track_stat <- function(x,framerate=30,pxsize=100){ x\$X <- (x\$X*pxsize)/1000 x\$Y <- (x\$Y*pxsize)/1000 out <- ddply(x,.variables = "track",.fun= function(x) { speed <- 0 for (i in 2:nrow(x)){ speed <- speed + (x\$X[i]-x\$X[i-1])^2+(x\$Y[i]-x\$Y[i-1])^2/((x\$frame[i]-x\$frame[i-1])*framerate) } speed <- speed/nrow(x) coord <- cbind(x\$X,x\$Y) # use pricipal component analysis on X and Y coordinates to get eigenvectors: major and minor axis D <- princomp(coord) angle <- atan2(D\$loadings[2,1],D\$loadings[1,1]) #calculate convex hull and futher statistics y <- chull(coord) area <- pracma::polyarea(coord[rev(y),1], coord[rev(y),2]) perimeter <- pracma::poly_length(coord[rev(y),1], coord[rev(y),2]) D_chull <- princomp(coord[y,]) #return(data.frame("sd"=((sd(x\$X)+sd(x\$Y))/2)*2.35,"N"=nrow(x),"channel"=1)) # return(data.frame(,"N"=nrow(x),"channel"=1)) return(data.frame("N"=nrow(x),"meanX"=mean(x\$X),"meanY"=mean(x\$Y),"meanspeed"=speed , "sd"=((sd(x\$X)+sd(x\$Y))/2),"sdpri"=((D\$sdev[1]+D\$sdev[2])/2),"major"=D\$sdev[1],"minor"=D\$sdev[2], "width"=(max(D\$scores[,1])-min(D\$scores[,1])),"ratio"=(D\$sdev[1]/D\$sdev[2]),"angle"=angle, "chull_area"=area,"chull_perimeter"=perimeter,"chull_major"=D_chull\$sdev[1],"chull_minor"=D_chull\$sdev[2])) }) return(out) } TRACK_STAT <- function(x,framerate=30,pxsize=100){ UseMethod("TRACK_STAT") } TRACK_STAT.default <- function(x,framerate=30,pxsize=100){ stop("TRACK_STAT requires data frame") } TRACK_STAT.data.frame <- function(x,framerate=30,pxsize=100){ track_stat(x,framerate,pxsize) } TRACK_STAT.list <- function(x,framerate=30,pxsize=100){ llply(x,function(x){ TRACK_STAT(x,framerate,pxsize) }) } segment_stat <- function(x){ get_angle <- function(x){ seg_angle <- vector() for(i in 1:(nrow(x)-2)){ A <- as.numeric(x[i,2:3]) B <- as.numeric(x[i+1,2:3]) C <- as.numeric(x[i+2,2:3]) AB <- B-A CB <- C-B #dAB <- sqrt((B[1]-A[1])^2+(B[2]-A[2])^2) #dBC <- sqrt((C[1]-B[1])^2+(C[2]-B[2])^2) #Formula obtained from https://gitlab.com/anders.sejr.hansen/anisotropy angle <- abs(atan2(det(cbind(AB,CB)),AB%*%CB)) angle <- angle/pi*180 seg_angle <- c(seg_angle,angle) } seg_angle <- c(-1,seg_angle,-1) return(seg_angle) } result <- ddply(x,.variables = "track",function(x){ if(nrow(x)>4){x\$angle <- get_angle(x)}else{ x\$angle<- 0 } if(!is.null(x\$displacement)){ x\$disp_squared <- x\$displacement^2 x\$disp_squared[x\$displacement==-1] <- -1 } return(x) } ) return(result) } SEGMENT_STAT <- function(x){ UseMethod("SEGMENT_STAT") } SEGMENT_STAT.default <- function(x){ stop("SEGMENT_STAT requires data frame") } SEGMENT_STAT.data.frame <- function(x){ segment_stat(x) } SEGMENT_STAT.list <- function(x){ result <- llply(x,function(x){ SEGMENT_STAT(x) }) return(result) }