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LISTSERV Web Interface 16.52020-06-02T12:49:59ZBotero Arias, Robinson2020-05-28T18:19:50+00:002020-05-28T18:19:50+00:00Re: Online Workshop Instructor Signuphttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;dea3c154.20Hi Eve,<br><br>I have assigned the spreadsheet, as a helper! It’s my first experience.<br><br>Thank you<br><br>Robin<br><br>From: UF R Users List <R-USERS-L@LISTS.UFL.EDU> on behalf of "Bohnett,Eve" <evebohnett@UFL.EDU><br>Reply-To: UF R Users List <R-USERS-L@LISTS.UFL.EDU><br>Date: Thursday, May 28, 2020 at 11:29 AM<br>To: "R-USERS-L@LISTS.UFL.EDU" <R-USERS-L@LISTS.UFL.EDU><br>Subject: Re: Online Workshop Instructor Signup<br><br>Great thanks Audrey. I'm so glad you've decided to volunteer again! How nice. [...]Rahmani,Haqiqurahman2020-05-28T17:13:17+00:002020-05-28T17:13:17+00:00Re: Online Workshop Instructor Signuphttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;49f2db45.20Hi Eve,<br><br>I would also like to volunteer in the carpentry workshop, probably as a helper as my first experience.<br><br>Regards,<br>Haqiq Bohnett,Eve2020-05-28T15:27:55+00:002020-05-28T15:27:55+00:00Re: Online Workshop Instructor Signuphttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;66d0e281.20Great thanks Audrey. I'm so glad you've decided to volunteer again! How nice.<br><br>I thought to send this to everyone in this R-users group in case there was interest in knowing a few more details Since now the website has not been officially set up (firstI wanted to see how many people volunteered to teach and help ). Here is some additional info. [...] Smith,Audrey Culver2020-05-28T14:12:01+00:002020-05-28T14:12:01+00:00Re: Online Workshop Instructor Signuphttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;4e756d67.20Hi Eve-<br><br>I am definitely interested in volunteering, most likley as either as a helper or moderator. I'm still not confident in my skills to be an instructor at this time, but I will review the material to see if there is a portion of the workshop that I may be able to cover as instructor. [...] Bohnett,Eve2020-05-28T13:17:43+00:002020-05-28T13:17:43+00:00Re: Online Workshop Instructor Signuphttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;9202c721.20Greetings James,<br><br>Yes, you are welcome to contact me at this email. If you have any questions about volunteering for the UF Carpentries Club, then please let me know.<br><br>Best,<br>Eve Bohnett Colee,James C2020-05-28T13:06:34+00:002020-05-28T13:06:34+00:00Re: Online Workshop Instructor Signuphttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c039dbbe.20Is there any contact information for about volunteering? Bohnett,Eve2020-05-27T21:33:26+00:002020-05-27T21:33:26+00:00Online Workshop Instructor Signuphttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;9e35561d.20Greetings everyone,<br><br>The UF Carpentries Club is hosting an online Zoom workshop for Data Carpentry for Ecology in R specifically limited to IFAS Rec Centers on June 29th and 30th<br><br>We are currently in the process of recruiting helpers and instructors.<br><br>The curriculum will follow the standard data carpentry curriculum with modules, plus some potential extra modules from the NEON website or other Ecology web tutorials. [...] Rahmani,Haqiqurahman2020-05-07T17:15:59+00:002020-05-07T17:15:59+00:00Re: Data Carpentry Online Workshop Instructor Recruitment.https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;e6cdf8cf.20Hi Eve,<br><br>Is there spaces life open in the data carpentry online workshop?<br><br>I would like to participate in the two-day course. Please kindly include me in for this in case there is space or if someone cancels their spot at the last minute.<br><br>Thanks,<br>Haqiq Bohnett,Eve2020-04-17T22:06:07+00:002020-04-17T22:06:07+00:00Data Carpentry Online Workshop Instructor Recruitment.https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;71573280.20Greetings everyone,<br><br>The UF Carpentries Club is hosting an online Zoom workshop: Geospatial meets NEON on May 18th-19th.<br><br>We are currently in the process of recruiting helpers and instructors.