R/estSummary.R
In tranlm/lrecImpact: Analyzing the impact of a Low Risk Express Care program
###############################################################################
# Description: Add comment
#
# Author: Linh Tran <tranlm@berkeley.edu>
# Date: Apr 10, 2015
###############################################################################
estSummary = function(estimator, fileloc, gloc=NULL, file, timepts){
######################
## LOADS EXCEL FILE ##
######################
parms = loadWorkbook(file=file)
sheets = getSheets(parms)
cs0 <- CellStyle(parms) + DataFormat("#,##0")
cs2 <- CellStyle(parms) + DataFormat("#,##0.00")
cs4 <- CellStyle(parms) + DataFormat("#,##0.0000")
colStyle = list('1'=cs4, '2'=cs4, '3'=cs4, '4'=cs4, '5'=cs4, '6'=cs4, '7'=cs4, '8'=cs4, '9'=cs4, '10'=cs4, '11'=cs4, '12'=cs4)
## ASSIGNS FILE NAME FITS SAVED AS ##
if(grepl("unadjusted", tolower(estimator))) {
filename = "null"
} else if(grepl("glm", tolower(estimator))) {
filename = "glm"
} else if(grepl("sl", tolower(estimator))) {
filename = "SL"
}
###################
## g-FITS (LONG) ##
###################
if(grepl("long", tolower(estimator))) {
if(grepl("glm", tolower(estimator))) {
gA1.fit = readRDS(paste0(gloc, "/glm/disc90/A1.glm.RDS"))
gA2.fit = readRDS(paste0(gloc, "/glm/disc90/A2.glm.RDS"))
gC1.fit = readRDS(paste0(gloc, "/glm/disc90/C1.glm.RDS"))
gC2.fit = readRDS(paste0(gloc, "/glm/disc90/C2.glm.RDS"))
## COEF ##
addDataFrame(x = summary(gA1.fit)$coef, sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = TRUE, startColumn = 1, startRow=4, colStyle=colStyle)
addDataFrame(x = summary(gA2.fit)$coef, sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = TRUE, startColumn = 7, startRow=4, colStyle=colStyle)
addDataFrame(x = summary(gC1.fit)$coef, sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = TRUE, startColumn = 13, startRow=4, colStyle=colStyle)
addDataFrame(x = summary(gC2.fit)$coef, sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = TRUE, startColumn = 19, startRow=4, colStyle=colStyle)
} else if(grepl("sl", tolower(estimator))) {
gA1.fit = readRDS(paste0(gloc, "/SL/disc90/A1.SL.RDS"))
gA2.fit = readRDS(paste0(gloc, "/SL/disc90/A2.SL.RDS"))
gC1.fit = readRDS(paste0(gloc, "/SL/disc90/C1.SL.psi_00.RDS"))
gC2.fit = readRDS(paste0(gloc, "/SL/disc90/C2.SL.RDS"))
## CV-RISK ##
addDataFrame(x = as.matrix(gA1.fit$cvRisk), sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = FALSE, startColumn = 1, startRow=47, colStyle=colStyle)
addDataFrame(x = as.matrix(gA2.fit$cvRisk), sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = FALSE, startColumn = 7, startRow=47, colStyle=colStyle)
addDataFrame(x = as.matrix(gC1.fit$cvRisk), sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = FALSE, startColumn = 13, startRow=47, colStyle=colStyle)
addDataFrame(x = as.matrix(gC2.fit$cvRisk), sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = FALSE, startColumn = 19, startRow=47, colStyle=colStyle)
## COEF ##
addDataFrame(x = as.matrix(gA1.fit$coef), sheet = sheets[["g-LONG"]], row.names = FALSE, col.names = FALSE, startColumn = 3, startRow=47, colStyle=colStyle)
addDataFrame(x = as.matrix(gA2.fit$coef), sheet = sheets[["g-LONG"]], row.names = FALSE, col.names = FALSE, startColumn = 9, startRow=47, colStyle=colStyle)
addDataFrame(x = as.matrix(gC1.fit$coef), sheet = sheets[["g-LONG"]], row.names = FALSE, col.names = FALSE, startColumn = 15, startRow=47, colStyle=colStyle)
addDataFrame(x = as.matrix(gC2.fit$coef), sheet = sheets[["g-LONG"]], row.names = FALSE, col.names = FALSE, startColumn = 21, startRow=47, colStyle=colStyle)
}
}
########################################
## LOADS AND EXECUTES EACH TIME POINT ##
########################################
for(t in 1:timepts) {
psi_00 = readRDS(paste0(fileloc, "/", estimator, "/psi_00.", filename, ".tmle-t", t, ".RDS"))
psi_10 = readRDS(paste0(fileloc, "/", estimator, "/psi_10.", filename, ".tmle-t", t, ".RDS"))
psi_11 = readRDS(paste0(fileloc, "/", estimator, "/psi_11.", filename, ".tmle-t", t, ".RDS"))
if(!grepl("LONG", estimator)) {
gcmp_00 = readRDS(paste0(fileloc, "/", estimator, "/psi_00.", filename, ".gcmp-t", t, ".RDS"))
gcmp_10 = readRDS(paste0(fileloc, "/", estimator, "/psi_10.", filename, ".gcmp-t", t, ".RDS"))
gcmp_11 = readRDS(paste0(fileloc, "/", estimator, "/psi_11.", filename, ".gcmp-t", t, ".RDS"))
}
## VARIABLE NAMES ##
if(t==1 & (grepl("GLM_WIDE", estimator))) {
## AVAILABILITY ##
gA1names = names(coef(psi_00$fit$g[[paste0("avail.",t-1)]]))
gA1names[16:length(gA1names)] = sub(paste0("\\.", t-1,"$"), ".t", gA1names[16:length(gA1names)])
addDataFrame(x = gA1names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 1, startRow=4)
gA1names = names(coef(psi_10$fit$g[[paste0("avail.",t-1)]]))
gA1names[16:length(gA1names)] = sub(paste0("\\.", t-1,"$"), ".t", gA1names[16:length(gA1names)])
addDataFrame(x = gA1names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15, startRow=4)
gA1names = names(coef(psi_11$fit$g[[paste0("avail.",t-1)]]))
gA1names[16:length(gA1names)] = sub(paste0("\\.", t-1,"$"), ".t", gA1names[16:length(gA1names)])
addDataFrame(x = gA1names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29, startRow=4)
## ENROLLMENT ##
gA2names = names(coef(psi_10$fit$g[[paste0("enroll.",t-1)]]))
gA2names[16:length(gA2names)] = sub(paste0("\\.", t-1,"$"), ".t", gA2names[16:length(gA2names)])
addDataFrame(x = gA2names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15, startRow=38)
gA2names = names(coef(psi_11$fit$g[[paste0("enroll.",t-1)]]))
gA2names[16:length(gA2names)] = sub(paste0("\\.", t-1,"$"), ".t", gA2names[16:length(gA2names)])
addDataFrame(x = gA2names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29, startRow=38)
## TRANSFER ##
gC1names = names(coef(psi_00$fit$g[[paste0("transfer.",t-1)]]))
gC1names[16:length(gC1names)] = sub(paste0("\\.", t-1,"$"), ".t", gC1names[16:length(gC1names)])
addDataFrame(x = gC1names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 1, startRow=74)
gC1names = names(coef(psi_10$fit$g[[paste0("transfer.",t-1)]]))
gC1names[16:length(gC1names)] = sub(paste0("\\.", t-1,"$"), ".t", gC1names[16:length(gC1names)])
addDataFrame(x = gC1names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15, startRow=74)
gC1names = names(coef(psi_11$fit$g[[paste0("transfer.",t-1)]]))
gC1names[16:length(gC1names)] = sub(paste0("\\.", t-1,"$"), ".t", gC1names[16:length(gC1names)])
