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agdamsbo 2019-12-13 11:58:21 +01:00
parent 6bd9e0508b
commit 36a0862645
2 changed files with 157 additions and 175 deletions
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DESCRIPTION
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@ -1,6 +1,6 @@
Package: daDoctoR Package: daDoctoR
Title: Functions For Health Research Title: Functions For Health Research
Version: 0.19.11 Version: 0.19.12
Year: 2019 Year: 2019
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>

330
R/strobe_pred.R
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@ -27,165 +27,156 @@ strobe_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
if(is.factor(m)){ if(is.factor(m)){
## Crude ORs ## Crude ORs
dfcr<-data.frame(matrix(NA,ncol = 3)) dfcr<-data.frame(matrix(NA,ncol = 3))
names(dfcr)<-c("pred","or_ci","pv") names(dfcr)<-c("pred","or_ci","pv")
n.mn<-c() n.mn<-c()
nref<-c() nref<-c()
for(i in 1:ncol(ads)){ for(i in 1:ncol(ads)){
dat<-data.frame(m=m,ads[,i]) dat<-data.frame(m=m,ads[,i])
names(dat)<-c("m",names(ads)[i]) names(dat)<-c("m",names(ads)[i])
mn<-glm(m~.,family = binomial(),data=dat) mn<-glm(m~.,family = binomial(),data=dat)
n.mn<-c(n.mn,nrow(mn$model)) n.mn<-c(n.mn,nrow(mn$model))
suppressMessages(ci<-exp(confint(mn))) suppressMessages(ci<-exp(confint(mn)))
l<-round(ci[-1,1],dec) l<-round(ci[-1,1],dec)
u<-round(ci[-1,2],dec) u<-round(ci[-1,2],dec)
or<-round(exp(coef(mn))[-1],dec) or<-round(exp(coef(mn))[-1],dec)
or_ci<-paste0(or," (",l," to ",u,")") or_ci<-paste0(or," (",l," to ",u,")")
pv<-round(tidy(mn)$p.value[-1],dec+1) pv<-round(tidy(mn)$p.value[-1],dec+1)
x1<-ads[,i] x1<-ads[,i]
if (is.factor(x1)){ if (is.factor(x1)){
pred<-paste0(names(ads)[i],levels(x1)[-1]) pred<-paste0(names(ads)[i],levels(x1)[-1])
}
else {
pred<-names(ads)[i]
}
dfcr<-rbind(dfcr,cbind(pred,or_ci,pv))
}
## Mutually adjusted ORs
dat<-data.frame(m=m,ads)
ma <- glm(m ~ .,family = binomial(), data = dat)
miss<-length(ma$na.action)
actable <- coef(summary(ma))
pa <- actable[,4]
pa<-ifelse(pa<0.001,"<0.001",round(pa,3))
pa <- ifelse(pa<=0.05|pa=="<0.001",paste0("*",pa),
ifelse(pa>0.05&pa<=0.1,paste0(".",pa),pa))
apv<-pa[1:length(coef(ma))]
aco<-round(exp(coef(ma)),dec)
suppressMessages(aci<-round(exp(confint(ma)),dec))
alo<-aci[,1]
aup<-aci[,2]
aor_ci<-paste0(aco," (",alo," to ",aup,")")
# names(dat2)<-c(var,names(ads))
nq<-c()
nall<-length(!is.na(dat[,1]))
if (n.by.adj==TRUE){
dat2<-ma$model[,-1]
# 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 { else {
pred<-names(ads)[i] dat2<-dat[!is.na(dat[,1]),][,-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]
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 <- length(num[!is.na(num)])
rt <- paste0(n, " (", round(n/nall * 100, 0), "%)")
nq <- rbind(nq, cbind(names(dat2)[i], rt))
}
}
} }
dfcr<-rbind(dfcr,cbind(pred,or_ci,pv)) rnames<-c()
}
## Mutually adjusted ORs
dat<-data.frame(m=m,ads)
ma <- glm(m ~ .,family = binomial(), data = dat)
miss<-length(ma$na.action)
actable <- coef(summary(ma))
pa <- actable[,4]
pa<-ifelse(pa<0.001,"<0.001",round(pa,3))
pa <- ifelse(pa<=0.05|pa=="<0.001",paste0("*",pa),
ifelse(pa>0.05&pa<=0.1,paste0(".",pa),pa))
apv<-pa[1:length(coef(ma))]
aco<-round(exp(coef(ma)),dec)
suppressMessages(aci<-round(exp(confint(ma)),dec))
alo<-aci[,1]
aup<-aci[,2]