<br><br>The curriculum will follow the standard data carpentry curriculum with modules for Introduction to Geospatial Raster and Vector Data with R. https://urldefense.proofpoint.com/v2/url?u=https-3A__datacarpentry.org_r-2Draster-2Dvector-2Dgeospatial_&d=DwIFAw&c=sJ6xIWYx-zLMB3EPkvcnVg&r=DuhgWCeXalOWlep4QHjULlX1EKUvc1kolmPuGxHK4VU&m=MWLJNK88wjwG6j3Lsu2ysQkyM2miliAxv1IwenTTTNM&s=VtfgXU4T2oR_D3i-tsIP6RRc8sH-2sZe4JeQQO3LNEI&e=<br>The workshop will also host NEON representative, Felipe Sanchez, who is going to introduce downloading and working with NEON data. [...] Kathe Todd-Brown2020-04-14T14:53:22-04:002020-04-14T14:53:22-04:00Summer undergraduate research positionhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;f46e0840.20I have a summer position available for UF undergraduates in my lab. The research relies heavily on R as the primary tool to investigate carbon cycling in northern latitudes. Here is a link with some more details (I’m also looking for a PhD student on more general computational biogeochemistry):<br><br>https://urldefense.proofpoint.com/v2/url?u=http-3A__ktoddbrown.github.io_openpositions.html&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=DuhgWCeXalOWlep4QHjULlX1EKUvc1kolmPuGxHK4VU&m=8dj1PocG4WTTuxw5VY1yHtfmHVO-a5TKkn9R9n2coSU&s=O3OuLTM2ukNgLqsCS8gW5GwCS0OmVwjoXc2tnHGjWP0&e=<br><br>Feel free to forward this to anyone you think might be interested!<br>Best,<br>-Kathe [...]Maxwell,Daniel2020-04-09T19:19:51+00:002020-04-09T19:19:51+00:00Re: undergraduate internship using Rhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;f877653f.20Mark - will keep my eyes and ears open!<br><br>Dan<br><br>From: UF R Users List <R-USERS-L@LISTS.UFL.EDU> On Behalf Of Girson,Mark A<br>Sent: Thursday, April 9, 2020 12:45 PM<br>To: R-USERS-L@LISTS.UFL.EDU<br>Subject: undergraduate internship using R<br><br>Hello,<br><br>The UF Bureau of Economic and Business Research is seeking an undergraduate intern for a remote summer internship. Please see the attached document for details. Send me your resume if interested in applying. [...] Girson,Mark A2020-04-09T16:44:48+00:002020-04-09T16:44:48+00:00undergraduate internship using Rhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;2ca9ca11.20Hello,<br><br>The UF Bureau of Economic and Business Research is seeking an undergraduate intern for a remote summer internship. Please see the attached document for details. Send me your resume if interested in applying.<br><br>Thank you.<br><br>Mark Girson<br>Special Projects Coordinator<br>Bureau of Economic and Business Research<br>University of Florida<br>352-392-2908 x 114<br><br>This list strives to be beginner friendly. However, we still ask that you<br>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html<br>and provide commented, minimal, self-contained, reproducible code. Sinha,Puja2020-03-03T14:02:40+00:002020-03-03T14:02:40+00:00Re: Need assistance in plotting values in ggplot2https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;2c858b37.20Hi Joe,<br><br>Yes, these are transcription factors and the values are the enrichment score.<br><br>From: UF R Users List <R-USERS-L@LISTS.UFL.EDU> On Behalf Of Wu,Zhuoxi<br>Sent: Monday, March 02, 2020 5:30 PM<br>To: R-USERS-L@LISTS.UFL.EDU<br>Subject: Re: Need assistance in plotting values in ggplot2<br><br>Hi Puja -<br><br>So the entries under column TF - are these transcription factors? Just trying to understand what you are measuring. [...]Wu,Zhuoxi2020-03-02T22:30:10+00:002020-03-02T22:30:10+00:00Re: Need assistance in plotting values in ggplot2https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;945d6a10.20Hi Puja -<br><br>So the entries under column TF - are these transcription factors? Just trying to understand what you are measuring.<br><br>On Mar 2, 2020, at 3:32 PM, Toh,Kok Ben <kokbent@ufl.edu> wrote:<br><br><br>Computer sees 1e-1000 as exact zero so it really doesn’t matter how you transform your scale… to computer log(1e-1000) = log(0) = -Inf [...]Klarenberg,Geraldine2020-03-02T21:10:11+00:002020-03-02T21:10:11+00:00Tidy Tuesday - tomorrow!https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;226fae58.20Below a message from R-Ladies Gainesville:<br><br>Practice your data wrangling and visualization R skills with other members of R-Ladies! Tidy Tuesdays are designed by the R for Data Science Online Learning Community to help R users learn in a fun and real-world context. Every Tuesday a new data set is released and we practice tidying and visualizing data, mostly using tidyverse packages. [...] Toh,Kok Ben2020-03-02T20:35:04+00:002020-03-02T20:35:04+00:00Re: Solve and plot implicit function in Rhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;b5391017.20That’s because fct(12,…) is NaN. You need to set the upper bound of t such that fct(t,…) won’t return NA or NaN.<br><br>Also I’m not sure what you’re trying to achieve here but uniroots require you to provide a lower bound of x such that f(x) is negative and an upper bound of x such that f(x) is positive. It can be the other way round, but the idea is that the interval has to contain f(x) = 0. Your current interval doesn’t contain f(x) = 0. [...]Toh,Kok Ben2020-03-02T20:32:13+00:002020-03-02T20:32:13+00:00Re: Need assistance in plotting values in ggplot2https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;5a9a93c6.20Computer sees 1e-1000 as exact zero so it really doesn’t matter how you transform your scale… to computer log(1e-1000) = log(0) = -Inf<br><br>You will have to do it manually, i.e. log with base 10 of 1e-1234 is -1234.<br><br>From: UF R Users List <R-USERS-L@LISTS.UFL.EDU> On Behalf Of Sinha,Puja<br>Sent: Monday, March 2, 2020 3:03 PM<br>To: R-USERS-L@LISTS.UFL.EDU<br>Subject: Re: Need assistance in plotting values in ggplot2 [...]Sinha,Puja2020-03-02T20:02:30+00:002020-03-02T20:02:30+00:00Re: Need assistance in plotting values in ggplot2https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;3fadadfd.20Hi Ben,<br><br>I agree with your log transformation step and I was trying to do so but not successful as I am not able to figure out whether to use this scale_y_log10() or scale_y_continuous() in the code.<br><br>Hoping for the solution.<br><br>Thanks,<br>Puja<br><br>From: UF R Users List <R-USERS-L@LISTS.UFL.EDU> On Behalf Of Toh,Kok Ben<br>Sent: Monday, March 02, 2020 1:44 PM<br>To: R-USERS-L@LISTS.UFL.EDU<br>Subject: Re: Need assistance in plotting values in ggplot2 [...]Nicolas,Floyid2020-03-02T19:26:08+00:002020-03-02T19:26:08+00:00Re: Solve and plot implicit function in Rhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;fc0aedc9.20Hi everyone,<br><br>I am back with my issues since I have been trying to get a solution to go forward.<br>Solving for t, I rewrite the equation and use uniroot function I get a bunch of NA values.<br>Here are my lines of code:<br>rm(list = ls())<br>#soil parameters<br>Ks= 17000;<br>Beta= 1.3;<br># Eta= 4.5;<br>Eta= 4;<br>Theta_s= 0.33;<br>Theta_r= 0.03;<br>Psi_Water= -300;<br># Psi_Water = 80<br>Delta=Eta/Beta [...]Toh,Kok Ben2020-03-02T18:43:39+00:002020-03-02T18:43:39+00:00Re: Need assistance in plotting values in ggplot2https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;fd7598f0.20Hi Puja,<br><br>I’m not sure what kind of data you’re dealing with that goes so small and still quantifiable. I just tested it out in my R console, R (and computer in general) reads any number that is smaller than 1e-334 as zero. Therefore R would think you want it to plot a range of zeroes with some other very small number. Additionally, plotting your range of values on a linear scale does not make any sense, it’s like plotting 1, 10 and 100000. You might want to consider log transformation. [...]Sinha,Puja2020-02-28T16:47:31+00:002020-02-28T16:47:31+00:00Need assistance in plotting values in ggplot2https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;74e91b60.20Hi All,<br><br>I have the data in the following format:<br>TF<br><br>YT_YC<br><br>MT_MC<br><br>AT_AC<br><br>GRHL2<br><br>1e-2597<br><br>1e-2789<br><br>1e-281<br><br>Srebp1a<br><br>1e-1860<br><br>1e-1744<br><br>1e-944<br><br>EWS:ERG<br><br>1e-1831<br><br>1e-2127<br><br>1e-548<br><br>I am trying to make geom_tile in ggplot but after plotting there is no difference in gradient of colors may be because my values are very small ranging from (1.e-3700 to 0.01). I tried to use limits and breaks but it doesn't work. Can anyone suggest me which function I should use to plot these values. The code is below:<br>mat_data1 %>%<br>pivot_longer(<br>cols = c("YT_YC", "MT_MC", "AT_AC"),<br>names_to = "Age_group",<br>values_to = "Value"<br> [...] Klarenberg,Geraldine2020-02-27T13:24:07+00:002020-02-27T13:24:07+00:00Re: Solve and plot implicit function in Rhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c864eda9.20Your function is defined as only taking the argument t as input. In the parentheses after "function" you need to list *all* the input variables for your function.<br><br>I also don't see anywhere where you're defining the values for t.<br><br>Geraldine<br><br>On Feb 27, 2020 00:13, "Nicolas,Floyid" <floyid.nicolas@UFL.EDU> wrote:<br><br>Dear Geraldine,<br><br>Thank you for your reply. The error is the following: [...]Nicolas,Floyid2020-02-27T05:12:39+00:002020-02-27T05:12:39+00:00Re: Solve and plot implicit function in Rhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;ed58237.20Dear Geraldine,<br>Thank you for your reply. The error is the following:<br>Error in fct(Tp, EC50, p, Psi_Root, b, Ks, Eta, Theta_s, Theta_r, Psi_Water, :<br>unused arguments (EC50, p, Psi_Root, b, Ks, Eta, Theta_s, Theta_r, Psi_Water, gamma, I[j], EC[i], t)<br>But when I take, out the unused arguments from the function I still get error and can’t figure it out. [...]Klarenberg,Geraldine2020-02-27T04:59:44+00:002020-02-27T04:59:44+00:00Re: Solve and plot implicit function in Rhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c3bc58b5.20Since you haven't indicated what the error messages are that you are getting, it's hard to troubleshoot.