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Merge branch 'master' of github.com:agdamsbo/daDoctoR

# Conflicts:
#	DESCRIPTION
#	R/print_diff_bygroup.R
#	R/print_diff_byvar.R
#	R/print_log.R
#	R/print_olr.R
#	R/print_pred.R
This commit is contained in:
Andreas Gammelgaard Damsbo 2021-06-11 13:37:27 +02:00
commit 09719ea905
11 changed files with 77 additions and 5 deletions
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4
DESCRIPTION
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@ -1,6 +1,10 @@
Package: daDoctoR Package: daDoctoR
Title: Functions For Health Research Title: Functions For Health Research
<<<<<<< HEAD
Version: 0.21.7 Version: 0.21.7
=======
Version: 0.21.5
>>>>>>> d8ffa3dc7b67e43a846bbd58e055a141a010b304
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>

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R/print_diff_bygroup.R
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@ -18,7 +18,11 @@
#' mtcars$am<-factor(mtcars$am) #' mtcars$am<-factor(mtcars$am)
#' strobe_diff_bygroup(meas="mpg",var="vs",group = "am",adj=c("disp","wt"),data=mtcars) #' strobe_diff_bygroup(meas="mpg",var="vs",group = "am",adj=c("disp","wt"),data=mtcars)
<<<<<<< HEAD
print_diff_bygroup<-function(meas,var,group,adj,data,dec=2){ print_diff_bygroup<-function(meas,var,group,adj,data,dec=2){
=======
strobe_diff_bygroup<-function(meas,var,group,adj,data,dec=2){
>>>>>>> d8ffa3dc7b67e43a846bbd58e055a141a010b304
## meas: sdmt ## meas: sdmt
## var: rtreat ## var: rtreat

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R/print_diff_byvar.R
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#' mtcars$am<-factor(mtcars$am) #' mtcars$am<-factor(mtcars$am)
#' strobe_diff_byvar(meas="mpg",var="vs",group = "am",adj=c("disp","wt","hp"),data=mtcars) #' strobe_diff_byvar(meas="mpg",var="vs",group = "am",adj=c("disp","wt","hp"),data=mtcars)
<<<<<<< HEAD
print_diff_byvar<-function(meas,var,group,adj,data,dec=2){ print_diff_byvar<-function(meas,var,group,adj,data,dec=2){
=======
strobe_diff_byvar<-function(meas,var,group,adj,data,dec=2){
>>>>>>> d8ffa3dc7b67e43a846bbd58e055a141a010b304
## meas: sdmt ## meas: sdmt
## var: rtreat ## var: rtreat

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R/print_log.R
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#' @keywords logistic #' @keywords logistic
#' @export #' @export
<<<<<<< HEAD
print_log<-function(meas,var,adj,data,dec=2){ print_log<-function(meas,var,adj,data,dec=2){
=======
strobe_log<-function(meas,var,adj,data,dec=2){
>>>>>>> d8ffa3dc7b67e43a846bbd58e055a141a010b304
## Ønskeliste: ## Ønskeliste:
## ##
## - Sum af alle, der indgår (Overall N) ## - Sum af alle, der indgår (Overall N)

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R/print_olr.R
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#' @keywords olr #' @keywords olr
#' @export #' @export
<<<<<<< HEAD
print_olr<-function(meas,vars,data,dec=2,n.by.adj=FALSE){ print_olr<-function(meas,vars,data,dec=2,n.by.adj=FALSE){
=======
strobe_olr<-function(meas,vars,data,dec=2,n.by.adj=FALSE){
>>>>>>> d8ffa3dc7b67e43a846bbd58e055a141a010b304
## For calculation of p-value from t-value see rep_olr() ## For calculation of p-value from t-value see rep_olr()
require(MASS) require(MASS)

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R/print_pred.R
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#' @keywords logistic #' @keywords logistic
#' @export #' @export
<<<<<<< HEAD
print_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){ print_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
=======
strobe_pred<-function(meas,adj,data,dec=2,n.by.adj=FALSE,p.val=FALSE){
>>>>>>> d8ffa3dc7b67e43a846bbd58e055a141a010b304
## Wish list: ## Wish list:
## - SPEED, maybe flags to include/exclude time consuming tasks ## - SPEED, maybe flags to include/exclude time consuming tasks