addDataFrame(x = gC1names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29, startRow=74)
## EOFU ##
gC2names = names(coef(psi_00$fit$g[[paste0("eofu.",t-1)]]))
addDataFrame(x = gC2names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 1, startRow=109)
gC2names = names(coef(psi_10$fit$g[[paste0("eofu.",t-1)]]))
addDataFrame(x = gC2names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15, startRow=109)
gC2names = names(coef(psi_11$fit$g[[paste0("eofu.",t-1)]]))
addDataFrame(x = gC2names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29, startRow=109)
}
###########################################
## g-FITS (WIDE), Q-FITS, and Qstar-FITS ##
###########################################
if(estimator!="Unadjusted") {
if(grepl("GLM_WIDE", estimator)) {
## PSI_00 g ##
addDataFrame(x = coef(psi_00$fit$g[[paste0("avail.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 1+t, startRow=4, colStyle=colStyle)
addDataFrame(x = coef(psi_00$fit$g[[paste0("transfer.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 1+t, startRow=74, colStyle=colStyle)
addDataFrame(x = coef(psi_00$fit$g[[paste0("eofu.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 1+t, startRow=109, colStyle=colStyle)
## PSI_10 g ##
if(class(psi_10$fit$g[[paste0("avail.",t-1)]])[1] != "character") {
addDataFrame(x = coef(psi_10$fit$g[[paste0("avail.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15+t, startRow=4, colStyle=colStyle)
}
addDataFrame(x = coef(psi_10$fit$g[[paste0("enroll.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15+t, startRow=38, colStyle=colStyle)
addDataFrame(x = coef(psi_10$fit$g[[paste0("transfer.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15+t, startRow=74, colStyle=colStyle)
addDataFrame(x = coef(psi_10$fit$g[[paste0("eofu.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15+t, startRow=109, colStyle=colStyle)
## PSI_11 g ##
if(class(psi_11$fit$g[[paste0("avail.",t-1)]])[1] != "character") {
addDataFrame(x = coef(psi_11$fit$g[[paste0("avail.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29+t, startRow=4, colStyle=colStyle)
}
if(class(psi_11$fit$g[[paste0("enroll.",t-1)]])[1] != "character") {
addDataFrame(x = coef(psi_11$fit$g[[paste0("enroll.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29+t, startRow=38, colStyle=colStyle)
}
addDataFrame(x = coef(psi_11$fit$g[[paste0("transfer.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29+t, startRow=74, colStyle=colStyle)
addDataFrame(x = coef(psi_11$fit$g[[paste0("eofu.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29+t, startRow=109, colStyle=colStyle)
} else if(grepl("SL_WIDE", estimator)) {
cat("NEED TO SUMMARIZE SL G-FITS\n")
}
############
## Q-FITS ##
############
## GLM ##
if(grepl("GLM", estimator)) {
Qnames = names(coef(psi_00$fit$Q[[1]]))
Qnames[16:length(Qnames)] = sub(paste0("\\.0$"), ".t", Qnames[16:length(Qnames)])
Qfits_00 = matrix(NA, ncol=t, nrow=length(coef(psi_00$fit$Q[[1]])), dimnames=list(Qnames, paste0("t",1:t)))
Qfits_10 = matrix(NA, ncol=t, nrow=length(coef(psi_10$fit$Q[[1]])), dimnames=list(Qnames, paste0("t",1:t)))
Qfits_11 = matrix(NA, ncol=t, nrow=length(coef(psi_11$fit$Q[[1]])), dimnames=list(Qnames, paste0("t",1:t)))
for(i in 1:t) {
## PSI_00 ##
Qfits_00[,i] = coef(psi_00$fit$Q[[i]])
## PSI_10 ##
Qfits_10[,i] = coef(psi_10$fit$Q[[i]])
## PSI_11 ##
Qfits_11[,i] = coef(psi_11$fit$Q[[i]])
}
addDataFrame(x = Qfits_00, sheet = sheets[[paste0("Q-", estimator)]], row.names = TRUE, col.names = FALSE, startColumn = round(0.5*t^2+1.5*t-1), startRow=4, colStyle=colStyle)
addDataFrame(x = Qfits_10, sheet = sheets[[paste0("Q-", estimator)]], row.names = TRUE, col.names = FALSE, startColumn = round(0.5*t^2+1.5*t-1), startRow=41, colStyle=colStyle)
addDataFrame(x = Qfits_11, sheet = sheets[[paste0("Q-", estimator)]], row.names = TRUE, col.names = FALSE, startColumn = round(0.5*t^2+1.5*t-1), startRow=78, colStyle=colStyle)
## SL ##
} else if(grepl("SL", estimator)) {
Qfits_00.coef = Qfits_10.coef = Qfits_11.coef = matrix(NA, ncol=t, nrow=length(psi_00$fit$Q[[1]]$coef), dimnames=list(names(psi_00$fit$Q[[1]]$coef), paste0("t",1:t)))
Qfits_00.cvRisk = Qfits_10.cvRisk = Qfits_11.cvRisk = matrix(NA, ncol=t, nrow=length(psi_00$fit$Q[[1]]$cvRisk), dimnames=list(names(psi_00$fit$Q[[1]]$cvRisk), paste0("t",1:t)))
for(i in 1:t) {
## PSI_00 ##
Qfits_00.coef[,i] = psi_00$fit$Q[[i]]$coef
Qfits_00.cvRisk[,i] = psi_00$fit$Q[[i]]$cvRisk
## PSI_10 ##
Qfits_10.coef[,i] = psi_10$fit$Q[[i]]$coef
Qfits_10.cvRisk[,i] = psi_10$fit$Q[[i]]$cvRisk
## PSI_11 ##
Qfits_11.coef[,i] = psi_11$fit$Q[[i]]$coef
Qfits_11.cvRisk[,i] = psi_11$fit$Q[[i]]$cvRisk
}
addDataFrame(x = rownames(Qfits_00.coef), sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t-1), startRow=5)
addDataFrame(x = rownames(Qfits_10.coef), sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t-1), startRow=42)
addDataFrame(x = rownames(Qfits_11.coef), sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t-1), startRow=79)
for(i in 1:t) {
addDataFrame(x = Qfits_00.coef[,i], sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t+1+(i-1)*2), startRow=5, colStyle=colStyle)
addDataFrame(x = Qfits_00.cvRisk[,i], sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t+(i-1)*2), startRow=5, colStyle=colStyle)
addDataFrame(x = Qfits_10.coef[,i], sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t+1+(i-1)*2), startRow=42, colStyle=colStyle)
addDataFrame(x = Qfits_10.cvRisk[,i], sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t+(i-1)*2), startRow=42, colStyle=colStyle)
addDataFrame(x = Qfits_11.coef[,i], sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t+1+(i-1)*2), startRow=79, colStyle=colStyle)
addDataFrame(x = Qfits_11.cvRisk[,i], sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t+(i-1)*2), startRow=79, colStyle=colStyle)
}
}
################
## Qstar-FITS ##
################
Qstar_00.eps = Qstar_10.eps = Qstar_11.eps = matrix(NA, ncol=t, nrow=1)
Qstar_00.con = Qstar_10.con = Qstar_11.con = matrix(NA, ncol=t, nrow=1)
for(i in 1:t) {
## PSI_00 ##
if (class(psi_00$fit$Qstar[[i]])[1]=="glm") {
Qstar_00.eps[,i] = coef(psi_00$fit$Qstar[[i]])
Qstar_00.con[,i] = 1
} else if (class(psi_00$fit$Qstar[[i]])[1]=="list") {
Qstar_00.eps[,i] = psi_00$fit$Qstar[[i]]$par
Qstar_00.con[,i] = 0
}
## PSI_10 ##
if (class(psi_10$fit$Qstar[[i]])[1]=="glm") {
Qstar_10.eps[,i] = coef(psi_10$fit$Qstar[[i]])
Qstar_10.con[,i] = 1
} else if (class(psi_10$fit$Qstar[[i]])[1]=="list") {
Qstar_10.eps[,i] = psi_10$fit$Qstar[[i]]$par
