xpose-general — General talk and questions about Xpose is welcome to this list.

[Xpose-general] asking for help with xpose

[Helena C. C. <hel...@ub...>]

Dear Andrew,
I am writting you because  i have troubles with xpose. When i Try t oread the tables of a new model , xpose only reads sdtab and stops , giving me the message you can see below.
It is the first time that it happens to me, I have been using Xpose for a very long time.
I try to install the package magrittr  but the problema remains.

Last week i tried to install new packages for a PKsim workshop , could the problema be related to this?

Looking for NONMEM table files.
    Reading ./sdtab151

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  there is no package called 'magrittr'

The packages that i tried to install were as follows:
#Install dependencies
install.packages('R6')

# Install rClr from local file
install.packages(pathTorCLR.zip, repos = NULL)

# Install ospsuite-r from local file
install.packages(pathToOSPSuite.zip, repos = NULL)

I have also re-installed R studio, R and xpose but i could fix the problem

I would appreciate your help,
Best regards
helena


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[Xpose-general] Error reading in NONMEM output files

[Wayne L. <yu-...@mo...>]

Dear all

I am getting the following error when trying to read NONMEM output files
into xpose4. I have never seen this error before. Appreciate any comments.
Thanks.

Wayne Lin

Warning: 70580 parsing failures.
row   col expected                actual     file
  1 ID    a double  7.2012010000E+06     'sdtab1'
  1 TAD   a double      -2.6930E+02      'sdtab1'
  1 IPRED a double      1.0628806545E+03 'sdtab1'
  2 ID    a double  7.2012010000E+06     'sdtab1'
  2 TAD   a double      -1.1170E+00      'sdtab1'
... ..... ........ ..................... ........
See problems(...) for more details.

    Reading patab1
Warning: 99375 parsing failures.
row col expected            actual     file
  1  ID a double  7.2012010000E+06 'patab1'
  2  ID a double  7.2012010000E+06 'patab1'
  3  ID a double  7.2012010000E+06 'patab1'
  4  ID a double  7.2012010000E+06 'patab1'
  5  ID a double  7.2012010000E+06 'patab1'
... ... ........ ................. ........
See problems(...) for more details.

    Reading catab1
Warning: 66093 parsing failures.
row col expected            actual     file
  1  ID a double  7.2012010000E+06 'catab1'
  2  ID a double  7.2012010000E+06 'catab1'
  3  ID a double  7.2012010000E+06 'catab1'
  4  ID a double  7.2012010000E+06 'catab1'
  5  ID a double  7.2012010000E+06 'catab1'
... ... ........ ................. ........
See problems(...) for more details.

    Reading cotab1
Warning: 65369 parsing failures.
row col expected            actual     file
  1  ID a double  7.2012010000E+06 'cotab1'
  2  ID a double  7.2012010000E+06 'cotab1'
  3  ID a double  7.2012010000E+06 'cotab1'
  4  ID a double  7.2012010000E+06 'cotab1'
  5  ID a double  7.2012010000E+06 'cotab1'
... ... ........ ................. ........
See problems(...) for more details.

[Xpose-general] FW: Greetings _ Xpose

[Lohy d. J. p. d. [JRDUS] <JLo...@it...>]

Greeetings

Appreciate your help. The full code is as below:

run.number        <- "1005"                                          # define the run.number is ......
xpdb                     <- xpose.data(run.number)          # Object of the data
###############################################
#  using xpdb as data.frame
#---------------------------------------------#
#  using xpdb to plot out of xpose                            #
xpdb<-xpdb@Data
xpdb

write.csv(xpdb,file="xpdb_XX.csv",sep=",",row.names=F)
# --renaming eta_scatterplot of etas----------#
#---change the level names -------------------#
names(xpdb)[names(xpdb) == 'BQL_LATEST'] <- 'BQL'
names(xpdb)[names(xpdb) == 'ETA2'] <- 'IIV_V2'

From: Lohy das, Jesmin permala das [JRDUS]
Sent: Sunday, November 11, 2018 6:18 PM
To: 'rik...@fa...' <rik...@fa...>
Subject: FW: Greetings _ Xpose
Importance: High



From: Lohy das, Jesmin permala das [JRDUS]
Sent: Sunday, November 11, 2018 6:17 PM
To: 'rik...@fa...' <rik...@fa...<mailto:rik...@fa...>>
Subject: Greetings _ Xpose
Importance: High

Hi Rikard

Greetings. Hope to find you well.
How is everyone doing in Uppsala - my regards to all.

