yjlee168
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Kaohsiung, Taiwan,
2013-03-20 11:53
(4422 d 03:04 ago)

Posting: # 10244
Views: 12,523
 

 Preview of bear v2.5.4 [🇷 for BE/BA]

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Dear all,

I plan to release bear v2.5.4 recently. One thing is that R v3.0 will be released on April 3, 2013. I am wondering if I should wait until R v3.0, although I have tested bear v2.5.4 with nightly built of R v3.0 pre-release or alpha. Anyway, before that, I would like to share change logs of bear v2.5.4 here.
  1. grouping all output files for each run with random batch# and system date as leading characters for these output files; more output files will be generated from this version. and thus no more overwrite output files from previous runs now.
  2. outlier detection analysis (ODA) is taken away from routine run; and also ODA outputs are separated (plots & text output files);
  3. max. data point selections for lambda_z estimation was increased to 6 (2-6);
  4. single plot (1x1) for point selection now (used to be 2x2 plots) with manual data point selection for lambda_z estimation;
  5. fix inconsistent outputs for unbalanced dataset (between anova & stat summary output files);
  6. incomplete dataset will be blocked before being analyzed (hopefully);
  7. use "file.choose()" for data file selections; no more limit to working directory for data files anymore; however, all output files still go to working directory;
  8. summary lambda_z selections outputs as .csv format of total subjects; this still not available for demo runs currently; also fixed the outputs in nca_output files for manual selection list;
  9. pivotal and misc pk parameters output file as .csv format;
  10. add "/extdata" directory to store demo data files as .rda format;
  11. fixed error due to lineplot.ci() (from sciplot package) to successfully generate NCA plots with R 3.0 pre-release/alpha? (though it is be OK with R v2.15.3);
  12. add "extdata" directory to store demo data files as .rda format; thus remove data() call for good practice (users won't feel this change at all).

I will update this change log later if necessary. User can install updated version with R console (menu-> Packages-> Update packages...) from CRAN mirror site after successful submission. Thank you for your interest in bear and have a nice day.
—
All the best,
-- Yung-jin Lee
bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here
 
yjlee168
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Kaohsiung, Taiwan,
2013-03-27 23:22
(4414 d 15:35 ago)

@ yjlee168
Posting: # 10301
Views: 10,721
 

 Pre-release of bear v2.5.4

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Dear all,

If you like to have a look at pre-rlease bear v2.5.4, please click here and go to folder '/package' to click 'readme.txt' for more information. Files under the folder '/single-dose run' are some output files generated by bear of this pre-release. Please only install this pre-release under R 2.15.3. Try it yourself. Have fun.
—
All the best,
-- Yung-jin Lee
bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here
 
yjlee168
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Kaohsiung, Taiwan,
2013-04-04 15:48
(4407 d 00:09 ago)

@ yjlee168
Posting: # 10342
Views: 10,681
 

 Release of bear v2.5.4

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Dear all,

After two more years of last update (v2.5.3) (excuse my laziness :-D), bear v2.5.4 has been submitted and accepted by CRAN core team on April 04, 2013. To upgrade, you have to delete 'bear' directory (folder) under /program files/R/library (if your OS is Windows) completely. And type install.packages("bear") under R console to install it back again. After installation from CRAN, please remember to update all your current R packages to assure that bear can run perfectly. bear should be able to run under R3.0.0 (released on April 03, 2013) very well.

For any problem of using bear, please report to this Forum - R for BE/BA http://forum.bebac.at/?category=19

Thank you for using bear.
—
All the best,
-- Yung-jin Lee
bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here
 
elba.romero
☆    

Guadalajara, Mexico,
2013-04-14 01:47
(4397 d 14:09 ago)

@ yjlee168
Posting: # 10407
Views: 10,427
 

 error in file (file, "rt") bear v2.5.4

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❝ Dear all,

❝

❝ After two more years of last update (v2.5.3) (excuse my laziness :-D), bear v2.5.4 has been submitted and accepted by CRAN core team on April 04, 2013. To upgrade, you have to delete 'bear' directory (folder) under /program files/R/library (if your OS is Windows) completely. And type install.packages("bear") under R console to install it back again. After installation from CRAN, please remember to update all your current R packages to assure that bear can run perfectly. bear should be able to run under R3.0.0 (released on April 03, 2013) very well.

❝

❝ For any problem of using bear, please report to this Forum - R for BE/BA http://forum.bebac.at/?category=19

❝

❝ Thank you for using bear.


Dear Yung-jin Lee:
I have already worked with previous version of BEAR v2.5.3. (Windows 7). After installed the new version and tried to run the NCA demo (2x2x2 design, single dose) just to confirm if everything is doing well, the results are given in my R console but there is a legend at the end: "Error in file(file,"rt"). The XXX_nca.pk.txt and XXX_stat_sum.txt files are empty. There is no problem with the concentration time plots in .pdf format. I have uninstalled and installed again R 3.0.0, bear v.2.5.4 and updated my library.
I can not figure out what it is happening! :confused: Any help will be really appreciated. Thank you in advance.
Regards,
—
Regards,

--
Elba Romero
Área de Farmacometría
Universidad de Guadalajara, México lindo y querido...
 
yjlee168
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Kaohsiung, Taiwan,
2013-04-14 02:25
(4397 d 13:32 ago)

@ elba.romero
Posting: # 10408
Views: 10,497
 

 error in file (file, "rt") bear v2.5.4

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Dear elba.romero,

Did you input any file name? Usually the error occurs when one inputs a file name with file extension. I have tried my best to have the least input when using bear with v2.5.4. All file names will be generated automatically. However, you said you were playing with demo. Then it should be no file name required. I have no idea how it happened. I just ran the 2x2x2 crossover single-dose demo without any problem. So could you please log the error messages from R console and post here? It would be better to trace the error by typing 'traceback()' immediately when you are stuck with error. Thanks,

❝ I have already worked with previous version of BEAR v2.5.3. (Windows 7). After installed the new version and tried to run the NCA demo (2x2x2 design, single dose) just to confirm if everything is doing well, the results are given in my R console but there is a legend at the end: "Error in file(file,"rt"). The XXX_nca.pk.txt and XXX_stat_sum.txt files are empty. There is no problem with the concentration time plots in .pdf format. I have uninstalled and installed again R 3.0.0, bear v.2.5.4 and updated my library.

—
All the best,
-- Yung-jin Lee
bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here
 
elba.romero
☆    

Guadalajara, Mexico,
2013-04-16 05:46
(4395 d 10:11 ago)

(edited on 2013-04-16 18:43)
@ yjlee168
Posting: # 10420
Views: 10,389
 

 error in file (file, "rt") bear v2.5.4

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Dear yjlee168:
This is the error prompted in my R console and the results after typing traceback()

****************************************************************************
Error in file(file, "rt") : cannot open the connection
> traceback()
>

As you can see, there are no arguments prompted to investigate after typing 'traceback()' function. In fact, at this point there are no options to go back to the main menu. I need to close R program to start again.

Edit: Full quote removed. Please delete everything from the text of the original poster which is not necessary in understanding your answer; see also this post! [Ohlbe]
—
Regards,

--
Elba Romero
Área de Farmacometría
Universidad de Guadalajara, México lindo y querido...
 
yjlee168
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Kaohsiung, Taiwan,
2013-04-16 10:32
(4395 d 05:25 ago)

@ elba.romero
Posting: # 10422
Views: 10,479
 

 error in file (file, "rt") bear v2.5.4

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Dear elba.romero,

I wish that I can reproduce the error as described on my computer. Could you log all stuffs from R console? If the content of all stuffs that you log from R console are too many characters, please save them and post it as an attachment.

❝ ...

❝ This is the error prompted in my R console and the results after typing traceback()

❝

❝ ****************************************************************************

❝ Error in file(file, "rt") : cannot open the connection

❝ > traceback()

❝ >

❝ ...


As my experience, the content of traceback() may be entrapped into one of .txt output files (in bear, it's usually xxx_nca_output.txt.); otherwise, it will tell you 'No traceback available.' Next time if you have such an error, please just press 'Esc' key to stop computation (under Windows). You don't need to close whole R session.
—
All the best,
-- Yung-jin Lee
bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here
 
elba.romero
☆    

Guadalajara, Mexico,
2013-04-18 02:22
(4393 d 13:35 ago)

@ yjlee168
Posting: # 10430
Views: 10,302
 

 error in file (file, "rt") bear v2.5.4-traceback file

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Dear yjlee:
Because I do not have a webhoster available to upload the content of the traceback file (4 sheets), I hope is not a drawback that it has been sent to your email.

Best regards,
—
Regards,

--
Elba Romero
Área de Farmacometría
Universidad de Guadalajara, México lindo y querido...
 
yjlee168
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Homepage
Kaohsiung, Taiwan,
2013-04-18 12:30
(4393 d 03:27 ago)

@ elba.romero
Posting: # 10432
Views: 10,369
 

 Yes, it's a bug -> error in file (file, "rt")

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Dear elba romero,

Thanks for your messages. I've fixed the bug and upload it (bear v2.5.5) to my cloud storage (wuala). You can download it here. The error occurs when running NCA demo alone or NCA alone. When I added the new function to display the section containing the means (SD) for each formulation (by time point) in NCA output file, I just tested it with "NCA -> Statistical analysis." Thus I ignore the situation of running NCA alone. I was thinking that it should be fixed at the same time. Unfortunately, it is not. So I fixed that part this morning, including running NCA alone (also the replicate crossover with NCA alone). Sorry about the error.
—
All the best,
-- Yung-jin Lee
bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here
 
elba.romero
☆    

Guadalajara, Mexico,
2013-04-20 05:19
(4391 d 10:38 ago)

@ yjlee168
Posting: # 10440
Views: 10,214
 

 Yes, it's a bug -> error in file (file, "rt")

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Dear yjlee:
I have been installed bear v2.5.5 and yes, it now works perfectly! no just the demo but a real data set.
Thank you!
—
Regards,

--
Elba Romero
Área de Farmacometría
Universidad de Guadalajara, México lindo y querido...
 
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