package metafor: error when setting 'col' and 'at' for a forest plot

-----Original Message-----
From: r-help-bounces at r-project.org 
[mailto:r-help-bounces at r-project.org]
On Behalf Of Brian Z Ring
Sent: Sunday, January 06, 2013 05:48
To: 'David Winsemius'; r-help at r-project.org
Subject: Re: [R] package metafor: error when setting 'col' and 'at' 
for a forest plot

Good suggestion, and yes, the given examples work. Using a 
modification of one of the supplied examples, where in the final line 
I only added the parameter col=c(1,2,3):

data(dat.bcg)
dat <- escalc(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, 
data=dat.bcg, append=TRUE) forest(dat$yi, dat$vi, 
slab=paste(dat$author, dat$year, sep=", "), atransf=exp, 
at=log(c(.05,.25,1,4,20)), col=c(1,2,3))

I get a plot similar to what I want to achieve. My code:

forest(forest$OR, ci.lb=forest$Low, ci.ub=forest$High,  col=c(1,2,3), 
at=log(c(.05, .25, 1, 10)), slab=forest$SNP, atransf=exp)

differs in the data and using confidence intervals instead of vi 
(sample variance). The parameters being changed in my line of code are 
fairly simple, just color of each row and the x axis tick marks. 
Setting each of these independently with my data works fine, it's only 
when I try to do both that it fails. I'm still stuck.

Here is some example data that should reproduce the error:
SNP	Group	High	Low	OR
rs1137101	A	1.21	0.87	1.03
rs1137101	B	2.11	1.21	1.6
rs1137101	C	2.9	1.42	2.03
rs1042522	A	1.12	0.84	0.97
rs1042522	B	1.15	0.79	0.95
rs1042522	C	0.92	0.5	0.7
rs1625895	A	1.14	0.76	0.93
rs1625895	B	1.15	0.75	0.93
rs1625895	C	NA	NA	NA
ACEI/D	A	1.55	0.79	1.11
ACEI/D	B	1.25	0.76	0.98
ACEI/D	C	0.85	0.41	0.59

-----Original Message-----
From: David Winsemius [mailto:dwinsemius at comcast.net]
Sent: Sunday, January 06, 2013 2:31 AM
To: Brian Z Ring
Cc: r-help at r-project.org
Subject: Re: [R] package metafor: error when setting 'col' and 'at' 
for a forest plot


On Jan 4, 2013, at 9:13 PM, Brian Z Ring wrote:

I am using metafor to create forest plots. This code gives me the 
expected plot (setting x axis tick marks):

forest(forest$OR, ci.lb=forest$Low, ci.ub=forest$High,  at=log(c(.
05, .25,
1, 10)), slab=forest$SNP, atransf=exp)

As does this (setting colors):

forest(forest$OR, ci.lb=forest$Low, ci.ub=forest$High,  
col=c(1,2,3), slab=forest$SNP, atransf=exp)

But if I try to set both 'at' and 'col':

forest(forest$OR, ci.lb=forest$Low, ci.ub=forest$High,  
col=c(1,2,3), at=log(c(.05, .25, 1, 10)), slab=forest$SNP, 
atransf=exp)

I receive this error:
Error in polygon(x = c(alim[2], alim[2] - (1.4/100) * cex * (xlim[2]
-  :
 formal argument "col" matched by multiple actual arguments

Any help greatly appreciated.

Can you reproduce this using the examples in the package help pages?

--

David Winsemius, MD
Alameda, CA, USA

Windows 7
R 2.12.1
I am trying to write a function (see sample code below) that will take the output of a t-test and produce results suitable for a table.
I have two questions
(1) You will note that the name of the outcome variable, which is "value" in the input is replaced by the string "outcome by class" in the data frame produced by my function. How can I make my function put the name of the variable being analyzed,, i.e "value" in the output data frame
(2) How can I pass the entire input data to the function so my call to the function will not have to be in its current ugly form, i.e.
Table1(data$value,data$sex)
and instead could just be
Table1(value,sex,data=data)


x <- data.frame(value=rnorm(20)  ,sex=rep("Male",  20))
y <- data.frame(value=rnorm(20,4),sex=rep("Female",20))
data <- rbind(x,y)
temp <- t.test(value~sex,data=data)
temp
v<-data.frame(dep=temp$data.name,
           female=temp$estimate[1],male=temp$estimate[2],
           p=temp$p.value,
           CILow=temp$conf.int[1],CIHigh=temp$conf.int[2])
row.names(v) <- NULL



Table1 <- function(outcome,class) {
temp <- t.test(outcome~ class)
mydf <- data.frame(dep=temp$data.name,
             female=temp$estimate[1],male=temp$estimate[2],
             p=temp$p.value,
             CILow=temp$conf.int[1],CIHigh=temp$conf.int[2])
row.names(mydf) <- NULL
mydf}
Table1(data$value,data$sex)



Thank you,
John



John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for ...{{dropped:27}}

Hello,

A simple change to your function partly answers to both questions.


Table2 <- function(formula, data) {
      temp <- t.test(formula, data)
      mydf <- data.frame(dep=temp$data.name,
               female=temp$estimate[1],male=temp$estimate[2],
               p=temp$p.value,
               CILow=temp$conf.int[1],CIHigh=temp$conf.int[2])
      row.names(mydf) <- NULL
      mydf
}
Table2(value ~ sex, data)


If you want the outcome variable to be called just "value", inside the
function use

dname <- rownames(attr(terms(formula), "factors"))[1]
mydf <- data.frame(dep=dname, [...etc...]


Hope this helps,

Rui Barradas


Em 07-01-2013 14:44, John Sorkin escreveu:

Windows 7
R 2.12.1
I am trying to write a function (see sample code below) that will take the output of a t-test and produce results suitable for a table.
I have two questions
(1) You will note that the name of the outcome variable, which is "value" in the input is replaced by the string "outcome by class" in the data frame produced by my function. How can I make my function put the name of the variable being analyzed,, i.e "value" in the output data frame
(2) How can I pass the entire input data to the function so my call to the function will not have to be in its current ugly form, i.e.
Table1(data$value,data$sex)
and instead could just be
Table1(value,sex,data=data)
   
   
x <- data.frame(value=rnorm(20)  ,sex=rep("Male",  20))
y <- data.frame(value=rnorm(20,4),sex=rep("Female",20))
data <- rbind(x,y)
temp <- t.test(value~sex,data=data)
temp
v<-data.frame(dep=temp$data.name,
             female=temp$estimate[1],male=temp$estimate[2],
             p=temp$p.value,
             CILow=temp$conf.int[1],CIHigh=temp$conf.int[2])
row.names(v) <- NULL
   
   
   
Table1 <- function(outcome,class) {
temp <- t.test(outcome~ class)
mydf <- data.frame(dep=temp$data.name,
               female=temp$estimate[1],male=temp$estimate[2],
               p=temp$p.value,
               CILow=temp$conf.int[1],CIHigh=temp$conf.int[2])
row.names(mydf) <- NULL
mydf}
Table1(data$value,data$sex)
   
   
   
Thank you,
John
   
   
   
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for ...{{dropped:13}}