[英]How to calculate distance between different IDs over time by group?
我的(示例)数据结构如下...其中参与者的 X 和 Y 坐标在不同条件下记录,随时间收集:
Individ <- data.frame(Participant = c("Bill", "Bill", "Bill", "Bill", "Bill", "Harry", "Harry", "Harry", "Harry","Harry", "Paul", "Paul", "Paul", "Paul", "Paul"),
Time = c(0.01, 0.02, 0.03, 0.04, 0.05, 0.01, 0.02, 0.03, 0.04, 0.05, 0.01, 0.02, 0.03, 0.04, 0.05),
Condition = c("Expr", "Expr", "Expr", "Expr", "Expr", "Con", "Con", "Con", "Con", "Con", "Nor", "Nor", "Nor", "Nor", "Nor"),
X = c(26.07, 26.06, 26.05, 26.09, 26.04, 26.65, 26.64, 26.62, 26.63, 26.62, 27.99, 28.01, 28.01, 28.02, 28.02),
Y = c(-5.01, -5.12, -5.14, -5.18, -5.2065, -12.37, 12.36, -12.35, -12.34, 12.33, -5.52, -5.514, -5.51, -5.50, -5.4962))
X 和 Y 坐标是从同一位置捕获的。 我可以使用以下方法计算每个参与者覆盖的距离:
require(plyr)
require(dplyr)
DistanceOutput <- Individ %>%
arrange(Participant, Time, Condition) %>%
group_by(Participant, Condition) %>%
mutate( lagX = lag(X, order_by=Time), lagY = lag(Y, order_by=Time)) %>%
rowwise() %>%
mutate(Distance = dist( matrix( c(X,Y,lagX,lagY),nrow=2,byrow=TRUE) )) %>%
select(-lagX, -lagY)
但是,我怎么能计算出每个之间的距离Participant
超过Time
,根据自己的Condition
。 例如,比尔和哈利之间的距离,比尔和保罗加上哈利和保罗随着时间的推移?
我的数据集是 179,800 obs。 所以理想情况下,首选快速解决方案。 谢谢!
这是一种计算每个参与者在每个时间点之间距离的方法。 我怀疑这是最有效的方法,但也许其他人会提出更优雅的解决方案。
您说过要计算每个Condition
参与者之间的距离。 在您的示例数据中,每个条件只有一个参与者。 但是,除了Time
之外,下面的解决方案可以很容易地扩展到Condition
应用。
library(reshape2)
library(dplyr)
# Calculate distance matrix for each Time
res = lapply(unique(Individ$Time), function(i) {
mat = as.matrix(Individ[Individ$Time==i, c("X","Y")])
rownames(mat) = Individ$Participant[Individ$Time==i]
# Distance matrix
d = as.matrix(dist(mat))
# Keep only lower triangle
d[upper.tri(d, diag=TRUE)] = NA
# Return data frame with distances, time and participants
data.frame(Time=i, d) %>% add_rownames("P1")
})
# Combine all time points into single long data frame of distances
res = bind_rows(res) %>%
melt(id.var=c("Time","P1"), variable.name="P2", value.name="Distance") %>%
filter(!is.na(Distance)) %>%
rowwise %>%
mutate(Pair = paste(sort(c(as.character(P1), as.character(P2))), collapse="-")) %>%
select(Pair, Time, Distance) %>%
arrange(Pair, Time)
res
Pair Time Distance 1 Bill-Harry 0.01 7.382818 2 Bill-Harry 0.02 17.489620 3 Bill-Harry 0.03 7.232496 4 Bill-Harry 0.04 7.180334 5 Bill-Harry 0.05 17.546089 6 Bill-Paul 0.01 1.986580 7 Bill-Paul 0.02 1.989406 8 Bill-Paul 0.03 1.994618 9 Bill-Paul 0.04 1.956349 10 Bill-Paul 0.05 2.001081 11 Harry-Paul 0.01 6.979835 12 Harry-Paul 0.02 17.926427 13 Harry-Paul 0.03 6.979807 14 Harry-Paul 0.04 6.979807 15 Harry-Paul 0.05 17.881091
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