NCA failed with some data.

[RamomNF]

Hi,

I've been testing the NonCompart package for some time and I've found some datasets which the package function fails or prints a message somewhat strange.

I'll be reporting one issue at time. So, I've submitted a dataset where I'm not being able to use neither sNCA nor tblNCA.

fail1.xlsx

It just prints the message below and fails

Error in [<-.data.frame(*tmp*, Res[, 2] == 0 | Res[, 2] == Inf, 2, :
missing values are not allowed in subscripted assignments of data frames

Thank you.

[shanmdphd]

Thanks for sharing your issue. However, the following codes performed NCA without any errors. We could not reproduce the error you got.

Would you please provide the full script and the output of devtools::session_info() here?

library(readxl)
library(NonCompart)

Data = as.data.frame(read_excel('fail1.xlsx'))
Res = tblNCA(Data, key=c("Subject", "Period", "Formulation"), 
             colTime="Time", colConc="Concentration", 
             dose=150, doseUnit="ug", concUnit="ug/mL", R2ADJ=0)

knitr::kable(head(Res[ , 1:10]))

Subject	Period	Formulation	b0	CMAX	CMAXD	TMAX	TLAG	CLST	CLSTP
1	2	B	-0.5861514	14.723	0.0981533	2.00	1.00	0.064	0.0651636
1	4	B	0.5897648	13.691	0.0912733	2.25	1.50	0.174	0.1740333
1	1	A	1.0589757	20.138	0.1342533	2.50	1.75	0.341	0.1422012
1	3	A	1.3231138	13.898	0.0926533	2.00	1.25	0.241	0.0842974
2	1	B	0.7028187	28.106	0.1873733	2.25	1.50	0.052	0.0599840
2	3	B	0.4132031	23.075	0.1538333	2.25	1.25	0.123	0.1412312

Environment

devtools::session_info()

## - Session info ----------------------------------------------------------
##  setting  value                       
##  version  R version 3.6.1 (2019-07-05)
##  os       Windows 10 x64              
##  system   x86_64, mingw32             
##  ui       RTerm                       
##  language (EN)                        
##  collate  Korean_Korea.949            
##  ctype    Korean_Korea.949            
##  tz       Asia/Seoul                  
##  date     2019-09-17                  
## 
## - Packages --------------------------------------------------------------
##  package     * version date       lib source        
##  assertthat    0.2.1   2019-03-21 [1] CRAN (R 3.6.1)
##  backports     1.1.4   2019-04-10 [1] CRAN (R 3.6.0)
##  callr         3.3.1   2019-07-18 [1] CRAN (R 3.6.1)
##  cellranger    1.1.0   2016-07-27 [1] CRAN (R 3.6.1)
##  cli           1.1.0   2019-03-19 [1] CRAN (R 3.6.1)
##  crayon        1.3.4   2017-09-16 [1] CRAN (R 3.6.1)
##  desc          1.2.0   2018-05-01 [1] CRAN (R 3.6.1)
##  devtools      2.2.0   2019-09-07 [1] CRAN (R 3.6.1)
##  digest        0.6.20  2019-07-04 [1] CRAN (R 3.6.1)
##  DT            0.8     2019-08-07 [1] CRAN (R 3.6.1)
##  ellipsis      0.2.0.1 2019-07-02 [1] CRAN (R 3.6.1)
##  evaluate      0.14    2019-05-28 [1] CRAN (R 3.6.1)
##  fs            1.3.1   2019-05-06 [1] CRAN (R 3.6.1)
##  glue          1.3.1   2019-03-12 [1] CRAN (R 3.6.1)
##  highr         0.8     2019-03-20 [1] CRAN (R 3.6.1)
##  htmltools     0.3.6   2017-04-28 [1] CRAN (R 3.6.1)
##  htmlwidgets   1.3     2018-09-30 [1] CRAN (R 3.6.1)
##  knitr         1.24    2019-08-08 [1] CRAN (R 3.6.1)
##  magrittr      1.5     2014-11-22 [1] CRAN (R 3.6.1)
##  memoise       1.1.0   2017-04-21 [1] CRAN (R 3.6.1)
##  NonCompart  * 0.4.4   2018-07-19 [1] CRAN (R 3.6.0)
##  pillar        1.4.2   2019-06-29 [1] CRAN (R 3.6.1)
##  pkgbuild      1.0.5   2019-08-26 [1] CRAN (R 3.6.1)
##  pkgconfig     2.0.2   2018-08-16 [1] CRAN (R 3.6.1)
##  pkgload       1.0.2   2018-10-29 [1] CRAN (R 3.6.1)
##  prettyunits   1.0.2   2015-07-13 [1] CRAN (R 3.6.1)
##  processx      3.4.1   2019-07-18 [1] CRAN (R 3.6.1)
##  ps            1.3.0   2018-12-21 [1] CRAN (R 3.6.1)
##  R6            2.4.0   2019-02-14 [1] CRAN (R 3.6.1)
##  Rcpp          1.0.2   2019-07-25 [1] CRAN (R 3.6.1)
##  readxl      * 1.3.1   2019-03-13 [1] CRAN (R 3.6.1)
##  remotes       2.1.0   2019-06-24 [1] CRAN (R 3.6.1)
##  rlang         0.4.0   2019-06-25 [1] CRAN (R 3.6.1)
##  rmarkdown     1.15    2019-08-21 [1] CRAN (R 3.6.1)
##  rprojroot     1.3-2   2018-01-03 [1] CRAN (R 3.6.1)
##  sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 3.6.1)
##  stringi       1.4.3   2019-03-12 [1] CRAN (R 3.6.0)
##  stringr       1.4.0   2019-02-10 [1] CRAN (R 3.6.1)
##  testthat      2.2.1   2019-07-25 [1] CRAN (R 3.6.1)
##  tibble        2.1.3   2019-06-06 [1] CRAN (R 3.6.1)
##  usethis       1.5.1   2019-07-04 [1] CRAN (R 3.6.1)
##  withr         2.1.2   2018-03-15 [1] CRAN (R 3.6.1)
##  xfun          0.9     2019-08-21 [1] CRAN (R 3.6.1)
##  yaml          2.2.0   2018-07-25 [1] CRAN (R 3.6.0)
## 
## [1] C:/Users/cmc/Rlib
## [2] C:/Program Files/R/R-3.6.1/library

