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R-USERS-L List Archives2020-09-28T06:57:48ZPowered by L-Soft's LISTSERV mailing list manager
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http://www.lsoft.com/images/listserv_small.gifIntro to Program R Workshop
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;607a2c3f.20
The UF Carpentries Club is offering a two-day Intro to Program R workshop<https://urldefense.proofpoint.com/v2/url?u=https-3A__uf-2Dcarpentry.github.io_2020-2D09-2D28-2DIntro-5Fto-5FR_&d=DwIFAw&c=sJ6xIWYx-zLMB3EPkvcnVg&r=DuhgWCeXalOWlep4QHjULlX1EKUvc1kolmPuGxHK4VU&m=zFeqSJPecodiY1AIcRDNqNiyrs7tojOoBulC0Vj29Sc&s=kpxT9b9df2dulFioHW2pQPW8Pk3L40SGUQvHZw-bhXM&e= > Monday-Tuesday, Sept 28th-29th, 2020, to help the new graduates and even undergraduate students in learning program R.<br><br>Need to learn some programming for a class? Want to collaborate effectively with your peers? We were there once too. Come start learning with us. [...]
2020-09-23T03:12:42+00:00Bohnett,Evehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;607a2c3f.20Fall course advertisement and resources
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;fd3430f9.20
Hi everyone,<br><br>Hope you’re ready for the Fall semester! For those of us who are looking to learn the foundation of statistics with focus on R, check out the following course. Also, here’s a very useful shiny app compilation of stats courses in UF: https://urldefense.proofpoint.com/v2/url?u=https-3A__ufstatscourses.shinyapps.io_shiny-5Ftutorial_&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=DuhgWCeXalOWlep4QHjULlX1EKUvc1kolmPuGxHK4VU&m=yO6VRPkNy4CYRTvQC_buxDRT0_E9syBm-OFT1Dm3yVY&s=zC80VQX1iPKrG8T_QsmqW1e5kH4Hgpq_aYqKtT6SFWw&e= .<br><br>Fall 2020 ABE 6933 section PROB, periods T6, R6-7, 100% web [...]
2020-08-24T20:19:53+00:00Toh,Kok Benhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;fd3430f9.20Re: adding shaded standard deviation to lines plotted in ggplot2 for multiple variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;155f6c5b.20
Thank you! I was able to make it! ?? ??<br><br>Bests<br>Hang
2020-08-04T15:18:00+00:00Duong,Hang Thttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;155f6c5b.20Re: adding shaded standard deviation to lines plotted in ggplot2 for multiple variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;7a30109b.20
You should be able to remove (unsubscribe) yourself here:<br>https://lists.ufl.edu/cgi-bin/wa?A0=R-USERS-L<br><br>On 8/3/20 6:58 PM, Idrisi, Nasseer@Wildlife wrote:<br>><br>> Please remove me from the list-serv.<br>><br>> Thanks, Nasseer<br>><br>> *From:* UF R Users List <R-USERS-L@LISTS.UFL.EDU> *On Behalf Of<br>> *Duong,Hang T<br>> *Sent:* Monday, August 3, 2020 1:27 PM<br>> *To:* R-USERS-L@LISTS.UFL.EDU<br>> *Subject:* adding shaded standard deviation to lines plotted in<br>> ggplot2 for multiple variables<br>><br>> *Warning:*This email originated from outside of CDFW and should be<br>> treated with extra caution.<br>><br>> Hi everyone,<br>><br>> I have a data set like this:<br> [...]
2020-08-03T19:01:02-04:00Ben Bolkerhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;7a30109b.20Re: adding shaded standard deviation to lines plotted in ggplot2 for multiple variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;8e450a78.20
Please remove me from the list-serv.<br>Thanks, Nasseer<br><br>From: UF R Users List <R-USERS-L@LISTS.UFL.EDU> On Behalf Of Duong,Hang T<br>Sent: Monday, August 3, 2020 1:27 PM<br>To: R-USERS-L@LISTS.UFL.EDU<br>Subject: adding shaded standard deviation to lines plotted in ggplot2 for multiple variables<br><br>Warning: This email originated from outside of CDFW and should be treated with extra caution. [...]
