rewritten olr_strobe

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: daDoctoR
 Title: Functions For Health Research
-Version: 0.19.3
+Version: 0.19.4
 Year: 2019
 Author: Andreas Gammelgaard Damsbo <agdamsbo@pm.me>
 Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@pm.me>

R/strobe_olr.R

@@ -1,72 +1,132 @@
 #' Print ordinal logistic regression results according to STROBE
 #'
-#' Printable table of ordinal logistic regression analysis oaccording to STROBE. Uses polr() funtion of the MASS-package.
+#' Printable table of ordinal logistic regression with bivariate and multivariate analyses.
-#' @param meas outcome meassure variable name in data-data.frame as a string. Can be numeric or factor. Result is calculated accordingly.
+#' Table according to STROBE. Uses polr() funtion of the MASS-package.
+#' Formula analysed is the most simple m~v1+v2+vn. The is no significance test. Results are point estimates with 95 percent CI.
+#' @param meas outcome meassure variable name or response in data-data.frame as a string. Should be factor, preferably ordered.
 #' @param vars variables to compare against. As vector of columnnames.
 #' @param data dataframe of data.
 #' @param dec decimals for results, standard is set to 2. Mean and sd is dec-1.
+#' @param n.by.adj flag to indicate wether to count number of patients in adjusted model or overall for outcome meassure not NA.
 #' @keywords olr
 #' @export
 
-strobe_olr<-function(meas,vars,data,dec=2){
+strobe_olr<-function(meas,vars,data,dec=2,n.by.adj=FALSE){
 
   require(MASS)
   require(dplyr)
 
   d<-data
   m<-d[,c(meas)]
-  v<-d[,c(vars)]
 
-  dat<-data.frame(m,v)
+  ads<-d[,c(vars)]
 
-  ma <- polr(m ~ ., data = dat, Hess=TRUE)
+  if(!is.factor(m)){stop("'meas' should be a factor, preferably ordered.")}
 
-  actable <- coef(summary(ma))
+  if(is.factor(m)){
-  pa <- pnorm(abs(actable[, "t value"]), lower.tail = FALSE) * 2
-  pa<-ifelse(pa<0.001,"<0.001",round(pa,3))
-  pa <- ifelse(pa<=0.05|pa=="<0.001",paste0("*",pa),
-               ifelse(pa>0.05&pa<=0.1,paste0(".",pa),pa))
 
-  apv<-pa[1:length(coef(ma))]
+    ## Crude ORs
+
+    dfcr<-data.frame(matrix(NA,ncol = 2))
+    names(dfcr)<-c("pred","or_ci")
+    n.mn<-c()
+    nref<-c()
+
+    for(i in 1:ncol(ads)){
+      dat<-data.frame(m=m,ads[,i])
+      names(dat)<-c("m",names(ads)[i])
+      mn<-polr(m ~ ., data = dat, Hess=TRUE)
+      n.mn<-c(n.mn,nrow(mn$model))
+
+      suppressMessages(ci<-matrix(exp(confint(mn)),ncol=2))
+      l<-round(ci[,1],dec)
+      u<-round(ci[,2],dec)
+      or<-round(exp(coef(mn)),dec)
+      or_ci<-paste0(or," (",l," to ",u,")")
+
+      x1<-ads[,i]
+
+      if (is.factor(x1)){
+        pred<-paste0(names(ads)[i],levels(x1)[-1])
+      }
+
+      else {
+        pred<-names(ads)[i]
+      }
+
+      dfcr<-rbind(dfcr,cbind(pred,or_ci))
+    }
+
+
+    ## Mutually adjusted  ORs
+
+    dat<-data.frame(m=m,ads)
+    ma <-polr(m ~ ., data = dat, Hess=TRUE)
+    miss<-length(ma$na.action)
 
     aco<-round(exp(coef(ma)),dec)
-  aci<-round(exp(confint(ma)),dec)
+    suppressMessages(aci<-round(exp(confint(ma)),dec))
     alo<-aci[,1]
     aup<-aci[,2]
     aor_ci<-paste0(aco," (",alo," to ",aup,")")
 
-  dat2<-ma$model[,-1]
-  # names(dat2)<-c(var,names(ads))
     nq<-c()
 