<br>However, I'd like to offer an observation: you're looping over the length of EC with index i, and over I with index j - but in the function in the loop you're indexing EC with j and I with i. That might be causing an issue?<br>But please share the error messages so we have an idea of the problem. [...]Nicolas,Floyid2020-02-27T04:31:03+00:002020-02-27T04:31:03+00:00Solve and plot implicit function in Rhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;b661e631.20Here are the equation and my lines of codes.<br>I am trying to solve that equation below (see image) for “t” in R but got stuck in the scripts. I tried some functions such as uniroot, optim and optimize but could still get something. Any help is welcome.<br><br>[cid:image001.png@01D5ECE3.A9A93E30]<br><br>#soil parameters<br>Ks= 17000;<br>Beta= 1.3;<br>Eta= 4.5;<br>Theta_s= 0.33;<br>Theta_r= 0.03;<br>Psi_Water= -80;<br>Delta=Eta/Beta [...]Yawo Kokuvi2020-02-20T11:22:03-05:002020-02-20T11:22:03-05:00Re: Crosstabs - More than 2 Variableshttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;a5266c06.20Thanks so much -- it worked.<br><br>I will follow the examples in the blog to change the color of the bars ...<br><br>best - cY<br><br>On Thu, Feb 20, 2020 at 11:04 AM Krenz,Till <till.krenz@ufl.edu> wrote:<br><br>> Hi Yawo,<br>><br>><br>><br>> substituting that line with<br>><br>><br>><br>> geom_bar(aes(y = ..prop.., group = Animal), position = "dodge") +<br>><br>><br>><br>> will plot the bars as proportions within each animal group.<br>><br>><br>><br>> The whole thing would look like this:<br>><br>><br>><br>> CatsDogs %>%<br>><br>> haven::as_factor() %>%<br>><br>> ggplot(aes(Dance, fill [...]Krenz,Till2020-02-20T16:04:26+00:002020-02-20T16:04:26+00:00Re: Crosstabs - More than 2 Variableshttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;915a70e.20Hi Yawo,<br><br>substituting that line with<br><br>geom_bar(aes(y = ..prop.., group = Animal), position = "dodge") +<br><br>will plot the bars as proportions within each animal group.<br><br>The whole thing would look like this:<br><br>CatsDogs %>%<br>haven::as_factor() %>%<br>ggplot(aes(Dance, fill = Training)) +<br>geom_bar(aes(y = ..prop.., group = Animal), position = "dodge") +<br>ylab("Proportion") +<br>facet_wrap(~Animal)<br><br>If you’d rather have the values shown as Percent, the following example does a good job at that. [...]Yawo Kokuvi2020-02-20T08:49:57-05:002020-02-20T08:49:57-05:00Re: Crosstabs - More than 2 Variableshttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;67f4ce9e.20Thanks so much, Mr. Till.<br>I implemented the tidyverse solution you suggested using ggplot, all worked<br>well for the percent counts, the only issue is that this command:<br><br>* geom_bar(aes(y = (..count..)/sum(..count..)), position = "dodge") + *<br><br>is giving total percents, instead of the percents over column variables. I<br>suspect it has to do with the count function ... can it be changed? I am<br>looking also. [...]Klarenberg,Geraldine2020-02-18T14:46:04+00:002020-02-18T14:46:04+00:00R-Ladies Tidy Tuesdays [TODAY]https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;ab15d365.20Practice your data wrangling and visualization R skills with other members of R-Ladies! Tidy Tuesdays are designed by the R for Data Science Online Learning Community to help R users learn in a fun and real-world context. Everyone is welcome.<br><br>Read more about Tidy Tuesdays here: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.tidytuesday.com_&d=DwIFAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=DuhgWCeXalOWlep4QHjULlX1EKUvc1kolmPuGxHK4VU&m=-_vFKl0WPYaaFBNDqXJwPVL09cDtUMzo3pT5S7NtUBg&s=Wro-3-ECPet1q02EHN27NPyUqTn8m7iKhAljSON6UxI&e=<br><br>Join us at the UF Biodiversity Institute / UF Informatics Institute during lunch to work on the Tidy Tuesday challenge as a group. Food will not be provided, but you are welcome to bring your own. Please bring your laptop. These events will supplement, not replace, our monthly meetings. Hope to see you [...] Krenz,Till2020-02-17T23:05:56+00:002020-02-17T23:05:56+00:00Re: Crosstabs - More than 2 Variableshttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;895f5ae1.20Hi Yawo,<br><br>let me suggest a [tidyverse](https://urldefense.proofpoint.com/v2/url?u=http-3A__www.tidyverse.org&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=DuhgWCeXalOWlep4QHjULlX1EKUvc1kolmPuGxHK4VU&m=wMyhh_b6N4wBwS02IzsfPTscgE5yQqfdTwnlF-m2Ry4&s=UFTzBNsz0NSG1xFo9Folx_v97qwejBIOZufZqkQqByc&e= ) approach for this. As I can<br>see from your `dput()` output you are using the haven package, which means<br>you are at least with one foot in the tidyverse already.<br><br>Before creating any outputs from the data, you probably<br>read in with a command from the haven library, you want to apply the<br>`as_factor()` command from the same library to your data, in order to<br>turn the labelled data into factors and thusly being able to create<br>tables and plots with human readable labels instead of zeros and ones. [...]Toh,Kok Ben2020-02-17T22:49:47+00:002020-02-17T22:49:47+00:00Re: Crosstabs - More than 2 Variableshttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;df8310b8.20You can use the prop.table function:<br>tmp <- table(df[,c("Dance", "Training", "Animal")])<br>prop.table(tmp)<br><br>If you check the function the second argument sets the margin; say if you want to calculate the % based on a type of animal instead of across all cell-table, then since animal is third column of the table input,<br>prop.table(tmp, margin = 3) [...]Yawo Kokuvi2020-02-17T14:14:12-05:002020-02-17T14:14:12-05:00Re: Crosstabs - More than 2 Variableshttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;e84b6fe1.20Thanks so much for this -<br><br>is there any way to amend this table command/function to produce column and<br>row percentages, as well as the row/column marginals?<br><br>wih much appreciation.<br><br>best - Yawo<br><br>On Mon, Feb 17, 2020 at 2:10 PM Toh,Kok Ben <kokbent@ufl.edu> wrote:<br><br>> I tried reading through the CrossTable function I don’t think it allows<br>> crosstab of more than two variables. Here’s an alternative:<br>><br>><br>><br>> df <- data.frame(<br>><br>> Animal = rbinom(20, 1, 0.5),<br>><br>> Training = rbinom(20, 1,.5),<br>><br>> Dance = rbinom(20, 1,.5)<br>><br>> )<br>><br>><br>><br> [...]Toh,Kok Ben2020-02-17T19:10:14+00:002020-02-17T19:10:14+00:00Re: Crosstabs - More than 2 Variableshttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;f2289921.20I tried reading through the CrossTable function I don’t think it allows crosstab of more than two variables. Here’s an alternative:<br><br>df <- data.frame(<br>Animal = rbinom(20, 1, 0.5),<br>Training = rbinom(20, 1,.5),<br>Dance = rbinom(20, 1,.5)<br>)<br><br>table(df[,c("Dance", "Training", "Animal")])<br><br>Cheers,<br>Ben<br><br>From: UF R Users List <R-USERS-L@LISTS.UFL.EDU> On Behalf Of Yawo Kokuvi<br>Sent: Saturday, February 15, 2020 1:27 PM<br>To: R-USERS-L@LISTS.UFL.EDU<br>Subject: Crosstabs - More than 2 Variables [...]Yawo Kokuvi2020-02-15T13:27:09-05:002020-02-15T13:27:09-05:00Crosstabs - More than 2 Variableshttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;d55f88d2.20Hello<br><br>Good evening folks.<br><br>I am trying to run a crosstabulation between two variables, but controlling<br>for a 3rd one, and then draw a bar chart (vertical / horizontal) to display<br>the results.<br><br>I am using a CrossTable function (part of the gmodels package) and so far,<br>I am only able to do handle the main effects without the elaborated<br>variable, using the following command [...]Nicolas,Floyid2020-02-13T21:04:26+00:002020-02-13T21:04:26+00:00Re: Initial guess for non linear modelhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;da3d3fbf.20Thank you Ben. You explain everything I could not understand.<br><br>Floyid Nicolas<br>Master Student<br>Depart. of Agricultural and Biological Engineering<br>University of Florida<br>1741 Museum Rd, Gainesville, FL 32603|Office 141<br>+1 (352)-204-6156| floyid.nicolas@ufl.edu<br><br>On 2/12/20, 2:12 PM, "UF R Users List on behalf of Ben Bolker" <R-USERS-L@LISTS.UFL.EDU on behalf of bbolker@GMAIL.COM> wrote:<br><br>[External Email]<br><br>These problems are usually a combination of trial and<br>error/knowing enough about the shape of the function being fitted and<br>how the parameters relate to the characteristics of the curve. [...]Toh,Kok Ben2020-02-13T02:44:45+00:002020-02-13T02:44:45+00:00FW: Invitation to 2020 Southeast SACNAS Regional Conferencehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;822c2502.20Hi everyone,<br><br>One of our group member wants to share this event with you.<br><br>Cheers,<br>Ben<br><br>Greetings!