DRP về thời gian truyền của các hóa chất trong phác đồ FOLFOX
Duy Nguyen
3/8/2020
library(DescTools)
library(ggpubr)## Loading required package: ggplot2## Loading required package: magrittrlibrary(rcompanion)
library(gridExtra)
options(scipen = 999)
t = "C:\\Users\\Admin\\Google Drive\\HOC TAP\\NCKH\\Data ung thu\\Viet bai\\R code\\Xu ly du lieu lan 2\\thoigian_folfox2.csv"
duy = read.csv(t)
duy1 = subset(duy, duy$hoachat != "5-FU bolus")
duy2 = subset(duy, duy$hoachat == "5-FU bolus")
attach(duy)
head(duy)## bv phacdo hoachat thoigian drp drp_thoigian
## 1 TB FOLFOX4 5-FU bolus 400 Co DRP-Cao
## 2 TB FOLFOX4 5-FU bolus 400 Co DRP-Cao
## 3 TB FOLFOX4 5-FU bolus 400 Co DRP-Cao
## 4 TB FOLFOX4 5-FU bolus 400 Co DRP-Cao
## 5 TB FOLFOX4 5-FU bolus 400 Co DRP-Cao
## 6 TB FOLFOX4 5-FU bolus 400 Co DRP-CaoThống kê thời gian truyền hóa chất theo phác đồ
Desc(phacdo ~ hoachat, data = duy)## ------------------------------------------------------------------------------
## phacdo ~ hoachat
##
##
## Summary:
## n: 3'870, rows: 2, columns: 4
##
## Pearson's Chi-squared test:
## X-squared = 59.282, df = 3, p-value = 0.0000000000008366
## Likelihood Ratio:
## X-squared = 55.49, df = 3, p-value = 0.000000000005397
## Mantel-Haenszel Chi-squared:
## X-squared = 29.907, df = 1, p-value = 0.00000004533
##
## Phi-Coefficient 0.124
## Contingency Coeff. 0.123
## Cramer's V 0.124
##
##
## hoachat 5-FU bolus 5-FU iv leucovorin oxaliplatin Sum
## phacdo
##
## FOLFOX4 freq 828 828 828 414 2'898
## perc 21.4% 21.4% 21.4% 10.7% 74.9%
## p.row 28.6% 28.6% 28.6% 14.3% .
## p.col 77.3% 77.3% 77.3% 63.0% .
##
## mFOLFOX6 freq 243 243 243 243 972
## perc 6.3% 6.3% 6.3% 6.3% 25.1%
## p.row 25.0% 25.0% 25.0% 25.0% .
## p.col 22.7% 22.7% 22.7% 37.0% .
##
## Sum freq 1'071 1'071 1'071 657 3'870
## perc 27.7% 27.7% 27.7% 17.0% 100.0%
## p.row . . . . .
## p.col . . . . .
## 
Biểu đồ tích lũy thời gian truyền của 5-FU bolus
p1 = ggplot(duy2, aes(thoigian, colour = hoachat)) + scale_x_continuous(name = "Relative duration (%)") + scale_y_continuous(name = "Cumulative percentage of prescriptions", breaks = seq(0,1,0.2)) + stat_ecdf() + theme(legend.position="top") + theme(legend.position="top") + geom_vline(xintercept=c(85,90,110,115), linetype="dashed", color = "purple", size=1.2)
p1
Biểu đồ tích lũy thời gian truyền của 5-FU iv, Leucovorin và Oxaliplatin
p2 = ggplot(duy1, aes(thoigian, colour = hoachat)) + scale_x_continuous(name = "Relative duration (%)") + scale_y_continuous(name = "Cumulative percentage of prescriptions", breaks = seq(0,1,0.2)) + stat_ecdf() + theme(legend.position="top") + theme(legend.position="top") + geom_vline(xintercept=c(85,90,110,115), linetype="dashed", color = "purple", size=1.2)
p2
Thống kê cho 5-FU bolus
#Biểu đồ tích lũy thời gian truyền của 5-FU bolus
fu_bolus = subset(duy, hoachat == "5-FU bolus")
fu_iv = subset(duy, hoachat == "5-FU iv")
