u

R/strobe_print.R

@@ -1,7 +1,7 @@
 #' Print regression results according to STROBE
 #'
 #' Printable table of linear regression analysis of group vs var for meas.
-#' @param meas outcome meassure variable name in data-data.frame as a string.
+#' @param meas outcome meassure variable name in data-data.frame as a string. Can be numeric or factor. Result is calculated accordingly.
 #' @param var exposure variable to compare against (active vs placebo). As string.
 #' @param groups groups to compare, as string.
 #' @param adj variables to adjust for, as string.
@@ -28,40 +28,81 @@ strobe_print<-function(meas,var,group,adj,data,dec=2){
   dat<-data.frame(m,v,g,ads)
 
   df<-data.frame(matrix(ncol=7))
-  names(df)<-c("grp",paste0("N.",substr(levels(v)[1],1,3)),paste0("M.",substr(levels(v)[1],1,3)),paste0("N.",substr(levels(v)[2],1,3)),paste0("M.",substr(levels(v)[2],1,3)),"diff","ad.diff")
 
-  for (i in 1:length(levels(g))){
+  if(!is.factor(m)){
-    grp<-levels(dat$g)[i]
-    di<-dat[dat$g==grp,][,-3]
 
-    mod<-lm(m~v,data=di)
+    for (i in 1:length(levels(g))){
-    co<-round(coef(mod)[-1],dec)
+      grp<-levels(dat$g)[i]
-    lo<-round(confint(mod)[-1,1],dec)
+      di<-dat[dat$g==grp,][,-3]
-    up<-round(confint(mod)[-1,2],dec)
 
-    ci<-paste0(co," (",lo," to ",up,")")
+      mod<-lm(m~v,data=di)
+      co<-round(coef(mod)[-1],dec)
+      lo<-round(confint(mod)[-1,1],dec)
+      up<-round(confint(mod)[-1,2],dec)
 
-    amod<-lm(m~.,data=di)
+      ci<-paste0(co," (",lo," to ",up,")")
-    aco<-round(coef(amod)[2],dec)
-    alo<-round(confint(amod)[2,1],dec)
-    aup<-round(confint(amod)[2,2],dec)
 
-    aci<-paste0(aco," (",alo," to ",aup,")")
+      amod<-lm(m~.,data=di)
+      aco<-round(coef(amod)[2],dec)
+      alo<-round(confint(amod)[2,1],dec)
+      aup<-round(confint(amod)[2,2],dec)
 
-    nr<-c()
+      aci<-paste0(aco," (",alo," to ",aup,")")
 
-    for (r in 1:2){
+      nr<-c()
-      vr<-levels(di$v)[r]
+
-      dr<-di[di$v==vr,]
+      for (r in 1:2){
-      n<-as.numeric(nrow(dr[!is.na(dr$m),]))
+        vr<-levels(di$v)[r]
-      mean<-round(mean(dr$m,na.rm = TRUE),dec-1)
+        dr<-di[di$v==vr,]
-      sd<-round(sd(dr$m,na.rm = TRUE),dec-1)
+        n<-as.numeric(nrow(dr[!is.na(dr$m),]))
-      ms<-paste0(mean," (",sd,")")
+        mean<-round(mean(dr$m,na.rm = TRUE),dec-1)
+        sd<-round(sd(dr$m,na.rm = TRUE),dec-1)
+        ms<-paste0(mean," (",sd,")")
+
+        nr<-c(nr,n,ms)
+      }
+      irl<-c(grp,nr,ci,aci)
+      df<-rbind(df,irl)
+      names(df)<-c("grp",paste0("N.",substr(levels(v)[1],1,3)),paste0("M.",substr(levels(v)[1],1,3)),paste0("N.",substr(levels(v)[2],1,3)),paste0("M.",substr(levels(v)[2],1,3)),"diff","ad.diff")
+    }}
+
+  if(is.factor(m)){
+
+    for (i in 1:length(levels(g))){
+      grp<-levels(dat$g)[i]
+      di<-dat[dat$g==grp,][,-3]
+
+      mod<-glm(m~v,family=binomial(),data=di)
+      co<-round(exp(coef(mod)[-1]),dec)
+      lo<-round(exp(confint(mod)[-1,1]),dec)
+      up<-round(exp(confint(mod)[-1,2]),dec)
+
+      ci<-paste0(co," (",lo," to ",up,")")
+
+      amod<-glm(m~.,family=binomial(),data=di)
+      aco<-round(exp(coef(amod)[2]),dec)
+      alo<-round(exp(confint(amod)[2,1]),dec)
+      aup<-round(exp(confint(amod)[2,2]),dec)
+
+      aci<-paste0(aco," (",alo," to ",aup,")")
+
+      nr<-c()
+
+      for (r in 1:2){
+        vr<-levels(di$v)[r]
+        dr<-di[di$v==vr,]
+        n<-as.numeric(nrow(dr[!is.na(dr$m),]))
+        nl<-levels(m)[2]
+        out<-nrow(dr[dr$m==nl&!is.na(dr$m),])
+        pro<-round(out/n*100,0)
+        rt<-paste0(out," (",pro,"%)")
+
+        nr<-c(nr,n,rt)
+      }
+      irl<-c(grp,nr,ci,aci)
+      df<-rbind(df,irl)
+      names(df)<-c("grp",paste0("N.",substr(levels(v)[1],1,3)),paste0(nl,".",substr(levels(v)[1],1,3)),paste0("N.",substr(levels(v)[2],1,3)),paste0(nl,".",substr(levels(v)[2],1,3)),"OR","ad.OR")
+    }}
 
-      nr<-c(nr,n,ms)
-    }
-    irl<-c(grp,nr,ci,aci)
-    df<-rbind(df,irl)
-  }
   return(df)
 }

man/strobe_print.Rd

@@ -7,7 +7,7 @@
 strobe_print(meas, var, group, adj, data, dec = 2)
 }
 \arguments{
-\item{meas}{outcome meassure variable name in data-data.frame as a string.}
+\item{meas}{outcome meassure variable name in data-data.frame as a string. Can be numeric or factor. Result is calculated accordingly.}
 
 \item{var}{exposure variable to compare against (active vs placebo). As string.}