<br><br>The UF chapter of the Society for the Advancement of Chicanos/Hispanics and Native Americans in Science invites the UF Informatics Institute to participate in the inaugural 2020 Southeast SACNAS Regional Meeting! Our program features keynote speakers representing various professional backgrounds in STEM, oral and poster presentations and awards, networking events and workshops, graduate program recruitment booths, and more. The conference aims to help students from diverse backgrounds, disciplines, and universities develop their presentations skills, learn about career opportunities, and build professional networks. [...] Ben Bolker2020-02-12T17:11:35-05:002020-02-12T17:11:35-05:00Re: Initial guess for non linear modelhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;a1094b22.20These problems are usually a combination of trial and<br>error/knowing enough about the shape of the function being fitted and<br>how the parameters relate to the characteristics of the curve.<br><br>## define function<br>Richards <- function (time, Vi, Vf, u, n) {<br>(Vi*Vf)/((Vi^n)+((Vf^n-(Vi^n))*exp(-u*time)))^(1/n)}<br><br>## explore function: plot curve, compare with logistic, look at<br>effects of shape parameter n<br>curve(Richards(x,Vi=20,Vf=260,u=1/20,n=1),from=0,to=500, ylim=c(0,280))<br>abline(h=c(20,260),lty=2) ## Vi/Vf are starting point/asymptote<br>## compare with logistic<br>## Vi -> location by guess<br>curve(260*plogis(x,location=50,scale=20),col="red",add=TRUE)<br>## change shape - Vi/Vf unmodified ... location and shape both change<br>curve(Richards(x,Vi=20,Vf=260,u=1/20,n=5),add=TRUE,col="blue") [...]Nicolas,Floyid2020-02-12T17:45:24+00:002020-02-12T17:45:24+00:00Re: Initial guess for non linear modelhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;8bd0c2a5.20Hi James,<br><br>I tried the minpack.lm function and I still can’t figure it out.<br><br>Is there any package that helps to do a better guess of the initial value?<br><br>Floyid Nicolas<br>Master Student<br>Depart. of Agricultural and Biological Engineering<br>University of Florida<br>1741 Museum Rd, Gainesville, FL 32603|Office 141<br>+1 (352)-204-6156| floyid.nicolas@ufl.edu<mailto:floyid.nicolas@ufl.edu><br><br>From: UF R Users List <R-USERS-L@LISTS.UFL.EDU> on behalf of "Martin,James L,III" <jamesmartin@UFL.EDU><br>Reply-To: UF R Users List <R-USERS-L@LISTS.UFL.EDU><br>Date: Wednesday, February 12, 2020 at 9:14 AM<br>To: "R-USERS-L@LISTS.UFL.EDU" <R-USERS-L@LISTS.UFL.EDU><br>Subject: Re: Initial guess for non linear model [...]Nicolas,Floyid2020-02-12T17:14:35+00:002020-02-12T17:14:35+00:00Re: Initial guess for non linear modelhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;22209b3a.20The data is the following:<br>dat1<br>time Volume<br>3 12<br>6 25<br>9 38<br>12 53<br>15 73<br>21 108<br>27 136<br>33 160<br>39 180<br>48 202<br>60 222<br>72 241<br>96 255<br><br>Floyid Nicolas<br>Master Student<br>Depart. of Agricultural and Biological Engineering<br>University of Florida<br>1741 Museum Rd, Gainesville, FL 32603|Office 141<br>+1 (352)-204-6156| floyid.nicolas@ufl.edu<br><br>On 2/12/20, 9:11 AM, "UF R Users List on behalf of Ben Bolker" <R-USERS-L@LISTS.UFL.EDU on behalf of bbolker@GMAIL.COM> wrote: [...]Martin,James L,III2020-02-12T17:12:46+00:002020-02-12T17:12:46+00:00Re: Initial guess for non linear modelhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;7013da3e.20Hi Floyid,<br><br>I usually try generating a scatter plot, then I'll play with the values of the parameters, plotting the resulting lines over the scatter plot each time until the curve fits the points some what closely. Your parameter starting values are probably off by a bit and if you try plotting the line it might not even show. It takes some messing around. [...] Ben Bolker2020-02-12T12:10:28-05:002020-02-12T12:10:28-05:00Re: Initial guess for non linear modelhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;1734a316.20Not sure about this richards model parameterization: I think Vf =<br>asymptotic value, u=initial rate of increase, n = shape, Vi= initial<br>value? n<0 (and Vi, Vf<0) are unusual in my experience, but maybe<br>you're modelling something different? If I'm right about the<br>parameterization you can often get Vi from first (or mean of the first<br>few) values, Vf from the last (or mean of the last few) values, u from<br>a log-linear regression on the first few values; I would set n=1 as a<br>starting value. What do your data look like? [...]Nicolas,Floyid2020-02-12T17:00:48+00:002020-02-12T17:00:48+00:00Initial guess for non linear modelhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;680c1c12.20Hi everyone,<br><br>I am trying to fit this Richards model but I am having a hard time with the initial guess.<br>Below are the function and the errors I got.