Bioequivalence and Bioavailability Forum • about package randomizeBE

yjlee168
★★

Kaohsiung, Taiwan,
2019-08-19 12:14

Posting: # 20502
Views: 1,339

about package randomizeBE [R for BE/BA]

Dear Detlew and all others,

I recently tried to re-write GUI for your developed R package randomizeBE. And I got some error messages about the function sequences. Here is what I got

require("randomizeBE")

tmts<- c("R","T")

tmts

[1] "R" "T"

sequences("parallel", tmts=tmts)

Error in if (!is.null(tmts) & length(tmts) != ntmt) { : 

  missing value where TRUE/FALSE needed

In addition: Warning message:

In sequences("parallel", tmts = tmts) : NAs introduced by coercion



sequences

function (design, tmts = NULL) 

{

    seqs <- character()

    ntmt <- as.numeric(substr(design, 1, 1))           ### Q1: if this works for design=="parallel" too?

    if (!is.null(tmts) & length(tmts) != ntmt) { 

        stop("Treatment codes must have ", ntmt, " entries!")

    }

    if (design == "2x2" | design == "2x2x2") 

        seqs <- c("AB", "BA")

    if (design == "parallel")                          ### Q2: not working if tmts=c("R","T")?

        seqs <- c("A", "B")

    if (design == "3x3" | design == "3x3x3") {

        seqs <- c("ABC", "BCA", "CAB")

        seqs <- randLS(seqs)

...

}

sequences("parallel")

[1] "A" "B"

Warning message:

In sequences("parallel") : NAs introduced by coercion  ### Q3: is this warning message normal? 

sequences("parallel", tmts=c("R","T1","T2"))           ### Q4: not implemented yet for this?

Error in if (!is.null(tmts) & length(tmts) != ntmt) { : 

  missing value where TRUE/FALSE needed

In addition: Warning message:

In sequences("parallel", tmts = c("R", "T1", "T2")) :

  NAs introduced by coercion

Thanks in advanced.

—
All the best,
-- Yung-jin Lee
bear v2.8.7:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan http://pkpd.kmu.edu.tw/bear
Download link (updated) -> here

yjlee168
★★

Kaohsiung, Taiwan,
2019-08-20 14:04

@ yjlee168
Posting: # 20505
Views: 1,136

about package randomizeBE

Post reply

Dear all,

I re-checked the codes and found

as.numeric(substr("parallel", 1, 1))

[1] NA   ### from 'as.numeric("p")'

sequences("parallel")

[1] "A" "B"

Warning message:

In sequences("parallel") : NAs introduced by coercion

Q1: So this is where that warning message comes from.
Q2: Nope, cannot do it with sequences("parallel",tmts=c("R","T")).
Q3: Ok, it still works and it just happens to design=="parallel".
Q4: not implemented yet for sure.

—
All the best,
-- Yung-jin Lee
bear v2.8.7:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan http://pkpd.kmu.edu.tw/bear
Download link (updated) -> here

d_labes
★★★

Berlin, Germany,
2019-08-24 16:26

@ yjlee168
Posting: # 20512
Views: 1,073

about package randomizeBE

Post reply

Dear Yung-jin,

» I re-checked the codes and found
»

as.numeric(substr("parallel", 1, 1))

» [1] NA   ### from 'as.numeric("p")'
» sequences("parallel")
» [1] "A" "B"
» Warning message:
» In sequences("parallel") : NAs introduced by coercion

»
» Q1: So this is where that warning message comes from.

Correct. You have discovered a bug. Congratulation :-D

.

» Q2: Nope, cannot do it with sequences("parallel",tmts=c("R","T")).

Warning still alive.

» Q3: Ok, it still works and it just happens to design=="parallel".

Also correct. It works, but with a stupid warning.

» Q4: not implemented yet for sure.

Correct, not implemented yet.

A new version with bug fix is on its way to CRAN.

—
Regards,

Detlew

yjlee168 ★★ Kaohsiung, Taiwan, 2019-08-24 19:32 @ d_labes Posting: # 20514 Views: 1,067	about package randomizeBE Post reply
	Dear Detlew, Thank you so much for your replied messages. It confirms what I found. — All the best, -- Yung-jin Lee bear v2.8.7:- created by Hsin-ya Lee & Yung-jin Lee Kaohsiung, Taiwan http://pkpd.kmu.edu.tw/bear Download link (updated) -> here

Helmut
★★★

Vienna, Austria,
2019-08-25 13:43

@ yjlee168
Posting: # 20515
Views: 1,073

randomizeBE 0.3-5

Post reply

Dear Yung-jin,

sources of randomizeBE 0.3-5 on CRAN since yesterday.

Your test cases:

library(randomizeBE) tmts <- c("R", "T") # [1] "R" "T" sequences("parallel") # [1] "A" "B" sequences("parallel", tmts=c("R", "T1", "T2")) Error in sequences("parallel", tmts = c("R", "T1", "T2")) : Treatment codes must have 2 entries!

—
Cheers,
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

yjlee168
★★

Kaohsiung, Taiwan,
2019-08-25 15:19

@ Helmut
Posting: # 20516
Views: 1,052

randomizeBE 0.3-5

Post reply

Dear Helmut,

» sources of randomizeBE 0.3-5 on CRAN since yesterday.

Thank you for your messages. I just got upgraded.

packageVersion("randomizeBE")

[1] ‘0.3.5’

»...
» sequences("parallel")
» [1] "A" "B"
»
» sequences("parallel", tmts=c("R", "T1", "T2"))
» Error in sequences("parallel", tmts = c("R", "T1", "T2")) :
» Treatment codes must have 2 entries![/code][/indent]

Right. Though sequences() dose not work with tmts=c("R","T") or tmts=c("R","T1","T2"), RL4() still works very well.

RL4(24,seqs=c("R","T"))

Randomization table          created: 2019-08-25 20:13:13 

(seed: 886436 blocksize: 4 )



 subject seqno sequence

       1     1        R

       2     1        R

       3     2        T

       4     2        T

       5     1        R

       6     1        R

       7     2        T

       8     2        T

       9     1        R

      10     2        T

      11     1        R

      12     2        T

      13     1        R

      14     1        R

      15     2        T

      16     2        T

      17     2        T

      18     2        T

      19     1        R

      20     1        R

      21     2        T

      22     1        R

      23     2        T

      24     1        R



RL4(24,seqs=c("R","T1","T2"))

Randomization table          created: 2019-08-25 20:15:06 

(seed: 3637764 blocksize: 6 )



 subject seqno sequence

       1     2       T1

       2     3       T2

       3     3       T2

       4     2       T1

       5     1        R

       6     1        R

       7     1        R

       8     3       T2

       9     2       T1

      10     3       T2

      11     2       T1

      12     1        R

      13     3       T2

      14     2       T1

      15     1        R

      16     1        R

      17     3       T2

      18     2       T1

      19     3       T2

      20     2       T1

      21     2       T1

      22     1        R

      23     3       T2

      24     1        R

That means I cannot use RL4(...,seqs=seqs) where seqs=squences(...) if I prefer using "R", "T", "T1", "T2" for treatment abbreviated, instead of "A", "B", "C" etc.. Am I correct?

—
All the best,
-- Yung-jin Lee
bear v2.8.7:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan http://pkpd.kmu.edu.tw/bear
Download link (updated) -> here

Helmut
★★★

Vienna, Austria,
2019-08-25 16:26

@ yjlee168
Posting: # 20517
Views: 1,038

randomizeBE 0.3-5

Post reply

Hi Yung-jin,

» That means I cannot use RL4(...,seqs=seqs) where seqs=squences(...) if I prefer using "R", "T", "T1", "T2" for treatment abbreviated, instead of "A", "B", "C" etc.. Am I correct?

I’m not sure whether I understand you correctly. See ?sequences. Only designs listed there are implemented. Hence, you can’t randomize a parallel design with >2 groups.
However,

sequences("4x4", tmts=c("R1", "R2", "T1", "T2")) # [1] "R1T2R2T1" "R2T1T2R1" "T1R2R1T2" "T2R1T1R2" williams(ntmt=4, tmts=c("R1", "R2", "T1", "T2")) # [1] "R1T2T1R2" "R2T1T2R1" "T1R1R2T2" "T2R2R1T1"

work as designed.

—
Cheers,
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

yjlee168
★★

Kaohsiung, Taiwan,
2019-08-25 17:08

@ Helmut
Posting: # 20518
Views: 1,033

randomizeBE 0.3-5

Post reply

Dear Helmut,

You're right. Great and many thanks. I just get confused. It is much more convenient to use seqs=sequences(...) in RL4(...,seqs=seqs). Sorry about that. :-D

» ... I’m not sure whether I understand you correctly. See ?sequences. Only designs listed there are implemented. Hence, you can’t randomize a parallel design with >2 groups.

—
All the best,
-- Yung-jin Lee
bear v2.8.7:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan http://pkpd.kmu.edu.tw/bear
Download link (updated) -> here

d_labes
★★★

Berlin, Germany,
2019-08-25 19:39

@ Helmut
Posting: # 20519
Views: 1,027

randomizeBE 0.3-5

Post reply

Dear both,

sequences() and williams() are only convenience functions to give you the sequences of a design from its short-hand name.
And as Helmut already stated: "parallel" is the short hand for 2-group parallel design and can't therefore used with the treatment codes T1, T2 and R.

But main function RL4() accepts of course the "sequences" (aka groups) T1, T2 and R as noticed above and gives you a randomization list also for that design (3-group parallel) not listed in sequences().

BTW: Since today randomizeBE v0.3-5 is available at CRAN also as windows binaries.

—
Regards,

Detlew