Qstar_10.con[,i] = 0
}
## PSI_11 ##
if (class(psi_11$fit$Qstar[[i]])[1]=="glm") {
Qstar_11.eps[,i] = coef(psi_11$fit$Qstar[[i]])
Qstar_11.con[,i] = 1
} else if (class(psi_11$fit$Qstar[[i]])[1]=="list") {
Qstar_11.eps[,i] = psi_11$fit$Qstar[[i]]$par
Qstar_11.con[,i] = 0
}
}
i.col = 3*(estimator=="GLM_WIDE") + 12*(estimator=="GLM_LONG") + 21*(estimator=="SL_WIDE") + 30*(estimator=="SL_LONG")
addDataFrame(x = Qstar_00.eps, sheet = sheets[["Qstar-FITS"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=3+t, colStyle=colStyle)
addDataFrame(x = Qstar_10.eps, sheet = sheets[["Qstar-FITS"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=12+t, colStyle=colStyle)
addDataFrame(x = Qstar_11.eps, sheet = sheets[["Qstar-FITS"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=21+t, colStyle=colStyle)
addDataFrame(x = Qstar_00.con, sheet = sheets[["Qstar-FITS"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=31+t, colStyle=colStyle)
addDataFrame(x = Qstar_10.con, sheet = sheets[["Qstar-FITS"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=47+t, colStyle=colStyle)
addDataFrame(x = Qstar_11.con, sheet = sheets[["Qstar-FITS"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=63+t, colStyle=colStyle)
}
##################
## CUMULATIVE-G ##
##################
cumgStyle = list('1'=cs4, '2'=cs4, '3'=cs4, '4'=cs4, '5'=cs4, '6'=cs4, '7'=cs0)
i.col = 2*(estimator=="Unadjusted") + 11*(estimator=="GLM_WIDE") + 20*(estimator=="GLM_LONG") + 29*(estimator=="SL_WIDE") + 38*(estimator=="SL_LONG")
addDataFrame(x = t(as.matrix(summary(psi_00$cum.g[,ncol(psi_00$cum.g)]))), sheet = sheets[["cum.g"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=3+t, colStyle=cumgStyle)
addDataFrame(x = t(as.matrix(summary(psi_10$cum.g[,ncol(psi_10$cum.g)]))), sheet = sheets[["cum.g"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=19+t, colStyle=cumgStyle)
addDataFrame(x = t(as.matrix(summary(psi_11$cum.g[,ncol(psi_11$cum.g)]))), sheet = sheets[["cum.g"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=35+t, colStyle=cumgStyle)
###############
## ESTIMATES ##
###############
## psi_00 ##
i.col = 3*(estimator=="Unadjusted") + 7*(estimator=="GLM_WIDE") + 11*(estimator=="GLM_LONG") + 15*(estimator=="SL_WIDE") + 19*(estimator=="SL_LONG")
addDataFrame(x = do.call('cbind', summary(psi_00, est="tmle")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=10+t, colStyle=colStyle)
addDataFrame(x = do.call('cbind', summary(psi_00, est="iptw")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=26+t, colStyle=colStyle)
## psi_10 ##
i.col = 25*(estimator=="Unadjusted") + 29*(estimator=="GLM_WIDE") + 33*(estimator=="GLM_LONG") + 37*(estimator=="SL_WIDE") + 41*(estimator=="SL_LONG")
addDataFrame(x = do.call('cbind', summary(psi_10, est="tmle")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=10+t, colStyle=colStyle)
addDataFrame(x = do.call('cbind', summary(psi_10, est="iptw")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=26+t, colStyle=colStyle)
## psi_11 ##
i.col = 47*(estimator=="Unadjusted") + 51*(estimator=="GLM_WIDE") + 55*(estimator=="GLM_LONG") + 59*(estimator=="SL_WIDE") + 63*(estimator=="SL_LONG")
addDataFrame(x = do.call('cbind', summary(psi_11, est="tmle")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=10+t, colStyle=colStyle)
addDataFrame(x = do.call('cbind', summary(psi_11, est="iptw")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=26+t, colStyle=colStyle)
## GCOMP ##
if(!grepl("LONG", estimator)) {
i.col = 3*(estimator=="Unadjusted") + 7*(estimator=="GLM_WIDE") + 11*(estimator=="GLM_LONG") + 15*(estimator=="SL_WIDE") + 19*(estimator=="SL_LONG")
addDataFrame(x = do.call('cbind', summary(gcmp_00, est="gcomp")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=42+t, colStyle=colStyle)
i.col = 25*(estimator=="Unadjusted") + 29*(estimator=="GLM_WIDE") + 33*(estimator=="GLM_LONG") + 37*(estimator=="SL_WIDE") + 41*(estimator=="SL_LONG")
addDataFrame(x = do.call('cbind', summary(gcmp_10, est="gcomp")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=42+t, colStyle=colStyle)
i.col = 47*(estimator=="Unadjusted") + 51*(estimator=="GLM_WIDE") + 55*(estimator=="GLM_LONG") + 59*(estimator=="SL_WIDE") + 63*(estimator=="SL_LONG")
addDataFrame(x = do.call('cbind', summary(gcmp_11, est="gcomp")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=42+t, colStyle=colStyle)
}
################
## TX EFFECTS ##
################
i.row = 4*(estimator=="Unadjusted") + 13*(estimator=="GLM_WIDE") + 22*(estimator=="GLM_LONG") + 31*(estimator=="SL_WIDE") + 40*(estimator=="SL_LONG")
# psi_10 vs psi_00 #
tmle.10v00 = summary(psi_10, psi_00, estimator="tmle")$effect.measures
iptw.10v00 = summary(psi_10, psi_00, estimator="iptw")$effect.measures
# psi_11 vs psi_10 #
tmle.11v10 = summary(psi_11, psi_10, estimator="tmle")$effect.measures
iptw.11v10 = summary(psi_11, psi_10, estimator="iptw")$effect.measures
# GCOMP #
if(!grepl("LONG", estimator)) {
gcmp.10v00 = summary(gcmp_10, gcmp_00, estimator="gcomp")$effect.measures
gcmp.11v10 = summary(gcmp_11, gcmp_10, estimator="gcomp")$effect.measures
}
##############################
## AVERAGE TREATMENT EFFECT ##
##############################
# TMLE (10v00) #
addDataFrame(x = tmle.10v00$ATE$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 3, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = tmle.10v00$ATE$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 4, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(tmle.10v00$ATE$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 5, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# IPTW (10v00) #
addDataFrame(x = iptw.10v00$ATE$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 3+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = iptw.10v00$ATE$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 4+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(iptw.10v00$ATE$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 5+13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# GCMP (10v00) #
if(!grepl("LONG", estimator)) {
addDataFrame(x = gcmp.10v00$ATE$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 3+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = gcmp.10v00$ATE$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 4+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(gcmp.10v00$ATE$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 5+26, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
