Bioequivalence and Bioavailability Forum • Tracking down error

Tracking down error [Power / Sample Size]

posted by Helmut – Vienna, Austria, 2020-05-12 13:49 (1706 d 12:15 ago) – Posting: # 21427
Views: 10,427

Hi Alyssa,

❝ Then i continued with the following command but it appeared error: […]

Let’s try to figure it out. Execute this code:

library(PowerTOST)

CVwR    <- 0.426

CV      <- rep(CVwR, 2)

designs <- c("2x3x3", "2x2x3", "2x2x4")

target  <- c(0.80, 0.85, 0.90)

res     <- data.frame(design = rep(designs, each = length(target)),

                      target = target, n = NA, power = NA)

for (j in 1:nrow(res)) {

  res[j, 3:4] <- sampleN.scABEL(CV = CV, design = res$design[j],

                                targetpower = res$target[j],

                                print = FALSE, details = FALSE)[8:9]


}

print(res, row.names = FALSE)

If it works now, fine. If you get the same error, try:

res[1, 3:4] <- sampleN.scABEL(CV = CV, design = "2x3x3",

                              targetpower = 0.8, print = FALSE,

                              details = FALSE)[8:9]


print(res[1, ], row.names = FALSE)

Expected:

 design target  n   power

  2x3x3    0.8 42 0.81976

If you get an error (or something else), let’s see what you have installed. Try this:

p <- c("PowerTOST", "mvtnorm", "stats", "utils",

       "graphics", "grDevices", "cubature",

       "TeachingDemos", "crossdes", "devtools")

i <- data.frame(name = c("R", p),

                version = c(noquote(as.character(getRversion())),

                            rep(NA, length(p))),

                status = c("-", rep("required", 8),

                           rep("suggested", 2)))

for (j in 2:nrow(i)) {

  i[j, 2] <- noquote(as.character(packageVersion(i[j, 1])))

}

print(i, row.names = FALSE)

On my machine:

          name    version    status

             R      4.0.0         -

     PowerTOST 1.4.9.9999  required

       mvtnorm      1.1.0  required

         stats      4.0.0  required

         utils      4.0.0  required

      graphics      4.0.0  required

     grDevices      4.0.0  required

      cubature      2.0.4  required

 TeachingDemos       2.12  required

      crossdes      1.1.1 suggested

      devtools      2.3.0 suggested

If you have [image]

<4.0.0, I suggest to update. Then copy the entire library-folder of the old installation over the new installation. When asked whether newer files should be overwritten, answer No. Open the console of the new [image]

and execute:
update.packages(checkBuilt = TRUE, ask = FALSE)
Once done, it should look similar to mine. 1.4.9.9999 is the development version of PowerTOST; on your machine it should be 1.4.9. If one is missing (<NA> in the column version), download/install it.
To get more information about you installation, execute:
devtools::session_info()
On my machine:

- Session info ---------------------------------------------------------------

 setting  value                       

 version  R version 4.0.0 (2020-04-24)

 os       Windows 7 x64 SP 1          

 system   x86_64, mingw32             

 ui       Rgui                        

 language EN                          

 collate  German_Germany.1252         

 ctype    German_Germany.1252         

 tz       Europe/Vienna               

 date     2020-05-12                  



- Packages -------------------------------------------------------------------

 package       * version    date       lib source        

 assertthat      0.2.1      2019-03-21 [1] CRAN (R 4.0.0)

 backports       1.1.6      2020-04-05 [1] CRAN (R 4.0.0)

 callr           3.4.3      2020-03-28 [1] CRAN (R 4.0.0)

 cli             2.0.2      2020-02-28 [1] CRAN (R 4.0.0)

 crayon          1.3.4      2017-09-16 [1] CRAN (R 4.0.0)

 cubature        2.0.4      2019-12-04 [1] CRAN (R 4.0.0)

 desc            1.2.0      2018-05-01 [1] CRAN (R 4.0.0)

 devtools        2.3.0      2020-04-10 [1] CRAN (R 4.0.0)

 digest          0.6.25     2020-02-23 [1] CRAN (R 4.0.0)

 ellipsis        0.3.0      2019-09-20 [1] CRAN (R 4.0.0)

 fansi           0.4.1      2020-01-08 [1] CRAN (R 4.0.0)

 fs              1.4.1      2020-04-04 [1] CRAN (R 4.0.0)

 glue            1.4.0      2020-04-03 [1] CRAN (R 4.0.0)

 magrittr        1.5        2014-11-22 [1] CRAN (R 4.0.0)

 memoise         1.1.0      2017-04-21 [1] CRAN (R 4.0.0)

 mvtnorm         1.1-0      2020-02-24 [1] CRAN (R 4.0.0)

 pkgbuild        1.0.8      2020-05-07 [1] CRAN (R 4.0.0)

 pkgload         1.0.2      2018-10-29 [1] CRAN (R 4.0.0)

 PowerTOST     * 1.4.9.9999 2020-05-11 [1] local         

 prettyunits     1.1.1      2020-01-24 [1] CRAN (R 4.0.0)

 processx        3.4.2      2020-02-09 [1] CRAN (R 4.0.0)

 ps              1.3.3      2020-05-08 [1] CRAN (R 4.0.0)

 R6              2.4.1      2019-11-12 [1] CRAN (R 4.0.0)

 Rcpp            1.0.4.6    2020-04-09 [1] CRAN (R 4.0.0)

 remotes         2.1.1      2020-02-15 [1] CRAN (R 4.0.0)

 rlang           0.4.6      2020-05-02 [1] CRAN (R 4.0.0)

 rprojroot       1.3-2      2018-01-03 [1] CRAN (R 4.0.0)

 sessioninfo     1.1.1      2018-11-05 [1] CRAN (R 4.0.0)

 TeachingDemos   2.12       2020-04-07 [1] CRAN (R 4.0.0)

 testthat        2.3.2      2020-03-02 [1] CRAN (R 4.0.0)

 usethis         1.6.1      2020-04-29 [1] CRAN (R 4.0.0)

 withr           2.2.0      2020-04-20 [1] CRAN (R 4.0.0)



[1] D:/Program Files/R/R-4.0.0/library

Likely your list will be shorter; please post here what you got.

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Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
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Complete thread:

Sample size calculation (Pilot study result vs literature) Alyssa 2020-05-04 04:35 [Power / Sample Size]
- Sample size calculation (Pilot study result vs literature) Dr_Dan 2020-05-04 08:46
  - Sample size calculation (Pilot study result vs literature) Alyssa 2020-05-04 09:26
- Estimation of CVw and/or CVwR Helmut 2020-05-04 12:07
  - Estimation of CVw and/or CVwR ElMaestro 2020-05-04 12:14
    - Mea culpa! Helmut 2020-05-04 12:40
      - It must be Myco ElMaestro 2020-05-04 13:46
        
        It is, it is! Helmut 2020-05-04 14:07
        
        It is.... Alyssa 2020-05-05 05:00
        
        Tutorial Helmut 2020-05-05 12:45
        
        Tutorial Alyssa 2020-05-08 06:48
        
        library d_labes 2020-05-08 11:16
        Tutorial (from the start) Helmut 2020-05-08 13:08
        
        Tutorial (from the start) Alyssa 2020-05-12 04:05
        
        Tracking down errorHelmut 2020-05-12 11:49
        
        Tracking down error: stringsAsFactors d_labes 2020-05-13 11:34
        
        R <4.0.0 Helmut 2020-05-13 12:07
        
        R <4.0.0 ElMaestro 2020-05-13 14:18
        
        R <4.0.0? Helmut 2020-05-13 14:21
        
        PowerTOST’s functions with as.character(design) d_labes 2020-05-13 18:50
        
        PowerTOST’s functions with as.character(design) Helmut 2020-05-13 18:55
        
        Tracking down error Alyssa 2020-05-15 05:08
        
        All’s well that ends well. Helmut 2020-05-15 10:52