Thanks so much for your help, Clément, your suggestion helped solve one of my questions, it identified the animal that had less than 3 relocations (98391), but it gave me an error when trying to implement the MCP:
> any(table(all.id)<5) [1] TRUE > ta <- table(all.id)<5 > ta[ta<5] all.id 76790 76792 76793 76794 76795 76796 76797 76798 87942 87943 87944 87945 87946 87947 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 87948 87949 87950 87951 87952 87953 87954 87955 87956 98382 98383 98384 98385 98386 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE 98387 98388 98389 98391 FALSE FALSE FALSE TRUE > out <- names(ta[ta<5]) > pc <- mcp(all.xy[!(all.id%in%out),], factor(all.id[!(all.id%in%out)])) Error in apply(df.t, 1, dist.cdg) : dim(X) must have a positive length In addition: Warning message: In min(table(id)) : no non-missing arguments to min; returning Inf I fixed the issue by removing all the rows from the data.frame that contained that particular animal using: gaz.sub = subset(all.frame, Name != 98391) And then tried the MCP with success. Also, I solved the two-week issue by creating a variable for each two-week interval to include in the analysis: start.date = '2007-09-04' end.date = '2010-01-09' two.weeks = seq(from = as.Date(start.date) , to = as.Date(end.date), by = 14) I apologize for the duplicate posting in the AniMov listserv, I didn't know the same subscribers were on lists hosted on different servers. All the best, Hakim _________________________________ Abdulhakim Abdi, M.Sc. Research Intern Conservation GIS/Remote Sensing Lab Smithsonian Conservation Biology Institute phone: +1-540-635-6578 fax: +1-540-635-6506 email: [email protected] From: Clément Calenge [mailto:[email protected]] Sent: Friday, June 04, 2010 4:50 AM To: Abdi, Abdulhakim Cc: [email protected] Subject: Re: [R-sig-eco] Adehabitat: creating MCPs every two weeks for 32 different animals Several answers to your question are already available here: http://lists.faunalia.it/pipermail/animov/2010-June/000601.html http://lists.faunalia.it/pipermail/animov/2010-June/000602.html Please avoid cross-posting, Best, Clément Calenge On 06/03/2010 04:18 PM, Abdi, Abdulhakim wrote: Dear List, I'm trying to detect patterns in the movements of a nomadic gazelle species during the breeding season. Basically, I would like to create MCPs (minimum convex polygons representing home ranges) for each of the 32 gazelles every two weeks starting on September 4th 2007. I have satellite tracking points from September 2007 to January 2010. The point of this exercise is to see whether the animals converge at particular areas during the breeding season or whether the site selection is random. Before going into the date loop procedure I attempted to create MCPs for the animals without regard for the two-week interval: Here is what my data.frame looks like: head(all.frame) Name Status X Y Date 1 76792 capture 1356206 2196167 2007-09-04 2 76795 capture 1354434 2209845 2007-09-04 3 76797 capture 1354434 2209845 2007-09-04 And here is the output of the command, as you can see I get an error statement: all.xy = all.frame[,c("X","Y")] all.id = all.frame$Name all.mcp = mcp(all.xy, all.id, percent=95) Error in mcp(all.xy, all.id, percent = 95) : At least 5 relocations are required to fit an home range Next, I ran MCPs for the "puechabon$loc" data.frame that comes with Adehabitat and it worked without producing any errors, so I compared my data.frame with puechabon$loc. head(puechabon$loc) Name Age Sex X Y Date 1 Brock 2 1 699889 3161559 930701 2 Brock 2 1 700046 3161541 930703 3 Brock 2 1 698840 3161033 930706 Looking at the structure of both, my dataset has the date set to class 'Date' while in the Puechabon dataset it's set to 'Integer' and the dates are concatenated as "yymmdd": str(all.frame) 'data.frame': 5059 obs. of 5 variables: $ Name : Factor w/ 32 levels "76790","76792",..: 2 5 7 7 1 3 5 8 7 7 ... $ Status: Factor w/ 3 levels "argos","capture",..: 2 2 2 3 2 2 1 2 3 3 ... $ X : int 1356206 1354434 1354434 1349773 1362802 1362802 1357468 1362802 1345648 1345387 ... $ Y : int 2196167 2209845 2209845 2211725 2216920 2216920 2176051 2216920 2213362 2213572 ... $ Date :Class 'Date' num [1:5059] 13760 13760 13760 13761 13761 ... str(puechabon$loc) 'data.frame': 119 obs. of 6 variables: $ Name: Factor w/ 4 levels "Brock","Calou",..: 1 1 1 1 1 1 1 1 1 1 ... $ Age : int 2 2 2 2 2 2 2 2 2 2 ... $ Sex : int 1 1 1 1 1 1 1 1 1 1 ... $ X : int 699889 700046 698840 699809 698627 698719 698991 698626 698879 699756 ... $ Y : int 3161559 3161541 3161033 3161496 3160941 3160989 3161015 3160768 3160964 3161449 ... $ Date: int 930701 930703 930706 930707 930708 930709 930713 930714 930715 930720 ... I tried to convert my dates to the "yymmdd" format, without any luck as the new column came out exactly the same as the original one: all.frame$Date2 = as.Date(all.frame$Date, format="%y/%m%/d") head(all.frame) Name Status X Y Date Date2 1 76792 capture 1356206 2196167 2007-09-04 2007-09-04 2 76795 capture 1354434 2209845 2007-09-04 2007-09-04 3 76797 capture 1354434 2209845 2007-09-04 2007-09-04 So, I have three questions: is it only a date format issue or am I missing something else? If it is a date format issue, then, how would it be possible to convert my dates in "YYyy-mm-dd" into "yymmdd"? and finally what loop functions or steps could I take to create MCPs for the animals every two weeks. Any help is greatly appreciated. Regards, Hakim Abdi _________________________________ Abdulhakim Abdi, M.Sc. Research Intern Conservation GIS/Remote Sensing Lab Smithsonian Conservation Biology Institute 1500 Remount Road Front Royal, VA phone: +1-540-635-6578 fax: +1-540-635-6506 email: [email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]> [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list [email protected]<mailto:[email protected]> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Clément CALENGE Cellule d'appui à l'analyse de données Office national de la chasse et de la faune sauvage Saint Benoist - 78610 Auffargis tel. (33) 01.30.46.54.14 [[alternative HTML version deleted]]
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