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6
DESCRIPTION
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Package: daDoctoR Package: daDoctoR
Title: Functions For Health Research Title: Functions For Health Research
<<<<<<< HEAD Version: 0.21.8
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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#' REWRITE UNDERWAY #' Print regression results in table
#' #'
#' Print regression results according to STROBE #' New function ready for revision / rewrite
#' #'
#' 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.
@ -16,14 +16,9 @@
#' data('mtcars') #' data('mtcars')
#' 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) #' print_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
## group: genotype ## group: genotype

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R/print_diff_byvar.R
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#' REWRITE UNDERWAY #' Printable table of three dimensional regression analysis
#' #'
#' Print regression results according to STROBE #' New function ready for revision
#' #'
#' 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.
#' @param meas outcome meassure variable name in data-data.frame as a string. Can be numeric or factor. Result is calculated accordingly. #' @param meas outcome meassure variable name in data-data.frame as a string. Can be numeric or factor. Result is calculated accordingly.
@ -9,20 +9,15 @@
#' @param adj variables to adjust for, as string. #' @param adj variables to adjust for, as string.
#' @param data dataframe of data. #' @param data dataframe of data.
#' @param dec decimals for results, standard is set to 2. Mean and sd is dec-1. #' @param dec decimals for results, standard is set to 2. Mean and sd is dec-1.
#' @keywords strobe #' @keywords table
#' @export #' @export
#' @examples #' @examples
#' data('mtcars') #' data('mtcars')
#' 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) #' print_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
## group: genotype ## group: genotype

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R/print_log.R
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#' Print regression results according to STROBE #' Print regression results in table
#' #'
#' Printable table of logistic regression analysis according to STROBE. #' New function ready for revision
#'
#' Printable table of logistic regression analysis. Leaves out other variables from results.
#' @param meas outcome meassure variable name in data-data.frame as a string. Can be numeric or factor. Result is calculated accordingly. #' @param meas outcome meassure variable name in data-data.frame as a string. Can be numeric or factor. Result is calculated accordingly.
#' @param var exposure variable to compare against (active vs placebo). As string. #' @param var exposure variable to compare against (active vs placebo). As string.
#' @param adj variables to adjust for, as string. #' @param adj variables to adjust for, as string.
@ -9,11 +11,7 @@
#' @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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#' Print ordinal logistic regression results according to STROBE #' Print ordinal logistic regression results in table
#' #'
#' Printable table of ordinal logistic regression with bivariate and multivariate analyses. #' Printable table of ordinal logistic regression with bivariate and multivariate analyses.
#' Table according to STROBE. Uses polr() funtion of the MASS-package. #' Uses polr() funtion of the MASS-package. Prints table.
#' Formula analysed is the most simple m~v1+v2+vn. The is no significance test. Results are point estimates with 95 percent CI. #' 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 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 vars variables to compare against. As vector of columnnames.
@ -11,11 +11,7 @@
#' @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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#' Regression model of predictors according to STROBE, bi- and multivariable. #' Regression model of predictors according to STROBE, bi- and multivariable. Printable result.
#' #'
#' Printable table of regression model according to STROBE for linear or binary outcome-variables. #' Printable table of regression model according to STROBE for linear or binary outcome-variables.
#' Includes both bivariate and multivariate in the same table. #' Includes both bivariate and multivariate in the same table.
@ -14,11 +14,7 @@
#' @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/print_diff_bygroup.Rd
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% Please edit documentation in R/print_diff_bygroup.R % Please edit documentation in R/print_diff_bygroup.R
\name{print_diff_bygroup} \name{print_diff_bygroup}
\alias{print_diff_bygroup} \alias{print_diff_bygroup}
\title{REWRITE UNDERWAY} \title{Print regression results in table}
\usage{ \usage{
print_diff_bygroup(meas, var, group, adj, data, dec = 2) print_diff_bygroup(meas, var, group, adj, data, dec = 2)
} }
@ -20,7 +20,7 @@ print_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 New function ready for revision / rewrite
} }
\details{ \details{
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
@ -30,6 +30,6 @@ Group and variable has to be dichotomous factor.
data('mtcars') data('mtcars')
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) print_diff_bygroup(meas="mpg",var="vs",group = "am",adj=c("disp","wt"),data=mtcars)
} }
\keyword{strobe} \keyword{strobe}