After some time, I tried to use the xpose using my old codes (as below):
But I am having some issue - can you advice ? I never had any issue using these codes before.

Ps: I also attached the lst file here here.

run.number  <- "1005"                                        # define the run.number is ......
xpdb              <- xpose.data(run.number)          # Object of the data

[cid:image001.png@01D479EA.9ED2CBB0]

[cid:image002.png@01D479EA.B6CE7980]

[Xpose-general] xpose.data reading in Error

[Jun S. <jun...@gm...>]

Dear xpose users,

It was working fine when I call xpose.data() to read in the NM output
files. Then all of sudden, I got this error. I typically have sdtab, patab,
cotab and catab. I have never seen this error before. Appreciate any
comments. Thanks.

Jun

Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  scan() expected 'a real', got '"1"'

[Xpose-general] Error Message

[Jon C. <jc...@ya...>]

Hello everybody,


I've been trying to generate plots using xpose 4 for my base model. The model successfully converged in NONMEM with the covariance step. I also asked for the various tables patab, and sdtab in the control stream needed for xpose 4 plots.


I created my xpdb in R, and it says table files read. Copied belowxpdb <- xpose.data(runno="11")

Looking for NONMEM table files.
    Reading sdtab11 
    Reading patab11 
Table files read.
    Reading run11.phi 



However, when I run any of the plot commands in R, such as dv.vs.ipred(xpdb1), I get the following error in R

cwres.vs.idv(xpdb)
Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow = nr,  : 
  'data' must be of a vector type, was 'NULL'

I checked all the data is in an xpose.data file format.Additionally I imported the same files into the xpose library package that uses ggplot and the plotting functions worked fine.  I ran the example file from xpose4 simpraz.xpdb and everything worked fine.  Is there anyway to check somewhere in Formal Class xpose.data file what the problem is? System VersionsComputer: WINDOWS operating system-64 bitR system is R-3.4.2xpose4 4.6.0



Thank you very much!
Jon Collins 

[Xpose-general] Error while running xpose

[Srinivasan, M. <Mee...@un...>]

Hello everybody,


I've been trying to generate plots using xpose for my base model. The model successfully converged in NONMEM with the covariance step. I also asked for the various tables PATAB, COTAB, CATAB and SDTAB in the control stream needed for xpose plots.


I created my xpdb in R, and it says table files read.


However, when I run any of the plot commands in R, such as dv.vs.ipred(xpdb1), I get the following error in R

Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow = nr,  :
  'data' must be of a vector type, was 'NULL'

I tried the same in another computer with NONMEM and I got the same error in R.
Could you tell me what the possible issue might be and how to rectify this?

Thank you very much!

Sincerely,
Meenakshi

[Xpose-general] Main.menu function not found

[Manuel I. <mi...@fq...>]

Dear all,

I have a problem associated to Xpose main.menu() function. When loading the
Xpose package in R studio from pirana, all tables are read. The only error
that comes up after running *main.menu()* is:

*Error in main.menu(): could not find function "main.menu"*

I've been using Xpose in several computers with no issues. This error
appeared in two different installations, both with R version 3.4.0
(2017-04-21), one in Windows 10 (64-bit) and the other in Windows 7
(64-bit).

Do you have any idea how can I fix this? I'm aware that it is a basic menu,
Xpose functions run OK when coded directly in R.

Thanks in advance,

Best wishes.
Manuel
____________________________________________________________
__________________

Dr. Manuel Ibarra
Profesor Adj. Área de Biofarmacia y Terapéutica
Centro de Evaluación de Biodisponibilidad y Bioequivalencia de Medicamentos
(CEBIOBE)
Departamento de Ciencias Farmacéuticas.
Facultad de Química, Universidad de la República - Uruguay
www.cebiobe.edu.uy
Tel: +(598) 22097899 int 216 <+598%202209%207899>/217

[Xpose-general] Problems with dOFV.vs.id(xpdb1, xpdb2)

[Kragh, Å. <asa...@as...>]

Hi,

I'm trying to use the dOFV.vs.id(xpdp1, xpdb2) function for comparison of individual OFVs between two nested runs. However, I get the following error message:

Error in 1:max.rank : result would be too long a vector
In addition: Warning message:
In max(comp.frame$rnk) : no non-missing arguments to max; returning -Inf

and to me, it seems like the phi-file is not read in correctly, but I have no idea how to fix the problem.