}
# TMLE (11v10) #
addDataFrame(x = tmle.11v10$ATE$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 3, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = tmle.11v10$ATE$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 4, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(tmle.11v10$ATE$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 5, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# IPTW (11v10) #
addDataFrame(x = iptw.11v10$ATE$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 3+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = iptw.11v10$ATE$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 4+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(iptw.11v10$ATE$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 5+13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# GCMP (11v10) #
if(!grepl("LONG", estimator)) {
addDataFrame(x = gcmp.11v10$ATE$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 3+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = gcmp.11v10$ATE$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 4+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(gcmp.11v10$ATE$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 5+26, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
}
###################
## RELATIVE RISK ##
###################
# TMLE (10v00) #
addDataFrame(x = tmle.10v00$RR$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 7, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = tmle.10v00$RR$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 8, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(tmle.10v00$RR$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 9, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# IPTW (10v00) #
addDataFrame(x = iptw.10v00$RR$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 7+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = iptw.10v00$RR$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 8+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(iptw.10v00$RR$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 9+13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# GCMP (10v00) #
if(!grepl("LONG", estimator)) {
addDataFrame(x = gcmp.10v00$RR$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 7+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = gcmp.10v00$RR$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 8+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(gcmp.10v00$RR$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 9+26, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
}
# TMLE (11v10) #
addDataFrame(x = tmle.11v10$RR$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 7, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = tmle.11v10$RR$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 8, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(tmle.11v10$RR$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 9, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# IPTW (11v10) #
addDataFrame(x = iptw.11v10$RR$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 7+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = iptw.11v10$RR$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 8+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(iptw.11v10$RR$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 9+13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# GCMP (11v10) #
if(!grepl("LONG", estimator)) {
addDataFrame(x = gcmp.11v10$RR$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 7+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = gcmp.11v10$RR$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 8+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(gcmp.11v10$RR$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 9+26, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
}
################
## ODDS RATIO ##
################
# TMLE (10v00) #
addDataFrame(x = tmle.10v00$OR$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 11, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = tmle.10v00$OR$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 12, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(tmle.10v00$OR$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# IPTW (10v00) #
addDataFrame(x = iptw.10v00$OR$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 11+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = iptw.10v00$OR$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 12+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(iptw.10v00$OR$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 13+13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# GCMP (10v00) #
if(!grepl("LONG", estimator)) {
addDataFrame(x = gcmp.10v00$OR$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 11+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = gcmp.10v00$OR$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 12+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(gcmp.10v00$OR$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 13+26, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
}
# TMLE (11v10) #
addDataFrame(x = tmle.11v10$OR$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 11, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = tmle.11v10$OR$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 12, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(tmle.11v10$OR$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# IPTW (11v10) #
addDataFrame(x = iptw.11v10$OR$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 11+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = iptw.11v10$OR$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 12+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(iptw.11v10$OR$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 13+13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# GCMP (11v10) #
if(!grepl("LONG", estimator)) {
addDataFrame(x = gcmp.11v10$OR$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 11+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = gcmp.11v10$OR$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 12+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(gcmp.11v10$OR$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 13+26, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
}
}
saveWorkbook(parms, file=file)
}
tranlm/lrecImpact documentation built on May 31, 2019, 7:45 p.m.