2020-08-03T22:58:44+00:00Idrisi, Nasseer@Wildlifehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;8e450a78.20Re: adding shaded standard deviation to lines plotted in ggplot2 for multiple variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;6355f6fc.20
To tack on to Ben and Ben's advice, I recommend using the clean_names() function from the {janitor} package to easily make the column names "legal".<br>https://urldefense.proofpoint.com/v2/url?u=http-3A__sfirke.github.io_janitor_&d=DwIFAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=DuhgWCeXalOWlep4QHjULlX1EKUvc1kolmPuGxHK4VU&m=ADg3WGgkcyhibKF0oUT-S1g64iAJQZkvXFezQHLcEUc&s=uIrUMa678tE57TihowE4jo-zWKMPJFp2qrkXeVgejSg&e=<br><br>From: UF R Users List <R-USERS-L@LISTS.UFL.EDU> On Behalf Of Toh,Kok Ben<br>Sent: 03 August 2020 17:00<br>To: R-USERS-L@LISTS.UFL.EDU<br>Subject: Re: adding shaded standard deviation to lines plotted in ggplot2 for multiple variables [...]
2020-08-03T21:17:56+00:00Millar,Justin Jhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;6355f6fc.20Re: adding shaded standard deviation to lines plotted in ggplot2 for multiple variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;a0071664.20
On 8/3/20 5:00 PM, Toh,Kok Ben wrote:<br>><br>> I agree with Ben’s comment regarding the “legal” R variable names. R<br>> doesn’t like hyphen (‘-‘) in variable names. And it’s less cumbersome<br>> to just rename and change it to say underscore (‘_’).<br>><br>> To expand on the tidyr::pivot_longer(), you basically want to make a<br>> table like this:<br>><br>> DOY<br>><br>><br>><br>> Variable<br>><br>><br>><br>> mean<br>><br>><br>><br>> STDEV<br>><br>> 1<br>><br>><br>><br>> LO-VPD<br>><br>><br>><br>> 0.459527<br>><br>><br>><br>> 0.29131<br>><br>> 2<br> [...]
2020-08-03T17:04:01-04:00Ben Bolkerhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;a0071664.20Re: adding shaded standard deviation to lines plotted in ggplot2 for multiple variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c3ad4ac.20
I agree with Ben's comment regarding the "legal" R variable names. R doesn't like hyphen ('-') in variable names. And it's less cumbersome to just rename and change it to say underscore ('_').<br><br>To expand on the tidyr::pivot_longer(), you basically want to make a table like this:<br><br>DOY<br><br>Variable<br><br>mean<br><br>STDEV<br><br>1<br><br>LO-VPD<br><br>0.459527<br><br>0.29131<br><br>2<br><br>LO-VPD<br><br>0.458673<br><br>0.309112<br><br>1<br><br>LO-Rn<br><br>0.439308<br><br>0.335118<br><br>2<br><br>LO-Rn<br><br>0.432799<br><br>0.385561<br><br>1<br><br>Mag-VPD<br><br>0.368959<br><br>0.489372<br><br>2<br><br>Mag-VPD<br><br>0.3417<br><br>0.48302<br><br>This allows you to do:<br>+ geom_line(aes(x=DOY, y=mean, colour=Variable)) + geom_ribbon(aes(x=DOY, ymin=mean-STDEV, ymax=mean+STDEV, colour=Variable)) [...]
2020-08-03T21:00:08+00:00Toh,Kok Benhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c3ad4ac.20Re: adding shaded standard deviation to lines plotted in ggplot2 for multiple variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;e61c12ad.20
For a *single* variable:<br><br> + geom_ribbon(aes(ymin=`LO-Rn`-`LO-Rn-STDEV`,<br>ymax=`LO-RN`+`LO-Rn-STDEV`), alpha=0.2, colour=NA)<br><br>alpha makes sure the ribbons are transparent<br><br>colour=NA turns off the boundary lines, which you usually don't want<br><br>if you are differentiating lines by colour you may want to add a fill=<br>mapping<br><br> Others may disagree, but I would say it is best practice to adjust<br>your variables (e.g. using `dplyr::rename()`) so that they are legal R<br>variable names, so you don't have to mess with back-ticks `` in your<br>code as much (then use `labs=` to get the axis labels the way you want<br>them, which is probably [...]