[nskoch]

I have the same error message.
Any idea or what's going on?
Best regards
Nicolas

[nskoch]

Error in [<-.data.frame(*tmp*, Res[, 2] == 0 | Res[, 2] == Inf, 2, :
missing values are not allowed in subscripted assignments of data frames

[shanmdphd]

@nskoch ,

It's mainly due to an input of the key argument.
Or you can check if there're duplicates of time and concentration data for a given subject.

It would be nice if you could provide minimal working example (MWE), and I will sort out the problem for you.

Pil

[nskoch]

Hi I work with simulated data, 2 groups of subjects (n=2x500) with 2 full profiles by subject. When I limit my dataset to 20 pk profiles, it runs bu I have to define the slope manually which is not possible for 1000 subject. My interest is on AUCall, Tmax and Cmax, I do not need slope. Is it possible with the package ? Best regards Nicolas <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Garanti sans virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> Le sam. 10 avr. 2021 à 06:43, Sungpil Han ***@***.***> a écrit :

…

@nskoch <https://github.com/nskoch> , It's mainly due to an input of the key argument. Or you can check if there're duplicates of time and concentration data for a given subject. It would be nice if you could provide minimal working example (MWE), and I will sort out the problem for you. Pil — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKBGW6HNGDKEDJSCC77TPX3TH7JNRANCNFSM4IXCTT7Q> .

-- Pharmacology & Pharmacokinetic Consultant Professor of Medicine, University of Aix-Marseille Head of the Department of Clinical Pharmacology, Ste Marguerite Hospital Office: +33 49 106 5874 Mobile: +33 63 339 1765

[ksbae]

Use R2ADJ=0 option 나의 iPhone에서 보냄

…

2021. 4. 10. 23:57, Simon ***@***.***> 작성:  Hi I work with simulated data, 2 groups of subjects (n=2x500) with 2 full profiles by subject. When I limit my dataset to 20 pk profiles, it runs bu I have to define the slope manually which is not possible for 1000 subject. My interest is on AUCall, Tmax and Cmax, I do not need slope. Is it possible with the package ? Best regards Nicolas <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Garanti sans virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> Le sam. 10 avr. 2021 à 06:43, Sungpil Han ***@***.***> a écrit : > @nskoch <https://github.com/nskoch> , > > It's mainly due to an input of the key argument. > Or you can check if there're duplicates of time and concentration data for > a given subject. > > It would be nice if you could provide minimal working example (MWE), and I > will sort out the problem for you. > > Pil > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#1 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AKBGW6HNGDKEDJSCC77TPX3TH7JNRANCNFSM4IXCTT7Q> > . > -- Pharmacology & Pharmacokinetic Consultant Professor of Medicine, University of Aix-Marseille Head of the Department of Clinical Pharmacology, Ste Marguerite Hospital Office: +33 49 106 5874 Mobile: +33 63 339 1765 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[ksbae]

