Merge branch 'master' into master

jinseob2kim · Feb 28, 2024 · 5504b77 · 5504b77
2 parents ad027da + ed24d3f
commit 5504b77
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Showing 3 changed files with 29 additions and 25 deletions.
diff --git a/R/forestcox.R b/R/forestcox.R
@@ -48,7 +48,7 @@
 #' @importFrom survey svycoxph regTermTest
 #' @importFrom stats confint coefficients
 #' @importFrom utils tail
- 
+
 
 TableSubgroupCox <- function(formula, var_subgroup = NULL, var_cov = NULL, data, time_eventrate = 3 * 365, decimal.hr = 2, decimal.percent = 1, decimal.pvalue = 3) {
   . <- NULL
@@ -85,38 +85,35 @@ TableSubgroupCox <- function(formula, var_subgroup = NULL, var_cov = NULL, data,
   xlabel <- setdiff(as.character(formula)[[3]], "+")[1]
 
   ncoef <- ifelse(any(class(data) == "survey.design"), ifelse(length(levels(data$variables[[xlabel]])) <= 2, 1, length(levels(data$variables[[xlabel]])) - 1),
-    ifelse(length(levels(data[[xlabel]])) <= 2||is.numeric(data[[xlabel]]), 1, length(levels(data[[xlabel]])) - 1)
+    ifelse(length(levels(data[[xlabel]])) <= 2 || is.numeric(data[[xlabel]]), 1, length(levels(data[[xlabel]])) - 1)
   )
 
   if (is.null(var_subgroup)) {
-
     if (!is.null(var_cov)) {
       formula <- as.formula(paste0(deparse(formula), " + ", paste(var_cov, collapse = "+")))
     }
     if (any(class(data) == "survey.design")) {
       model <- survey::svycoxph(formula, design = data, x = T)
       # if (!is.null(model$xlevels) & length(model$xlevels[[1]]) != 2) stop("Categorical independent variable must have 2 levels.")
-      if(is.numeric(data[[xlabel]])){
-        prop<-NULL
-      }
-      else{
-      res.kap <- survey::svykm(formula.km, design = data)
-      prop <- round(100 * sapply(res.kap, function(x) {
-        1 - x[["surv"]][which.min(abs(x[["time"]] - time_eventrate))]
-      }), decimal.percent)
-      names(prop) <- model$xlevels[[1]]
+      if (is.numeric(data[[xlabel]])) {
+        prop <- NULL
+      } else {
+        res.kap <- survey::svykm(formula.km, design = data)
+        prop <- round(100 * sapply(res.kap, function(x) {
+          1 - x[["surv"]][which.min(abs(x[["time"]] - time_eventrate))]
+        }), decimal.percent)
+        names(prop) <- model$xlevels[[1]]
       }
     } else {
       model <- survival::coxph(formula, data = data, x = TRUE)
       # if (!is.null(model$xlevels) & length(model$xlevels[[1]]) != 2) stop("Categorical independent variable must have 2 levels.")
-      if(is.numeric(data[[xlabel]])){
-        prop<-NULL
-      }
-      else{
-      res.kap <- survival::survfit(formula.km, data = data)
-      res.kap.times <- summary(res.kap, times = time_eventrate, extend = T)
-      prop <- round(100 * (1 - res.kap.times[["surv"]]), decimal.percent)
-      names(prop) <- model$xlevels[[1]]
+      if (is.numeric(data[[xlabel]])) {
+        prop <- NULL
+      } else {
+        res.kap <- survival::survfit(formula.km, data = data)
+        res.kap.times <- summary(res.kap, times = time_eventrate, extend = T)
+        prop <- round(100 * (1 - res.kap.times[["surv"]]), decimal.percent)
+        names(prop) <- model$xlevels[[1]]
       }
       # out.kap <- paste(res.kap.times[["n.event"]], " (", round(100 * (1 - res.kap.times[["surv"]]), decimal.percent), ")", sep = "")
     }
@@ -223,13 +220,11 @@ TableSubgroupCox <- function(formula, var_subgroup = NULL, var_cov = NULL, data,
           coefficients()
         pv_int <- round(pvs_int[nrow(pvs_int), ncol(pvs_int)], decimal.pvalue)
         # if (!is.null(xlev) & length(xlev[[1]]) != 2) stop("Categorical independent variable must have 2 levels.")
-
       } else {
         model.int$call$formula <- as.formula(gsub(xlabel, paste0(xlabel, "*", var_subgroup), deparse(formula)))
         model.int$call$data <- as.name("data")
         pv_anova <- anova(model.int)
         pv_int <- round(pv_anova[nrow(pv_anova), 4], decimal.pvalue)
-
       }
     }
 

diff --git a/R/forestglm.R b/R/forestglm.R
@@ -141,8 +141,8 @@ TableSubgroupGLM <- function(formula, var_subgroup = NULL, var_cov = NULL, data,
         coefficients()
       pv_int <- round(pvs_int[nrow(pvs_int), ncol(pvs_int)], decimal.pvalue)
       # if (!is.null(xlev) & length(xlev[[1]]) != 2) stop("Categorical independent variable must have 2 levels.")
-      data.design<-data
-      if(family=='binomial'){
+      data.design <- data
+      if (family == "binomial") {
         model.int <- survey::svyglm(as.formula(gsub(xlabel, paste(xlabel, "*", var_subgroup, sep = ""), deparse(formula))), design = data.design, family = quasibinomial())
       }else if(family=='gaussian'){
         model.int <- survey::svyglm(as.formula(gsub(xlabel, paste(xlabel, "*", var_subgroup, sep = ""), deparse(formula))), design = data.design, family = gaussian())

diff --git a/cla/cla.json b/cla/cla.json
@@ -1,3 +1,12 @@
 {
-   "signedContributors": []
+  "signedContributors": [
+    {
+      "name": "cyk0315",
+      "id": 91959343,
+      "comment_id": 1922935084,
+      "created_at": "2024-02-02T06:13:52Z",
+      "repoId": 135014959,
+      "pullRequestNo": 16
+    }
+  ]
 }