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man/strobe_diff_bygroup.Rd
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% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/strobe_diff_bygroup.R % Please edit documentation in R/print_diff_bygroup.R, R/strobe_diff_bygroup.R
\name{strobe_diff_bygroup} \name{strobe_diff_bygroup}
\alias{strobe_diff_bygroup} \alias{strobe_diff_bygroup}
\title{REWRITE UNDERWAY - replaced by 'print_diff_bygroup'} \title{REWRITE UNDERWAY - replaced by 'print_diff_bygroup'}
\usage{ \usage{
strobe_diff_bygroup(meas, var, group, adj, data, dec = 2)
strobe_diff_bygroup(meas, var, group, adj, data, dec = 2) strobe_diff_bygroup(meas, var, group, adj, data, dec = 2)
} }
\arguments{ \arguments{
@ -20,9 +22,14 @@ strobe_diff_bygroup(meas, var, group, adj, data, dec = 2)
\item{dec}{decimals for results, standard is set to 2. Mean and sd is dec-1. pval has 3 decimals.} \item{dec}{decimals for results, standard is set to 2. Mean and sd is dec-1. pval has 3 decimals.}
} }
\description{ \description{
Print regression results according to STROBE
Print regression results according to STROBE Print regression results according to STROBE
} }
\details{ \details{
Printable table of two dimensional regression analysis of group vs variable for outcome measure. By group. Includes p-value
Group and variable has to be dichotomous factor.
Printable table of two dimensional regression analysis of group vs variable for outcome measure. By group. Includes p-value Printable table of two dimensional regression analysis of group vs variable for outcome measure. By group. Includes p-value
Group and variable has to be dichotomous factor. Group and variable has to be dichotomous factor.
} }
@ -31,5 +38,9 @@ Group and variable has to be dichotomous factor.
mtcars$vs<-factor(mtcars$vs) mtcars$vs<-factor(mtcars$vs)
mtcars$am<-factor(mtcars$am) mtcars$am<-factor(mtcars$am)
strobe_diff_bygroup(meas="mpg",var="vs",group = "am",adj=c("disp","wt"),data=mtcars) strobe_diff_bygroup(meas="mpg",var="vs",group = "am",adj=c("disp","wt"),data=mtcars)
data('mtcars')
mtcars$vs<-factor(mtcars$vs)
mtcars$am<-factor(mtcars$am)
strobe_diff_bygroup(meas="mpg",var="vs",group = "am",adj=c("disp","wt"),data=mtcars)
} }
\keyword{strobe} \keyword{strobe}

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man/strobe_diff_byvar.Rd
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@ -1,9 +1,11 @@
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/strobe_diff_byvar.R % Please edit documentation in R/print_diff_byvar.R, R/strobe_diff_byvar.R
\name{strobe_diff_byvar} \name{strobe_diff_byvar}
\alias{strobe_diff_byvar} \alias{strobe_diff_byvar}
\title{REWRITE UNDERWAY - replaced by 'print_diff_byvar'} \title{REWRITE UNDERWAY - replaced by 'print_diff_byvar'}
\usage{ \usage{
strobe_diff_byvar(meas, var, group, adj, data, dec = 2)
strobe_diff_byvar(meas, var, group, adj, data, dec = 2) strobe_diff_byvar(meas, var, group, adj, data, dec = 2)
} }
\arguments{ \arguments{
@ -20,9 +22,13 @@ strobe_diff_byvar(meas, var, group, adj, data, dec = 2)
\item{dec}{decimals for results, standard is set to 2. Mean and sd is dec-1.} \item{dec}{decimals for results, standard is set to 2. Mean and sd is dec-1.}
} }
\description{ \description{
Print regression results according to STROBE
Print regression results according to STROBE Print regression results according to STROBE
} }
\details{ \details{
Printable table of three dimensional regression analysis of group vs var for meas. By var. Includes p-values.
Printable table of three dimensional regression analysis of group vs var for meas. By var. Includes p-values. Printable table of three dimensional regression analysis of group vs var for meas. By var. Includes p-values.
} }
\examples{ \examples{
@ -30,5 +36,9 @@ Printable table of three dimensional regression analysis of group vs var for mea
mtcars$vs<-factor(mtcars$vs) mtcars$vs<-factor(mtcars$vs)
mtcars$am<-factor(mtcars$am) mtcars$am<-factor(mtcars$am)
strobe_diff_byvar(meas="mpg",var="vs",group = "am",adj=c("disp","wt","hp"),data=mtcars) strobe_diff_byvar(meas="mpg",var="vs",group = "am",adj=c("disp","wt","hp"),data=mtcars)
data('mtcars')
mtcars$vs<-factor(mtcars$vs)
mtcars$am<-factor(mtcars$am)
strobe_diff_byvar(meas="mpg",var="vs",group = "am",adj=c("disp","wt","hp"),data=mtcars)
} }
\keyword{strobe} \keyword{strobe}

