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Paleocave Blog Trust us, we’re scientists Menu Home Privacy About the header image Search for: Your 2014 Winter Solstice Gift Guide! 1 December, 2014 Ryan’s Ramblings gift , guide , nerd , paleopals , recommendations , science , science... sort of , Solstice , suggestion , winter Ryan The days are short, the nights are long, the only solace we can take from the coming cold and darkness is to give each other gifts. If you’re a nerd like us maybe you want those gifts to have a science bent? Well we are here to help you out with that with our annual gift guide for the geek in your life! Each of the Paleopals (in alphabetical order) has contributed something to this list to make your holiday shopping season as easy as can be, so let’s dive right in! Continue reading Your 2014 Winter Solstice Gift Guide! → One comment so far Strange behavior from the cut function with dates in R 12 August, 2014 Patrick’s Ponderables bugs , code , cut , dates , R , Statistics , work around Patrick Update: @hadlywickham tweeted to me to let me know that daylight savings time was the culprit. Though this explains the behavior I document in the first part of this post, the behavior of the cut function using truncated dates (discussed further down the post) is still unexplained. I recently encountered some strange behavior from R when using the cut.POSIXt method with day” as the interval specification. This function isn’t working as I intended and I doubt that it is working properly. I’ll show you the behavior I’m seeing (and what I was expecting) then I’ll show you my current base R workaround. To generate a reproducible example, I’ll use this latemail function I gleaned from this stack overflow post . latemail - function(N, st="2013/01/01", et="2013/12/31") { st - as.POSIXct(as.Date(st)) et - as.POSIXct(as.Date(et)) dt - as.numeric(difftime(et,st,unit="sec")) ev - sort(runif(N, 0, dt)) rt - st + ev } And generate some data… set.seed(7110) #generate 1000 random POSIXlt dates and times bar-data.frame("date"=latemail(1000, st="2013/03/02", et="2013/03/30")) # assign factors based on the day portion of the POSIXlt object bar$dateCut - cut(bar$date, "day", labels = FALSE) I expected that all rows with the date 2013-03-01 would receive factor 1, all rows with the date 2013-03-02 would receive factor 2, and so on. At first glance this seems to be what is happening. head(bar, 10) date dateCut 1 2013-03-01 19:10:31 1 2 2013-03-01 19:31:31 1 3 2013-03-01 19:55:02 1 4 2013-03-01 20:09:36 1 5 2013-03-01 20:13:32 1 6 2013-03-01 22:15:42 1 7 2013-03-01 22:16:06 1 8 2013-03-01 23:41:50 1 9 2013-03-02 00:30:53 2 10 2013-03-02 01:08:52 2 Note that at row 9 the date changes from March 1 to March 2 and the factor (dateCut) changes from 1 to 2. So far so good. But we shall see some strange things in the midnight hour. Continue reading Strange behavior from the cut function with dates in R → View all 6 comments Insert random NAs in a vector in R 30 July, 2014 Patrick’s Ponderables , Uncategorized code , R , Statistics , stats Patrick I was recently writing a function which was going to need to deal with NAs in some kind of semi-intelligent way. I wanted to test it with some fake data, meaning that I was going to need a vector with some random NAs sprinkled in. After a few disappointing google searches and a stack overflow post or two that left something to be desired, I sat down, thought for a few minutes, and came up with this. #create a vector of random values foo - rnorm(n=100, mean=20, sd=5) #randomly choose 15 indices to replace #this is the step in which I thought I was clever #because I use which() and %in% in the same line ind - which(foo %in% sample(foo, 15)) #now replace those indices in foo with NA foo[ind]-NA #here is our vector with 15 random NAs foo Not especially game changing but more elegant than any of the solutions I found on the interwebs, so there it is FTW. View all 10 comments GIS in R: Part 1 27 March, 2014 Uncategorized GIS , Maps , R , Statistics Patrick I messed around with R for years without really learning how to use it properly. I think it’s because I could always throw my hands up when the going got tough and run back and cling the skirts of Excel or JMP or Systat. I finally learned how to use R when I needed to do a fairly hefty GIS project and I didn’t have access to a computer with ArcGIS and couldn’t afford to buy it (who can?). So I started looking into R’s spatial abilities. Admittedly R might not be the most obvious choice for free GIS options, combinations of QGIS (http://www.qgis.org/), GRASS (http://grass.osgeo.org/), PostGIS (http://postgis.refractions.net/), or OpenGeo (http://boundlessgeo.com/solutions/opengeo-suite/download/) might pop up in google searches before R. R might not even be the first general purpose programming language you think of for GIS, especially now that ArcGIS relies on Python for much of its modeling. However, all of these tools have a significant learning curve, and I was farther along in R than any of these alternatives, so I started googling and watching tutorial videos. So should you be using R for analyzing and displaying spatial data? If you already know a little or a lot of R, if you need a cross platform solution, or need to do some fairly heavy stats applications to your spatial data, R just might be a good solution for you. It turns out R has lots of support for spatial data and does a great job displaying it too. There are a number of packages useful for analyzing and displaying your spatial data. I think the 4 most useful right out of the gate are sp, rgdal, maptools, and raster. If you haven’t installed packages before do this… install.packages(sp”) install.packages(raster”) install.packages(maptools”) …and if you are on a Windows machine… install.packages(rgdal”) If you’re on a Mac, installing rgdal is a little tricky. Give this a try setRepositories(ind=1:2) install.packages(rgdal”) If that doesn’t work read this over. Installing rgdal on a Mac After installing the packages, if you want to use the functions contained in that package you need to load the library. To use the functions in the sp package, you should type library(sp) to load the rgdal package… library(rgdal) etc. One comment so far Science… sort of DC Meetup 2014! 7 January, 2014 Ryan’s Ramblings DC , meetup , podcast , science club Ryan We’ve noticed through the magic of download statistics that we have a nice cluster of listeners in the DC metro area. With Patrick always nearby and Ryan in town for a bit, we figured a meet up would be fun. So on Thursday, January 9th, starting around 7:30pm EST we’ll be convening at the Science Club bar to hang out, meet some new people, and share some drinks. We hope that you’ll join us if you can. More details about the event can be found on our Eventbrite page here: Science… sort of DC Meetup 2014 For those who RSVP on the Evenbrite page, your first drink of the evening is on us. See y’all soon! Leave a comment Winter Solstice Survival Guide 2013 27 November, 2013 Patrick’s Ponderables , Ryan’s Ramblings books , electronics , gadgets , gift guide , gifts , science , science... sort of , sonic screwdriver , survival gear , Winter Solstice Patrick The most wonderful time of the year, obviously. ’tis the season to consume! But for this part of the year, as the Winter Solstice approaches, we consume not for ourselves, but for others, and that’s generally a good thing. Each year we here at Science… sort of like to put together a list of suggestions for the science-inclined in your life. Whether you’re looking to give the gift of science, or fleshing out your own list to send to your regionally-appropriate gift giving elf-spirit, this list should have you covered. We begin with Patrick , who really went above and beyond with contribution, earning him well-deserved top billing. Continue reading Winter Solstice Survival Guide 2013 → View all 2 comments Science link fest for the week of the 27th 27 July, 2013 Brownian...