2020-08-03T16:39:18-04:00Ben Bolkerhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;e61c12ad.20adding shaded standard deviation to lines plotted in ggplot2 for multiple variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;3d6caf30.20
Hi everyone,<br><br>I have a data set like this:<br><br>DOY LO-VPD LO-VPD-STDEV LO-Rn LO-Rn-STDEV Mag-VPD Mag-VPD-STDEV<br>1 0.465075 0.459527 0.29131 0.471788 0.60554 0.209158<br>2 0.483584 0.458673 0.309112 0.478904 0.574919 0.256222<br>3 0.50656 0.439308 0.335118 0.418182 0.579301 0.257089<br>4 0.532272 0.432799 0.385561 0.417886 0.590181 0.245088<br>5 0.561662 0.368959 0.489372 0.307806 0.591651 0.239143<br>6 0.563379 0.3417 0.48302 0.305674 0.594346 0.231368<br>7 0.570645 0.316844 0.493578 0.307564 0.601119 0.229896<br>8 0.58487 0.27565 0.549339 0.266864 0.598576 0.246463 [...]
2020-08-03T20:27:14+00:00Duong,Hang Thttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;3d6caf30.20Re: internship opportunity
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;fc0b088a.20
Hi Mark,<br><br>Can you comment on why the internship is unpaid? ~10 hours per week doing<br>data processing in R and Excel is rather a lot of time doing highly skilled<br>labor.<br><br>I bring this up because there are well-known issues with unpaid internships<br>being a barrier to inclusion and equity in STEM. See the attached cover<br>letter to the Society for Marine Mammalogy Leadership. [...]
2020-07-30T09:01:13-04:00Hao Yehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;fc0b088a.20internship opportunity
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;59eeea29.20
Hello,<br><br>The UF Bureau of Economic and Business Research has an undergraduate remote internship opportunity for the fall 2020 semester for a data processor with Excel and R skills. Please see attached for more details and feel free to pass along to anyone you think might be interested.<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 [...]
2020-07-30T12:09:42+00:00Girson,Mark Ahttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;59eeea29.20RFP for inclusive virtual events in open data science
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c117a97.20
Hi,<br><br>Some of you may have already seen this, but Code for Science and Society<br>has a call for virtual events to promote open data science. Submission<br>deadline is *August 25*.<br><br>https://urldefense.proofpoint.com/v2/url?u=https-3A__eventfund.codeforscience.org_request-2Dfor-2Dproposals_&d=DwIFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=DuhgWCeXalOWlep4QHjULlX1EKUvc1kolmPuGxHK4VU&m=RLtjHlHL1LVjnfC52QzwN-ERGlvElfB4bmMhVRKSOqs&s=F3TUSrp51MHhO7tdxTVGSAEJcbfMspe0_pZb-kvisbA&e=<br><br>We aim to improve access to open data science practices and tools and<br>> support communities in open data science to grow sustainably and<br>> inclusively. We will support these communities with grants for virtual<br>> events focused on improving or connecting research-driven data science<br>> tools, practices, and the communities themselves. Proposals must<br>> demonstrate the educational and scientific purposes of the event (or series<br>> of [...]
2020-07-09T10:53:33-04:00Hao Yehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c117a97.20Re: adding superscript to rmarkdown table
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;909c722a.20
Hi Emilio,<br><br>I’ve posted to the stackoverflow regarding my suggestion. It is hacky and by no means elegant but if you’re looking for a quick fix it might be a good way.<br><br>Cheers,<br>Ben<br><br>From: UF R Users List <R-USERS-L@LISTS.UFL.EDU> On Behalf Of Bruna, Emilio M.<br>Sent: Friday, June 26, 2020 1:04 PM<br>To: R-USERS-L@LISTS.UFL.EDU<br>Subject: adding superscript to rmarkdown table [...]