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man/strobe_log.Rd
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% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/strobe_log.R % Please edit documentation in R/print_log.R, R/strobe_log.R
\name{strobe_log} \name{strobe_log}
\alias{strobe_log} \alias{strobe_log}
\title{OBSOLETE - use 'print_log'} \title{OBSOLETE - use 'print_log'}
\usage{ \usage{
strobe_log(meas, var, adj, data, dec = 2)
strobe_log(meas, var, adj, data, dec = 2) strobe_log(meas, var, adj, data, dec = 2)
} }
\arguments{ \arguments{
@ -18,6 +20,11 @@ strobe_log(meas, var, adj, data, dec = 2)
\item{dec}{decimals for results, standard is set to 2. Mean and sd is dec-1.} \item{dec}{decimals for results, standard is set to 2. Mean and sd is dec-1.}
} }
\description{ \description{
Print regression results according to STROBE
}
\details{
Printable table of logistic regression analysis according to STROBE.
Print regression results according to STROBE Print regression results according to STROBE
} }
\details{ \details{

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man/strobe_olr.Rd
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% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/strobe_olr.R % Please edit documentation in R/print_olr.R, R/strobe_olr.R
\name{strobe_olr} \name{strobe_olr}
\alias{strobe_olr} \alias{strobe_olr}
\title{OBSOLETE - use 'print_olr'} \title{OBSOLETE - use 'print_olr'}
\usage{ \usage{
strobe_olr(meas, vars, data, dec = 2, n.by.adj = FALSE)
strobe_olr(meas, vars, data, dec = 2, n.by.adj = FALSE) strobe_olr(meas, vars, data, dec = 2, n.by.adj = FALSE)
} }
\arguments{ \arguments{
@ -18,6 +20,13 @@ strobe_olr(meas, vars, data, dec = 2, n.by.adj = FALSE)
\item{n.by.adj}{flag to indicate wether to count number of patients in adjusted model or overall for outcome meassure not NA.} \item{n.by.adj}{flag to indicate wether to count number of patients in adjusted model or overall for outcome meassure not NA.}
} }
\description{ \description{
Print ordinal logistic regression results according to STROBE
}
\details{
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.
Print ordinal logistic regression results according to STROBE Print ordinal logistic regression results according to STROBE
} }
\details{ \details{

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man/strobe_pred.Rd
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% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/strobe_pred.R % Please edit documentation in R/print_pred.R, R/strobe_pred.R
\name{strobe_pred} \name{strobe_pred}
\alias{strobe_pred} \alias{strobe_pred}
\title{OBSOLETE - use 'print_pred'} \title{OBSOLETE - use 'print_pred'}
\usage{ \usage{
strobe_pred(meas, adj, data, dec = 2, n.by.adj = FALSE, p.val = FALSE)
strobe_pred(meas, adj, data, dec = 2, n.by.adj = FALSE, p.val = FALSE) strobe_pred(meas, adj, data, dec = 2, n.by.adj = FALSE, p.val = FALSE)
} }
\arguments{ \arguments{
@ -20,6 +22,15 @@ strobe_pred(meas, adj, data, dec = 2, n.by.adj = FALSE, p.val = FALSE)
\item{p.val}{flag to include p-values in table, set to FALSE as standard.} \item{p.val}{flag to include p-values in table, set to FALSE as standard.}
} }
\description{ \description{
Regression model of predictors according to STROBE, bi- and multivariable.
}
\details{
Printable table of regression model according to STROBE for linear or binary outcome-variables.
Includes both 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 continuous outcome variable. Linear regression will give estimated adjusted true mean in list.
For logistic regression gives count of outcome variable pr variable level.
Regression model of predictors according to STROBE, bi- and multivariable. Regression model of predictors according to STROBE, bi- and multivariable.
} }
\details{ \details{