Bioequivalence and Bioavailability Forum • bear v2.7.8 released (GUI)

yjlee168
★★★

Kaohsiung, Taiwan,
2017-04-13 23:58
(2894 d 16:48 ago)

(edited on 2017-04-14 08:00)
Posting: # 17237
Views: 18,737

bear v2.7.8 released (GUI) [🇷 for BE/BA]

Dear all,

I have uploaded bear v2.7.8 to SF. Please note that, if you like speed and menu-driven mode as bear v2.7.7, you do not need to upgrade to v2.7.8. The new release has a graphic user interface (GUI) for setup and data manipulation. So it is slower than the menu-driven mode under Windows (not too bad if running under Ubuntu/Linux and iMac OS X.) If you like to watch its demo video, you can find it on Youtube.

Installation

Java installation: this step needs to be done first before all steps, if you have not installed any Java before. It is because we will install the package rChoiceDialogs and this package requires rJava.
- Windows: go to Oracle to download JAVA, and select Java for consumers to continue and follow the steps.
- iMac OS X: I really got confused when I worked with iMac OS X Sierra. What I did was to install Java obtained from Oracle first, this enabled the package rChoiceDialogs be installed successfully. Then I run bear and the terminal showed that I need to install Java and brought me to a web page to download it. After installing the second Java, it run OK. Unfortunately, I don't remember that web page. It should be no problem for iMac users to figure out.
- Ubuntu/Linux: OpenJDK works well. Please go to browse this website for more details. Since I have Java installed on my system, I just do sudo R CMD javareconf and it works fine.
GTK drivers (and related files for GUI toolkit): if you are the first time to install bear, you need to do this. Please go and browse my previous post.
installations of required packages: only do this step after the above two steps have finished successfully. The fastest way is to download preinst.r from SF and place it in your R working directory. Finally, run it from R console/terminal by typing source("preinst.r") and select bear from the menu and type 0 to exist.
Finally, you can install bear v2.7.8 now from a local zip file (Windows).

Major update logs

used fread() from package data.table to load all csv data files now; fread() can recognize the file format of *.csv automatically.
automatically saved manual selection of data points; no more ask users to save or not to save.
fixed the errors of NCAplot(); thanks to Dr. Mahmoud Hassan Teaima (2016-07-28).
added data check after loading from a csv file when doing NCA, like this, and probably this too.
displayed plots on screen (device) again for Rgui/X11 or running with RStudio.
added nonparametric statistics for Tmax for 2x2x2 crossover (please see this thread) as an optional selection. The output is like
--- statistical analysis of Tmax --- 90% CI Z-value* P-value* PE (T-R) Lower Upper 0.847 0.415 0.25 -0.250 0.750 -------------------------------------------------- *: Exact Wilcoxon-Mann-Whitney Test alternative hypothesis: true mu is not equal to 0 -> Tmax has no statistical difference. refs: http://forum.bebac.at/mix_entry.php?id=5904

That's all. Sorry for this lengthy post and thanks for reading.

—
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

jag009 ★★★ NJ, 2019-01-06 06:51 (2262 d 08:55 ago) @ yjlee168 Posting: # 19733 Views: 11,479	bear v2.7.8 released (GUI) Post reply
	HI yjlee168, How do I install GTK drivers? I looked around and found GTK+ download which requires me to install msys2? But then I got stuck inside msys2 because the following line could not be executed inside msys2 --> "pacman -S mingw-w64-x86_64-gtk3" Was I getting the correct GTK? Thanks John

yjlee168
★★★

Kaohsiung, Taiwan,
2019-01-06 08:23
(2262 d 07:24 ago)

@ jag009
Posting: # 19734
Views: 11,534

install GTK+ driver for bear

Post reply

Dear John,

Nope, you don't need msys2 to install GTK+ driver. It can be easier.

Windows OS: you should run source("preinst.r") first under R console. This installs all required R packages for bear. Then type library(bear) (Enter), followed by go(). There is a pop-up dialogue asking if you want to install GTK+ driver. Click 'Yes, to install GTK+ driver' menu. It's done. You only need to do this step once. After these steps, you can install bear packages from the menu of R console (install packages from a local zip file.)
macOS: you will need to Homebrew GTK+ driver first before running source("preinst.r"). You should have Homebrew installed on your macOS first. To install Homebrew, under the terminal program, type and run /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
(use copy-and-paste to avoid typo here; or you can google it about how to install Homebrew.) Then same in the terminal program, type and run brew install gtk+ cairo pkg-config. Sit and wait for a while. After it finishes, you can run source("preinst.r") under R console now. Unlike Windows OS, there will be no pop-up dialogue since you have already installed GTK+ driver on your macOS.Now you can install bear package now.
linux PC distros: the procedures are pretty same as macOS, it means that you need to install GTK+ driver first before source("preinst.r"). Here I just mention Ubuntu distro. Under the terminal program, type sudo apt-get install -y libgtk2.0-dev. Then you can run source("preinst.r") under R console now. Finally you can install bear package now. The names of GTK+ driver may differ a little bit with other distros. Let me know if you use Fedora or archlinux distros.

Hope this can help.

❝ [...]

❝ Was I getting the correct GTK?

—
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

jag009 ★★★ NJ, 2019-01-07 02:06 (2261 d 13:40 ago) @ yjlee168 Posting: # 19737 Views: 11,394	install GTK+ driver for bear Post reply
	Thank you. I will try again tonight. John

yjlee168
★★★

Kaohsiung, Taiwan,
2019-01-07 09:47
(2261 d 05:59 ago)

@ jag009
Posting: # 19738
Views: 11,366

install GTK+ driver for bear

Post reply

Hi John

I have tried to install GTK+ driver on Windows like what you did with no luck. It did not work at all. GTK+ driver on Windows seems provided by the developer (package gWidgets & gWidgets2) himself. It is kind of out of date (2014 or earlier?) and looks ugly a little bit when compared to that in Linux. But it works anyway.

—
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

Astea ★★ Russia, 2019-02-17 20:05 (2219 d 19:41 ago) @ yjlee168 Posting: # 19930 Views: 11,007	strange misc.pk for replicate Post reply
	Dear yjlee168! Can you please check the ouput data for misc.pk parameters while doing NCA only for replicate studies? For SingleRep_demo.csv I've got extremely strange data like T_max=8,8 and not correct λ. What could be the problem? — "Being in minority, even a minority of one, did not make you mad"

yjlee168
★★★

Kaohsiung, Taiwan,
2019-02-18 10:15
(2219 d 05:32 ago)

@ Astea
Posting: # 19931
Views: 10,905

strange misc.pk for replicate

Post reply

Dear Astea,

Thank you so much for reporting the error. The error has been confirmed. I will fix that error asap. It affects Tmax and λ in replicated crossover. The error might be introduced when I was adding data analysis of partial AUC. I also need to fix the output file - nca_pk.txt together. Very sorry about that.

❝ ... I've got extremely strange data like T_max=8,8 and not correct λ. What could be the problem?

—
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
★★★

Kaohsiung, Taiwan,
2019-02-21 21:47
(2215 d 17:59 ago)

@ Astea
Posting: # 19965
Views: 10,874

bear v2.8.3-3 released

Post reply

Dear Astea and all,

I just uploaded bear v2.8.3-3 to Sourceforge. Major fixes include: (1) two output files (misc_pk.csv & pivotal.csv) for both replicated crossover and parallel BE study; and (2) fixed some output files formats (such as digits after decimal points, etc.). No extra R package is required for this release. So it can be installed directly.

❝ ... I've got extremely strange data like T_max=8,8 and not correct λ. What could be the problem?

The error resulted from that T_max was pointed to MRT. However, the value of λ in the misc_pk.csv was the average of two periods. So it was correct. It might be confusing with previous misc_pk.csv layout. That's because the column of 'subj' is not corretly presented. Same for the parallel design. I added one more output file for replicate crossover to show more details for this release. Very 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

yjlee168
★★★

Kaohsiung, Taiwan,
2019-07-08 13:22
(2079 d 03:24 ago)

@ yjlee168
Posting: # 20380
Views: 9,331

install GTK+ driver for bear

Post reply

For macOS users,

Please read this post. Thanks.

❝

Windows OS: ...
macOS: you will need to Homebrew GTK+ driver first before running source("preinst.r"). You should have Homebrew installed on your macOS first. To install Homebrew, under the terminal program, type and run /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
❝ (use copy-and-paste to avoid typo here; or you can google it about how to install Homebrew.) Then same in the terminal program, type and run brew install gtk+ cairo pkg-config. Sit and wait for a while. After it finishes, you can run source("preinst.r") under R console now. Unlike Windows OS, there will be no pop-up dialogue since you have already installed GTK+ driver on your macOS.Now you can install bear package now.
linux PC distros: ...

—
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