I'm using Xpose4 version 4.5.3 in R version 3.2.4.

Thanks for your help!

Kind regards,
Åsa


Åsa Kragh, PhD
Clinical Pharmacometrician
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Re: [Xpose-general] bug fix read.phi xpose4_4.6.0

[Andrew H. <And...@fa...>]

Hi

This function is not exported from the xpose namespace (something I changed for this xpose4 release).  To use the function you can use

xpose4:::read.phi()

Best regards,
Andrew

Andrew Hooker, Ph.D.
Associate Professor of Pharmacometrics
Dept. of Pharmaceutical Biosciences
Uppsala University
Box 591, 751 24, Uppsala, Sweden
Phone: +46 18 471 4355
Mobile: +46 768 000 725
www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>







On 26 Jun 2017, at 10:39 , Timothy Mutsvari <Tim...@ar...<mailto:Tim...@ar...>> wrote:

Dear xpose4 team,

I am failing to run the model read.phi function in xpose4_4.6.0 with error message:

> PK_params_cov <- read.phi(paste0(cov_))
Error in read.phi(paste0(cov_)) : could not find function "read.phi"


>



Any bug fixes?

Timothy Mutsvari
Manager Statistics & Pharmacometrics

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Office (Mont-St-Guibert) :  +32 (0) 10 46 10 19
Mobile: +32 (0) 488 358 133
Website : www.arlenda.com<http://www.arlenda.com/>

A Company of the PharmaLex Group

<image002.jpg><http://www.pharmalex.com/>

www.pharmalex.com<http://www.pharmalex.com/>
––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
Meet our experts @ booth #1705 at the BIO International Convention in San Diego, CA,USA on June 19th – 22nd, 2017!
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Meet our experts @ booth #2357 at the DIA Annual Meeting in Chicago, IL,USA on June 18th – 22nd, 2017!
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<image005.jpg><http://thebiosimilarsgroup.com/>

Registered office: Friedrichsdorf • Commercial Register No: HRB 13017 • Local Court of Bad Homburg
Managing Directors: Dr. Thomas Dobmeyer, Dr. Tilo Netzer
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[Xpose-general] bug fix read.phi xpose4_4.6.0

[Timothy M. <Tim...@ar...>]

Dear xpose4 team,

I am failing to run the model read.phi function in xpose4_4.6.0 with error message:

> PK_params_cov <- read.phi(paste0(cov_))
Error in read.phi(paste0(cov_)) : could not find function "read.phi"


>



Any bug fixes?

Timothy Mutsvari
Manager Statistics & Pharmacometrics

[arlenda_mail_150]

Office (Mont-St-Guibert) :  +32 (0) 10 46 10 19
Mobile: +32 (0) 488 358 133
Website : www.arlenda.com<http://www.arlenda.com/>

A Company of the PharmaLex Group

[PLX_Logo-4C-300dpi]<http://www.pharmalex.com/>

www.pharmalex.com<http://www.pharmalex.com/>
--------------------------------------------------------------------------------------
Meet our experts @ booth #1705 at the BIO International Convention in San Diego, CA,USA on June 19th - 22nd, 2017!
[cid:image006.jpg@01D2C7FE.9C8CF5F0]

Meet our experts @ booth #2357 at the DIA Annual Meeting in Chicago, IL,USA on June 18th - 22nd, 2017!
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------------------------------------------------------------------------------------
PharmaLex is a member of THE BIOSIMILARS GROUP
[The Biosimilars Group]<http://thebiosimilarsgroup.com/>

Registered office: Friedrichsdorf ∙ Commercial Register No: HRB 13017 ∙ Local Court of Bad Homburg
Managing Directors: Dr. Thomas Dobmeyer, Dr. Tilo Netzer
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or legally privileged. If you are not the intended recipient or a person responsible for delivering this
transmission to the intended recipient, you are hereby notified that any disclosure, copying, distribution
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the sender immediately and destroy the original transmission and its attachments and destroy any hardcopies.
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Re: [Xpose-general] Xpose4 installation

[Xiaoping Z. <zha...@gm...>]

Hi Andrew,
Got it. Thank you very much for your comments.
Regards
Xiaoping

On Tue, May 2, 2017 at 12:03 AM, Andrew Hooker <And...@fa...>
wrote:

> Hi
>
> This is normal behavior and nothing to worry about.
>
> Best regards,
> Andrew
>
> Andrew Hooker, Ph.D.
> Associate Professor of Pharmacometrics
> Dept. of Pharmaceutical Biosciences
> Uppsala University
> Box 591, 751 24, Uppsala, Sweden
> Phone: +46 18 471 4355 <+46%2018%20471%2043%2055>
> Mobile: +46 768 000 725
> www.farmbio.uu.se/research/researchgroups/pharmacometrics/
>
>
>
>
>
>
>
> On 1 May 2017, at 1:30 , Xiaoping Zhang <zha...@gm...> wrote:
>
> Hi Guys,
> When I install Xpose4 in R x64 3.3.3. it says that "The following object
> is masked from ‘package:base’: list.dirs". I was wondering  if it is normal
> or  if it indicts that something is wrong.
> Thank you very much for your help and comments.
> Regards
> Annie
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
> _________________________________________
> Xpose-general mailing list
> Xpo...@li...
> https://lists.sourceforge.net/lists/listinfo/xpose-general
>
>
>

Re: [Xpose-general] Xpose4 installation

[Andrew H. <And...@fa...>]

Hi

This is normal behavior and nothing to worry about.

Best regards,
Andrew

Andrew Hooker, Ph.D.
Associate Professor of Pharmacometrics
Dept. of Pharmaceutical Biosciences
Uppsala University
Box 591, 751 24, Uppsala, Sweden
Phone: +46 18 471 4355
Mobile: +46 768 000 725
www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>







On 1 May 2017, at 1:30 , Xiaoping Zhang <zha...@gm...<mailto:zha...@gm...>> wrote:

Hi Guys,
When I install Xpose4 in R x64 3.3.3. it says that "The following object is masked from ‘package:base’: list.dirs". I was wondering  if it is normal or  if it indicts that something is wrong.
Thank you very much for your help and comments.
Regards
Annie

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[Xpose-general] Xpose4 installation

[Xiaoping Z. <zha...@gm...>]

Hi Guys,
When I install Xpose4 in R x64 3.3.3. it says that "The following object is
masked from ‘package:base’: list.dirs". I was wondering  if it is normal or
 if it indicts that something is wrong.
Thank you very much for your help and comments.
Regards
Annie

Re: [Xpose-general] error reading in files

[Al C. <acp...@gm...>]

Also cannot have ‘FIRSTONLY’ in some of the $TABLE statements (D’Oh!  :().  All is working well now.

 

Thanks,

 

Al Corey, Principal
AC Pharmaco, LLC
1043 Heather Lane
Wake Forest, NC 27587
240-644-8827
acp...@gm... <mailto:acp...@gm...> 

This communication, including any attachments, is intended only for the person or entity to which it is addressed and may contain confidential material. Any review, retransmission, distribution or other use of this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please destroy any copies, contact the sender and delete the material from any computer. Thank you.

 

From: Krina Mehta [mailto:kr...@gm...] 
Sent: Friday, February 3, 2017 9:49 AM
To: Al Corey <acp...@gm...>
Cc: xpo...@li...
Subject: RE: [Xpose-general] error reading in files

 

All your table files need to have that table number heading, i am assuming.

 

On Feb 2, 2017 7:01 PM, "Al Corey" <acp...@gm... <mailto:acp...@gm...> > wrote:

Thanks, that took care of that error.  N ow I just have to deal with:

The table files associated with this run number ( ) appear

to have different lengths.

You will have to sort this out and try again!

Table files not read!

,but I remember seeing something in the archives about that.

 

 

Al Corey, Principal
AC Pharmaco, LLC
1043 Heather Lane
Wake Forest, NC 27587
240-644-8827 <tel:(240)%20644-8827> 
acp...@gm... <mailto:acp...@gm...> 

This communication, including any attachments, is intended only for the person or entity to which it is addressed and may contain confidential material. Any review, retransmission, distribution or other use of this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please destroy any copies, contact the sender and delete the material from any computer. Thank you.

 

From: Krina Mehta [mailto:kr...@gm... <mailto:kr...@gm...> ] 
Sent: Thursday, February 2, 2017 7:16 PM
To: Al Corey <acp...@gm... <mailto:acp...@gm...> >
Cc: xpo...@li... <mailto:xpo...@li...> 
Subject: Re: [Xpose-general] error reading in files

 

Hello Al Corey,

 

Try taking out NOTITLE from your table statement. I believe xpose4 requires that "Table No. xx" on the top in sdtab file to read in correctly. I have had that issue before and by simply adding "TABLE NO.  3" at the top of my sdtab file, it got resolved.

