coxph: Add uni and multivariate analysis

coxph.R

@@ -51,6 +51,46 @@ sma_coxph_univ <- function() {
 	univ_results <- lapply(univ_models, sma_cox_res)
 	res <- t(as.data.frame(univ_results, check.names = FALSE))
 
+	cat("\nUnivariate coxph with multiple covariates:\n")
+	cat("##########################################\n\n")
+	print(as.data.frame(res))
+
+	cat("\nUnivariat coxph with multiple covariates (HR over 1):\n")
+	cat("#####################################################\n\n")
+	# Convert from factor to double then filter
+	resgt <- as.data.frame(res)
+	resgt$HR <- as.double(as.character(resgt$HR))
+	resgt <- filter(resgt, HR > 1.0)
+	resgt$HR <- sprintf("%0.2f", resgt$HR)
+	print(resgt)
+
+	cat("\nUnivariat coxph with multiple covariates (HR lower or 1):\n")
+	cat("#########################################################\n\n")
+	# Convert from factor to double then filter
+	resle <- as.data.frame(res)
+	resle$HR <- as.double(as.character(resle$HR))
+	resle <- filter(resle, HR <= 1.0)
+	resle$HR <- sprintf("%0.2f", resle$HR)
+	print(resle)
+
+	cat("\nCoxph model assumptions (check for non-significance)\n")
+	cat("###################################################\n\n")
+	coxzph <- lapply(univ_models, cox.zph)
+	print(coxzph)
+}
+
+#
+# Univariate Cox ph analysis with multiple covariates.
+#
+sma_coxph_univ_hr <- function() {
+	univ_formulas <- sapply(covariates, function(x) as.formula(
+				paste('Surv(time_at_risk, time_at_risk_status) ~ ',
+				x)))
+	univ_models <- lapply(univ_formulas,
+			      function(x) {coxph(x, data = secmal)})
+	univ_results <- lapply(univ_models, sma_cox_res)
+	res <- t(as.data.frame(univ_results, check.names = FALSE))
+
 	print("Univariate coxph with multiple covariates:")
 	print(as.data.frame(res))
 }