EMbC R-package (v.1.1) Tutorial
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1 EMbC Expectation Maximization binary Clustering EMbC R-package (v.1.1) Tutorial J.Garriga, J.R.Palmer, A.Oltra, F.Bartumeus ICREA - Movement Ecology Lab (CEAB-CSIC) 28 April 2014
2 Behavioural Annotation of Movement Trajectories segmentation/labelling of a trajectory into behavioural modes approach esimate movement variables (e.g velocity, turning angle, tourtuosity,fpt) and apply a classification algorithm challenges unsupervised problem parameterization and prior assumptions uncertainty in the data (geopositioning inaccuracies, sampling hetereogeneity) capture sufficiently general and biologically meaningful semantics
3 EMbC variant of the GMM maximum likelihood estimation algorithm (EMC) EMC goods unsupervised, multivariate clustering algorithm. EMC bads prior assumptions or restarts interpretability of the output EMbC novelty implements potential uncertainty in the data binary clustering: variables take either High or Low values (meaningful clustering) number of clusters bounded to 2^(number of variables) parameter free, no prior assumptions
4 EMbC R-package API classes objects with attributes (slots) containing input/output variables constructors commands to build the objects (process inputs and computes outputs) methods commands to manipulate the objects (give access to attributes for analysis or visualization) parameters modifiers of the commands
5 EMbC R-package API Classes binclst (dataset) Move Move Move R-package R-package binclstpath (trajectory) binclstmove (Move obj.) binclstpathstck (set of of trajectories) binclstmovestck (set of of Move objs.)
6 EMbC R-package API Constructors general (broad applicability) binclst embc(signature,parameters) (v.1.1 only bivariant) specific for movement trajectory analysis (behavioural annotation) binclstpath stbc(signature,parameters) binclstmove stbc(signature,parameters) (v.1.1 only speed/turn analysis)
7 constructor binclst embc(signature,params) signature (matrix) data points matrix (n data points, m variables) returns binclst > mybc <- embc(mydatamtx) parameters (U,stDv,maxItr,vrb)
8 constructor binclstpath/binclstmove stbc(signature,params) signature: (data.frame) trajectory as (timestamps, lons, lats,...) returns binclstpath > mybcp <- stbc(mypathdf) signature (Move object) returns binclstmove > mybcm <- stbc(mymoveobj) parameters inherited (stdv,maxitr,vrb) (not U!!) specific (spdlim,smth)
9 input matrix(n,m); data-points internal integer; number of data points integer; number of variables integer; max. number of clusters (2^(m)) output matrix(n,k); likelihood weights numeric(iters); step likelihoods matrix(k,2*m); delimiters numeric(n); cluster assignments (1:LL,2:LH,3:HL,4:HH)
10 all inherited from binclst self trajectory numeric(n); span times distances bearings uncertainty
11 all inherited from binclstpth all inherited from Move
12 EMbC R-package API Methods clustering information (statistics) plotting (input/output variables) visualization (clustering, annotated path) comparison (clusters, labels)
13 methods stts(signature) clustering statistics (mean, stdv, marginal distribution) signature (binclst), (binclstpath), (binclstmove) parameters: none : > stts(mybc)
14 methods sctr(signature) bivariate clustering scatterplot signatures (matrix) (binclst), (binclstpath), (binclstmove) parameters none > sctr(mybcp) >
15 binclstpath methods lblp(signature) plots labeling profile signature (binclstpath), (binclstmove) parameters none > lblp(mybcp) > lblp(bcp1,bcp2) > lblp(mybcp,explbl)
16 methods binclstpath/binclstmove smth(signature) a posteriori smoothing of local labelling signatures (binclstpath), (binclstmove) parameters none returns a smoothed copy of the binclstpath/binclstmove input instance > mysmoothedbcp <- smth(mybcp)
17 binclst methods comparing/validating results comparison of clustering scatterplots sctr(binclst,binclst) sctr(binclst,numeric) comparison of labellings lblp(binclst,binclst) lblp(binclst,numeric) parameters none > sctr(bc1,bc2) > sctr(bc1,exp) > lblp(bc1,exp)
18 binclstpath methods pkml(signature) / bkml(signature) generates pointwise/burstwise kmldoc (Google-Earth) signature (binclstpath), (binclstmove) parameters folder::character ('~/embcdocs') path where to save the kmldoc file name system_datetime.kml markerradius::numeric (5) size of markers in pixels display::bool (FALSE) open Google-Earth > pkml(mybcp,display=true) > bkml(mybcp)
19 binclstpath methods pmap(signature) / bmap(signature) generates pointwise/burstwise htmldoc (browser) signature (binclstpath),(binclstmove) parameters folder::character ('~/embcdocs') path where to save the kmldoc file name system_datetime.html markerradius::numeric (5) size of markers in pixels display::bool (FALSE) open browser maptype::character ('SATELLITE') background map (see doc. help) > pmap(mybcp,display=true,markerradius=25) > bmap(mybcp,display=true)
20 binclstpath methods varp(signature) plots binclstpath/binclstmove data signature (binclstpath), (binclstmove) (matrix) (numeric) parameters none > varp(mybcp) > > >
21 binclstpath methods view(signature) fast visualization of the trajectory signature (binclstpath), (binclstmove) parameters none > view(mybcp)
22 binclst methods setc(signature,params) sets a k-color palette from a color family in the RColorBrewer R-package signature (binclst), (binclstpath), (binclstmove) parameters fam:: character a color family name from the RColorBrewer s > brewer.pal.info; lists all color families (name, type, max.colors) > display.brewer.pal(8,'rdylbu') > setc(mybc,'rdylbu') alternatively: >mybc@c <- c("#fdae61","#d7191c","#abd9e9","#2c7bb6","#525252")
23 embc/stbc constructors parameters (iteration process control) maxitr = integer stop criterium in case of slow convergence default,(200) > mybc <- stbc(mypthdf,maxitr=1) vrb = integer if vrb=0 shows compact step information if vrb=1 shows expanded (statistics) step information default, (0) > mybc <- embc(x=data,,stdv=c(1,1),vrb=1)
24 stbc constructor specific parameters spdlim:: float speed limit for outliers (m/s) default, (40) > mybcp <- stbc(mypthdf,spdlim=20) smth:: float smoothing time window (hours) default, (0) > mybcp <- stbc(mypthdf,smth=6)
25 embc/stbc constructors parameters (clustering control) U = matrix(n,m) uncertainty matrix (same dimension as X!!) default, (matrix(rep(1,n*m),c(n,m))) > mybc <- embc(mydatamtx,u=myuncmtx) stdv = numeric(m) minimum standard deviation (variable specific) default, (rep(10e-32,m)) > mybc <- embc(mydatamtx,stdv=myminstdv)
26 Thanks for your attention! acknowledgments Raymond Klaassen (Migration Ecology Group, Department of Animal Ecology. Lund University, Sweden), who has kindly provided the Osprey trajectory Dina Dechmann (Max Plank Institute of Ornithology, MPIO, Germany) who has kindly povided the Straw-colored fruit bat data test package ask at available for linux/windows (please, indicate your OS) any feedback welcome questions?????
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