I want to do. But the other advantage of this is it does provide some commentary on why I want to do things and what I'm trying to do. So we will get going with this. And what we're going to do is two types of analysis I've already mentioned. We're going to measure the degree of splitting. And to do that, we're going to group the data by the region within the success gene, the threshold, as well as the genome. And then we're going to count for each of the, for this combination, basically for each genome at each threshold and each region, how many Amplicon sequence variants are there? And if there's more than one, then we want to know what fraction of the genomes have more than one Amplicon sequence variant. Now, the measured degree of lumping is basically the same thing, except instead of including genome ID for pooling our data together, aggregating our data, we're going to include the exact or Amplicon sequence variant information. And then we're going to ask how many genomes have more than one Amplicon sequence variant. So here, how many genomes have more than one Amplicon sequence variant? Here, how many Amplicon sequence variants have more than one genome, okay? And this will then allow us to calculate the two fractions. We'll then pull those two data frames together, and we will then generate a few plots where we are fastening the data by different types of information. So this is great to get us going, and so let's get to it. So metadata, EASV, we will then pipe that to a group by, wherever we see group data by, we want to do group by. So region, threshold, genome ID, we will then pipe that to a summarize function, where we will then do N EASV equals N distinct, and we will then do EASV. And so within each of these groupings, we're going to say how many distinct Amplicon sequence variants are there, and that's going to be our N EASV. And then we will say is split, because this is a measure of splitting the data. So is split, and that will be true if N EASVs is greater than one. We could have done this all in one line, but I kind of like to be explicit in how I lay out my logic. Another sign of being explicit about my logic is to do the dot groups equals drop, which will then remove our grouping variables. And then I can pipe that to group by, and we will then group by region and threshold, and we will then pipe that to a summarize function. For each region, each threshold, we want to know the fraction of splitting, and that will then be the sum of is split divided by the end function, okay? And we will then do dot groups equals drop and be in good shape. As this is running, something to note is that this function splitting uses the sum is split. And that might look weird to some of you, but know that is split is a logical variable made of trues and falses. Numerically, a true is one, and a false is a zero. So if you sum over a logical column, the number you get out is the number of true values, and then that is the sum, right? Another trick that we could have done in place of this would have been to say mean is split, without dividing by the end function. So the mean of 0 and 1 is 0.5, and that will then tell you the fraction of rows, or fraction of genomes in this case, where they are split. Again, more than one way to skin a cat, and this works pretty well. And what we see from the output, at least for the first ten lines from the V19 region, is that as we increase the threshold in the second column, we decrease the level of splitting, which is what we'd expect. And so I'm gonna call this splitting data, and we will load that, and we will then move on to looking at lumping, right? And so we will do metadata, EASV, and we'll then pipe that to a group by function, and again the syntax is gonna be largely the same. Group by region, threshold, EASV, and we will then pipe that to our summarize function. Again, like we saw before, we will then do nLumped, and that is gonna be nDistinct, EASV, I'm sorry, nDistinct genome ID. And we will then say, isLumped, and that's gonna be some, or no, sorry, that's gonna be nLumped, greater than one. Or I shouldn't say lumped, cuz that's not the right thing. So I'll say nGenomes. So how many genomes is each EASV found in? And so that's an nGenomes, greater than one, is a sign that that is being lumped. Okay, we can also then do dot groups equals false, sorry, dot groups equals drop. And we can then pipe that to another group by, where again we'll do region, threshold, summarize, summarize, and we will then do fLumped. And maybe we'll do, yeah, lumped. I don't know why you're splitting up here. So I'll do, where was it, fSplit. And then fLumped is, again, gonna be some isLumped divided by the n function. And