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###############################################################################
# Description: Add comment
#
# Author: Linh Tran <tranlm@berkeley.edu>
# Date: Apr 10, 2015
###############################################################################
estSummary = function(estimator, fileloc, gloc=NULL, file, timepts){
######################
## LOADS EXCEL FILE ##
######################
parms = loadWorkbook(file=file)
sheets = getSheets(parms)
cs0 <- CellStyle(parms) + DataFormat("#,##0")
cs2 <- CellStyle(parms) + DataFormat("#,##0.00")
cs4 <- CellStyle(parms) + DataFormat("#,##0.0000")
colStyle = list('1'=cs4, '2'=cs4, '3'=cs4, '4'=cs4, '5'=cs4, '6'=cs4, '7'=cs4, '8'=cs4, '9'=cs4, '10'=cs4, '11'=cs4, '12'=cs4)
## ASSIGNS FILE NAME FITS SAVED AS ##
if(grepl("unadjusted", tolower(estimator))) {
filename = "null"
} else if(grepl("glm", tolower(estimator))) {
filename = "glm"
} else if(grepl("sl", tolower(estimator))) {
filename = "SL"
}
###################
## g-FITS (LONG) ##
###################
if(grepl("long", tolower(estimator))) {
if(grepl("glm", tolower(estimator))) {
gA1.fit = readRDS(paste0(gloc, "/glm/disc90/A1.glm.RDS"))
gA2.fit = readRDS(paste0(gloc, "/glm/disc90/A2.glm.RDS"))
gC1.fit = readRDS(paste0(gloc, "/glm/disc90/C1.glm.RDS"))
gC2.fit = readRDS(paste0(gloc, "/glm/disc90/C2.glm.RDS"))
## COEF ##
addDataFrame(x = summary(gA1.fit)$coef, sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = TRUE, startColumn = 1, startRow=4, colStyle=colStyle)
addDataFrame(x = summary(gA2.fit)$coef, sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = TRUE, startColumn = 7, startRow=4, colStyle=colStyle)
addDataFrame(x = summary(gC1.fit)$coef, sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = TRUE, startColumn = 13, startRow=4, colStyle=colStyle)
addDataFrame(x = summary(gC2.fit)$coef, sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = TRUE, startColumn = 19, startRow=4, colStyle=colStyle)
} else if(grepl("sl", tolower(estimator))) {
gA1.fit = readRDS(paste0(gloc, "/SL/disc90/A1.SL.RDS"))
gA2.fit = readRDS(paste0(gloc, "/SL/disc90/A2.SL.RDS"))
gC1.fit = readRDS(paste0(gloc, "/SL/disc90/C1.SL.psi_00.RDS"))
gC2.fit = readRDS(paste0(gloc, "/SL/disc90/C2.SL.RDS"))
## CV-RISK ##
addDataFrame(x = as.matrix(gA1.fit$cvRisk), sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = FALSE, startColumn = 1, startRow=47, colStyle=colStyle)
addDataFrame(x = as.matrix(gA2.fit$cvRisk), sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = FALSE, startColumn = 7, startRow=47, colStyle=colStyle)
addDataFrame(x = as.matrix(gC1.fit$cvRisk), sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = FALSE, startColumn = 13, startRow=47, colStyle=colStyle)
addDataFrame(x = as.matrix(gC2.fit$cvRisk), sheet = sheets[["g-LONG"]], row.names = TRUE, col.names = FALSE, startColumn = 19, startRow=47, colStyle=colStyle)
## COEF ##
addDataFrame(x = as.matrix(gA1.fit$coef), sheet = sheets[["g-LONG"]], row.names = FALSE, col.names = FALSE, startColumn = 3, startRow=47, colStyle=colStyle)
addDataFrame(x = as.matrix(gA2.fit$coef), sheet = sheets[["g-LONG"]], row.names = FALSE, col.names = FALSE, startColumn = 9, startRow=47, colStyle=colStyle)
addDataFrame(x = as.matrix(gC1.fit$coef), sheet = sheets[["g-LONG"]], row.names = FALSE, col.names = FALSE, startColumn = 15, startRow=47, colStyle=colStyle)
addDataFrame(x = as.matrix(gC2.fit$coef), sheet = sheets[["g-LONG"]], row.names = FALSE, col.names = FALSE, startColumn = 21, startRow=47, colStyle=colStyle)
}
}
########################################
## LOADS AND EXECUTES EACH TIME POINT ##
########################################
for(t in 1:timepts) {
psi_00 = readRDS(paste0(fileloc, "/", estimator, "/psi_00.", filename, ".tmle-t", t, ".RDS"))
psi_10 = readRDS(paste0(fileloc, "/", estimator, "/psi_10.", filename, ".tmle-t", t, ".RDS"))
psi_11 = readRDS(paste0(fileloc, "/", estimator, "/psi_11.", filename, ".tmle-t", t, ".RDS"))
if(!grepl("LONG", estimator)) {
gcmp_00 = readRDS(paste0(fileloc, "/", estimator, "/psi_00.", filename, ".gcmp-t", t, ".RDS"))
gcmp_10 = readRDS(paste0(fileloc, "/", estimator, "/psi_10.", filename, ".gcmp-t", t, ".RDS"))
gcmp_11 = readRDS(paste0(fileloc, "/", estimator, "/psi_11.", filename, ".gcmp-t", t, ".RDS"))
}
## VARIABLE NAMES ##
if(t==1 & (grepl("GLM_WIDE", estimator))) {
## AVAILABILITY ##
gA1names = names(coef(psi_00$fit$g[[paste0("avail.",t-1)]]))
gA1names[16:length(gA1names)] = sub(paste0("\\.", t-1,"$"), ".t", gA1names[16:length(gA1names)])
addDataFrame(x = gA1names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 1, startRow=4)
gA1names = names(coef(psi_10$fit$g[[paste0("avail.",t-1)]]))
gA1names[16:length(gA1names)] = sub(paste0("\\.", t-1,"$"), ".t", gA1names[16:length(gA1names)])
addDataFrame(x = gA1names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15, startRow=4)
gA1names = names(coef(psi_11$fit$g[[paste0("avail.",t-1)]]))
gA1names[16:length(gA1names)] = sub(paste0("\\.", t-1,"$"), ".t", gA1names[16:length(gA1names)])
addDataFrame(x = gA1names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29, startRow=4)
## ENROLLMENT ##
gA2names = names(coef(psi_10$fit$g[[paste0("enroll.",t-1)]]))
gA2names[16:length(gA2names)] = sub(paste0("\\.", t-1,"$"), ".t", gA2names[16:length(gA2names)])
addDataFrame(x = gA2names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15, startRow=38)
gA2names = names(coef(psi_11$fit$g[[paste0("enroll.",t-1)]]))
gA2names[16:length(gA2names)] = sub(paste0("\\.", t-1,"$"), ".t", gA2names[16:length(gA2names)])
addDataFrame(x = gA2names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29, startRow=38)
## TRANSFER ##
gC1names = names(coef(psi_00$fit$g[[paste0("transfer.",t-1)]]))
gC1names[16:length(gC1names)] = sub(paste0("\\.", t-1,"$"), ".t", gC1names[16:length(gC1names)])
addDataFrame(x = gC1names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 1, startRow=74)
gC1names = names(coef(psi_10$fit$g[[paste0("transfer.",t-1)]]))
gC1names[16:length(gC1names)] = sub(paste0("\\.", t-1,"$"), ".t", gC1names[16:length(gC1names)])
addDataFrame(x = gC1names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15, startRow=74)
gC1names = names(coef(psi_11$fit$g[[paste0("transfer.",t-1)]]))
gC1names[16:length(gC1names)] = sub(paste0("\\.", t-1,"$"), ".t", gC1names[16:length(gC1names)])
addDataFrame(x = gC1names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29, startRow=74)
## EOFU ##
gC2names = names(coef(psi_00$fit$g[[paste0("eofu.",t-1)]]))
addDataFrame(x = gC2names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 1, startRow=109)
gC2names = names(coef(psi_10$fit$g[[paste0("eofu.",t-1)]]))
addDataFrame(x = gC2names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15, startRow=109)
gC2names = names(coef(psi_11$fit$g[[paste0("eofu.",t-1)]]))
addDataFrame(x = gC2names, sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29, startRow=109)
}
###########################################
## g-FITS (WIDE), Q-FITS, and Qstar-FITS ##
###########################################
if(estimator!="Unadjusted") {
if(grepl("GLM_WIDE", estimator)) {
## PSI_00 g ##
addDataFrame(x = coef(psi_00$fit$g[[paste0("avail.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 1+t, startRow=4, colStyle=colStyle)
addDataFrame(x = coef(psi_00$fit$g[[paste0("transfer.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 1+t, startRow=74, colStyle=colStyle)
addDataFrame(x = coef(psi_00$fit$g[[paste0("eofu.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 1+t, startRow=109, colStyle=colStyle)
## PSI_10 g ##
if(class(psi_10$fit$g[[paste0("avail.",t-1)]])[1] != "character") {
addDataFrame(x = coef(psi_10$fit$g[[paste0("avail.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15+t, startRow=4, colStyle=colStyle)
}
addDataFrame(x = coef(psi_10$fit$g[[paste0("enroll.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15+t, startRow=38, colStyle=colStyle)
addDataFrame(x = coef(psi_10$fit$g[[paste0("transfer.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15+t, startRow=74, colStyle=colStyle)
addDataFrame(x = coef(psi_10$fit$g[[paste0("eofu.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 15+t, startRow=109, colStyle=colStyle)
## PSI_11 g ##
if(class(psi_11$fit$g[[paste0("avail.",t-1)]])[1] != "character") {
addDataFrame(x = coef(psi_11$fit$g[[paste0("avail.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29+t, startRow=4, colStyle=colStyle)
}
if(class(psi_11$fit$g[[paste0("enroll.",t-1)]])[1] != "character") {
addDataFrame(x = coef(psi_11$fit$g[[paste0("enroll.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29+t, startRow=38, colStyle=colStyle)
}
addDataFrame(x = coef(psi_11$fit$g[[paste0("transfer.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29+t, startRow=74, colStyle=colStyle)
addDataFrame(x = coef(psi_11$fit$g[[paste0("eofu.",t-1)]]), sheet = sheets[["g-GLM_WIDE"]], row.names = FALSE, col.names = FALSE, startColumn = 29+t, startRow=109, colStyle=colStyle)
} else if(grepl("SL_WIDE", estimator)) {
cat("NEED TO SUMMARIZE SL G-FITS\n")
}
############
## Q-FITS ##
############
## GLM ##
if(grepl("GLM", estimator)) {
Qnames = names(coef(psi_00$fit$Q[[1]]))
Qnames[16:length(Qnames)] = sub(paste0("\\.0$"), ".t", Qnames[16:length(Qnames)])
Qfits_00 = matrix(NA, ncol=t, nrow=length(coef(psi_00$fit$Q[[1]])), dimnames=list(Qnames, paste0("t",1:t)))
Qfits_10 = matrix(NA, ncol=t, nrow=length(coef(psi_10$fit$Q[[1]])), dimnames=list(Qnames, paste0("t",1:t)))
Qfits_11 = matrix(NA, ncol=t, nrow=length(coef(psi_11$fit$Q[[1]])), dimnames=list(Qnames, paste0("t",1:t)))
for(i in 1:t) {
## PSI_00 ##
Qfits_00[,i] = coef(psi_00$fit$Q[[i]])
## PSI_10 ##
Qfits_10[,i] = coef(psi_10$fit$Q[[i]])
## PSI_11 ##
Qfits_11[,i] = coef(psi_11$fit$Q[[i]])
}
addDataFrame(x = Qfits_00, sheet = sheets[[paste0("Q-", estimator)]], row.names = TRUE, col.names = FALSE, startColumn = round(0.5*t^2+1.5*t-1), startRow=4, colStyle=colStyle)
addDataFrame(x = Qfits_10, sheet = sheets[[paste0("Q-", estimator)]], row.names = TRUE, col.names = FALSE, startColumn = round(0.5*t^2+1.5*t-1), startRow=41, colStyle=colStyle)
addDataFrame(x = Qfits_11, sheet = sheets[[paste0("Q-", estimator)]], row.names = TRUE, col.names = FALSE, startColumn = round(0.5*t^2+1.5*t-1), startRow=78, colStyle=colStyle)
## SL ##
} else if(grepl("SL", estimator)) {
Qfits_00.coef = Qfits_10.coef = Qfits_11.coef = matrix(NA, ncol=t, nrow=length(psi_00$fit$Q[[1]]$coef), dimnames=list(names(psi_00$fit$Q[[1]]$coef), paste0("t",1:t)))
Qfits_00.cvRisk = Qfits_10.cvRisk = Qfits_11.cvRisk = matrix(NA, ncol=t, nrow=length(psi_00$fit$Q[[1]]$cvRisk), dimnames=list(names(psi_00$fit$Q[[1]]$cvRisk), paste0("t",1:t)))
for(i in 1:t) {
## PSI_00 ##
Qfits_00.coef[,i] = psi_00$fit$Q[[i]]$coef
Qfits_00.cvRisk[,i] = psi_00$fit$Q[[i]]$cvRisk
## PSI_10 ##
Qfits_10.coef[,i] = psi_10$fit$Q[[i]]$coef
Qfits_10.cvRisk[,i] = psi_10$fit$Q[[i]]$cvRisk
## PSI_11 ##
Qfits_11.coef[,i] = psi_11$fit$Q[[i]]$coef
Qfits_11.cvRisk[,i] = psi_11$fit$Q[[i]]$cvRisk
}
addDataFrame(x = rownames(Qfits_00.coef), sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t-1), startRow=5)
addDataFrame(x = rownames(Qfits_10.coef), sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t-1), startRow=42)
addDataFrame(x = rownames(Qfits_11.coef), sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t-1), startRow=79)
for(i in 1:t) {
addDataFrame(x = Qfits_00.coef[,i], sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t+1+(i-1)*2), startRow=5, colStyle=colStyle)
addDataFrame(x = Qfits_00.cvRisk[,i], sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t+(i-1)*2), startRow=5, colStyle=colStyle)
addDataFrame(x = Qfits_10.coef[,i], sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t+1+(i-1)*2), startRow=42, colStyle=colStyle)
addDataFrame(x = Qfits_10.cvRisk[,i], sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t+(i-1)*2), startRow=42, colStyle=colStyle)
addDataFrame(x = Qfits_11.coef[,i], sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t+1+(i-1)*2), startRow=79, colStyle=colStyle)
addDataFrame(x = Qfits_11.cvRisk[,i], sheet = sheets[["Q-SL_LONG"]], row.names = FALSE, col.names = FALSE, startColumn = round(t^2+t+(i-1)*2), startRow=79, colStyle=colStyle)
}
}
################
## Qstar-FITS ##
################
Qstar_00.eps = Qstar_10.eps = Qstar_11.eps = matrix(NA, ncol=t, nrow=1)
Qstar_00.con = Qstar_10.con = Qstar_11.con = matrix(NA, ncol=t, nrow=1)
for(i in 1:t) {
## PSI_00 ##
if (class(psi_00$fit$Qstar[[i]])[1]=="glm") {
Qstar_00.eps[,i] = coef(psi_00$fit$Qstar[[i]])
Qstar_00.con[,i] = 1
} else if (class(psi_00$fit$Qstar[[i]])[1]=="list") {
Qstar_00.eps[,i] = psi_00$fit$Qstar[[i]]$par
Qstar_00.con[,i] = 0
}
## PSI_10 ##
if (class(psi_10$fit$Qstar[[i]])[1]=="glm") {
Qstar_10.eps[,i] = coef(psi_10$fit$Qstar[[i]])
Qstar_10.con[,i] = 1
} else if (class(psi_10$fit$Qstar[[i]])[1]=="list") {
Qstar_10.eps[,i] = psi_10$fit$Qstar[[i]]$par
Qstar_10.con[,i] = 0
}
## PSI_11 ##
if (class(psi_11$fit$Qstar[[i]])[1]=="glm") {
Qstar_11.eps[,i] = coef(psi_11$fit$Qstar[[i]])
Qstar_11.con[,i] = 1
} else if (class(psi_11$fit$Qstar[[i]])[1]=="list") {
Qstar_11.eps[,i] = psi_11$fit$Qstar[[i]]$par
Qstar_11.con[,i] = 0
}
}
i.col = 3*(estimator=="GLM_WIDE") + 12*(estimator=="GLM_LONG") + 21*(estimator=="SL_WIDE") + 30*(estimator=="SL_LONG")
addDataFrame(x = Qstar_00.eps, sheet = sheets[["Qstar-FITS"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=3+t, colStyle=colStyle)
addDataFrame(x = Qstar_10.eps, sheet = sheets[["Qstar-FITS"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=12+t, colStyle=colStyle)
addDataFrame(x = Qstar_11.eps, sheet = sheets[["Qstar-FITS"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=21+t, colStyle=colStyle)
addDataFrame(x = Qstar_00.con, sheet = sheets[["Qstar-FITS"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=31+t, colStyle=colStyle)
addDataFrame(x = Qstar_10.con, sheet = sheets[["Qstar-FITS"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=47+t, colStyle=colStyle)
addDataFrame(x = Qstar_11.con, sheet = sheets[["Qstar-FITS"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=63+t, colStyle=colStyle)
}
##################
## CUMULATIVE-G ##
##################
cumgStyle = list('1'=cs4, '2'=cs4, '3'=cs4, '4'=cs4, '5'=cs4, '6'=cs4, '7'=cs0)
i.col = 2*(estimator=="Unadjusted") + 11*(estimator=="GLM_WIDE") + 20*(estimator=="GLM_LONG") + 29*(estimator=="SL_WIDE") + 38*(estimator=="SL_LONG")
addDataFrame(x = t(as.matrix(summary(psi_00$cum.g[,ncol(psi_00$cum.g)]))), sheet = sheets[["cum.g"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=3+t, colStyle=cumgStyle)
addDataFrame(x = t(as.matrix(summary(psi_10$cum.g[,ncol(psi_10$cum.g)]))), sheet = sheets[["cum.g"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=19+t, colStyle=cumgStyle)
addDataFrame(x = t(as.matrix(summary(psi_11$cum.g[,ncol(psi_11$cum.g)]))), sheet = sheets[["cum.g"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=35+t, colStyle=cumgStyle)
###############
## ESTIMATES ##
###############
## psi_00 ##
i.col = 3*(estimator=="Unadjusted") + 7*(estimator=="GLM_WIDE") + 11*(estimator=="GLM_LONG") + 15*(estimator=="SL_WIDE") + 19*(estimator=="SL_LONG")
addDataFrame(x = do.call('cbind', summary(psi_00, est="tmle")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=10+t, colStyle=colStyle)
addDataFrame(x = do.call('cbind', summary(psi_00, est="iptw")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=26+t, colStyle=colStyle)
## psi_10 ##
i.col = 25*(estimator=="Unadjusted") + 29*(estimator=="GLM_WIDE") + 33*(estimator=="GLM_LONG") + 37*(estimator=="SL_WIDE") + 41*(estimator=="SL_LONG")
addDataFrame(x = do.call('cbind', summary(psi_10, est="tmle")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=10+t, colStyle=colStyle)
addDataFrame(x = do.call('cbind', summary(psi_10, est="iptw")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=26+t, colStyle=colStyle)
## psi_11 ##
i.col = 47*(estimator=="Unadjusted") + 51*(estimator=="GLM_WIDE") + 55*(estimator=="GLM_LONG") + 59*(estimator=="SL_WIDE") + 63*(estimator=="SL_LONG")
addDataFrame(x = do.call('cbind', summary(psi_11, est="tmle")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=10+t, colStyle=colStyle)
addDataFrame(x = do.call('cbind', summary(psi_11, est="iptw")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=26+t, colStyle=colStyle)
## GCOMP ##
if(!grepl("LONG", estimator)) {
i.col = 3*(estimator=="Unadjusted") + 7*(estimator=="GLM_WIDE") + 11*(estimator=="GLM_LONG") + 15*(estimator=="SL_WIDE") + 19*(estimator=="SL_LONG")
addDataFrame(x = do.call('cbind', summary(gcmp_00, est="gcomp")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=42+t, colStyle=colStyle)
i.col = 25*(estimator=="Unadjusted") + 29*(estimator=="GLM_WIDE") + 33*(estimator=="GLM_LONG") + 37*(estimator=="SL_WIDE") + 41*(estimator=="SL_LONG")
addDataFrame(x = do.call('cbind', summary(gcmp_10, est="gcomp")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=42+t, colStyle=colStyle)
i.col = 47*(estimator=="Unadjusted") + 51*(estimator=="GLM_WIDE") + 55*(estimator=="GLM_LONG") + 59*(estimator=="SL_WIDE") + 63*(estimator=="SL_LONG")
addDataFrame(x = do.call('cbind', summary(gcmp_11, est="gcomp")$treatment[1:3]), sheet = sheets[["Estimates"]], row.names = FALSE, col.names = FALSE, startColumn = i.col, startRow=42+t, colStyle=colStyle)
}
################
## TX EFFECTS ##
################
i.row = 4*(estimator=="Unadjusted") + 13*(estimator=="GLM_WIDE") + 22*(estimator=="GLM_LONG") + 31*(estimator=="SL_WIDE") + 40*(estimator=="SL_LONG")
# psi_10 vs psi_00 #
tmle.10v00 = summary(psi_10, psi_00, estimator="tmle")$effect.measures
iptw.10v00 = summary(psi_10, psi_00, estimator="iptw")$effect.measures
# psi_11 vs psi_10 #
tmle.11v10 = summary(psi_11, psi_10, estimator="tmle")$effect.measures
iptw.11v10 = summary(psi_11, psi_10, estimator="iptw")$effect.measures
# GCOMP #
if(!grepl("LONG", estimator)) {
gcmp.10v00 = summary(gcmp_10, gcmp_00, estimator="gcomp")$effect.measures
gcmp.11v10 = summary(gcmp_11, gcmp_10, estimator="gcomp")$effect.measures
}
##############################
## AVERAGE TREATMENT EFFECT ##
##############################
# TMLE (10v00) #
addDataFrame(x = tmle.10v00$ATE$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 3, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = tmle.10v00$ATE$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 4, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(tmle.10v00$ATE$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 5, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# IPTW (10v00) #
addDataFrame(x = iptw.10v00$ATE$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 3+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = iptw.10v00$ATE$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 4+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(iptw.10v00$ATE$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 5+13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# GCMP (10v00) #
if(!grepl("LONG", estimator)) {
addDataFrame(x = gcmp.10v00$ATE$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 3+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = gcmp.10v00$ATE$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 4+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(gcmp.10v00$ATE$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 5+26, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
}
