update help file

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: forplot
 Title: Forest plots
-Version: 0.0.1
+Version: 0.0.2
 Authors@R: 
     person("Lukas", "Bütikofer", , "lukas.buetikofer@unibe.ch", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-0801-746X"))

NEWS.md

@@ -2,4 +2,9 @@ forplot 0.0.1
 ------------------
 add news file
 
-ordering of columns according to input
+ordering of columns according to input
+
+forplot 0.0.2
+------------------
+
+bug fix in help file

R/forest.R

@@ -49,15 +49,15 @@
 #'  x (vector with xpos), y (single y-position), text (character vector with labels), cex (text size),
 #'  the list can be >1 to define more than one header line
 #' @param ref reference line, list with x (xposition), extend (extension on top), lty (line type), col (line color), lwd (line width)
-#' @param bottomline lines at the bottom if not NA
-#' @param headline  1 line for header if not NA, 2 lines if 2
-#' @param headline_pos  vector with position of lower and upper headline (if applicable), default c(0,1)
-#' @param beta2 if not NULL a second forest is generated, needs variables beta2, beta2_lci and beta2_uci in dat
+#' @param bottomline line at the bottom if not NA
+#' @param headline line for header if not NA, 1 for one line at the bottom, 2 for a line at the bottom and top
+#' @param headline_pos vector with position of lower and upper headline (if applicable), default c(0,1)
+#' @param beta2 if not NULL a second forest is generated, needs variables beta2, beta_lci2 and beta_uci2 in dat
 #' @param xlab2 see xlab for 2nd forest
 #' @param xlab_text2 see xlab_text for 2nd forest
 #' @param xlim2 see xlim for 2nd forest
 #' @param xtitle2 see xtitle for 2nd forest
-#' @param ... options passed to ff_ci for formatting the effects (if beta_format not goven)
+#' @param ... options passed to ff_ci for formatting the effects (if beta_format not given)
 #'
 #' @return forest plot
 #'

README.Rmd

@@ -31,16 +31,16 @@ Note that `remotes` treats any warnings (e.g. that a certain package was built u
 Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = "true")
 ```
 
-## Overview
-`forpplot` and it's main function fplot needs a data frame with specific column names. 
+## Usage
+`forplot` and its main function `fplot` needs a data frame with specific column names. 
 
-- vlabel: a chr column with the variable labels printed on the left of the forest plot 
-- nx: any number of chr or num columns numbered sequentially (i.e. n1, n2, n3, ...). Printed in that seqence after the 
-	column label. May contain the number of observations and/or summary per group.
-- beta, beta_lci, beta_uci: three num columns with point estimates and confidence interval to be plotted as forest.
-- beta_format: optional chr column with formatted text to be prin§ted along forest, generated from beta if not given.
-- px: any number of chr or num columns numbered sequentially (i.e. p1, p2, p3, ...), printed on the very right of the plot.
-	May contain p-values.
+- *vlabel*: a *chr* column with the variable labels.
+- *nx*: any number of *chr* or *num* columns numbered sequentially (i.e. *n1*, *n2*, *n3*, ...). Could contain the number of observations and/or summary per group.
+- *beta*, *beta_lci*, *beta_uci*: three *num* columns with point estimates and confidence interval to be plotted as forest.
+- *beta_format*: optional *chr* column with formatted text to be printed along forest, generated from betas if not given.
+- *px*: any number of *chr* or *num* columns numbered sequentially (i.e. *p1*, *p2*, *p3*, ...). Could contain p-values.
+
+The order of the columns is kept for the plot.
 
 The package includes an example dataset with 10 variables:
 
@@ -54,23 +54,24 @@ data(forplotdata)
 forplotdata
 ```
 
-The nx columns included the number of observations and descritpives (mean (sd)) for each group, beta is a mean difference, p1 the p-value.
+The *nx* columns include the number of observations and descriptives (mean (sd)) for each group, *beta* is a mean difference, *p1* the p-value.
 
-The minimal plot only includes a label and the forest and needs columns vlabel, beta, beta_lci, beta_uci.
+The minimal plot only includes a label and the forest and needs columns *vlabel*, *beta*, *beta_lci*, *beta_uci*.
 
 ```{r, fig.height=3.5, fig.width=5}
 fplot(dat=forplotdata[,c("vlabel","beta","beta_lci","beta_uci")])
 ```
 
-We can add the nx and px columns:
+Adding *nx* and *px* columns:
 ```{r, fig.height=3.5, fig.width=8}
 fplot(dat=forplotdata)
 ```
 
-Set more sensible widths and heights.
-The widths has to be the same length as the number of columns for the input 
-	data plus two for the left and right margin.
-The length is usually three, header, body and footer.	
+Set more sensible widths and heights:
+
+- lwidths has to be the same length as the number of columns for the input 
+	data plus two for the left and right margin
+- lheight is usually of length three, for header, body and footer	
 
 ```{r, fig.height=3.5, fig.width=8}
 lwidths<-c(0.05,0.5,0.2,0.8,0.2,0.8,1.2,1.2,0.5,0.05)
@@ -81,8 +82,7 @@ fplot(dat=forplotdata,lwidths=lwidths,lheights=lheights)
 ```
 
 A header can be given using a character vector the same 
-	length as the number of columns of the input data, which then 
-	places it above the columns
+	length as the number of columns of the input data:
 
 ```{r, fig.height=3.5, fig.width=8}
 header<-c("","Group1\nN","Group0\nmean (sd)","Group2\nN","Group2\nmean (sd)",
@@ -92,21 +92,22 @@ fplot(dat=forplotdata,lwidths=lwidths,lheights=lheights,header=header)
 ```
 
 The header can also be placed at any x/y position using a list 
-	with one element per header line.
+	with one element per header line:
 
 ```{r, fig.height=3.5, fig.width=8}
-header<-list(list(y=0.7,
-	text=c("Group1","Group2","Mean difference (95% CI)","P-value"),
-	x=c(0.10,0.32,0.7,0.98)),
-	list(y=0.3,text=c("N","mean (sd)","N","mean (sd)"),
-	x=c(0.07,0.18,0.28,0.38)))
+header<-list(
+  list(y=0.7,text=c("Group1","Group2","Mean difference (95% CI)","P-value"),x=c(0.10,0.32,0.7,0.98)),
+  list(y=0.3,text=c("N","mean (sd)","N","mean (sd)"),x=c(0.07,0.18,0.28,0.38)))
 
 fplot(dat=forplotdata,header=header,lwidths=lwidths,lheights=lheights)
 ```
 
-A label can be placed below the x-axis using option xtitle.
-Option ref adds a vertical reference line and xlim specifies the 
-	limits for the axis.
+Further formatting options for the forest plot include:
+
+  - *xtitle*: a label below the x-axis
+  - *ref*: adds a vertical reference line
+  - *xlim*: limits for the x-axis
+
 
 ```{r, fig.height=3.5, fig.width=8}
 xtitle<-list(x=0.86,y=0.2,textl="Group 1 better  ",textr="  Group 2 better")
@@ -115,10 +116,10 @@ fplot(dat=forplotdata,header=header,lwidths=lwidths,lheights=lheights,
 	xtitle=xtitle,ref=list(x=0),xlim=c(-1,0.5))
 ```
 
-Note that arrows are shown if the limits of the CIs are not included within xlim.
+Note that arrows are shown if the limits of the confidence intervals are not included within *xlim*.
 
 There are further options for the reference line and we can shift the x-axis
-  if the gap at the bottom is too large.
+  if the gap at the bottom is too large:
 
 ```{r, fig.height=3.5, fig.width=8}
 xtitle<-list(x=0.86,y=0.6,textl="Group 1 better  ",textr="  Group 2 better")
@@ -129,7 +130,7 @@ fplot(dat=forplotdata,header=header,lwidths=lwidths,lheights=lheights,
 
 ```
 
-The points of the forest plots can also be formatted.
+The points of the forest plots can also be formatted:
 
 ```{r, fig.height=3.5, fig.width=8}
 set.seed(1345)
@@ -142,7 +143,7 @@ fplot(dat=forplotdata,header=header,lwidths=lwidths,lheights=lheights,
 
 ```
 
-Lines at the top and bottom can be added.
+Lines at the top and bottom can be added:
 
 ```{r, fig.height=3.5, fig.width=8}
 fplot(dat=forplotdata,header=header,lwidths=lwidths,lheights=lheights,
@@ -151,10 +152,9 @@ fplot(dat=forplotdata,header=header,lwidths=lwidths,lheights=lheights,
 	headline=2,bottomline=1)
 ```
 
-If effect measures are on the log-scale (e.g. for odds ratios), option lscale can be used to indicate that the text should contain the exponentiated values. Axis ticks and labels have to be adapted by hand.
+If effect measures are on the log-scale (e.g. for odds ratios), option *lscale* can be used to indicate that the text should contain the exponentiated values. Axis ticks and labels have to be adapted by hand.
 
 ```{r, fig.height=3.5, fig.width=8}
-
 xlab_text<-c(0.3,0.5,0.8,1.0,1.5)
 xlab<-log(xlab_text)
 xlim<-log(c(min(xlab_text),max(xlab_text)))
@@ -165,14 +165,14 @@ fplot(dat=forplotdata,header=header,lwidths=lwidths,lheights=lheights,
 	xtitle=xtitle,shift_xaxis=0.3,xlab_line=-0.8,
   xlim=xlim,xlab=xlab, xlab_text=xlab_text,
 	headline=2,bottomline=1)
-
 ```
 
 ## Under development
 
-A feature under development is adding a second forest plot (e.g. to show a risk difference and ratio).
-That needs a beta, beta_lci2 and beta_uci2 column in the dataset (just copied over in the example below).
-Options xlab2,xlab_text2,xlim2 and xtitle2 are available to format the second plot.
+A feature under development is adding a second forest plot (e.g. to show a risk difference and ratio)
+  by setting *beta2 = TRUE*.
+That needs columns *beta2*, *beta_lci2* and *beta_uci2* in the dataset (just copied over in the example below).
+Options *xlab2*, *xlab_text2*, *xlim2* and *xtitle2* are available to format the second plot.
 
 ```{r, fig.height=3.5, fig.width=8}
 
@@ -186,7 +186,7 @@ forplotdata2$p1<-forplotdata$p1
 lwidths<-c(0.05,0.5,0.2,0.8,0.2,0.8,1.2,1.2,1.2,1.2,0.5,0.05)
 lheights<-c(0.14,1,0.08)
 
-fplot(dat=forplotdata2,beta2 = TRUE,
+fplot(dat=forplotdata2, beta2 = TRUE,
       lwidths=lwidths,lheights=lheights,
       xlim=c(-1,0.5),xlim2=c(-1,0.5),
       headline=2,bottomline=1)