<br><br>Richards <- function (time, Vi, Vf, u, n) {(Vi*Vf)/((Vi^n)+((Vf^n-(Vi^n))*exp(-u*time)))^(1/n)}<br>> Richards <- nls(Volume~Richards(time, Vi, Vf, u, n), data=dat1,start = c(Vi=-24,Vf=-200, u=.90, n=-10))<br>Error in numericDeriv(form[[3L]], names(ind), env) :<br>Missing value or an infinity produced when evaluating the model [...]Klarenberg,Geraldine2020-01-31T13:06:55+00:002020-01-31T13:06:55+00:00Re: Implicite equations in R - helphttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;24277e8e.20Floyid, FYI, when I run<br><br>Equation_12a(I=I[i], EC=EC[j], Ti[i], Tp=Tp,<br>EC50=EC50, p=p, Psi_Root=Psi_Root,<br>b=b, Ks=Ks, Eta=Eta, Theta_s=Theta_s,<br>Theta_r=Theta_r, Psi_Water=Psi_Water, gamma=gamma)<br><br>I get a result (not sure if it’s the result you want, but it works).<br>Running it inside uniroot() gives some issues though. I’m not familiar with this function, but it needs more arguments apparently. (Do ?uniroot in the console to see the help file that specifies the arguments).. [...]Klarenberg,Geraldine2020-01-31T05:43:48+00:002020-01-31T05:43:48+00:00Re: Implicite equations in R - helphttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;8d39d83d.20After you create the function Equation_12a, when you call it, you have to specify the arguments - in this case, since EC and I are in the loop, I’m pretty sure you need to specify I=i, EC=j. Probably also Ti[I]. Because from looking at the function, I don’t think you can use vectors in those calculations (didn’t have much time to check carefully though).<br>And I think got the function uniroot(), you also need to define an interval. (Check the help file that shows what arguments go in the function). [...]Nicolas,Floyid2020-01-31T04:15:58+00:002020-01-31T04:15:58+00:00Re: Implicite equations in R - helphttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;bc382012.20It gives me that as error:<br><br>Error in f(lower, ...) : argument "I" is missing, with no default<br><br>Floyid Nicolas<br>Master Student<br>Depart. of Agricultural and Biological Engineering<br>University of Florida<br>1741 Museum Rd, Gainesville, FL 32603|Office 141<br>+1 (352)-204-6156| floyid.nicolas@ufl.edu<mailto:floyid.nicolas@ufl.edu><br><br>From: UF R Users List <R-USERS-L@LISTS.UFL.EDU> on behalf of "Klarenberg,Geraldine" <gklarenberg@UFL.EDU><br>Reply-To: UF R Users List <R-USERS-L@LISTS.UFL.EDU><br>Date: Thursday, January 30, 2020 at 8:12 PM<br>To: "R-USERS-L@LISTS.UFL.EDU" <R-USERS-L@LISTS.UFL.EDU><br>Subject: Re: Implicite equations in R - help [...]Klarenberg,Geraldine2020-01-31T04:12:21+00:002020-01-31T04:12:21+00:00Re: Implicite equations in R - helphttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;6ca1fa8b.20Could you let us know what errors or warnings you're getting?<br><br>Geraldine<br><br>On Jan 30, 2020 22:09, "Nicolas,Floyid" <floyid.nicolas@UFL.EDU> wrote:<br>Hello,<br><br>I am trying to resolve this implicit equation in R with T as the only unknown parameter. I created a function and use uniroot to get the solution, I could not get the codes working. Does someone have any idea on how to solve this please?<br>This script that I tried : [...] Nicolas,Floyid2020-01-31T03:08:31+00:002020-01-31T03:08:31+00:00Implicite equations in R - helphttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;5259b3e.20Hello,<br><br>I am trying to resolve this implicit equation in R with T as the only unknown parameter. I created a function and use uniroot to get the solution, I could not get the codes working. Does someone have any idea on how to solve this please?<br>This script that I tried : [...]Bohnett,Eve2020-01-28T20:58:21+00:002020-01-28T20:58:21+00:00UF Carpentries Club Spring Socialhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;4301f353.20Hello,<br><br>On January 29, the UF Carpentries Club is hosting a spring social at the UF Informatics/Biodiversity Institute<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.google.com_maps_place_University-2Bof-2BFlorida-2BInformatics-2BInstitute_-4029.6483302-2C-2D82.3464802-2C17z_data-3D-213m1-214b1-214m5-213m4-211s0x88e8a39d48bf22b3-3A0xebce44d3b6d7530-218m2-213d29.6483256-214d-2D82.3442915&d=DwMFAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=CiNvPnxpyXzm3hjY-tTpoAO4rVu2ODiwimxRrSmk3fVo-8UM-EPU64LUYF-jm75s&m=OI-TcRIeEQw9pEx-KNDnayVvQtPznRHxUbXVx-dK5Nw&s=5r-g64R-SPxVXKDnxLA6b4GnQomJHK4njRdW45pC0uo&e=> from 11:30 AM - 1:30 PM. This is a free, informal, come-and-go event, and we'll have pizza!<br><br>In case you are not familiar with us, we run workshops to help members of the UF community learn basic software, computer programming, data management, and data analysis skills. (In spite of our name, we don't teach woodworking.) [...] Nicolas,Floyid2020-01-20T19:55:17+00:002020-01-20T19:55:17+00:00Re: Multiple datasetshttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;53c5db22.20Thank you, I’ll try it out.<br><br>Floyid<br><br>From: UF R Users List <R-USERS-L@LISTS.UFL.EDU> on behalf of "Klarenberg,Geraldine" <gklarenberg@UFL.EDU><br>Reply-To: UF R Users List <R-USERS-L@LISTS.UFL.EDU><br>Date: Sunday, January 19, 2020 at 10:14 PM<br>To: "R-USERS-L@LISTS.UFL.EDU" <R-USERS-L@LISTS.UFL.EDU><br>Subject: Re: Multiple datasets<br><br>I'm not sure if this is exactly what you need but with<br><br>matrix(rnorm(1000*5, 10, 2), ncol = 5)<br><br>you get a matrix with 5 columns (your observations) and 1000 draws from rnorm().<br>(Adjusted from https://urldefense.proofpoint.com/v2/url?u=https-3A__clayford.github.io_dwir_dwr-5F12-5Fgenerating-5Fdata.html&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=DuhgWCeXalOWlep4QHjULlX1EKUvc1kolmPuGxHK4VU&m=DHzaBeaY35S9KDzHQBXVzl-Z3yqrcDKnzi41U2x7K5g&s=AcyWQmWcMaKcapqh0wg2mQArvUzIFWTdRWy_pHSIdYE&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__clayford.github.io_dwir_dwr-5F12-5Fgenerating-5Fdata.html&d=DwQGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=DuhgWCeXalOWlep4QHjULlX1EKUvc1kolmPuGxHK4VU&m=1zrwt_mBNV8b4ZBmUaPuLrCED15tnYW2Iqwl4TmRzNg&s=gaWEkVstRdFCFNc7FV5gIa-bFnOzwlnS4lkWx1QHhJA&e=>) [...]Klarenberg,Geraldine2020-01-20T06:14:33+00:002020-01-20T06:14:33+00:00Re: Multiple datasetshttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;ab269fdc.20I'm not sure if this is exactly what you need but with<br><br>matrix(rnorm(1000*5, 10, 2), ncol = 5)<br><br>you get a matrix with 5 columns (your observations) and 1000 draws from rnorm().<br>(Adjusted from https://urldefense.proofpoint.com/v2/url?u=https-3A__clayford.github.io_dwir_dwr-5F12-5Fgenerating-5Fdata.html&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=DuhgWCeXalOWlep4QHjULlX1EKUvc1kolmPuGxHK4VU&m=1zrwt_mBNV8b4ZBmUaPuLrCED15tnYW2Iqwl4TmRzNg&s=gaWEkVstRdFCFNc7FV5gIa-bFnOzwlnS4lkWx1QHhJA&e= )<br><br>Geraldine<br><br>On Jan 20, 2020 00:38, "Nicolas,Floyid" <floyid.nicolas@UFL.EDU> wrote:<br><br>Hi all,<br><br>How can I create 1000 datasets of 5 observations each using the rnorm function with a mean of 10 and standard deviation of 2. [...]Nicolas,Floyid2020-01-20T05:38:22+00:002020-01-20T05:38:22+00:00Multiple datasetshttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;6b98a500.20Hi all,<br><br>How can I create 1000 datasets of 5 observations each using the rnorm function with a mean of 10 and standard deviation of 2.<br><br>Thanks in advance for your help.<br><br>Floyid<br><br>This list strives to be beginner friendly. However, we still ask that you<br>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html<br>and provide commented, minimal, self-contained, reproBohnett,Eve2020-01-18T16:04:06+00:002020-01-18T16:04:06+00:00Data Carpentry for Social Sciences - Carpentries Instructor Recruitmenthttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;66921619.20Greetings everyone,<br><br>The UF carpentries club is hosting an "Data Carpentry for Social Sciences" workshop Feb 10-11th.<br><br>We are currently in the process of recruiting helpers and instructors. The curriculum will follow the standard curriculum with modules for Excel, OpenRefine, R, and SQL. If you would like to teach a module about excel, sql or openrefine then you do not need to have experience with R to teach those lessons. [...] Klarenberg,Geraldine2020-01-17T01:27:36+00:002020-01-17T01:27:36+00:00Re: R meetuphttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;827bb04d.20Hi<br><br>Right now there is nothing happening, but we’re trying to get something started this semester. It will be announced on this listserv if something is organized.<br>If there are any volunteers interested in helping out occasionally, let me know!<br><br>Kind regards<br><br>Geraldine Klarenberg, PhD<br>Lecturer - Quantitative Data Science<br>UF/IFAS School of Forest Resources and Conservation<br>430 McCarty Hall C, PO Box 110410, Gainesville, FL 32611-0410<br>University of Florida<br>Tel: 352-273-0792<br>Email: gklarenberg@ufl.edu<mailto:gklarenberg@ufl.edu> [...]Sinha,Puja2020-01-13T16:51:48+00:002020-01-13T16:51:48+00:00R meetuphttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;2a859382.20Hi,<br><br>Just wanted to know is there any R meetup going this week or anytime.<br><br>Thanks,<br><br>Puja<br><br>This list strives to be beginner friendly. However, we still ask that you<br>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html<br>and provide commented, minimal, self-contained, reproducible code.