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beat_by_beat_analysis.R
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library(ggplot2)
library(stringr)
library(plyr)
library(dplyr)
library(lubridate)
library(reshape2)
library(scales)
library(ggthemes)
library(Metrics)
data <- read.csv("r2plus1d_18_32_2_pretrained_test_predictions.csv", header = FALSE)
str(data)
dataNoAugmentation <- data[data$V2 == 0,]
str(dataNoAugmentation)
dataGlobalAugmentation <- data %>% group_by(V1) %>% summarize(meanPrediction = mean(V3), sdPred = sd(V3))
str(dataGlobalAugmentation)
sizeData <- read.csv("size.csv")
sizeData <- sizeData[sizeData$ComputerSmall == 1,]
str(sizeData)
sizeRelevantFrames <- sizeData[c(1,2)]
sizeRelevantFrames$Frame <- sizeRelevantFrames$Frame - 32
sizeRelevantFrames[sizeRelevantFrames$Frame < 0,]$Frame <- 0
beatByBeat <- merge(sizeRelevantFrames, data, by.x = c("Filename", "Frame"), by.y = c("V1", "V2"))
beatByBeat <- beatByBeat %>% group_by(Filename) %>% summarize(meanPrediction = mean(V3), sdPred = sd(V3))
str(beatByBeat)
### For use, need to specify file directory
fileLocation <- "/Users/davidouyang/Local Medical Data/"
ActualNumbers <- read.csv(paste0(fileLocation, "FileList.csv", sep = ""))
ActualNumbers <- ActualNumbers[c(1,2)]
str(ActualNumbers)
dataNoAugmentation <- merge(dataNoAugmentation, ActualNumbers, by.x = "V1", by.y = "Filename", all.x = TRUE)
dataNoAugmentation$AbsErr <- abs(dataNoAugmentation$V3 - dataNoAugmentation$EF)
str(dataNoAugmentation)
summary(abs(dataNoAugmentation$V3 - dataNoAugmentation$EF))
# Mean of 4.216
rmse(dataNoAugmentation$V3,dataNoAugmentation$EF)
## 5.56
modelNoAugmentation <- lm(dataNoAugmentation$EF ~ dataNoAugmentation$V3)
summary(modelNoAugmentation)$r.squared
# 0.79475
beatByBeat <- merge(beatByBeat, ActualNumbers, by.x = "Filename", by.y = "Filename", all.x = TRUE)
summary(abs(beatByBeat$meanPrediction - beatByBeat$EF))
# Mean of 4.051697
rmse(beatByBeat$meanPrediction, beatByBeat$EF)
# 5.325237
modelBeatByBeat <- lm(beatByBeat$EF ~ beatByBeat$meanPrediction)
summary(modelBeatByBeat)$r.squared
# 0.8093174
beatByBeatAnalysis <- merge(sizeRelevantFrames, data, by.x = c("Filename", "Frame"), by.y = c("V1", "V2"))
str(beatByBeatAnalysis)
MAEdata <- data.frame(counter = 1:500)
MAEdata$sample <- -9999
MAEdata$error <- -9999
str(MAEdata)
for (i in 1:500){
samplingBeat <- sample_n(beatByBeatAnalysis %>% group_by(Filename), 1 + floor((i-1)/100), replace = TRUE) %>% group_by(Filename) %>% dplyr::summarize(meanPred = mean(V3))
samplingBeat <- merge(samplingBeat, ActualNumbers, by.x = "Filename", by.y = "Filename", all.x = TRUE)
samplingBeat$error <- abs(samplingBeat$meanPred - samplingBeat$EF)
MAEdata$sample[i] <- 1 + floor((i-1)/100)
MAEdata$error[i] <- mean(samplingBeat$error )
}
str(MAEdata)
beatBoxPlot <- ggplot(data = MAEdata) + geom_boxplot(aes(x = sample, y = error, group = sample), outlier.shape = NA
) + theme_classic() + theme(legend.position = "none", axis.text.y = element_text( size=7)) + xlab("Number of Sampled Beats") + ylab("Mean Absolute Error") + scale_fill_brewer(palette = "Set1", direction = -1)
beatBoxPlot