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fix n.by.adj flag function for print_pred

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AG Damsbo 2021-10-06 13:19:21 +02:00
parent 5728450087
commit d7ce0e0faf
4 changed files with 13 additions and 9 deletions
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.DS_Store vendored
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2
DESCRIPTION
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@ -1,6 +1,6 @@
Package: daDoctoR Package: daDoctoR
Title: Functions For Health Research Title: Functions For Health Research
Version: 0.21.13 Version: 0.21.14
Year: 2021 Year: 2021
Author: Andreas Gammelgaard Damsbo <agdamsbo@pm.me> Author: Andreas Gammelgaard Damsbo <agdamsbo@pm.me>
Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@pm.me> Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@pm.me>

17
R/print_pred.R
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@ -88,10 +88,11 @@ print_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
nq<-c() nq<-c()
nall<-length(!is.na(dat[,1])) nall<-length(!is.na(dat[,1]))
nalt<-c()
if (n.by.adj==TRUE){ if (n.by.adj==TRUE){
dat2<-ma$model dat2<-ma$model
# nalt<-nrow(dat2) nalt<-nrow(dat2)
for (i in 2:ncol(dat2)) { for (i in 2:ncol(dat2)) {
if (is.factor(dat2[, i])) { if (is.factor(dat2[, i])) {
vec <- dat2[, i] vec <- dat2[, i]
@ -120,6 +121,7 @@ print_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
else { else {
dat2<-dat[!is.na(dat[,1]),] dat2<-dat[!is.na(dat[,1]),]
nalt<-nall
for (i in 2:ncol(dat2)) { for (i in 2:ncol(dat2)) {
if (is.factor(dat2[, i])) { if (is.factor(dat2[, i])) {
vec <- dat2[, i] vec <- dat2[, i]
@ -184,12 +186,12 @@ print_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
if (p.val==TRUE){ if (p.val==TRUE){
ref<-data.frame(c(NA,rona),re[,"N"],re[,"N.out"],re[,"or_ci"],re[,"pv"],re[,"aor_ci"],re[,"apv"]) 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),paste0("N, ",meas," is ",levels(m)[2]),"Crude OR (95 % CI)","p-value","Mutually adjusted OR (95 % CI)","A p-value") names(ref)<-c("Variable",paste0("N=",nalt),paste0("N, ",meas," is ",levels(m)[2]),"Crude OR (95 % CI)","p-value","Mutually adjusted OR (95 % CI)","A p-value")
} }
else{ else{
ref<-data.frame(c(NA,rona),re[,"N"],re[,"N.out"],re[,"or_ci"],re[,"aor_ci"]) ref<-data.frame(c(NA,rona),re[,"N"],re[,"N.out"],re[,"or_ci"],re[,"aor_ci"])
names(ref)<-c("Variable",paste0("N=",nall),paste0("N, ",meas," is ",levels(m)[2]),"Crude OR (95 % CI)","Mutually adjusted OR (95 % CI)") names(ref)<-c("Variable",paste0("N=",nalt),paste0("N, ",meas," is ",levels(m)[2]),"Crude OR (95 % CI)","Mutually adjusted OR (95 % CI)")
} }
ls<-list(tbl=ref,miss,nall,nrow(d)) ls<-list(tbl=ref,miss,nall,nrow(d))
@ -259,10 +261,11 @@ print_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
nq<-c() nq<-c()
nall<-length(!is.na(dat[,1])) nall<-length(!is.na(dat[,1]))
nalt<-c()
if (n.by.adj==TRUE){ if (n.by.adj==TRUE){
dat2<-ma$model[,-1] dat2<-ma$model[,-1]
# nalt<-nrow(dat2) nalt<-nrow(dat2)
for (i in 1:ncol(dat2)){ for (i in 1:ncol(dat2)){
if (is.factor(dat2[,i])){ if (is.factor(dat2[,i])){
vec<-dat2[,i] vec<-dat2[,i]
@ -283,6 +286,7 @@ print_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
else { else {
dat2<-dat[!is.na(dat[,1]),][,-1] dat2<-dat[!is.na(dat[,1]),][,-1]
nalt<-nall
for (i in 1:ncol(dat2)) { for (i in 1:ncol(dat2)) {
if (is.factor(dat2[, i])) { if (is.factor(dat2[, i])) {
vec <- dat2[, i] vec <- dat2[, i]
@ -342,12 +346,12 @@ print_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
if (p.val==TRUE){ 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[,2],re[,5],re[,6],re[,3],re[,4])
names(ref)<-c("Variable",paste0("N=",nall),"Difference (95 % CI)","p-value","Mutually adjusted difference (95 % CI)","A p-value") names(ref)<-c("Variable",paste0("N=",nalt),"Difference (95 % CI)","p-value","Mutually adjusted difference (95 % CI)","A p-value")
} }
else{ else{
ref<-data.frame(c(NA,rona),re[,2],re[,5],re[,3]) ref<-data.frame(c(NA,rona),re[,2],re[,5],re[,3])
names(ref)<-c("Variable",paste0("N=",nall),"Difference (95 % CI)","Mutually adjusted difference (95 % CI)") names(ref)<-c("Variable",paste0("N=",nalt),"Difference (95 % CI)","Mutually adjusted difference (95 % CI)")
} }
ls<-list(tbl=ref,miss,nall,nrow(d),mean_est) ls<-list(tbl=ref,miss,nall,nrow(d),mean_est)
@ -357,3 +361,4 @@ print_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
return(ls) return(ls)
} }

1
packing.R
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@ -1,6 +1,5 @@
library(roxygen2, devtools) library(roxygen2, devtools)
setwd("/Users/au301842/daDoctoR")
source("updatePackageVersion.R") source("updatePackageVersion.R")
updatePackageVersion() updatePackageVersion()