From richard.baxter at ieu.uzh.ch Mon Oct 13 20:55:03 2014 From: richard.baxter at ieu.uzh.ch (richard.baxter at ieu.uzh.ch) Date: Mon, 13 Oct 2014 20:55:03 +0200 Subject: [tlocoh-info] (no subject) Message-ID: Dear T-Locoh list, Really enjoying using this package at the moment, however, I have some methodological questions: 1) First up is, was there any resolution to the thread 'showing duration of visit and visitation rate'?15 Jul 2014 ? As visualizing? movement data, UDs or movement paths, is essential for communication. 2) Related to the first, but hopefully much simpler: I'm a fan of the trajectory plots with the differing colours for different times but i was wondering how this could be refined to show the movement from start to end...as in, green at the start of the movement path (or first timepoint), red at the last time point with a graduated colour palette in between the points. It's possible to do in other packages but working with T-Locoh is much more intuitive for me except for the plotting. Is this possible? This would be awesome for migratory animals. 3) related to plotting: I'm plotting data for between 31 individuals so when I plot the lxy, the command returns the plots in grid form or a lattice. Is it possible to separate the plots for the into individuals plot windows? 4) Not sure what is wrong with the data or my coding but when looking at my sampling freq, there is also bursts below tau0.2 (See attached) similar to the T-LoCoh tutorial, but when i run the code I get the following error: > mal.lxy <- lxy.thin.bursts(mal.lxy, thresh=0.2) No bursts were found for id MIDC_01 No bursts were found for id MIDCST_02 New No bursts were found for id MIDIN_01 New No bursts were found for id MIDIN_02 No bursts were found for id MLB_01 No bursts were found for id MLB_02 Error in lxy[["pts"]][-idx.remove, ] : error in evaluating the argument 'i' in selecting a method for function '[': Error in -idx.remove : invalid argument to unary operator What is wrong? Any help would be most appreciated as I'm due to give a presentation about this for our R-lunch course! Best, Rich -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sampling freq.jpeg Type: application/octet-stream Size: 198354 bytes Desc: not available URL: From lyons.andy at gmail.com Wed Oct 15 08:12:44 2014 From: lyons.andy at gmail.com (Andy Lyons) Date: Tue, 14 Oct 2014 23:12:44 -0700 Subject: [tlocoh-info] Custom colors ramp; error msg In-Reply-To: References: Message-ID: <543E105C.7070901@gmail.com> Hi Richard, Thanks for your good questions, see replies below: On 10/13/2014 11:55 AM, richard.baxter at ieu.uzh.ch wrote: > Dear T-Locoh list, > > Really enjoying using this package at the moment, however, I have some > methodological questions: > > 1) First up is, was there any resolution to the thread 'showing > duration of visit and visitation rate' 15 Jul 2014? As visualizing > movement data, UDs or movement paths, is essential for communication. I don't remember if we finished that discussion, but let me look back at that thread and get back to you. > 2) Related to the first, but hopefully much simpler: > I'm a fan of the trajectory plots with the differing colours for > different times but i was wondering how this could be refined > to show the movement from start to end...as in, green at the start of > the movement path (or first timepoint), red at the last time point > with a graduated colour palette in between the points. > It's possible to do in other packages but working with T-Locoh is much > more intuitive for me except for the plotting. > Is this possible? This would be awesome for migratory animals. Yes you can change the colors that are used to display locations when plotting a locoh-xy object. From the help file for plot.locoh.lxy: col: A single value or vector of color values. Can also be 'auto' (default) in which case the colors saved in the locoh-xy object will be used (which are rainbow by default). If you wanted all the locations to be the same color, you could pass a single color value as col. For example: plot(toni.lxy, col="darkblue") To use a custom color ramp, you can create a vector of color values (same length as the number of points) and pass that as col. To display the locations green to red, for example, you could run: n <- nrow(toni.lxy$pts) green.to.red <- colorRampPalette(c("#00FF00","#FF0000"))(n) plot(toni.lxy, col=green.to.red) Granted that the plotting functions in tlocoh have a lot of options that can make them klunky to use. Note however you can easily grab the SpatialPointsDataFrame of a locoh-xy object, which is saved in the pts element: x <- toni.lxy$pts summary(x) > 3) related to plotting: I'm plotting data for between 31 individuals > so when I plot the lxy, the command returns the plots in grid form or > a lattice. > Is it possible to separate the plots for the into individuals plot > windows? Yes, set overlay=TRUE > > 4) Not sure what is wrong with the data or my coding but when looking > at my sampling freq, there is also bursts below tau0.2 (See attached) > similar to the T-LoCoh tutorial, but when i run the code I get the > following error: > > mal.lxy <- lxy.thin.bursts(mal.lxy, thresh=0.2) No bursts were found for id > MIDC_01 No bursts were found for id MIDCST_02 New No bursts were found > for id MIDIN_01 New No bursts were found for id MIDIN_02 No bursts > were found for id MLB_01 No bursts were found for id MLB_02 Error in > lxy[["pts"]][-idx.remove, ] : error in evaluating the argument 'i' in > selecting a method for function '[': Error in -idx.remove : invalid > argument to unary operator > > What is wrong? This sounds like a bug, or an untrapped error. Let me send you some suggestions in a separate message. > > Any help would be most appreciated as I'm due to give a presentation > about this for our R-lunch course! > > Best, > Rich > > > _______________________________________________ > Tlocoh-info mailing list > Tlocoh-info at lists.r-forge.r-project.org > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/tlocoh-info -------------- next part -------------- An HTML attachment was scrubbed... URL: