dplyr's arrange function - 3 solutions received - 1 New Question

On Jun 16, 2016, at 6:12 AM, Muhuri, Pradip (AHRQ/CFACT) <Pradip.Muhuri at ahrq.hhs.gov> 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[ mixedorder(mydata$prevalence_c, decreasing=TRUE),  ]

3)  Thanks to Jim Lemon's for his  solution. I  have prepended a minus sign to reverse the order.

numprev<-as.numeric(sapply(strsplit(trimws(mydata$prevalence_c)," 
"),"[",1)) mydata[order(-numprev), ]


(New)Question for solution 2:

I want to keep only 2 variables  (say, indicator and prevalence_c) in the output.  Where to insert the additional code? Why does the following code fail?

mydata[ mixedorder(mydata$prevalence_c, decreasing=TRUE), 
c(mydata$indicator, mydata$prevalence_c) ]

Error in `[.data.frame`(mydata, mixedorder(mydata$prevalence_c, decreasing = TRUE),  : 
 undefined columns selected

********************

str(mydata)

Classes 'tbl_df', 'tbl' and 'data.frame':	10 obs. of  10 variables:
$ indicator   : chr  "1. Health check-up" "2. Blood cholesterol checked " "3. Recieved flu vaccine" "4. Blood pressure checked" ...
$ subgroup    : chr  "Both sexes, ages =35 yrs""| __truncated__ "Both sexes, ages =35 yrs""| __truncated__ "Both sexes, ages =35 yrs""| __truncated__ "Both sexes, ages =35 yrs""| __truncated__ ...
$ n           : num  2117 2127 2124 2135 1027 ...
$ prevalence_c: chr  "74.7 (1.20)" "90.3 (0.89)" "51.7 (1.35)" "93.2 (0.70)" ...
$ prevalence_p: chr  "77.2 (1.19)" "84.5 (1.14)" "50.0 (1.33)" "88.7 (0.88)" ...
$ sensitivity : chr  "87.4 (1.10)" "99.2 (0.27)" "97.0 (0.62)" "99.0 (0.27)" ...
$ specificity : chr  "68.3 (2.80)" "58.2 (3.72)" "93.5 (0.90)" "52.7 (3.90)" ...
$ ppv         : chr  "90.4 (0.94)" "92.8 (0.85)" "93.7 (0.87)" "94.3 (0.63)" ...
$ npv         : chr  "61.5 (3.00)" "92.8 (2.27)" "96.9 (0.63)" "87.5 (3.27)" ...
$ kappa       : chr  "0.536 (0.029)" "0.676 (0.032)" "0.905 (0.011)" "0.626 (0.035)" ...

Pradip K. Muhuri,  AHRQ/CFACT
5600 Fishers Lane # 7N142A, Rockville, MD 20857
Tel: 301-427-1564




-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Daniel 
Nordlund
Sent: Wednesday, June 15, 2016 6:37 PM
To: r-help at r-project.org
Subject: Re: [R] dplyr's arrange function

On 6/15/2016 2:08 PM, Muhuri, Pradip (AHRQ/CFACT) wrote:

Hello,

I am using the dplyr's arrange() function to sort  one of the  many data frames  on a character variable (named "prevalence").

Issue: I am not getting the desired output  (line 7 is the problem, which should be the very last line in the sorted data frame) because the sorted field is character, not numeric.

The reproducible example and the output are appended below.

Is there any work-around  to convert/treat  this character variable (named "prevalence" in the data frame below)  as numeric before using the arrange() function within the dplyr package?

Any hints will be appreciated.

Thanks,

Pradip Muhuri

# Reproducible Example

library("readr")
testdata <- read_csv(
"indicator,  prevalence
1. Health check-up, 77.2 (1.19)
2. Blood cholesterol checked,  84.5 (1.14) 3. Recieved flu vaccine,
50.0 (1.33) 4. Blood pressure checked, 88.7 (0.88) 5. Aspirin 
use-problems, 11.7 (1.02) 6.Colonoscopy, 60.2 (1.41) 7. 
Sigmoidoscopy,
6.1 (0.61) 8. Blood stool test, 14.6 (1.00) 9.Mammogram,  72.6 (1.82) 
10. Pap Smear test, 73.3 (2.37)")

# Sort on the character variable in descending order 
arrange(testdata,
desc(prevalence))

# Results from Console

                     indicator  prevalence
                         (chr)       (chr)
1     4. Blood pressure checked 88.7 (0.88)
2  2. Blood cholesterol checked 84.5 (1.14)
3            1. Health check-up 77.2 (1.19)
4            10. Pap Smear test 73.3 (2.37)
5                   9.Mammogram 72.6 (1.82)
6                 6.Colonoscopy 60.2 (1.41)
7              7. Sigmoidoscopy  6.1 (0.61)
8       3. Recieved flu vaccine 50.0 (1.33)
9           8. Blood stool test 14.6 (1.00)
10      5. Aspirin use-problems 11.7 (1.02)


Pradip K. Muhuri,  AHRQ/CFACT
5600 Fishers Lane # 7N142A, Rockville, MD 20857
Tel: 301-427-1564

The problem is that you are sorting a character variable.

testdata$prevalence

 [1] "77.2 (1.19)" "84.5 (1.14)" "50.0 (1.33)" "88.7 (0.88)" "11.7 (1.02)"
 [6] "60.2 (1.41)" "6.1 (0.61)"  "14.6 (1.00)" "72.6 (1.82)" "73.3 (2.37)"

Notice that the 7th element is "6.1 (0.61)".  The first CHARACTER is a "6", so it is going to sort BEFORE the "50.0 (1.33)" (in descending order).  If you want the character value of line 7 to sort last, it would need to be "06.1 (0.61)" or " 6.1 (0.61)" (notice the leading space).

Hope this is helpful,

Dan

Daniel Nordlund
Port Townsend, WA USA