나의 iPhone에서 보냄 2021. 4. 11. 06:57, Bae Kyun-Seop ***@***.***> 작성:  Use R2ADJ=0 option 나의 iPhone에서 보냄 2021. 4. 10. 23:57, Simon ***@***.***> 작성:  Hi I work with simulated data, 2 groups of subjects (n=2x500) with 2 full profiles by subject. When I limit my dataset to 20 pk profiles, it runs bu I have to define the slope manually which is not possible for 1000 subject. My interest is on AUCall, Tmax and Cmax, I do not need slope. Is it possible with the package ? Best regards Nicolas <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Garanti sans virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> Le sam. 10 avr. 2021 à 06:43, Sungpil Han ***@***.***> a écrit :

…

@nskoch <https://github.com/nskoch> , It's mainly due to an input of the key argument. Or you can check if there're duplicates of time and concentration data for a given subject. It would be nice if you could provide minimal working example (MWE), and I will sort out the problem for you. Pil — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKBGW6HNGDKEDJSCC77TPX3TH7JNRANCNFSM4IXCTT7Q> .

-- Pharmacology & Pharmacokinetic Consultant Professor of Medicine, University of Aix-Marseille Head of the Department of Clinical Pharmacology, Ste Marguerite Hospital Office: +33 49 106 5874 Mobile: +33 63 339 1765 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#1 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACKQA4RCXC6RDVS4RYCAQ3TTIBROHANCNFSM4IXCTT7Q>.

[nskoch]

Hi many thanks, it works fine. My two groups received different dose, is it possible to take it into account? In the examples, only one dose value is given. Further each subject has 2 profiles, is it possible to compute PK parameters for each profile? I have created 2 ID for each subject (one for each profile) but that's not elegant. Best regards Nicolas <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Garanti sans virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> Le dim. 11 avr. 2021 à 00:24, Kyun-Seop Bae ***@***.***> a écrit :

…

나의 iPhone에서 보냄 2021. 4. 11. 06:57, Bae Kyun-Seop ***@***.***> 작성:  Use R2ADJ=0 option 나의 iPhone에서 보냄 2021. 4. 10. 23:57, Simon ***@***.***> 작성:  Hi I work with simulated data, 2 groups of subjects (n=2x500) with 2 full profiles by subject. When I limit my dataset to 20 pk profiles, it runs bu I have to define the slope manually which is not possible for 1000 subject. My interest is on AUCall, Tmax and Cmax, I do not need slope. Is it possible with the package ? Best regards Nicolas < https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Garanti sans virus. www.avast.com < https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> Le sam. 10 avr. 2021 à 06:43, Sungpil Han ***@***.***> a écrit : > @nskoch <https://github.com/nskoch> , > > It's mainly due to an input of the key argument. > Or you can check if there're duplicates of time and concentration data for > a given subject. > > It would be nice if you could provide minimal working example (MWE), and I > will sort out the problem for you. > > Pil > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > < #1 (comment)>, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AKBGW6HNGDKEDJSCC77TPX3TH7JNRANCNFSM4IXCTT7Q> > . > -- Pharmacology & Pharmacokinetic Consultant Professor of Medicine, University of Aix-Marseille Head of the Department of Clinical Pharmacology, Ste Marguerite Hospital Office: +33 49 106 5874 Mobile: +33 63 339 1765 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub< #1 (comment)>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ACKQA4RCXC6RDVS4RYCAQ3TTIBROHANCNFSM4IXCTT7Q>. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKBGW6G3MTGSREMCMA2QARTTIDF3JANCNFSM4IXCTT7Q> .

-- Pharmacology & Pharmacokinetic Consultant Professor of Medicine, University of Aix-Marseille Head of the Department of Clinical Pharmacology, Ste Marguerite Hospital Office: +33 49 106 5874 Mobile: +33 63 339 1765

[ksbae]

The necessary option is similar to the following; ...( , key=c(“ID”, “Period”), ...) 2021. 4. 11. 18:03, Simon ***@***.***> 작성:  Hi many thanks, it works fine. My two groups received different dose, is it possible to take it into account? In the examples, only one dose value is given. Further each subject has 2 profiles, is it possible to compute PK parameters for each profile? I have created 2 ID for each subject (one for each profile) but that's not elegant. Best regards Nicolas <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Garanti sans virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> Le dim. 11 avr. 2021 à 00:24, Kyun-Seop Bae ***@***.***> a écrit :

…

나의 iPhone에서 보냄 2021. 4. 11. 06:57, Bae Kyun-Seop ***@***.***> 작성:  Use R2ADJ=0 option 나의 iPhone에서 보냄 2021. 4. 10. 23:57, Simon ***@***.***> 작성:  Hi I work with simulated data, 2 groups of subjects (n=2x500) with 2 full profiles by subject. When I limit my dataset to 20 pk profiles, it runs bu I have to define the slope manually which is not possible for 1000 subject. My interest is on AUCall, Tmax and Cmax, I do not need slope. Is it possible with the package ? Best regards Nicolas < https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Garanti sans virus. www.avast.com < https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> Le sam. 10 avr. 2021 à 06:43, Sungpil Han ***@***.***> a écrit : > @nskoch <https://github.com/nskoch> , > > It's mainly due to an input of the key argument. > Or you can check if there're duplicates of time and concentration data for > a given subject. > > It would be nice if you could provide minimal working example (MWE), and I > will sort out the problem for you. > > Pil > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > < #1 (comment)>, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AKBGW6HNGDKEDJSCC77TPX3TH7JNRANCNFSM4IXCTT7Q> > . > -- Pharmacology & Pharmacokinetic Consultant Professor of Medicine, University of Aix-Marseille Head of the Department of Clinical Pharmacology, Ste Marguerite Hospital Office: +33 49 106 5874 Mobile: +33 63 339 1765 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub< #1 (comment)>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ACKQA4RCXC6RDVS4RYCAQ3TTIBROHANCNFSM4IXCTT7Q>. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKBGW6G3MTGSREMCMA2QARTTIDF3JANCNFSM4IXCTT7Q> .

-- Pharmacology & Pharmacokinetic Consultant Professor of Medicine, University of Aix-Marseille Head of the Department of Clinical Pharmacology, Ste Marguerite Hospital Office: +33 49 106 5874 Mobile: +33 63 339 1765 — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#1 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACKQA4UQSHGK2Y3IOGR7Z23TIFQW3ANCNFSM4IXCTT7Q>.

[nskoch]

Many thanks That’s fine Nicolas

…

Le 11 avr. 2021 à 11:43, Kyun-Seop Bae ***@***.***> a écrit :  The necessary option is similar to the following; ...( , key=c(“ID”, “Period”), ...) 2021. 4. 11. 18:03, Simon ***@***.***> 작성:  Hi many thanks, it works fine. My two groups received different dose, is it possible to take it into account? In the examples, only one dose value is given. Further each subject has 2 profiles, is it possible to compute PK parameters for each profile? I have created 2 ID for each subject (one for each profile) but that's not elegant. Best regards Nicolas <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Garanti sans virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> Le dim. 11 avr. 2021 à 00:24, Kyun-Seop Bae ***@***.***> a écrit : > > > > > 나의 iPhone에서 보냄 > 2021. 4. 11. 06:57, Bae Kyun-Seop ***@***.***> 작성: > >  > Use R2ADJ=0 option > > > > > 나의 iPhone에서 보냄 > 2021. 4. 10. 23:57, Simon ***@***.***> 작성: > >  > > Hi > > I work with simulated data, 2 groups of subjects (n=2x500) with 2 full > profiles by subject. > When I limit my dataset to 20 pk profiles, it runs bu I have to define the > slope manually which is not possible for 1000 subject. > My interest is on AUCall, Tmax and Cmax, I do not need slope. Is it > possible with the package ? > > Best regards > Nicolas > > > < > https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> > > Garanti > sans virus. www.avast.com > < > https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > Le sam. 10 avr. 2021 à 06:43, Sungpil Han ***@***.***> a > écrit : > > > @nskoch <https://github.com/nskoch> , > > > > It's mainly due to an input of the key argument. > > Or you can check if there're duplicates of time and concentration data > for > > a given subject. > > > > It would be nice if you could provide minimal working example (MWE), and > I > > will sort out the problem for you. > > > > Pil > > > > — > > You are receiving this because you were mentioned. > > Reply to this email directly, view it on GitHub > > < > #1 (comment)>, > > > or unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/AKBGW6HNGDKEDJSCC77TPX3TH7JNRANCNFSM4IXCTT7Q> > > > . > > > > > -- > Pharmacology & Pharmacokinetic Consultant > Professor of Medicine, University of Aix-Marseille > Head of the Department of Clinical Pharmacology, Ste Marguerite Hospital > Office: +33 49 106 5874 > Mobile: +33 63 339 1765 > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub< > #1 (comment)>, > or unsubscribe< > https://github.com/notifications/unsubscribe-auth/ACKQA4RCXC6RDVS4RYCAQ3TTIBROHANCNFSM4IXCTT7Q>. > > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#1 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AKBGW6G3MTGSREMCMA2QARTTIDF3JANCNFSM4IXCTT7Q> > . > -- Pharmacology & Pharmacokinetic Consultant Professor of Medicine, University of Aix-Marseille Head of the Department of Clinical Pharmacology, Ste Marguerite Hospital Office: +33 49 106 5874 Mobile: +33 63 339 1765 — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#1 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACKQA4UQSHGK2Y3IOGR7Z23TIFQW3ANCNFSM4IXCTT7Q>. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.