we'll do dot groups equals drop. And running that takes a moment or two for it to run. And we see, again, for the v19, that as we increase the threshold, the level of splitting goes up, okay? And let's go ahead and we call this first data frame splitting data. And let's call this lumping data, and that will run nicely. So now what we wanna do is join our lumping and splitting data together. So there's two general ways we could do this. So we could do bind rows, splitting data, and lumping data. And we saw this in a previous episode, maybe two or three episodes ago, we were trying to lump together all of our countable data. And the problem with this is that it pulls together or combines columns that have the same names. But in one of our data frames we have fSplit and the other we have fLumped. And so if one of those columns is missing from the other data frame, it fills it with na values. So bind rows isn't really what we want. We could change the name of the column like we did in that other episode. But I think what would be easier to do would be to inner join and ooh, one of the cool things we get to see here is how to join two data frames by more than one column. We've got two columns that we wanna join on. So before we would say do buy region, right? But we also wanna join using region and the threshold. So let's see how we do that. So we create a vector and the vector are the names of those columns that we want to join by. So we will do region and threshold and add that extra parentheses here. And now what we see is we have a data frame. We don't have those annoying na values. And we have four columns, region, threshold, fSplit and fLumped. We've joined the two data frames using the region and the threshold. Excellent. But I would like to tidy the data a bit so that I have a column indicating the type of approach we use, to measure the fraction of lumping or splitting, as well as a column for the measure of the fraction. Because I would like to make, say two lines, one for lumping and one for the rate of splitting. So we will do pivot longer and the calls will be fSplit and fLumped. And names two will be methods. I'll say method and values two will be fraction. And so then we see that we get region, threshold, method, fraction, or in good shape. And I'm gonna call this lumping splitting data, we'll run all that. And now we're ready to make our plots. So we've got a couple different ways that we can try to do our faceting. And so if we have lumping splitting data, we can then pipe that to ggplot.  And in this case, excuse me, I'm gonna put lumping and splitting as separate lines, and we're gonna facet by the region. So I will then do color equals method. And I will then do a geom line because I want line plot. And then I will do facet, wrap, and I will do tilde region. And what this will give me then is a different panel for each region that I'm looking at. And I don't know why I do this. I always seem to put color in quotes, the method in quotes. Eh, so here we go. This looks much better. And again, what we see in these panels is that as we increase the threshold, we decrease the amount of splitting, but we increase the amount of lumping. You'll see that for several of these regions, basically every region except for v19, we do a pretty poor job of defining a species based on the 16S gene. Even if you allow for splitting genomes, right? And so what we saw with v19 is that like half of the genomes get split. Which is huge considering that there's genomes with not many operons in them. But even here, there's about 4 or 5% of EASVs that are found in multiple species. Again, a sign of lumping. So the 16S really doesn't have enough resolution to get at species level designation, at least as we humans have tried to impose our naming schemes onto bacteria. Again, that's a lot like, this case down here is a lot like Bacillus Sirius, Bacillus Anthracis, and Bacillus Thuringiensis, all getting pooled together or split apart as different species even though the 16S genes are the same. Okay, let's look at this a different way. And again, the syntax is going to be very similar. But let's look at regions as separate lines, but we will facet by our method of lumping or splitting. And our x will be our threshold again, our y will be fraction. And our color, without quotes, will be region. I'll do G online and we will then facet wrap by method. So we'll have two panels, one for lumping, one for splitting. And so again, we see that we have one panel for lumped and one for split. I frankly prefer this approach better than this approach. We've seen this before where we could play with the faceting so that we have a column with four rows. So that it's easier to see the threshold. I like this because it allows me to see within a region, how does the level of lumping and splitting compare. Whereas here, I have to compare back and back across. I don't really care necessarily how lumping compares across the four different regions. Okay, the final approach would be lumping splitting data. And we'll do G plot x equals threshold, y fraction. And I'm gonna leave it at that. And we'll do G online and we will then facet grid and we will do say region tilde method. And this will give us four rows and two columns in our plotting window. The four rows for each of the four regions and the two columns for the different approaches. We can flip the order here. Let me copy this and paste it down below. And I will do method tilde region. We now see that we have the four regions arrayed across the columns and the lumping versus splitting as two rows. And so this is a nice approach too. It keeps the two methods of measuring apart. Really the two y-axis aren't the same thing. It's a fraction of different things. And so this allows you to see for a given threshold, what is the level of lumping? What is the level of splitting? So I like this, I also like this first version too. And so some of it is a matter of personal preference. It's also a matter of what's your question, right? And so some of these other approaches where we faceted by whether we're lumping or splitting or this first approach to the facet grid weren't so attractive to me because they're forcing me to make a comparison with my eyes that I'm not really interested in. Okay, so I'll go ahead and save this and add some conclusions. So as we increase the threshold, splitting drops and lumping increases. Again, we need a decent sized threshold, say greater than 0.01, to reduce the level of splitting and would prefer to limit splitting over lumping because species designations are too squishy. I'll say they're human made rather than bacterial made. Okay, so I'll go ahead and save that and I will come back and open up my make file in Adam and I will add this target to the make file so we can go ahead and build it way down here at the bottom. We'll do exploratory 2020-30-lumpingandsplitting.md. I'll save that, copy the target and we'll go ahead and make it. This will run. I'll go ahead and commit the changes to the repository. I hope you found this description of how I go through an analysis useful. Couple new things that we talked about in here. One was joining two data frames on multiple columns as well as seeing how we can use facet wrap and facet grid to do faceting in different ways and to get our plots to have a different layout in the finally rendered figure. So I hope you can play with this with your own data. Perhaps you're generating different facets. The facet grid is really nice when you have two variables that you want to facet your data by. So again, please be sure to subscribe to the channel and tell your friends about what we're doing here on Code Club. I think there's a lot of great principles that I'm talking about in regards to doing research in a reproducible manner that people get a lot out of regardless of if they give a care about Amplicon sequence variants or bacteria. I don't know who doesn't care about bacteria but I'm sure there's a few people out there. Anyway, keep practicing and we'll see you next time for another episode of Code Club.


Maen nhw'n Mark Thomson, headteacher at St Helen's Primary School. A, it's just amazed to have won it. I mean, there are such inspirational headteachers out there. Just to be chosen as the winner of this award is just absolutely fantastic. Just a massive, massive thank you to the boys who nominated me to my family at home and everybody that I worked with. It means a lot to me because it's a recognition of all of the hard work that the school community puts into the school. And I think for a school that's often struggled in the past and not had the best of reputation. To have something like this is a real recognition of the hard work that we've put in. Just to give the children in the Samfields community the best possible opportunities in life. It's been an absolute privilege to be involved in it right from when I found out that I was nominated. Getting the email is extremely exciting to go through the judging processes. To have the films made and today has just been a fantastic day. Often people talk about workload and the difficulties that we have. We sometimes forget the good things that are going on in school. The wonderful things that people are doing in their jobs, the wonderful things that children are doing. And I think it's important just to recognise that and celebrate on days like this.


