Re: [R] svykappa using the survey package
hi pradip, this should give you what you want
library(foreign)
library(survey)
tf <- tempfile()
download.file( "
https://meps.ahrq.gov/mepsweb/data_files/pufs/h163ssp.zip; , tf , mode =
'wb' )
z <- unzip( tf , exdir = tempdir() )
x <- read.xport( z )
names( x ) <- tolower( names( x ) )
design <- svydesign(id=~varpsu,strat=~varstr, weights=~perwt13f,
data=x, nest=TRUE)
# include missings as "No" values here
design <-
update(design,
xbpchek53 = ifelse(bpchek53 ==1,'yes','no or missing'),
xcholck53 = ifelse(cholck53 ==1, 'yes','no or missing')
)
# subset out records that were missing for either variable
svykappa( ~ xbpchek53 + xcholck53 , subset(design, bpchek53 > 0 &
cholck53 > 0 ) )
On Mon, Jun 20, 2016 at 7:49 PM, Muhuri, Pradip (AHRQ/CFACT) <
pradip.muh...@ahrq.hhs.gov> wrote:
> Hello,
>
> My goal is to calculate the weighted kappa measure of agreement between
> two factors using the R survey package. I am getting the following error
> message (the console is appended below; sorry no data provided).
>
> > # calculate survey Kappa
> > svykappa(~xbpchek53+xcholck53, design)
> Error in names(probs) <- nms :
> 'names' attribute [15] must be the same length as the vector [8]
>
> I have followed the following major steps:
>
> 1) Used the "haven" package to read the sas data set into R.
> 2) Used the dplyr mutate() to create 2 new variables and converted to
> factors [required for the svykappa()?].
> 3) Created an object (named design) using the survey design variables and
> the data file.
> 4) Used the svykappa() to compute the kappa measure of agreement.
>
> I will appreciate if someone could give me hints on how to resolve the
> issue.
>
> Thanks,
>
> Pradip Muhuri
>
> ### The detailed console is appended below
>
>
> > setwd ("U:/A_PSAQ")
> > library(haven)
> > library(dplyr)
> > library(survey)
> > library(srvyr)
> > library(Hmisc)
> > my_hc2013_data <- read_sas("pc2013.sas7bdat")
> >
> > # Function to convert var names in upper cases to var names in lower
> cases
> > lower <- function (df) {
> + names(df) <- tolower(names(df))
> + df
> + }
> > my_hc2013_data <- lower(my_hc2013_data)
> >
> > # Check the contents - Hmisc package (as above) required
> > # contents(my_hc2013_data)
> >
> > # create two new variables
> > my_hc2013_data <- mutate(my_hc2013_data,
> + xbpchek53 = ifelse(bpchek53 ==1, 1,
> + ifelse(bpchek53 %in% 2:6, 2,NA)),
> + xcholck53 = ifelse(cholck53 ==1, 1,
> +ifelse(cholck53 %in% 2:6, 2,NA)))
> >
> > # convert the numeric variables to factors for the kappa measure
> > my_hc2013_data$xbpchek53 <- as.factor(my_hc2013_data$xbpchek53)
> > my_hc2013_data$xcholck53 <- as.factor(my_hc2013_data$xcholck53)
> >
> > # check whether the variables are factors
> > is.factor(my_hc2013_data$xbpchek53)
> [1] TRUE
> > is.factor(my_hc2013_data$xcholck53)
> [1] TRUE
> >
> >
> > # check the data from the cross table
> > addmargins(with(my_hc2013_data, table(bpchek53,xbpchek53 )))
> xbpchek53
> bpchek53 1 2 Sum
> -9 0 0 0
> -8 0 0 0
> -7 0 0 0
> -1 0 0 0
> 1 19778 0 19778
> 2 0 2652 2652
> 3 0 1014 1014
> 4 0 538 538
> 5 0 737 737
> 6 0 623 623
> Sum 19778 5564 25342
> > addmargins(with(my_hc2013_data, table(cholck53,xcholck53 )))
> xcholck53
> cholck53 1 2 Sum
> -9 0 0 0
> -8 0 0 0
> -7 0 0 0
> -1 0 0 0
> 1 14850 0 14850
> 2 0 3153 3153
> 3 0 1170 1170
> 4 0 696 696
> 5 0 909 909
> 6 0 3764 3764
> Sum 14850 9692 24542
> > addmargins(with(my_hc2013_data, table(xbpchek53,xcholck53 )))
> xcholck53
> xbpchek53 1 2 Sum
> 1 14667 4379 19046
> 2 163 5225 5388
> Sum 14830 9604 24434
> >
> > # create an object with design variables and data
> > design<-svydesign(id=~varpsu,strat=~varstr, weights=~perwt13f,
> data=my_hc2013_data, nest=TRUE)
> >
> > # calculate survey Kappa
> > svykappa(~xbpchek53+xcholck53, design)
> Error in names(probs) <- nms :
> 'names' attribute [15] must be the same length as the vector [8]
>
> #
>
> Pradip K. Muhuri, AHRQ/CFACT
> 5600 Fishers Lane # 7N142A, Rockville, MD 20857
> Tel: 301-427-1564
>
>
>
>
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Muhuri,
> Pradip (AHRQ/CFACT)
> Sent: Thursday, June 16, 2016 2:06 PM
> To: David Winsemius
> Cc: r-help@r-project.org
> Subject: Re: [R] dplyr's arrange function - 3 solutions
[R] svykappa using the survey package
Hello,
My goal is to calculate the weighted kappa measure of agreement between two
factors using the R survey package. I am getting the following error message
(the console is appended below; sorry no data provided).