2020-06-27T02:27:59+00:00Toh,Kok Benhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;909c722a.20adding superscript to rmarkdown table
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;eff12cb1.20
Hi all, I posted this o stack overflow but thought I’d try my luck here as well.<br><br>https://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_questions_62597592_add-2Da-2Dsuperscript-2Dto-2Done-2Dcell-2Dof-2Da-2Dtable-2Dformatted-2Dwith-2Dkable-2Dkableextra-2Dfor-2Dr&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=DuhgWCeXalOWlep4QHjULlX1EKUvc1kolmPuGxHK4VU&m=qYRK79GfcuoWAysMUdu5L1UQAlMyE8hg-ZhNM-XRjrM&s=RMsKymYQcBCEbHiKlhcUmtsEz4XDRNePX82nw6BjuCs&e=<br><br>I have a footnote in a table formatted with kableExtra for an Rmarkdown-generated pdf. I need one of the cells (in the example code below NYC) to have the superscript (NYC^1) to point to the footnote, but can't figure out how to do it. Any suggestions? [...]
2020-06-26T17:03:58+00:00Bruna, Emilio M.https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;eff12cb1.20Do you use git and github? Can you spare a few minutes to fill out a survey?
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c8427f09.20
Hi,<br><br>My colleagues, Sarah Nguyen and Vicky Steeves have a Sloan grant-funded<br>project titled Investigating & Archiving the Scholarly Git Experience --<br>https://urldefense.proofpoint.com/v2/url?u=https-3A__investigating-2Darchiving-2Dgit.gitlab.io_&d=DwIBaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=DuhgWCeXalOWlep4QHjULlX1EKUvc1kolmPuGxHK4VU&m=DrWGemRkgVrPjXXpk-co2uOBAVnWVfGMWXx8zKtYg44&s=sRtUx23IiOPTrXvU2DgcGTCHi7K9wFRl45voAAUiSDI&e=<br><br>1. As part of this project, they're looking for a focus group of a few<br>beginning/intermediate users of Git, GitHub, GitLab, etc.<br><br>2. There is a short survey about version control and usage that would be<br>great to get a broader set of responses to:<br>https://urldefense.proofpoint.com/v2/url?u=https-3A__nyu.qualtrics.com_jfe_form_SV-5F5ArtYnx6kWMXYNv&d=DwIBaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=DuhgWCeXalOWlep4QHjULlX1EKUvc1kolmPuGxHK4VU&m=DrWGemRkgVrPjXXpk-co2uOBAVnWVfGMWXx8zKtYg44&s=njqbOdmxfQ6cBF33rbOg-JowUW8wjguj4zKfbr8hfnA&e= [...]
2020-06-18T11:31:58-04:00Hao Yehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c8427f09.20Job advertisement with UF - Data Management Analyst II
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;fa9eb3b0.20
Hi everyone,<br><br>I wanted to share a job opportunity with UF's Family Nutrition Program. The are looking for a Data Management Analyst II. Full details for the position can be found here: https://explore.jobs.ufl.edu/en-us/job/514121/state-evaluation-specialist-family-nutrition-program.<br><br>Best,<br><br>Christine<br><br>[cid:image001.jpg@01D6449D.C7F49EE0]<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.
2020-06-17T15:52:32+00:00Schneider Swanson, Anna Christinehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;fa9eb3b0.20Re: Online Workshop Instructor Signup
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;dea3c154.20
Hi 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. [...]
2020-05-28T18:19:50+00:00Botero Arias, Robinsonhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;dea3c154.20Re: Online Workshop Instructor Signup
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;49f2db45.20
Hi 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
2020-05-28T17:13:17+00:00Rahmani,Haqiqurahmanhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;49f2db45.20Re: Online Workshop Instructor Signup
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;66d0e281.20
Great 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. [...]
2020-05-28T15:27:55+00:00Bohnett,Evehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;66d0e281.20Re: Online Workshop Instructor Signup
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;4e756d67.20
Hi 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. [...]
2020-05-28T14:12:01+00:00Smith,Audrey Culverhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;4e756d67.20Re: Online Workshop Instructor Signup
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;9202c721.20
Greetings 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
2020-05-28T13:17:43+00:00Bohnett,Evehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;9202c721.20Re: Online Workshop Instructor Signup
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c039dbbe.20
Is there any contact information for about volunteering?
2020-05-28T13:06:34+00:00Colee,James Chttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c039dbbe.20Online Workshop Instructor Signup
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;9e35561d.20
Greetings 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. [...]
2020-05-27T21:33:26+00:00Bohnett,Evehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;9e35561d.20Re: Data Carpentry Online Workshop Instructor Recruitment.
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;e6cdf8cf.20
Hi 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
2020-05-07T17:15:59+00:00Rahmani,Haqiqurahmanhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;e6cdf8cf.20Data Carpentry Online Workshop Instructor Recruitment.
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;71573280.20
Greetings 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. [...]
2020-04-17T22:06:07+00:00Bohnett,Evehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;71573280.20Summer undergraduate research position
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;f46e0840.20
I 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 [...]
2020-04-14T14:53:22-04:00Kathe Todd-Brownhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;f46e0840.20Re: undergraduate internship using R
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;f877653f.20
Mark - 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. [...]
2020-04-09T19:19:51+00:00Maxwell,Danielhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;f877653f.20undergraduate internship using R
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;2ca9ca11.20
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.<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.
2020-04-09T16:44:48+00:00Girson,Mark Ahttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;2ca9ca11.20Re: Need assistance in plotting values in ggplot2
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;2c858b37.20
Hi 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. [...]
2020-03-03T14:02:40+00:00Sinha,Pujahttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;2c858b37.20Re: Need assistance in plotting values in ggplot2
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;945d6a10.20
Hi 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 [...]
2020-03-02T22:30:10+00:00Wu,Zhuoxihttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;945d6a10.20Tidy Tuesday - tomorrow!
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;226fae58.20
Below 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. [...]
2020-03-02T21:10:11+00:00Klarenberg,Geraldinehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;226fae58.20Re: Solve and plot implicit function in R
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;b5391017.20
That’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. [...]
2020-03-02T20:35:04+00:00Toh,Kok Benhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;b5391017.20Re: Need assistance in plotting values in ggplot2
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;5a9a93c6.20
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<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 [...]
2020-03-02T20:32:13+00:00Toh,Kok Benhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;5a9a93c6.20Re: Need assistance in plotting values in ggplot2
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;3fadadfd.20
Hi 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 [...]
2020-03-02T20:02:30+00:00Sinha,Pujahttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;3fadadfd.20Re: Solve and plot implicit function in R
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;fc0aedc9.20
Hi 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 [...]
2020-03-02T19:26:08+00:00Nicolas,Floyidhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;fc0aedc9.20Re: Need assistance in plotting values in ggplot2
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;fd7598f0.20
Hi 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. [...]
2020-03-02T18:43:39+00:00Toh,Kok Benhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;fd7598f0.20Need assistance in plotting values in ggplot2
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;74e91b60.20
Hi 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> [...]
2020-02-28T16:47:31+00:00Sinha,Pujahttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;74e91b60.20Re: Solve and plot implicit function in R
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c864eda9.20
Your 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: [...]
2020-02-27T13:24:07+00:00Klarenberg,Geraldinehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c864eda9.20Re: Solve and plot implicit function in R
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;ed58237.20
Dear 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. [...]
2020-02-27T05:12:39+00:00Nicolas,Floyidhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;ed58237.20Re: Solve and plot implicit function in R
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c3bc58b5.20
Since 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. [...]
2020-02-27T04:59:44+00:00Klarenberg,Geraldinehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;c3bc58b5.20Solve and plot implicit function in R
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;b661e631.20
Here 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 [...]
2020-02-27T04:31:03+00:00Nicolas,Floyidhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;b661e631.20Re: Crosstabs - More than 2 Variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;a5266c06.20
Thanks 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 [...]
2020-02-20T11:22:03-05:00Yawo Kokuvihttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;a5266c06.20Re: Crosstabs - More than 2 Variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;915a70e.20
Hi 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. [...]
2020-02-20T16:04:26+00:00Krenz,Tillhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;915a70e.20Re: Crosstabs - More than 2 Variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;67f4ce9e.20
Thanks 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. [...]
2020-02-20T08:49:57-05:00Yawo Kokuvihttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;67f4ce9e.20R-Ladies Tidy Tuesdays [TODAY]
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;ab15d365.20
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. 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 [...]
2020-02-18T14:46:04+00:00Klarenberg,Geraldinehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;ab15d365.20Re: Crosstabs - More than 2 Variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;895f5ae1.20
Hi 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. [...]
2020-02-17T23:05:56+00:00Krenz,Tillhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;895f5ae1.20Re: Crosstabs - More than 2 Variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;df8310b8.20
You 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) [...]