aor_ci<-paste0(aco," (",alo," to ",aup,")")
# names(dat2)<-c(var,names(ads))
nq<-c()
if (n.by.adj==TRUE){
dat2<-ma$model[,-1]
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] rnames<-c(rnames,names(dat2)[i],paste0(names(dat2)[i],levels(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(length(dat2[,c(ns)]))
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])){ if (!is.factor(dat2[,i])){
num<-dat2[,i] rnames<-c(rnames,paste0(names(dat2)[i],".all"),names(dat2)[i])
nl<-names(dat2)[i] }
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(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])))
} }
if (!is.factor(dat2[,i])){ res<-cbind(aor_ci,apv)
rnames<-c(rnames,paste0(names(dat2)[i],".all"),names(dat2)[i]) rest<-data.frame(names=row.names(res),res,stringsAsFactors = F)
}
}
res<-cbind(aor_ci,apv)
rest<-data.frame(names=row.names(res),res,stringsAsFactors = F)
numb<-data.frame(names=nq[,c("nl")],N=nq[,c("rt")],stringsAsFactors = F) numb<-data.frame(names=nq[,1],N=nq[,2],stringsAsFactors = F)
namt<-data.frame(names=rnames,stringsAsFactors = F) namt<-data.frame(names=rnames,stringsAsFactors = F)
coll<-left_join(left_join(namt,numb,by="names"),rest,by="names") 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)[-1]),ncol = ncol(coll)),stringsAsFactors = F)
names(header)<-names(coll) names(header)<-names(coll)
df<-data.frame(rbind(header,coll),stringsAsFactors = F) df<-data.frame(rbind(header,coll),stringsAsFactors = F)
names(dfcr)[1]<-c("names") names(dfcr)[1]<-c("names")
suppressWarnings(re<-left_join(df,dfcr,by="names")) suppressWarnings(re<-left_join(df,dfcr,by="names"))
rona<-c() rona<-c()
for (i in 1:length(ads)){ for (i in 1:length(ads)){
if (is.factor(ads[,i])){ if (is.factor(ads[,i])){
rona<-c(rona,names(ads[i]),levels(ads[,i]))} rona<-c(rona,names(ads[i]),levels(ads[,i]))}
if (!is.factor(ads[,i])){ if (!is.factor(ads[,i])){
rona<-c(rona,names(ads[i]),"Per unit increase") rona<-c(rona,names(ads[i]),"Per unit increase")
} }
} }
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=",n.meas),"Crude OR (95 % CI)","p-value","Mutually adjusted OR (95 % CI)","A p-value") names(ref)<-c("Variable",paste0("N=",nall),"Crude OR (95 % CI)","p-value","Mutually adjusted OR (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=",n.meas),"Crude OR (95 % CI)","Mutually adjusted OR (95 % CI)") names(ref)<-c("Variable",paste0("N=",nall),"Crude OR (95 % CI)","Mutually adjusted OR (95 % CI)")
} }
ls<-list(tbl=ref,miss,n.meas,nrow(d)) ls<-list(tbl=ref,miss,nall,nrow(d))
names(ls)<-c("Printable table","Deleted due to missingness in adjusted analysis","Number of outcome observations","Length of dataframe") names(ls)<-c("Printable table","Deleted due to missingness in adjusted analysis","Number of outcome observations","Length of dataframe")
} }
if(!is.factor(m)){ if(!is.factor(m)){
@ -250,59 +241,50 @@ strobe_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
nq<-c() nq<-c()
nall<-length(!is.na(dat[,1]))
if (n.by.adj==TRUE){ if (n.by.adj==TRUE){
dat2<-ma$model[,-1] dat2<-ma$model[,-1]
# 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]
ns<-names(dat2)[i] ns<-names(dat2)[i]
for (r in 1:length(levels(vec))){ for (r in 1:length(levels(vec))){
vr<-levels(vec)[r] vr<-levels(vec)[r]
n<-as.numeric(length(vec[vec==vr&!is.na(vec)])) n<-length(vec[vec==vr&!is.na(vec)])