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Tom here from Lawrence Systems. We're going to talk about XCPNG, Zen Orchestra, and some of the latest updates to the project. Now if you're not familiar with XCPNG, I do have plenty of videos on the topic, including an entire Getting Started video I made for 2020, which is how to build a fully open source virtualization lab with XCPNG and Zen Orchestra. And if you're not familiar with the project, XCPNG is the base, essentially the hypervisor. Zen Orchestra is the add-on that runs as a virtual machine. Well, and they kind of are made by the same people, so I look at them as one product. But they are two separate things, and the Zen Orchestra updates have been really interesting lately. They got some really cool new features, so I'm going to dive into those. But first, if you'd like to learn more about me and my company, head over to LawrenceSystems.com. If you'd like to hire a short project, there's a hires button right at the top. If you'd like to help keep this channel sponsor-free and thank you to everyone who already has, there is a join button here for YouTube and a Patreon page. Your support is greatly appreciated. If you're looking for deals or discounts on products and services we offer on this channel, check out the affiliate links down below. They're in the description of all of our videos, including a link to our shirt store. We have a wide variety of shirts that we sell, and new designs come out, well, randomly, so check back frequently. And finally, our forums. Forums.LawrenceSystems.com is where you can have a more in-depth discussion about this video and other tech topics you've seen on this channel. Now, back to our content. And we'll start here. The XCP-NG documentation. So, the documentation has been, like, really updated. They've got an official site for it. It's xcpng.org slash docs. Now, this is for the XCP-NG hypervisor. And they were kind enough to feature some of my videos because I break down some comparisons and some history of the project. And this is actually part of a presentation I had did at a local group talking about it. And I do compare it to, like, VMware and I compare to Proxmox. So for those of you looking for a difference and looking for some history, I'll leave a link to this. And of course, it's right on the very first page of the documentation. Zen Orchestra, the add-on that runs on here, they've been really hard at work adding features to this. Now, the cool thing about Zen Orchestra, if you're not familiar with it, is it adds full functionality right down to the backups with XCP-NG. So, XCP-NG itself is all command line driven. Zen Orchestra gives you the nice web interface. That's a lot we're going to talk about. Now, we'll start with the 547. Now, I've done previous videos and everything leading up to this right here. The ones I haven't covered, 547 and 548. So, that's the latest updates from them right now. And it already supported OVA import. And if you're not familiar with the open virtualization application, a lot of different places provide a file. You can just download an import into your hypervisor and just, you know, something turnkey started up and running. They've added support for OVA too.  OVA import was nice. OVA2 import is nicer. Now, this, the SDN controller rules. This is a little bit more complicated. At some point, I will do a dedicated video on it because they're really ramping this up. Now, what this is is software defined networking and it is Zen Orchestra tying series of XCPNG servers together. This is a really cool concept. Now, it sounds kind of complicated but they do break it down. And essentially what you end up doing here is you take several XCPNG physical servers, several hosts, and you can have them all networked together. Even if they're not, let's say, even in the same data center, the same rack. And the advantage of this is being able to have virtual machines that have private network that don't directly access the rest of the network. It's really good for doing a private virtual lab. This is also really good if you're a security researcher and you need to do sandbox testing because you can put whatever firewall you want virtually in front, then design essentially entire network infrastructure that ties a series of servers together that only can talk to each other over private encrypted networks. And it's just really neat what they're doing with this. And they got now the ability to even create very specific traffic rules and going to be adding the option so you can actually apply the traffic rules on a per interface setting. So this is a project in development but really slick if you want to test it out. It's all, once again, free. There's no licenses needed for any of this. It's really cool. I've done a little bit of testing with it. Not enough to get in depth to do a video but I will in the future just do probably a video just focus on this software defined networking as it matures. So that's really cool. The LDAP over TLS config encryption. This is actually a feature I'm really happy they added the ability to when you download the config file out of Zen Orchestra, it didn't have an encryption option. Now I would just encrypt it myself when I do a backup of my config but it's really cool that they built it in. That's just, you know, the way it should be I think. Record failed user attempts to the audit log. Now they have an extensive audit log and one of the cool things that you can see with Zen Orchestra is everything that happened on a per user basis every change made. Now Zen Orchestra is actually used in a lot of data centers. We've done some consulting with some big companies that have this implemented and they have many users using Zen Orchestra and it's nice to have that audit trail of hey, who changed this or who did this with a virtual machine and they've got an entire audit log, audit trail, an integrity checker for it and a lot of data that you can gather from that. It also has a tamper proof system that they built in and it's just really nice. They're getting a lot more fine grained into that particular part of it and trust me audit logs are wonderful because