leuco = subset(duy, hoachat == "leucovorin")
oxa = subset(duy, hoachat == "oxaliplatin")
p3 = ggplot(fu_bolus, aes(thoigian, colour = phacdo)) + scale_x_continuous(name = "Relative duration (%)") + scale_y_continuous(name = "", breaks = seq(0,1,0.2)) + stat_ecdf() + theme(legend.position="top") + theme(legend.position="top") + geom_vline(xintercept=c(85,90,110,115), linetype="dashed", color = "purple", size=1.2) + ggtitle("5-FU bolus")
p3
# Tất cả các lượt truyền đều có DRP về thời gian bolus 5-FU
Desc(drp ~ phacdo, data = fu_bolus)## ------------------------------------------------------------------------------
## drp ~ phacdo
##
##
## Summary:
## n: 1'071, rows: 1, columns: 2
##
## Pearson's Chi-squared test:
## X-squared = 319.54, df = 1, p-value < 0.00000000000000022
## Likelihood Ratio:
## X-squared = 337.7, df = 1, p-value < 0.00000000000000022
## Mantel-Haenszel Chi-squared:
## X-squared = NaN, df = 1, p-value = NA
##
## Phi-Coefficient 0.546
## Contingency Coeff. 0.479
## Cramer's V Inf
##
##
## phacdo FOLFOX4 mFOLFOX6 Sum
## drp
##
## Co freq 828 243 1'071
## perc 77.3% 22.7% 100.0%
## p.row 77.3% 22.7% .
## p.col 100.0% 100.0% .
##
## Sum freq 828 243 1'071
## perc 77.3% 22.7% 100.0%
## p.row . . .
## p.col . . .
## 
Thống kê cho 5-FU iv
#Biểu đồ tích lũy thời gian truyền của 5-FU iv
p4 = ggplot(fu_iv, aes(thoigian, colour = phacdo)) + scale_x_continuous(name = "Relative duration (%)") + scale_y_continuous(name = "", breaks = seq(0,1,0.2)) + stat_ecdf() + theme(legend.position="top") + theme(legend.position="top") + geom_vline(xintercept=c(85,90,110,115), linetype="dashed", color = "purple", size=1.2) + ggtitle("5-FU iv")
p4
#So sánh DRP về thời gian truyền của 5-FU iv
#Phiên giải giá trị: Pearson's Chi-squared test (cont. adj)
Desc(drp ~ phacdo, data = fu_iv)## ------------------------------------------------------------------------------
## drp ~ phacdo
##
##
## Summary:
## n: 1'071, rows: 2, columns: 2
##
## Pearson's Chi-squared test (cont. adj):
## X-squared = 64.47, df = 1, p-value = 0.00000000000000098
## Fisher's exact test p-value = 0.00000000000004464
## McNemar's chi-squared = 46.239, df = 1, p-value = 0.00000000001047
##
## estimate lwr.ci upr.ci'
##
## odds ratio 4.343 2.987 6.313
## rel. risk (col1) 1.626 1.370 1.929
## rel. risk (col2) 0.374 0.302 0.464
##
##
## Phi-Coefficient 0.249
## Contingency Coeff. 0.241
## Cramer's V 0.249
##
##
## phacdo FOLFOX4 mFOLFOX6 Sum
## drp
##
## Co freq 760 175 935
## perc 71.0% 16.3% 87.3%
## p.row 81.3% 18.7% .
## p.col 91.8% 72.0% .
##
## Khong freq 68 68 136
## perc 6.3% 6.3% 12.7%
## p.row 50.0% 50.0% .
## p.col 8.2% 28.0% .
##
## Sum freq 828 243 1'071
## perc 77.3% 22.7% 100.0%
## p.row . . .
## p.col . . .
##
##
## ----------
## ' 95% conf. level
#Thống kê DPR về thời gian truyền của 5-FU iv
Desc(drp_thoigian ~ phacdo, data = fu_iv)## ------------------------------------------------------------------------------
## drp_thoigian ~ phacdo
##
##
## Summary:
## n: 1'071, rows: 3, columns: 2
##
## Pearson's Chi-squared test:
## X-squared = 170.96, df = 2, p-value < 0.00000000000000022
## Likelihood Ratio:
## X-squared = 151.09, df = 2, p-value < 0.00000000000000022
## Mantel-Haenszel Chi-squared:
## X-squared = 9.9238, df = 1, p-value = 0.001632
##
## Phi-Coefficient 0.400
## Contingency Coeff. 0.371
## Cramer's V 0.400
##
##
## phacdo FOLFOX4 mFOLFOX6 Sum
## drp_thoigian
##
## DRP-Cao freq 0 27 27
## perc 0.0% 2.5% 2.5%
## p.row 0.0% 100.0% .
## p.col 0.0% 11.1% .
##
## DRP-Thap freq 760 148 908
## perc 71.0% 13.8% 84.8%
## p.row 83.7% 16.3% .
## p.col 91.8% 60.9% .
##
## Khong freq 68 68 136
## perc 6.3% 6.3% 12.7%
## p.row 50.0% 50.0% .
## p.col 8.2% 28.0% .
##
## Sum freq 828 243 1'071
## perc 77.3% 22.7% 100.0%
## p.row . . .
## p.col . . .
## 
Thống kê cho Leucovorin
#Biểu đồ tích lũy thời gian truyền của Leucovorin
p5 = ggplot(leuco, aes(thoigian, colour = phacdo)) + scale_x_continuous(name = "Relative duration (%)") + scale_y_continuous(name = "", breaks = seq(0,1,0.2)) + stat_ecdf() + theme(legend.position="top") + theme(legend.position="top") + geom_vline(xintercept=c(85,90,110,115), linetype="dashed", color = "purple", size=1.2) + ggtitle("Leucovorin")
p5
#So sánh DRP về thời gian truyền của Leucovorin
#Phiên giải giá trị: Pearson's Chi-squared test (cont. adj)
Desc(drp ~ phacdo, data = leuco)## ------------------------------------------------------------------------------
## drp ~ phacdo
##
##
## Summary:
## n: 1'071, rows: 2, columns: 2
##
## Pearson's Chi-squared test (cont. adj):
## X-squared = 617.41, df = 1, p-value < 0.00000000000000022
## Fisher's exact test p-value < 0.00000000000000022
## McNemar's chi-squared = 439.56, df = 1, p-value < 0.00000000000000022
##
## estimate lwr.ci upr.ci'
##
## odds ratio 0.00358 0.00154 0.00835
## rel. risk (col1) 0.03896 0.01775 0.08550
## rel. risk (col2) 10.87470 8.80449 13.43170
##
##
## Phi-Coefficient 0.762
## Contingency Coeff. 0.606
## Cramer's V 0.762
##
##
## phacdo FOLFOX4 mFOLFOX6 Sum
## drp
##
## Co freq 6 163 169
## perc 0.6% 15.2% 15.8%
## p.row 3.6% 96.4% .
## p.col 0.7% 67.1% .
##
## Khong freq 822 80 902
## perc 76.8% 7.5% 84.2%
## p.row 91.1% 8.9% .
## p.col 99.3% 32.9% .
##
## Sum freq 828 243 1'071
## perc 77.3% 22.7% 100.0%
## p.row . . .
## p.col . . .
##
##
## ----------
## ' 95% conf. level
#Thống kê DPR về thời gian truyền của Leucovorin
Desc(drp_thoigian ~ phacdo, data = leuco)## ------------------------------------------------------------------------------
## drp_thoigian ~ phacdo
##
##
## Summary:
## n: 1'071, rows: 3, columns: 2
##
## Pearson's Chi-squared test:
## X-squared = 622.93, df = 2, p-value < 0.00000000000000022
## Likelihood Ratio:
## X-squared = 559.39, df = 2, p-value < 0.00000000000000022
## Mantel-Haenszel Chi-squared:
## X-squared = 554.03, df = 1, p-value < 0.00000000000000022
##
## Phi-Coefficient 0.763
## Contingency Coeff. 0.606
## Cramer's V 0.763
##
##
## phacdo FOLFOX4 mFOLFOX6 Sum
## drp_thoigian
##
## DRP-Cao freq 0 52 52
## perc 0.0% 4.9% 4.9%
## p.row 0.0% 100.0% .
## p.col 0.0% 21.4% .
##
## DRP-Thap freq 6 111 117
## perc 0.6% 10.4% 10.9%
## p.row 5.1% 94.9% .
## p.col 0.7% 45.7% .
##
## Khong freq 822 80 902
## perc 76.8% 7.5% 84.2%
## p.row 91.1% 8.9% .
## p.col 99.3% 32.9% .
##
## Sum freq 828 243 1'071
## perc 77.3% 22.7% 100.0%
## p.row . . .
## p.col . . .
## 
Thống kê cho Oxaliplatin
#Biểu đồ tích lũy thời gian truyền của Oxaliplatin
p6 = ggplot(oxa, aes(thoigian, colour = phacdo)) + scale_x_continuous(name = "Relative duration (%)") + scale_y_continuous(name = "", breaks = seq(0,1,0.2)) + stat_ecdf() + theme(legend.position="top") + theme(legend.position="top") + geom_vline(xintercept=c(85,90,110,115), linetype="dashed", color = "purple", size=1.2) + ggtitle("Oxaliplatin")
p6
#So sánh DRP về thời gian truyền của oxaliplatin
#Phiên giải giá trị: Pearson's Chi-squared test (cont. adj)
Desc(drp ~ phacdo, data = oxa)## ------------------------------------------------------------------------------
## drp ~ phacdo
##
##
## Summary:
## n: 657, rows: 2, columns: 2
##
## Pearson's Chi-squared test (cont. adj):
## X-squared = 460.98, df = 1, p-value < 0.00000000000000022
## Fisher's exact test p-value < 0.00000000000000022
## McNemar's chi-squared = 78.293, df = 1, p-value < 0.00000000000000022
##
## estimate lwr.ci upr.ci'
##
## odds ratio 0.0006116 0.0000838 0.0044614
## rel. risk (col1) 0.0057366 0.0008120 0.0405306
## rel. risk (col2) 9.3802198 7.1971197 12.2255189
##
##
## Phi-Coefficient 0.841
## Contingency Coeff. 0.644
## Cramer's V 0.841
##
##
## phacdo FOLFOX4 mFOLFOX6 Sum
## drp
##
## Co freq 1 194 195
## perc 0.2% 29.5% 29.7%
## p.row 0.5% 99.5% .
## p.col 0.2% 79.8% .
##
## Khong freq 413 49 462
## perc 62.9% 7.5% 70.3%
## p.row 89.4% 10.6% .
## p.col 99.8% 20.2% .
##
## Sum freq 414 243 657
## perc 63.0% 37.0% 100.0%
## p.row . . .
## p.col . . .
##
##
## ----------
## ' 95% conf. level
#Thống kê DPR về thời gian truyền của oxaliplatin
Desc(drp_thoigian ~ phacdo, data = oxa)## ------------------------------------------------------------------------------
## drp_thoigian ~ phacdo
##
##
## Summary:
## n: 657, rows: 2, columns: 2
##
## Pearson's Chi-squared test (cont. adj):
## X-squared = 460.98, df = 1, p-value < 0.00000000000000022
## Fisher's exact test p-value < 0.00000000000000022
## McNemar's chi-squared = 78.293, df = 1, p-value < 0.00000000000000022
##
## estimate lwr.ci upr.ci'
##
## odds ratio 0.0006116 0.0000838 0.0044614
## rel. risk (col1) 0.0057366 0.0008120 0.0405306
## rel. risk (col2) 9.3802198 7.1971197 12.2255189
##
##
## Phi-Coefficient 0.841
## Contingency Coeff. 0.644
## Cramer's V 0.841
##
##
## phacdo FOLFOX4 mFOLFOX6 Sum
## drp_thoigian
##
## DRP-Cao freq 1 194 195
## perc 0.2% 29.5% 29.7%
## p.row 0.5% 99.5% .
## p.col 0.2% 79.8% .
##
## Khong freq 413 49 462
## perc 62.9% 7.5% 70.3%
## p.row 89.4% 10.6% .
## p.col 99.8% 20.2% .
##
## Sum freq 414 243 657
## perc 63.0% 37.0% 100.0%
## p.row . . .
## p.col . . .
##
##
## ----------
## ' 95% conf. level
grid.arrange(p3, p4, p5,p6 + rremove("x.text"), ncol = 2, nrow = 2)