if(!require("pacman")) install.packages("pacman")
pacman::p_load(broom,epiR,knitr,tidyverse)
## Primray Efficacy ##
rate_rr_1 <- as.table(matrix(c(85,85/11.74,167,167/23.64), nrow = 2, byrow = TRUE))
rr_relativeraterisk <- epi.2by2(dat = rate_rr_1, method = "cohort.time", conf.level = 0.95, units = 100, outcome = "as.columns")
rr_relativeraterisk
## Outcome + Time at risk Inc rate *
## Exposed + 85 7.24 1174
## Exposed - 167 7.06 2364
## Total 252 14.30 1762
##
## Point estimates and 95% CIs:
## -------------------------------------------------------------------
## Inc rate ratio 0.50 (0.38, 0.65)
## Attrib rate * -1190.00 (-1626.85, -753.15)
## Attrib rate in population * -602.32 (-1021.67, -182.96)
## Attrib fraction in exposed (%) -101.36 (-164.64, -54.17)
## Attrib fraction in population (%) -34.19 (-38.02, -30.19)
## -------------------------------------------------------------------
## Wald confidence limits
## CI: confidence interval
## * Outcomes per 100 units of population time at risk
tidy(rr_relativeraterisk, parameters = "moa") %>% kable
| IRR.strata.wald |
0.4966159 |
0.3778774 |
0.6486139 |
| ARate.strata.wald |
-1190.0000000 |
-1626.8524487 |
-753.1475513 |
| PARate.strata.wald |
-602.3168882 |
-1021.6742229 |
-182.9595536 |
| AFRate.strata.wald |
-1.0136286 |
-1.6463606 |
-0.5417493 |
| PAFRate.strata.wald |
-0.3418985 |
-0.3802131 |
-0.3018822 |
tidy(rr_relativeraterisk, parameters = "stat") %>% kable
| chisq.strata |
1.704546 |
1 |
0.1916945 |
ve_relativeraterisk <- 1 - rr_relativeraterisk[["massoc"]][["IRR.strata.wald"]]
ve_relativeraterisk[c(1,3,2)]%>% kable
| 0.5033841 |
0.3513861 |
0.6221226 |
## Secondary Efficacy ##
rate_rr_2 <- as.table(matrix(c(7,7/0.97,31,31/4.39), nrow = 2, byrow = TRUE))
rr_relativeraterisk_2 <- epi.2by2(dat = rate_rr_2, method = "cohort.time", conf.level = 0.95, units = 100, outcome = "as.columns")
rr_relativeraterisk_2
## Outcome + Time at risk Inc rate *
## Exposed + 7 7.22 97
## Exposed - 31 7.06 439
## Total 38 14.28 266
##
## Point estimates and 95% CIs:
## -------------------------------------------------------------------
## Inc rate ratio 0.22 (0.08, 0.51)
## Attrib rate * -342.00 (-512.43, -171.57)
## Attrib rate in population * -172.86 (-349.04, 3.33)
## Attrib fraction in exposed (%) -352.58 (-1117.69, -95.52)
## Attrib fraction in population (%) -64.95 (-70.58, -58.37)
## -------------------------------------------------------------------
## Wald confidence limits
## CI: confidence interval
## * Outcomes per 100 units of population time at risk
tidy(rr_relativeraterisk_2, parameters = "moa") %>% kable
| IRR.strata.wald |
0.2209567 |
0.0821224 |
0.5114515 |
| ARate.strata.wald |
-342.0000000 |
-512.4261582 |
-171.5738418 |
| PARate.strata.wald |
-172.8562500 |
-349.0440343 |
3.3315343 |
| AFRate.strata.wald |
-3.5257732 |
-11.1769449 |
-0.9552197 |
| PAFRate.strata.wald |
-0.6494845 |
-0.7057766 |
-0.5837344 |
tidy(rr_relativeraterisk_2, parameters = "stat") %>% kable
| chisq.strata |
5.408648 |
1 |
0.0200372 |
ve_relativeraterisk_2 <- 1 - rr_relativeraterisk_2[["massoc"]][["IRR.strata.wald"]]
ve_relativeraterisk_2[c(1,3,2)] %>% kable
| 0.7790433 |
0.4885485 |
0.9178776 |
Source: Otavio Ranzani - otavio_ranzani