sometimes and it's not necessarily malicious of course it's great for reverse engineering when someone did something malicious. It's also sometimes people just make mistakes they did things and well people sometimes they don't remember doing them or may try to deny doing them that audit log is actually really helpful. Backup improvements. Backups are the core of Zen Orchestra working and improving them every day. This is something I'm going to show you in person is like the list of VMs not backed up. I really like this and this is our Zen Orchestra and specifically this is you see how it says no support. I like to show people I'm using the compiled version so all these features you can buy the paid version of Zen Orchestra and get them all and get full support or if you want to compile them yourself if you're using this in a lab or for testing I like to do that because I know a lot of people will are going to start out by putting this in their lab putting it's in a testing zone you can get access to all the features without any support through this so I'm using this version and I'm on the latest version but I can say backed up VMs or I can say not backed up VMs which it's going to show none right now because I have backups on all of them but this is just a really good feature so I've now changed it to filter not running VMs these are some lab stuff that I have so it doesn't show there's any backups on there. Related to the backups as well the next feature they added was the ability to check the health of the backups and this is interesting because with the backup system being fully integrated with XEP and G one of things is if you don't have a backup job but you somehow have a backup file it can show you that list and actually I do this quite a bit because I create temporary backups I'll create a job and say you know what I just need something because I was building it on those supermicros for a demo I did I want to still hold on to that file for a little while but I don't need the virtual machine anymore I can destroy it but leave all of these set up in there this is kind of a neat use case when you're building a lab or I don't need a clutter of a backup jobs but I can still have all of those backed up servers that I can have and you can see how they're listed right here as far as the actual back overview backup jobs are listed here restore jobs even if they don't have anything and healthy can say hey these are these files that you have that don't have any of the backup jobs related to them just kind of nice because they give you different ways to pivot data also when you're looking at any particular backup you can go now inside the virtual machine when you're looking at it and say hey right here's the backup it's enabled what was the last status of that backup successful go here look at it and say all right here's the how long it took to back up and by the way when you do delta backups are impressively fast so it only took a few seconds as it said a few seconds so from 835 to 840 803 235 seconds to do the transfer and then merge the backups to create the delta so I have a snapshot of this and this one actually runs every couple hours and of course they added the edit button right here for convenience so let's go back down the list and I believe that is it now this is one thing they do have faster backup listings so when there's a lot of backups it does they optimize the performance on there no timeouts I never have enough in there to the timeouts but for some of the clients with large volumes of backups on there and you know hundreds of VMs sometimes I guess it would time out if they didn't have enough speed and it would wait too long on there so that's been fixed and this is something interesting too there's people have talked about bottlenecks now one of the bottlenecks is the way the compression works when you turn the compression on and the file transfer combined with a few other factors it can be really trouble hard to troubleshoot the backup performance and they're adding more optimization in there one of the things I've noticed is sometimes it doesn't seem to spread the load across all the processors with the previous versions it seems to be doing a better job of that so the backups do seem to be running faster now but they're also doing the data collected thanks to tracers won't be displayed in your infrastructure the data is stored in the log server proxies this is all part of uh enhancements and this is one of things I really like is they're always looking at it going how can we make it better it doesn't just work it's what can we do to make it better now let's move on to the zen 548 update this is that filter backup jobs this is kind of enhancement so 547 they didn't add it to actually add in 548 which is the latest one right now so that was what I just showed you there the accidental deletion this is kind of neat and I always thought it maybe was too easy to delete a vm and because it's only giving you one prompt so this will stop you at that extra prompt so it's more steps to delete a vm they I mean I appreciate how easy they made it but I guess this is nice because when you have production stuff you don't want to go delete this vm it does ask if you're sure but you can just say yes now it just stops you at that point right there so prevent from accidental deletion it's just a little button you can hit nice minor little enhancement but may save some people some oops time on there of course you show you to have backups and don't rely on you know just having it there but still it saves you from that whoops uh copy clone vm templates when you're building the vm templates this is kind of cool I like the way that it does this as well so thin or thick provision so that's two different options and it depends on the type of storage repository you're using but you go to advanced now it just tells you now this was not in there before just you had to dig around a little bit to see if it was thicker than provisions so they've added it right there nice little enhancement you know it's a simple thing sometimes and they kind of explain the difference between them proper detection for pv drivers management agent