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included counting of outcomes

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agdamsbo 2019-12-13 12:39:42 +01:00
parent 36a0862645
commit e10228bdec
3 changed files with 48 additions and 35 deletions
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2
DESCRIPTION
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@ -1,6 +1,6 @@
Package: daDoctoR
Title: Functions For Health Research
Version: 0.19.12
Version: 0.19.13
Year: 2019
Author: Andreas Gammelgaard Damsbo <agdamsbo@pm.me>
Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@pm.me>

80
R/strobe_pred.R
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@ -4,6 +4,7 @@
#' Includes borth bivariate and multivariate in the same table.
#' Output is a list, with the first item being the main "output" as a dataframe.
#' Automatically uses logistic regression model for dichotomous outcome variable and linear regression model for continous outcome variable. Linear regression will give estimated adjusted true mean in list.
#' For logistic regression gives count of outcome variable pr variable level.
#' @param meas binary outcome meassure variable, column name in data.frame as a string. Can be numeric or factor. Result is calculated accordingly.
#' @param adj variables to adjust for, as string.
#' @param data dataframe of data.
@ -14,9 +15,6 @@
#' @export
strobe_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
## Ønskeliste:
##
## - Tæl selv antal a NA'er
require(dplyr)
@ -87,44 +85,58 @@ strobe_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
nall<-length(!is.na(dat[,1]))
if (n.by.adj==TRUE){
dat2<-ma$model[,-1]
dat2<-ma$model
# nalt<-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<-length(vec[vec==vr&!is.na(vec)])
rt<-paste0(n," (",round(n/nall*100,0),"%)")
nq<-rbind(nq,cbind(paste0(ns,levels(vec)[r]),rt))
}}
if (!is.factor(dat2[,i])){
num<-dat2[,i]
n<-as.numeric(length(num[!is.na(num)]))
rt<-paste0(n," (",round(n/nall*100,0),"%)")
nq<-rbind(nq,cbind(names(dat2)[i],rt))
}}
}
else {
dat2<-dat[!is.na(dat[,1]),][,-1]
for (i in 1:ncol(dat2)) {
for (i in 2: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]
## Counting all included in analysis
n <- length(vec[vec == vr & !is.na(vec)])
rt <- paste0(n, " (", round(n/nall * 100, 0), "%)")
nq <- rbind(nq, cbind(paste0(ns, levels(vec)[r]), rt))
## Counting all included in analysis with outcome
lvl<-levels(dat2[,1])[2]
no <- length(vec[vec == vr & dat2[,1]==lvl & !is.na(vec)])
ro <- paste0(no, " (", round(no/n * 100, 0), "%)")
## Combining
nq <- rbind(nq, cbind(paste0(ns, levels(vec)[r]), rt,ro))
}
}
if (!is.factor(dat2[, i])) {
num <- dat2[, i]
n <- length(num[!is.na(num)])
rt <- paste0(n, " (", round(n/nall * 100, 0), "%)")
nq <- rbind(nq, cbind(names(dat2)[i], rt))
nq <- rbind(nq, cbind(names(dat2)[i], rt,ro="-"))
}
}
}
else {
dat2<-dat[!is.na(dat[,1]),]
for (i in 2: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]
## Counting all included in analysis
n <- length(vec[vec == vr & !is.na(vec)])
rt <- paste0(n, " (", round(n/nall * 100, 0), "%)")
## Counting all included in analysis with outcome
lvl<-levels(dat2[,1])[2]
no <- length(vec[vec == vr & dat2[,1]==lvl & !is.na(vec)])
ro <- paste0(no, " (", round(no/n * 100, 0), "%)")
## Combining
nq <- rbind(nq, cbind(paste0(ns, levels(vec)[r]), rt,ro))
}
}
if (!is.factor(dat2[, i])) {
num <- dat2[, i]
n <- length(num[!is.na(num)])
rt <- paste0(n, " (", round(n/nall * 100, 0), "%)")
nq <- rbind(nq, cbind(names(dat2)[i], rt,ro="-"))
}
}
}
@ -141,12 +153,12 @@ strobe_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
res<-cbind(aor_ci,apv)
rest<-data.frame(names=row.names(res),res,stringsAsFactors = F)
numb<-data.frame(names=nq[,1],N=nq[,2],stringsAsFactors = F)
namt<-data.frame(names=rnames,stringsAsFactors = F)
numb<-data.frame(names=nq[,1],N=nq[,2],N.out=nq[,3],stringsAsFactors = F)
namt<-data.frame(names=tail(rnames,-3),stringsAsFactors = F)
coll<-left_join(left_join(namt,numb,by="names"),rest,by="names")
header<-data.frame(matrix(paste0("Chance of ",meas," is ",levels(m)[-1]),ncol = ncol(coll)),stringsAsFactors = F)
header<-data.frame(matrix(paste0("Chance of ",meas," is ",levels(m)[2]),ncol = ncol(coll)),stringsAsFactors = F)
names(header)<-names(coll)
df<-data.frame(rbind(header,coll),stringsAsFactors = F)
@ -165,14 +177,14 @@ strobe_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
}
if (p.val==TRUE){
ref<-data.frame(c(NA,rona),re[,2],re[,5],re[,6],re[,3],re[,4])
ref<-data.frame(c(NA,rona),re[,"N"],re[,"N.out"],re[,"or_ci"],re[,"pv"],re[,"aor_ci"],re[,"apv"])
names(ref)<-c("Variable",paste0("N=",nall),"Crude OR (95 % CI)","p-value","Mutually adjusted OR (95 % CI)","A p-value")
names(ref)<-c("Variable",paste0("N=",nall),paste0("N, ",meas," is ",levels(m)[2]),"Crude OR (95 % CI)","p-value","Mutually adjusted OR (95 % CI)","A p-value")
}
else{
ref<-data.frame(c(NA,rona),re[,2],re[,5],re[,3])
ref<-data.frame(c(NA,rona),re[,"N"],re[,"N.out"],re[,"or_ci"],re[,"aor_ci"])
names(ref)<-c("Variable",paste0("N=",nall),"Crude OR (95 % CI)","Mutually adjusted OR (95 % CI)")
names(ref)<-c("Variable",paste0("N=",nall),paste0("N, ",meas," is ",levels(m)[2]),"Crude OR (95 % CI)","Mutually adjusted OR (95 % CI)")
}
ls<-list(tbl=ref,miss,nall,nrow(d))

1
man/strobe_pred.Rd
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@ -25,5 +25,6 @@ Printable table of regression model according to STROBE for linear or binary out
Includes borth bivariate and multivariate in the same table.
Output is a list, with the first item being the main "output" as a dataframe.
Automatically uses logistic regression model for dichotomous outcome variable and linear regression model for continous outcome variable. Linear regression will give estimated adjusted true mean in list.
For logistic regression gives count of outcome variable pr variable level.
}
\keyword{logistic}