nall<-as.numeric(length(dat2[,c(ns)])) rt<-paste0(n," (",round(n/nall*100,0),"%)")
n.meas<-nall nq<-rbind(nq,cbind(paste0(ns,levels(vec)[r]),rt))
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])){ if (!is.factor(dat2[,i])){
num<-dat2[,i] num<-dat2[,i]
nl<-names(dat2)[i]
n<-as.numeric(length(num[!is.na(num)])) n<-as.numeric(length(num[!is.na(num)]))
nall<-as.numeric(nrow(dat2)) rt<-paste0(n," (",round(n/nall*100,0),"%)")
n.meas<-nall nq<-rbind(nq,cbind(names(dat2)[i],rt))
pro<-round(n/nall*100,0) }}
rt<-paste0(n," (",pro,"%)") }
nq<-rbind(nq,cbind(nl,rt))
}}}
else { else {
dat2<-dat[!is.na(dat[,1]),][,-1] dat2<-dat[!is.na(dat[,1]),][,-1]
n.meas<-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] ns <- names(dat2)[i]
ns<-names(dat2)[i] for (r in 1:length(levels(vec))) {
for (r in 1:length(levels(vec))){ vr <- levels(vec)[r]
vr<-levels(vec)[r] n <- length(vec[vec == vr & !is.na(vec)])
n<-as.numeric(length(vec[vec==vr&!is.na(vec)])) rt <- paste0(n, " (", round(n/nall * 100, 0), "%)")
nall<-as.numeric(n.mn[i]) nq <- rbind(nq, cbind(paste0(ns, levels(vec)[r]), rt))
nl<-paste0(ns,levels(vec)[r]) }
pro<-round(n/nall*100,0) }
rt<-paste0(n," (",pro,"%)") if (!is.factor(dat2[, i])) {
nq<-rbind(nq,cbind(nl,rt)) num <- dat2[, i]
}} n <- length(num[!is.na(num)])
if (!is.factor(dat2[,i])){ rt <- paste0(n, " (", round(n/nall * 100, 0), "%)")
num<-dat2[,i] nq <- rbind(nq, cbind(names(dat2)[i], rt))
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() rnames<-c()
@ -317,7 +299,7 @@ strobe_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
res<-cbind(amean_ci,apv) res<-cbind(amean_ci,apv)
rest<-data.frame(names=row.names(res),res,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) numb<-data.frame(names=nq[,1],N=nq[,2],stringsAsFactors = F)
namt<-data.frame(names=rnames,stringsAsFactors = F) namt<-data.frame(names=rnames,stringsAsFactors = F)
coll<-left_join(left_join(namt,numb,by="names"),rest,by="names") coll<-left_join(left_join(namt,numb,by="names"),rest,by="names")
@ -335,23 +317,23 @@ strobe_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
for (i in 1:length(ads)){ for (i in 1:length(ads)){
if (is.factor(ads[,i])){ if (is.factor(ads[,i])){
rona<-c(rona,names(ads[i]),levels(ads[,i]))} rona<-c(rona,names(ads[i]),levels(ads[,i]))}
if (!is.factor(ads[,i])){ if (!is.factor(ads[,i])){
rona<-c(rona,names(ads[i]),"Per unit increase") rona<-c(rona,names(ads[i]),"Per unit increase")
}
} }
}
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=",n.meas),"Difference (95 % CI)","p-value","Mutually adjusted difference (95 % CI)","A p-value") names(ref)<-c("Variable",paste0("N=",nall),"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=",n.meas),"Difference (95 % CI)","Mutually adjusted difference (95 % CI)") names(ref)<-c("Variable",paste0("N=",nall),"Difference (95 % CI)","Mutually adjusted difference (95 % CI)")
} }
ls<-list(tbl=ref,miss,n.meas,nrow(d),mean_est) ls<-list(tbl=ref,miss,nall,nrow(d),mean_est)
names(ls)<-c("Printable table","Deleted due to missingness in adjusted analysis","Number of outcome observations","Length of dataframe","Estimated true mean (95 % CI) in adjusted analysis") names(ls)<-c("Printable table","Deleted due to missingness in adjusted analysis","Number of outcome observations","Length of dataframe","Estimated true mean (95 % CI) in adjusted analysis")
} }