2020-02-17T22:49:47+00:00Toh,Kok Benhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;df8310b8.20Re: Crosstabs - More than 2 Variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;e84b6fe1.20
Thanks 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> [...]
2020-02-17T14:14:12-05:00Yawo Kokuvihttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;e84b6fe1.20Re: Crosstabs - More than 2 Variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;f2289921.20
I 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 [...]
2020-02-17T19:10:14+00:00Toh,Kok Benhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;f2289921.20Crosstabs - More than 2 Variables
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;d55f88d2.20
Hello<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 [...]
2020-02-15T13:27:09-05:00Yawo Kokuvihttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;d55f88d2.20Re: Initial guess for non linear model
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;da3d3fbf.20
Thank 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. [...]
2020-02-13T21:04:26+00:00Nicolas,Floyidhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;da3d3fbf.20FW: Invitation to 2020 Southeast SACNAS Regional Conference
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;822c2502.20
Hi 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. [...]
2020-02-13T02:44:45+00:00Toh,Kok Benhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;822c2502.20Re: Initial guess for non linear model
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;a1094b22.20
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.<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") [...]
2020-02-12T17:11:35-05:00Ben Bolkerhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;a1094b22.20Re: Initial guess for non linear model
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;8bd0c2a5.20
Hi 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 [...]
2020-02-12T17:45:24+00:00Nicolas,Floyidhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;8bd0c2a5.20Re: Initial guess for non linear model
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;22209b3a.20
The 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: [...]
2020-02-12T17:14:35+00:00Nicolas,Floyidhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;22209b3a.20Re: Initial guess for non linear model
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;7013da3e.20
Hi 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. [...]
2020-02-12T17:12:46+00:00Martin,James L,IIIhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;7013da3e.20Re: Initial guess for non linear model
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;1734a316.20
Not 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? [...]
2020-02-12T12:10:28-05:00Ben Bolkerhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;1734a316.20Initial guess for non linear model
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;680c1c12.20
Hi 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 [...]
2020-02-12T17:00:48+00:00Nicolas,Floyidhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;680c1c12.20Re: Implicite equations in R - help
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;24277e8e.20
Floyid, 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).. [...]
2020-01-31T13:06:55+00:00Klarenberg,Geraldinehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;24277e8e.20Re: Implicite equations in R - help
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;8d39d83d.20
After 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). [...]
2020-01-31T05:43:48+00:00Klarenberg,Geraldinehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;8d39d83d.20Re: Implicite equations in R - help
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;bc382012.20
It 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 [...]
2020-01-31T04:15:58+00:00Nicolas,Floyidhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;bc382012.20Re: Implicite equations in R - help
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;6ca1fa8b.20
Could 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 : [...]
2020-01-31T04:12:21+00:00Klarenberg,Geraldinehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;6ca1fa8b.20Implicite equations in R - help
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;5259b3e.20
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 : [...]
2020-01-31T03:08:31+00:00Nicolas,Floyidhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;5259b3e.20UF Carpentries Club Spring Social
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;4301f353.20
Hello,<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.) [...]
2020-01-28T20:58:21+00:00Bohnett,Evehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;4301f353.20Re: Multiple datasets
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;53c5db22.20
Thank 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=>) [...]
2020-01-20T19:55:17+00:00Nicolas,Floyidhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;53c5db22.20Re: Multiple datasets
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;ab269fdc.20
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=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. [...]
2020-01-20T06:14:33+00:00Klarenberg,Geraldinehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;ab269fdc.20Multiple datasets
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;6b98a500.20
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.<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, repro
2020-01-20T05:38:22+00:00Nicolas,Floyidhttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;6b98a500.20Data Carpentry for Social Sciences - Carpentries Instructor Recruitment
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;66921619.20
Greetings 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. [...]
2020-01-18T16:04:06+00:00Bohnett,Evehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;66921619.20Re: R meetup
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;827bb04d.20
Hi<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> [...]
2020-01-17T01:27:36+00:00Klarenberg,Geraldinehttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;827bb04d.20R meetup
https://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;2a859382.20
Hi,<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.
2020-01-13T16:51:48+00:00Sinha,Pujahttps://lists.ufl.edu/cgi-bin/wa?A2=R-USERS-L;2a859382.20