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man/print_diff_byvar.Rd
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% Please edit documentation in R/print_diff_byvar.R % Please edit documentation in R/print_diff_byvar.R
\name{print_diff_byvar} \name{print_diff_byvar}
\alias{print_diff_byvar} \alias{print_diff_byvar}
\title{REWRITE UNDERWAY} \title{Printable table of three dimensional regression analysis}
\usage{ \usage{
print_diff_byvar(meas, var, group, adj, data, dec = 2) print_diff_byvar(meas, var, group, adj, data, dec = 2)
} }
@ -20,7 +20,7 @@ print_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 New function ready for revision
} }
\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.
@ -29,6 +29,6 @@ Printable table of three dimensional regression analysis of group vs var for mea
data('mtcars') data('mtcars')
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) print_diff_byvar(meas="mpg",var="vs",group = "am",adj=c("disp","wt","hp"),data=mtcars)
} }
\keyword{strobe} \keyword{table}

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man/print_log.Rd
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% Please edit documentation in R/print_log.R % Please edit documentation in R/print_log.R
\name{print_log} \name{print_log}
\alias{print_log} \alias{print_log}
\title{Print regression results according to STROBE} \title{Print regression results in table}
\usage{ \usage{
print_log(meas, var, adj, data, dec = 2) print_log(meas, var, adj, data, dec = 2)
} }
@ -18,6 +18,9 @@ print_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{
Printable table of logistic regression analysis according to STROBE. New function ready for revision
}
\details{
Printable table of logistic regression analysis. Leaves out other variables from results.
} }
\keyword{logistic} \keyword{logistic}

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man/print_olr.Rd
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@ -2,7 +2,7 @@
% Please edit documentation in R/print_olr.R % Please edit documentation in R/print_olr.R
\name{print_olr} \name{print_olr}
\alias{print_olr} \alias{print_olr}
\title{Print ordinal logistic regression results according to STROBE} \title{Print ordinal logistic regression results in table}
\usage{ \usage{
print_olr(meas, vars, data, dec = 2, n.by.adj = FALSE) print_olr(meas, vars, data, dec = 2, n.by.adj = FALSE)
} }
@ -19,7 +19,7 @@ print_olr(meas, vars, data, dec = 2, n.by.adj = FALSE)
} }
\description{ \description{
Printable table of ordinal logistic regression with bivariate and multivariate analyses. Printable table of ordinal logistic regression with bivariate and multivariate analyses.
Table according to STROBE. Uses polr() funtion of the MASS-package. Uses polr() funtion of the MASS-package. Prints table.
Formula analysed is the most simple m~v1+v2+vn. The is no significance test. Results are point estimates with 95 percent CI. 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} \keyword{olr}

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man/print_pred.Rd
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% Please edit documentation in R/print_pred.R % Please edit documentation in R/print_pred.R
\name{print_pred} \name{print_pred}
\alias{print_pred} \alias{print_pred}
\title{Regression model of predictors according to STROBE, bi- and multivariable.} \title{Regression model of predictors according to STROBE, bi- and multivariable. Printable result.}
\usage{ \usage{
print_pred(meas, adj, data, dec = 2, n.by.adj = FALSE, p.val = FALSE) print_pred(meas, adj, data, dec = 2, n.by.adj = FALSE, p.val = FALSE)
} }

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man/strobe_diff_bygroup.Rd
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@ -1,11 +1,9 @@
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/print_diff_bygroup.R, R/strobe_diff_bygroup.R % Please edit documentation in 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{
@ -22,14 +20,9 @@ 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.
} }
@ -38,9 +31,5 @@ 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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@ -1,11 +1,9 @@
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/print_diff_byvar.R, R/strobe_diff_byvar.R % Please edit documentation in 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{
@ -22,13 +20,9 @@ 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{
@ -36,9 +30,5 @@ 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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@ -1,11 +1,9 @@
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/print_log.R, R/strobe_log.R % Please edit documentation in 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{
@ -20,11 +18,6 @@ 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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@ -1,11 +1,9 @@
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/print_olr.R, R/strobe_olr.R % Please edit documentation in 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{
@ -20,13 +18,6 @@ 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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@ -1,11 +1,9 @@
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/print_pred.R, R/strobe_pred.R % Please edit documentation in 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{
@ -22,15 +20,6 @@ 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{