new small function, and new forest plot function

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: daDoctoR
 Title: Functions For Health Research
-Version: 0.19.5
+Version: 0.19.7
 Year: 2019
 Author: Andreas Gammelgaard Damsbo <agdamsbo@pm.me>
 Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@pm.me>

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(age_calc)
+export(biv_olr_plot_col)
 export(calculate_overlap)
 export(col_fact)
 export(col_num)
@@ -16,6 +17,7 @@ export(hwe_app)
 export(hwe_geno)
 export(hwe_sum)
 export(plot_ord_odds)
+export(plot_ord_odds2)
 export(rep_biv)
 export(rep_epi_tests)
 export(rep_glm)

R/biv_olr_plot_col.R

@@ -0,0 +1,28 @@
+#' For collection of datapoints for bivariate ordinal logistic regression plotting.
+#'
+#' Use with plot_ord_odds(), model="df".
+#' @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 data dataframe of data.
+#' @keywords olr
+#' @export
+
+biv_olr_plot_col<-function(meas,vars,data){
+  d <- data
+  x <- data.frame(d[, c(ad)])
+  y <- d[, c(meas)]
+  dt <- cbind(y, x)
+  odds<-c(matrix(ncol = 3))
+  nms<-c("or","lo","hi")
+  for (i in 1:ncol(x)) {
+    dat <- data.frame(y = y, x[, i])
+    m <- polr(y ~ ., data = dat, Hess = TRUE)
+
+    mat<-suppressMessages(matrix(c(exp(coef(m)), exp(confint(m))),ncol=3,byrow=FALSE))
+    colnames(mat)<-nms
+
+    odd <- data.frame(mat)
+    odds<-rbind(odds,odd)
+  }
+  return(odds[-1,])
+}

R/plot_ord_odds.R

@@ -8,11 +8,11 @@
 #' @param hori labels the horizontal axis (this i the y axis as the plot is rotated)
 #' @param vert labels the horizontal axis (this i the x axis as the plot is rotated)
 #' @param short flag to half number of ticks on horizontal axis.
-#' @param input can be either "model", which is a olr model (polr()), or "df", which is a dataframe whith three columns for OR, lower CI and upper CI-
+#' @param input can be either "model", which is a olr model (polr()), or "df", which is a dataframe whith three columns for OR, lower CI and upper CI.
 #' @keywords forestplot
 #' @export
 
-plot_ord_odds<-function(x, title = NULL,dec=3,lbls=NULL,hori="OR (95 % CI)",vert="Variables",short=FALSE,input="model"){
+plot_ord_odds<-function(x, title = NULL,dec=3,lbls=NULL,hori="OR (95 % CI)",vert="Variables",short=FALSE,input=c("model","df")){
 
   require(ggplot2)
 

R/plot_ord_odds2.R

@@ -0,0 +1,75 @@
+#' Forrest plot from ordinal logistic regression, version2.
+#'
+#' Heavily inspired by https://www.r-bloggers.com/plotting-odds-ratios-aka-a-forrestplot-with-ggplot2/
+#' @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 data dataframe of data.
+#' @param title plot title
+#' @param dec decimals for labels
+#' @param lbls labels for variable names. Carefull, as the right order is not checked automatically!
+#' @param hori labels the horizontal axis (this i the y axis as the plot is rotated)
+#' @param vert labels the horizontal axis (this i the x axis as the plot is rotated)
+#' @param short flag to half number of ticks on horizontal axis.
+#' @param analysis can be either "biv", or "multi", for creation of forest plot from either bivariate (unadjusted) or multivariate (adjusted) ordinal logistic regression.
+#' @keywords forestplot
+#' @export
+
+plot_ord_odds2<-function(meas,vars,data, title = NULL,dec=3,lbls=NULL,hori="OR (95 % CI)",vert="Variables",short=FALSE,analysis=c("biv","multi")){
+
+  require(ggplot2)
+
+  d <- data
+  x <- data.frame(d[, c(ad)])
+  y <- d[, c(meas)]
+
+  if (analysis=="biv"){
+
+    dt <- cbind(y, x)
+    odds<-c(matrix(ncol = 3))
+    nms<-c("or","lo","hi")
+    for (i in 1:ncol(x)) {
+      dat <- data.frame(y = y, x[, i])
+      m <- polr(y ~ ., data = dat, Hess = TRUE)
+
+      mat<-suppressMessages(matrix(c(exp(coef(m)), exp(confint(m))),ncol=3,byrow=FALSE))
+      colnames(mat)<-nms
+
+      odd <- data.frame(mat)
+      odds<-rbind(odds,odd)
+    }
+
+  }
+
+  if (analysis=="multi"){
+
+    m<-polr(y~.,data = dta2,Hess = TRUE)
+    odds<-data.frame(cbind(exp(coef(m)), exp(confint(m))))
+  }
+  names(odds)<-c("or", "lo", "up")
+  rodds<-round(odds,digits = dec)
+
+  if (!is.null(lbls)){
+    odds$vars<-paste0(lbls," \n",paste0(rodds$or," [",rodds$lo,":",rodds$up,"]"))
+  }
+  else {
+    odds$vars<-paste0(row.names(odds)," \n",paste0(rodds$or," [",rodds$lo,":",rodds$up,"]"))
+  }
+
+  ticks<-c(seq(0, 1, by =.1), seq(1, 10, by =1), seq(10, 100, by =10))
+
+  if (short==TRUE){
+    ticks<-ticks[seq(1, length(ticks), 2)]
+  }
+  else {ticks<-ticks}
+
+  odds$ord<-c(nrow(odds):1)
+
+  ggplot(odds, aes(y= or, x = reorder(vars,ord))) +
+    geom_point() +
+    geom_errorbar(aes(ymin=lo, ymax=up), width=.2) +
+    scale_y_log10(breaks=ticks, labels = ticks) +
+    geom_hline(yintercept = 1, linetype=2) +
+    coord_flip() +
+    labs(title = title, x = vert, y = hori) +
+    theme_bw()
+}

man/biv_olr_plot_col.Rd

@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/biv_olr_plot_col.R
+\name{biv_olr_plot_col}
+\alias{biv_olr_plot_col}
+\title{For collection of datapoints for bivariate ordinal logistic regression plotting.}
+\usage{
+biv_olr_plot_col(meas, vars, data)
+}
+\arguments{
+\item{meas}{outcome meassure variable name or response in data-data.frame as a string. Should be factor, preferably ordered.}
+
+\item{vars}{variables to compare against. As vector of columnnames.}
+
+\item{data}{dataframe of data.}
+}
+\description{
+Use with plot_ord_odds(), model="df".
+}
+\keyword{olr}

man/plot_ord_odds.Rd

@@ -6,7 +6,7 @@
 \usage{
 plot_ord_odds(x, title = NULL, dec = 3, lbls = NULL,
   hori = "OR (95 \% CI)", vert = "Variables", short = FALSE,
-  input = "model")
+  input = c("model", "df"))
 }
 \arguments{
 \item{x}{input data.}
@@ -23,7 +23,7 @@ plot_ord_odds(x, title = NULL, dec = 3, lbls = NULL,
 
 \item{short}{flag to half number of ticks on horizontal axis.}
 
-\item{input}{can be either "model", which is a olr model (polr()), or "df", which is a dataframe whith three columns for OR, lower CI and upper CI-}
+\item{input}{can be either "model", which is a olr model (polr()), or "df", which is a dataframe whith three columns for OR, lower CI and upper CI.}
 }
 \description{
 Heavily inspired by https://www.r-bloggers.com/plotting-odds-ratios-aka-a-forrestplot-with-ggplot2/

man/plot_ord_odds2.Rd

@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_ord_odds2.R
+\name{plot_ord_odds2}
+\alias{plot_ord_odds2}
+\title{Forrest plot from ordinal logistic regression, version2.}
+\usage{
+plot_ord_odds2(meas, vars, data, title = NULL, dec = 3, lbls = NULL,
+  hori = "OR (95 \% CI)", vert = "Variables", short = FALSE,
+  analysis = c("biv", "multi"))
+}
+\arguments{
+\item{meas}{outcome meassure variable name or response in data-data.frame as a string. Should be factor, preferably ordered.}
+
+\item{vars}{variables to compare against. As vector of columnnames.}
+
+\item{data}{dataframe of data.}
+
+\item{title}{plot title}
+
+\item{dec}{decimals for labels}
+
+\item{lbls}{labels for variable names. Carefull, as the right order is not checked automatically!}
+
+\item{hori}{labels the horizontal axis (this i the y axis as the plot is rotated)}
+
+\item{vert}{labels the horizontal axis (this i the x axis as the plot is rotated)}
+
+\item{short}{flag to half number of ticks on horizontal axis.}
+
+\item{analysis}{can be either "biv", or "multi", for creation of forest plot from either bivariate (unadjusted) or multivariate (adjusted) ordinal logistic regression.}
+}
+\description{
+Heavily inspired by https://www.r-bloggers.com/plotting-odds-ratios-aka-a-forrestplot-with-ggplot2/
+}
+\keyword{forestplot}