# TMLE (11v10) #
addDataFrame(x = tmle.11v10$ATE$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 3, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = tmle.11v10$ATE$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 4, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(tmle.11v10$ATE$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 5, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# IPTW (11v10) #
addDataFrame(x = iptw.11v10$ATE$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 3+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = iptw.11v10$ATE$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 4+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(iptw.11v10$ATE$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 5+13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# GCMP (11v10) #
if(!grepl("LONG", estimator)) {
addDataFrame(x = gcmp.11v10$ATE$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 3+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = gcmp.11v10$ATE$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 4+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(gcmp.11v10$ATE$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 5+26, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
}
###################
## RELATIVE RISK ##
###################
# TMLE (10v00) #
addDataFrame(x = tmle.10v00$RR$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 7, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = tmle.10v00$RR$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 8, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(tmle.10v00$RR$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 9, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# IPTW (10v00) #
addDataFrame(x = iptw.10v00$RR$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 7+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = iptw.10v00$RR$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 8+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(iptw.10v00$RR$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 9+13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# GCMP (10v00) #
if(!grepl("LONG", estimator)) {
addDataFrame(x = gcmp.10v00$RR$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 7+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = gcmp.10v00$RR$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 8+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(gcmp.10v00$RR$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 9+26, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
}
# TMLE (11v10) #
addDataFrame(x = tmle.11v10$RR$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 7, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = tmle.11v10$RR$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 8, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(tmle.11v10$RR$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 9, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# IPTW (11v10) #
addDataFrame(x = iptw.11v10$RR$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 7+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = iptw.11v10$RR$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 8+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(iptw.11v10$RR$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 9+13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# GCMP (11v10) #
if(!grepl("LONG", estimator)) {
addDataFrame(x = gcmp.11v10$RR$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 7+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = gcmp.11v10$RR$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 8+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(gcmp.11v10$RR$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 9+26, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
}
################
## ODDS RATIO ##
################
# TMLE (10v00) #
addDataFrame(x = tmle.10v00$OR$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 11, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = tmle.10v00$OR$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 12, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(tmle.10v00$OR$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# IPTW (10v00) #
addDataFrame(x = iptw.10v00$OR$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 11+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = iptw.10v00$OR$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 12+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(iptw.10v00$OR$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 13+13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# GCMP (10v00) #
if(!grepl("LONG", estimator)) {
addDataFrame(x = gcmp.10v00$OR$estimate, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 11+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = gcmp.10v00$OR$pvalue, sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 12+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(gcmp.10v00$OR$CI,2), collapse=","), sheet = sheets[["TX-Effect-10v00"]], row.names = FALSE, col.names = FALSE, startColumn = 13+26, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
}
# TMLE (11v10) #
addDataFrame(x = tmle.11v10$OR$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 11, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = tmle.11v10$OR$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 12, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(tmle.11v10$OR$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# IPTW (11v10) #
addDataFrame(x = iptw.11v10$OR$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 11+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = iptw.11v10$OR$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 12+13, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(iptw.11v10$OR$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 13+13, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
# GCMP (11v10) #
if(!grepl("LONG", estimator)) {
addDataFrame(x = gcmp.11v10$OR$estimate, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 11+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = gcmp.11v10$OR$pvalue, sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 12+26, startRow=i.row+t, colStyle=list('1'=cs2))
addDataFrame(x = paste(round(gcmp.11v10$OR$CI,2), collapse=","), sheet = sheets[["TX-Effect-11v10"]], row.names = FALSE, col.names = FALSE, startColumn = 13+26, startRow=i.row+t, colStyle=list('1'=CellStyle(parms) + Alignment(h="ALIGN_CENTER", wrapText=FALSE)))
}
}
saveWorkbook(parms, file=file)
}
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