对于基于代理的建模项目,我正在考虑使用tidyverse的tibble
而不是matrix
。我用一个非常简单的ABM(请参阅下文)检查了两者的性能,在该模型中我模拟了一个人口老化,死亡和出生的人口。对于ABM典型,我使用的是for循环和索引。
在对两个数据结构进行基准测试时(请参见此处的图形:https://github.com/marcosmolla/tibble_vs_matrix),矩阵比平移要快得多。但是,对于10e6运行,此结果实际上是相反的。而且我不知道为什么。
很高兴了解这个结果,以告知我将来是否应该针对这种用例使用小块或矩阵。
谢谢大家的投入!
# This code benchmarks the speed of tibbles versus matrices. This should be useful for evaluating the suitability of tibbles in a ABM context where matrix data is frequently altered in matrices (or vectors).
library(tidyverse)
library(reshape2)
library(cowplot)
lapply(c(10^1, 10^2, 10^3, 10^4, 10^5, 10^6), function(runtime){
# Set up tibble
indTBL <- tibble(id=1:100,
type=sample(1:3, size=100, replace=T),
age=1)
# Set up matrix (from tibble)
indMAT <- as.matrix(indTBL)
# Simulation run with tibble
t <- Sys.time()
for(i in 1:runtime){
# increase age
indTBL$age <- indTBL[["age"]]+1
# replace individuals by chance or when max age
dead <- (1:100)[runif(n=100,min=0,max=1)<=0.01 | indTBL[["age"]]>100]
indTBL[dead, "age"] <- 1
indTBL[dead, "type"] <- sample(1:3, size=length(dead), replace=T)
}
tibbleTime <- as.numeric(Sys.time()-t)
# Simulation run with matrix
t <- Sys.time()
for(i in 1:runtime){
# increase age
indMAT[,"age"] <- indMAT[,"age"]+1
# replace individuals by chance or when max age
dead <- (1:100)[runif(n=100,min=0,max=1)<=0.01 | indMAT[,"age"]>100]
indMAT[dead, "age"] <- 1
indMAT[dead, "type"] <- sample(1:3, size=length(dead), replace=T)
}
matrixTime <- as.numeric(Sys.time()-t)
# Return both run times
return(data.frame(tibbleTime=tibbleTime, matrixTime=matrixTime))
}) %>% bind_rows() -> res
# Prepare data for ggplot
res$power <- 1:nrow(res)
res_m <- melt(data=res, id.vars="power")
# Line plot for results
ggplot(data=res_m, aes(x=power, y=value, color=variable)) + geom_point() + geom_line() + scale_color_brewer(palette="Paired") + ylab("Runtime in sec") + xlab(bquote("Simulation runs"~10^x))
答案 0 :(得分:0)
谢谢你们的答复。我使用microbenchmark
软件包进行了正确的基准测试。现在,我发现对于10e6运行,矩阵仍然更快。
indTBL <- tibble(id=1:100,
type=sample(1:3, size=100, replace=T),
age=1)
# Set up matrix (from tibble)
indMAT <- as.matrix(indTBL)
# Simulation run with tibble
runtime <- 10^6
microbenchmark(
tib=for(i in 1:runtime){
# increase age
indTBL$age <- indTBL[["age"]]+1
# replace individuals by chance or when max age
dead <- (1:100)[runif(n=100,min=0,max=1)<=0.01 | indTBL[["age"]]>100]
indTBL[dead, "age"] <- 1
indTBL[dead, "type"] <- sample(1:3, size=length(dead), replace=T)
},
# Simulation run with matrix
mat=for(i in 1:runtime){
# increase age
indMAT[,"age"] <- indMAT[,"age"]+1
# replace individuals by chance or when max age
dead <- (1:100)[runif(n=100,min=0,max=1)<=0.01 | indMAT[,"age"]>100]
indMAT[dead, "age"] <- 1
indMAT[dead, "type"] <- sample(1:3, size=length(dead), replace=T)
}, times=1
)
结果是
Unit: seconds
expr min lq mean median uq max neval cld
tib 80.22042 81.45051 82.26645 82.68061 83.28946 83.89831 3 b
mat 20.44746 20.66974 20.75168 20.89202 20.90378 20.91555 3 a
感谢Ilrs和MrFlick的提示。