they're now doing clear diff differentiation between management agent and the pv drivers therefore they are now able to detect both so this is when you load the zen tools it's uh has a little bit of a better understanding now this is actually something I like a lot and I'm going to hopefully ask I got to submit probably a request for this or maybe they'll watch the video and notice it they put the ip address next to the interface that's great the only other request I would have is and one I'll show you a couple of examples so when you're in a lot of different areas you can do things like copy to clipboard so this is copy the virtual id to the clipboard a little clipboard icon that shows up all over the place now what I'd like to see is also and we'll go over here like to where they show the network interface when you want to ssh into something you have a lot of them I just copy paste it they actually made it easier to copy and paste because of putting it next to each interface so if there's a list of interfaces you get a list of on there but I'd love the copy button next to it there I could just copy and then paste it right in the terminal when I got a ssh into something especially when I'm building a bunch of lab servers usually set the dhcp so they're gonna go ahead and grab another um ip address out of the pool and it'd be nice to just have that copy button so um because they actually have you can copy right here that would be the uuid for the interface which is also really handy because uuids are really long that's for some advanced uses where you want to apply very specific features at the command line level to any particular uuid which could be like a virtual interface I've got some other videos where I dive into that where I talk about applying parameters to the virtual interface so it's really nice that they have that there but it would be cool if they had that as well open flow rules this is why I was talking about the rules that are gonna be coming for the sdn controller and audit log fingerprints to the cloud this is obviously no audit log just sitting locally is always the best way to check integrity so setting it to the cloud so they will increase the security or in the audit log by providing optional store fingerprints uh to your online zen orcasha.com account this way fingerprints cannot be altered by malicious user locally without triggering us as part of the commercial version of zen orcasha but still you know really cool that they're adding that on there I'm really happy about all those little features because the question that comes up a lot is is this a commercially viable product can it be used in production all you have done tom has shown lab environments and yeah that's because I can't just show you people's production environments all the time obviously besides my own which we do run in production we've put this in production for quite a few clients and consulted with a lot of them on there now a couple other things I'm going to clearly mention on this if you are using this in production and you would like to buy and purchase like a support contract or anything around like that that is completely an option xcpng has and if we look over and look over to their main site so while xcpng is free and open source and that's xcpng.org or g and this is where you download this is where you get the fully open source software this is where you can buy support contracts from them so yes this is a completely commercially supported product that you can get for free and pay for support of that is how they sell their system so you if you wanted to buy fully support and have tickets and things like that or have different options reach out and talk to them they also have their forums and such for giving support they also have the free turn keys and orchestra appliance or different options for doing monthly support packages for zen orchestra as well so just want to make sure you're aware of all the different options are when it comes to supporting zen server if you know how to use it you just want to test it out without any support you can do that if you want to buy a support contract because you're going to deploy it at a large commercial enterprise environment and you go you know i really want to be able to have people to call people to talk to and a support line any you know agreements on this they have those options as well so it's free completely to test out your lab you're completely free to use it as a home user i have videos on how to compile zen orchestra from sources i'll leave links to the lab how to compile from sources all down below in the description so you you know can try it out for yourself and fully try it out no you know no features not included you do get some extra bells whistles and upgrades including some auto deployment options if you do get the paid version there is that because they have the option on the paid version for auto deploying some of the without getting an iso auto deploying virtual machines and things like that there's some add-ons you do get for the paid version but hundred percent everything you can do in terms of like backups and all those other features if you compile from source you can have all of that so go ahead and check out those other videos if you're interested in learning more about zen check out their blog and there's always new updates coming they also have a few conferences and a few details of the future of zen uh which is a highly active developed project with more and more features getting added all the time because i've seen a few people comment that they think zen is dead and zen is far from dead and check out my other videos you want to learn about the history of the project it's actually kind of interesting in a whole structure of how it was built and it's been around longer than you think thanks and thank you for making it to the end of the video if you like this video please give it a thumbs up if you'd like to see more content from the channel hit the subscribe button and hit the bell icon if you like youtube to notify you when new videos come out if you'd like to hire us head over to 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