+    if (n.by.adj==TRUE){
+      dat2<-ma$model[,-1]
       for (i in 1:ncol(dat2)){
         if (is.factor(dat2[,i])){
           vec<-dat2[,i]
           ns<-names(dat2)[i]
           for (r in 1:length(levels(vec))){
             vr<-levels(vec)[r]
-        dr<-vec[vec==vr]
+            n<-as.numeric(length(vec[vec==vr&!is.na(vec)]))
-        n<-as.numeric(length(dr))
+            nall<-as.numeric(length(dat2[,c(ns)]))
-        nall<-as.numeric(nrow(dat2))
+            n.meas<-nall
             nl<-paste0(ns,levels(vec)[r])
             pro<-round(n/nall*100,0)
             rt<-paste0(n," (",pro,"%)")
             nq<-rbind(nq,cbind(nl,rt))
-      }
+          }}
-    }
         if (!is.factor(dat2[,i])){
           num<-dat2[,i]
-      ns<-names(dat2)[i]
+          nl<-names(dat2)[i]
-      n<-as.numeric(nrow(dat2))
+          n<-as.numeric(length(num[!is.na(num)]))
           nall<-as.numeric(nrow(dat2))
+          n.meas<-nall
           pro<-round(n/nall*100,0)
           rt<-paste0(n," (",pro,"%)")
-      nq<-rbind(nq,cbind(ns,rt))
+          nq<-rbind(nq,cbind(nl,rt))
-    }
+        }}}
+
+    else {
+      dat2<-dat[!is.na(dat[,1]),][,-1]
+      n.meas<-nrow(dat2)
+      for (i in 1:ncol(dat2)){
+        if (is.factor(dat2[,i])){
+          vec<-dat2[,i]
+          ns<-names(dat2)[i]
+          for (r in 1:length(levels(vec))){
+            vr<-levels(vec)[r]
+            n<-as.numeric(length(vec[vec==vr&!is.na(vec)]))
+            nall<-as.numeric(n.mn[i])
+            nl<-paste0(ns,levels(vec)[r])
+            pro<-round(n/nall*100,0)
+            rt<-paste0(n," (",pro,"%)")
+            nq<-rbind(nq,cbind(nl,rt))
+          }}
+        if (!is.factor(dat2[,i])){
+          num<-dat2[,i]
+          nl<-names(dat2)[i]
+          n<-as.numeric(length(num[!is.na(num)]))
+          nall<-as.numeric(n.meas)
+          pro<-round(n/nall*100,0)
+          rt<-paste0(n," (",pro,"%)")
+          nq<-rbind(nq,cbind(nl,rt))
+        }}
     }
 
     rnames<-c()
-
     for (i in 1:ncol(dat2)){
       if (is.factor(dat2[,i])){
         rnames<-c(rnames,names(dat2)[i],paste0(names(dat2)[i],levels(dat2[,i])))
@@ -75,17 +135,39 @@ strobe_olr<-function(meas,vars,data,dec=2){
         rnames<-c(rnames,paste0(names(dat2)[i],".all"),names(dat2)[i])
       }
     }
-  res<-cbind(aor_ci,apv)
+    rest<-data.frame(names=names(aco),aor_ci,stringsAsFactors = F)
-  rest<-data.frame(names=row.names(res),res,stringsAsFactors = F)
 
     numb<-data.frame(names=nq[,c("nl")],N=nq[,c("rt")],stringsAsFactors = F)
     namt<-data.frame(names=rnames,stringsAsFactors = F)
 
     coll<-left_join(left_join(namt,numb,by="names"),rest,by="names")
 
-  df<-data.frame(coll)
+    header<-data.frame(matrix(paste0("Chance of higher ",meas),ncol = ncol(coll)),stringsAsFactors = F)
+    names(header)<-names(coll)
 
-  names(df)<-c("Variable","N","OR (95 % CI)","p value")
+    df<-data.frame(rbind(header,coll),stringsAsFactors = F)
 
-  return(df)
+    names(dfcr)[1]<-c("names")
+
+    suppressWarnings(re<-left_join(df,dfcr,by="names"))
+
+    rona<-c()
+    for (i in 1:length(ads)){
+      if (is.factor(ads[,i])){
+        rona<-c(rona,names(ads[i]),levels(ads[,i]))}
+      if (!is.factor(ads[,i])){
+        rona<-c(rona,names(ads[i]),"Per unit increase")
+      }
+    }
+
+    ref<-data.frame(c(NA,rona),re[,2],re[,4],re[,3])
+
+    names(ref)<-c("Variable",paste0("N=",n.meas),"Bivariate OLR (95 % CI)","Mutually adjusted OLR (95 % CI)")
+
+    ls<-list(tbl=ref,miss,n.meas,nrow(d))
+    names(ls)<-c("Printable table","Deleted due to missingness in adjusted analysis","Number of outcome observations","Length of dataframe")
+  }
+
+
+  return(ls)
 }

man/strobe_olr.Rd

@@ -4,18 +4,22 @@
 \alias{strobe_olr}
 \title{Print ordinal logistic regression results according to STROBE}
 \usage{
-strobe_olr(meas, vars, data, dec = 2)
+strobe_olr(meas, vars, data, dec = 2, n.by.adj = FALSE)
 }
 \arguments{
-\item{meas}{outcome meassure variable name in data-data.frame as a string. Can be numeric or factor. Result is calculated accordingly.}
+\item{meas}{outcome meassure variable name or response in data-data.frame as a string. Should be factor, preferably ordered.}
 
 \item{vars}{variables to compare against. As vector of columnnames.}
 
 \item{data}{dataframe of data.}
 
 \item{dec}{decimals for results, standard is set to 2. Mean and sd is dec-1.}
+
+\item{n.by.adj}{flag to indicate wether to count number of patients in adjusted model or overall for outcome meassure not NA.}
 }
 \description{
-Printable table of ordinal logistic regression analysis oaccording to STROBE. Uses polr() funtion of the MASS-package.
+Printable table of ordinal logistic regression with bivariate and multivariate analyses.
+Table according to STROBE. Uses polr() funtion of the MASS-package.
+Formula analysed is the most simple m~v1+v2+vn. The is no significance test. Results are point estimates with 95 percent CI.
 }
 \keyword{olr}