> # calculate survey Kappa
> svykappa(~xbpchek53+xcholck53, design)
Error in names(probs) <- nms :
'names' attribute [15] must be the same length as the vector [8]
I have followed the following major steps:
1) Used the "haven" package to read the sas data set into R.
2) Used the dplyr mutate() to create 2 new variables and converted to factors
[required for the svykappa()?].
3) Created an object (named design) using the survey design variables and the
data file.
4) Used the svykappa() to compute the kappa measure of agreement.
I will appreciate if someone could give me hints on how to resolve the issue.
Thanks,
Pradip Muhuri
### The detailed console is appended below
> setwd ("U:/A_PSAQ")
> library(haven)
> library(dplyr)
> library(survey)
> library(srvyr)
> library(Hmisc)
> my_hc2013_data <- read_sas("pc2013.sas7bdat")
>
> # Function to convert var names in upper cases to var names in lower cases
> lower <- function (df) {
+ names(df) <- tolower(names(df))
+ df
+ }
> my_hc2013_data <- lower(my_hc2013_data)
>
> # Check the contents - Hmisc package (as above) required
> # contents(my_hc2013_data)
>
> # create two new variables
> my_hc2013_data <- mutate(my_hc2013_data,
+ xbpchek53 = ifelse(bpchek53 ==1, 1,
+ ifelse(bpchek53 %in% 2:6, 2,NA)),
+ xcholck53 = ifelse(cholck53 ==1, 1,
+ifelse(cholck53 %in% 2:6, 2,NA)))
>
> # convert the numeric variables to factors for the kappa measure
> my_hc2013_data$xbpchek53 <- as.factor(my_hc2013_data$xbpchek53)
> my_hc2013_data$xcholck53 <- as.factor(my_hc2013_data$xcholck53)
>
> # check whether the variables are factors
> is.factor(my_hc2013_data$xbpchek53)
[1] TRUE
> is.factor(my_hc2013_data$xcholck53)
[1] TRUE
>
>
> # check the data from the cross table
> addmargins(with(my_hc2013_data, table(bpchek53,xbpchek53 )))
xbpchek53
bpchek53 1 2 Sum
-9 0 0 0
-8 0 0 0
-7 0 0 0
-1 0 0 0
1 19778 0 19778
2 0 2652 2652
3 0 1014 1014
4 0 538 538
5 0 737 737
6 0 623 623
Sum 19778 5564 25342
> addmargins(with(my_hc2013_data, table(cholck53,xcholck53 )))
xcholck53
cholck53 1 2 Sum
-9 0 0 0
-8 0 0 0
-7 0 0 0
-1 0 0 0
1 14850 0 14850
2 0 3153 3153
3 0 1170 1170
4 0 696 696
5 0 909 909
6 0 3764 3764
Sum 14850 9692 24542
> addmargins(with(my_hc2013_data, table(xbpchek53,xcholck53 )))
xcholck53
xbpchek53 1 2 Sum
1 14667 4379 19046
2 163 5225 5388
Sum 14830 9604 24434
>
> # create an object with design variables and data
> design<-svydesign(id=~varpsu,strat=~varstr, weights=~perwt13f,
> data=my_hc2013_data, nest=TRUE)
>
> # calculate survey Kappa
> svykappa(~xbpchek53+xcholck53, design)
Error in names(probs) <- nms :
'names' attribute [15] must be the same length as the vector [8]
#
Pradip K. Muhuri, AHRQ/CFACT
5600 Fishers Lane # 7N142A, Rockville, MD 20857
Tel: 301-427-1564
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Muhuri, Pradip
(AHRQ/CFACT)
Sent: Thursday, June 16, 2016 2:06 PM
To: David Winsemius
Cc: r-help@r-project.org
Subject: Re: [R] dplyr's arrange function - 3 solutions received - 1 New
Question
Hello David,
Your revisions to the earlier code have given me desired results.
library("gtools")
mydata[ mixedorder(mydata$prevalence_c, decreasing=TRUE), c("indicator",
"prevalence_c") ]
Thanks,
Pradip
Pradip K. Muhuri, AHRQ/CFACT
5600 Fishers Lane # 7N142A, Rockville, MD 20857
Tel: 301-427-1564
-Original Message-
From: David Winsemius [mailto:dwinsem...@comcast.net]
Sent: Thursday, June 16, 2016 12:54 PM
To: Muhuri, Pradip (AHRQ/CFACT)
Cc: r-help@r-project.org
Subject: Re: [R] dplyr's arrange function - 3 solutions received - 1 New
Question
> On Jun 16, 2016, at 6:12 AM, Muhuri, Pradip (AHRQ/CFACT)
> wrote:
>
> Hello,
>
> I got 3 solutions to my earlier code. Thanks to the contributors. May I
> bring your attention to a new question below (with respect to David's
> solution)?
>
> 1) Thanks to Daniel Nordlund for the tips - replacing leading space with a 0
> in the data.
>
> 2) Thanks to David Winsemius for his solution with the gtools::mixedorder
> function. I have added an argument to his.
>
> mydata[
