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

Thu Jun 16 20:06:14 CEST 2016

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:dwinsemius at comcast.net] 
Sent: Thursday, June 16, 2016 12:54 PM
To: Muhuri, Pradip (AHRQ/CFACT)
Cc: r-help at 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) <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) ]
> 

Try instead just a vector of names for the second argument to "["

 mydata[ mixedorder(mydata$prevalence_c, decreasing=TRUE), 
         c("indicator", "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
> 
> ______________________________________________
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> PLEASE do read the posting guide 
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> and provide commented, minimal, self-contained, reproducible code.
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA