NPDE installation

Issues related to the installation of Pmetrics and getting it to run on your system.
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SONIALU
Posts: 10
Joined: Fri Mar 04, 2016 4:26 am

NPDE installation

Post by SONIALU » Fri Dec 07, 2018 9:16 am

Good afternoon,

I am trying to install the NPDE with the following instruccions:d:
Download the archived 2.0 version here: https://cran.r-project.org/src/contrib/Archive/npde/

In R, execute the following commands:

install.packages(“mclust”)
install.packages(file.choose())

When you execute the second command, navigate to where the downloaded npde_2.0.tar.gz file is located and select it. That should install the package successfully.

But the following error message appeared:

Warning in install.packages :
installation of package ‘C:/Users/Sonialu/Downloads/npde_2.0.tar.gz’ had non-zero exit status

Could you help me?

Thank you
Sonia

praveenkumarpgiindia
Posts: 1
Joined: Sun Jan 08, 2017 9:56 am

Re: NPDE installation

Post by praveenkumarpgiindia » Tue Jan 01, 2019 2:54 am

I am also having a similar problem. My installation of Pmetrics was successful (checked with PMtest()). But during installation, npde failed to get installed. I then checked in the CRAN website and found that the package npde has been removed from the CRAN.

pharmpk
Posts: 34
Joined: Fri Dec 05, 2014 1:35 pm

Re: NPDE installation

Post by pharmpk » Fri Feb 08, 2019 12:54 pm

I was trying to run makeNPDE and got the message

Warning in install.packages :
package ‘npde’ is not available (for R version 3.5.0)

I'm running Pmetrics v1.5.2 with R Studio 1.1.453 R 3.5.0 on Mac 10.13.6

As mentioned by praveenkumarpgiindia node seems to have been removed from CRAN: https://cran.r-project.org/web/packages/npde/index.html

Package ‘npde’ was removed from the CRAN repository.
Formerly available versions can be obtained from the archive.
Archived on 2018-04-16 as check problems were not corrected in time.

Thanks, David

PS, good to see the forum back!!

pharmpk
Posts: 34
Joined: Fri Dec 05, 2014 1:35 pm

Re: NPDE installation

Post by pharmpk » Fri Feb 08, 2019 2:01 pm

I was able to download version 2.0 from CRAN archive: https://cran.r-project.org/src/contrib/Archive/npde/

I installed (RStudio) using the Install Package... using
> install.packages("~/Downloads/npde_2.0.tar.gz", repos = NULL, type = "source")
after an error message looking for mclust I install that package from CRAN using
> install.packages("mclust")
and reinstalled npde
I got this error "Note: break used in wrong context: no loop is visible " but continued

The command
> makeNPDE(20,limits=c(0,10),nsim=1000) << not sure what the limits=c(0,10) is doing here but attempting to get past some errors/warnings (from memory this had something to do with the parameter or data values going outside bounds)
e.g.
Simulating from subject 30 ...
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_OVERFLOW_FLAG IEEE_UNDERFLOW_FLAG

Processing continued with a few warning and the messages including

The following NpdeData object was successfully created:

---
Now using
npde.20 <- makeNPDE(20,limits=NA)

appears to be working with only one IEEE_INVALID_FLAG IEEE_OVERFLOW_FLAG IEEE_UNDERFLOW_FLAG warning

And I get ...

Saving results in file output.npde
Saving graphs in file output.eps
Selected plot type: default
Plotting QQ-plot of the distribution
Plotting histogram of the distribution
Plotting scatterplot versus X
Plotting scatterplot versus predictions

the .eps file has the graphs/plots !!!
Now I need to go back to the Pmetrics manual to interpret the graphs ;-)

It looks like the archived npde can work.

SONIALU
Posts: 10
Joined: Fri Mar 04, 2016 4:26 am

Re: NPDE installation

Post by SONIALU » Mon Feb 18, 2019 10:02 am

Dear all,

Thank you very much for the information.
I finally was able to install the NPDE and to do an analysis.

However, I got the same error message: IEEE_INVALID_FLAG IEEE_OVERFLOW_FLAG IEEE_UNDERFLOW_FLAG

Could anyone tell me what does it mean?
I also got these 2 file outputs: output.npde and output.eps

I have some questions about that:
- How can I open the output.npde file?
- How can interpret the graphs? (I looked in the manual and I did not find any information)

Thank you very much,

Sonia

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