 

Hope this helps.

Krina

 

On Thu, Feb 2, 2017 at 2:53 PM, Al Corey <acp...@gm... <mailto:acp...@gm...> > wrote:

Hi –

 

I’m getting the following error when trying to read NONMEM output files into xpose4:

Error in (function (cl, name, valueClass)  : 

  assignment of an object of class “logical” is not valid for @‘Data’ in an object of class “xpose.data”; is(value, "data.frame or NULL") is not TRUE

 

I’m running NONMEM 7.3.0 from the DOS command line, and am using R version 3.3.1 with Xpose 4.5.0.  The $TABLE statement used to generate the output file follows:

$TABLE NOPRINT ONEHEADER NOTITLE FILE=sdtab1

       ID EVID MDV TIME

A copy of the output file is attached.

 

 

I tried searching the archive, but didn’t find an answer for this;  any help would be appreciated.

 

Thanks,

 

 

Al Corey, Principal
AC Pharmaco, LLC
1043 Heather Lane
Wake Forest, NC 27587
240-644-8827 <tel:(240)%20644-8827> 
acp...@gm... <mailto:acp...@gm...> 

This communication, including any attachments, is intended only for the person or entity to which it is addressed and may contain confidential material. Any review, retransmission, distribution or other use of this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please destroy any copies, contact the sender and delete the material from any computer. Thank you.

 


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Re: [Xpose-general] error reading in files

[Krina M. <kr...@gm...>]

All your table files need to have that table number heading, i am assuming.

On Feb 2, 2017 7:01 PM, "Al Corey" <acp...@gm...> wrote:

> Thanks, that took care of that error.  N ow I just have to deal with:
>
> The table files associated with this run number ( ) appear
>
> to have different lengths.
>
> You will have to sort this out and try again!
>
> Table files not read!
>
> ,but I remember seeing something in the archives about that.
>
>
>
>
>
> Al Corey, Principal
> AC Pharmaco, LLC
> 1043 Heather Lane
> Wake Forest, NC 27587
> 240-644-8827 <(240)%20644-8827>
> acp...@gm...
>
> This communication, including any attachments, is intended only for the
> person or entity to which it is addressed and may contain confidential
> material. Any review, retransmission, distribution or other use of this
> information by persons or entities other than the intended recipient is
> prohibited. If you received this in error, please destroy any copies,
> contact the sender and delete the material from any computer. Thank you.
>
>
>
> *From:* Krina Mehta [mailto:kr...@gm...]
> *Sent:* Thursday, February 2, 2017 7:16 PM
> *To:* Al Corey <acp...@gm...>
> *Cc:* xpo...@li...
> *Subject:* Re: [Xpose-general] error reading in files
>
>
>
> Hello Al Corey,
>
>
>
> Try taking out NOTITLE from your table statement. I believe xpose4
> requires that "Table No. xx" on the top in sdtab file to read in correctly.
> I have had that issue before and by simply adding "TABLE NO.  3" at the top
> of my sdtab file, it got resolved.
>
>
>
> Hope this helps.
>
> Krina
>
>
>
> On Thu, Feb 2, 2017 at 2:53 PM, Al Corey <acp...@gm...> wrote:
>
> Hi –
>
>
>
> I’m getting the following error when trying to read NONMEM output files
> into xpose4:
>
> Error in (function (cl, name, valueClass)  :
>
>   assignment of an object of class “logical” is not valid for @‘Data’ in
> an object of class “xpose.data”; is(value, "data.frame or NULL") is not TRUE
>
>
>
> I’m running NONMEM 7.3.0 from the DOS command line, and am using R version
> 3.3.1 with Xpose 4.5.0.  The $TABLE statement used to generate the output
> file follows:
>
> $TABLE NOPRINT ONEHEADER NOTITLE FILE=sdtab1
>
>        ID EVID MDV TIME
>
> A copy of the output file is attached.
>
>
>
>
>
> I tried searching the archive, but didn’t find an answer for this;  any
> help would be appreciated.
>
>
>
> Thanks,
>
>
>
>
>
> Al Corey, Principal
> AC Pharmaco, LLC
> 1043 Heather Lane
> Wake Forest, NC 27587
> 240-644-8827 <(240)%20644-8827>
> acp...@gm...
>
> This communication, including any attachments, is intended only for the
> person or entity to which it is addressed and may contain confidential
> material. Any review, retransmission, distribution or other use of this
> information by persons or entities other than the intended recipient is
> prohibited. If you received this in error, please destroy any copies,
> contact the sender and delete the material from any computer. Thank you.
>
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> Xpose-general mailing list
> Xpo...@li...
> https://lists.sourceforge.net/lists/listinfo/xpose-general
>
>
>

Re: [Xpose-general] error reading in files

[Al C. <acp...@gm...>]

Thanks, that took care of that error.  N ow I just have to deal with:

The table files associated with this run number ( ) appear

to have different lengths.

You will have to sort this out and try again!

Table files not read!

,but I remember seeing something in the archives about that.

 

 

Al Corey, Principal
AC Pharmaco, LLC
1043 Heather Lane
Wake Forest, NC 27587
240-644-8827
acp...@gm... <mailto:acp...@gm...> 

This communication, including any attachments, is intended only for the person or entity to which it is addressed and may contain confidential material. Any review, retransmission, distribution or other use of this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please destroy any copies, contact the sender and delete the material from any computer. Thank you.

 

From: Krina Mehta [mailto:kr...@gm...] 
Sent: Thursday, February 2, 2017 7:16 PM
To: Al Corey <acp...@gm...>
Cc: xpo...@li...
Subject: Re: [Xpose-general] error reading in files

 

Hello Al Corey,

 

Try taking out NOTITLE from your table statement. I believe xpose4 requires that "Table No. xx" on the top in sdtab file to read in correctly. I have had that issue before and by simply adding "TABLE NO.  3" at the top of my sdtab file, it got resolved.

 

Hope this helps.

Krina

 

On Thu, Feb 2, 2017 at 2:53 PM, Al Corey <acp...@gm... <mailto:acp...@gm...> > wrote:

Hi –

 

I’m getting the following error when trying to read NONMEM output files into xpose4:

Error in (function (cl, name, valueClass)  : 

  assignment of an object of class “logical” is not valid for @‘Data’ in an object of class “xpose.data”; is(value, "data.frame or NULL") is not TRUE

 

I’m running NONMEM 7.3.0 from the DOS command line, and am using R version 3.3.1 with Xpose 4.5.0.  The $TABLE statement used to generate the output file follows:

$TABLE NOPRINT ONEHEADER NOTITLE FILE=sdtab1

       ID EVID MDV TIME

A copy of the output file is attached.

 

 

I tried searching the archive, but didn’t find an answer for this;  any help would be appreciated.

 

Thanks,

 

 

Al Corey, Principal
AC Pharmaco, LLC
1043 Heather Lane
Wake Forest, NC 27587
240-644-8827 <tel:(240)%20644-8827> 
acp...@gm... <mailto:acp...@gm...> 

This communication, including any attachments, is intended only for the person or entity to which it is addressed and may contain confidential material. Any review, retransmission, distribution or other use of this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please destroy any copies, contact the sender and delete the material from any computer. Thank you.

 


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Re: [Xpose-general] error reading in files

[Krina M. <kr...@gm...>]

Hello Al Corey,

Try taking out NOTITLE from your table statement. I believe xpose4 requires
that "Table No. xx" on the top in sdtab file to read in correctly. I have
had that issue before and by simply adding "TABLE NO.  3" at the top of my
sdtab file, it got resolved.

Hope this helps.
Krina

On Thu, Feb 2, 2017 at 2:53 PM, Al Corey <acp...@gm...> wrote:

> Hi –
>
>
>
> I’m getting the following error when trying to read NONMEM output files
> into xpose4:
>
> Error in (function (cl, name, valueClass)  :
>
>   assignment of an object of class “logical” is not valid for @‘Data’ in
> an object of class “xpose.data”; is(value, "data.frame or NULL") is not TRUE
>
>
>
> I’m running NONMEM 7.3.0 from the DOS command line, and am using R version
> 3.3.1 with Xpose 4.5.0.  The $TABLE statement used to generate the output
> file follows:
>
> $TABLE NOPRINT ONEHEADER NOTITLE FILE=sdtab1
>
>        ID EVID MDV TIME
>
> A copy of the output file is attached.
>
>
>
>
>
> I tried searching the archive, but didn’t find an answer for this;  any
> help would be appreciated.
>
>
>
> Thanks,
>
>
>
>
>
> Al Corey, Principal
> AC Pharmaco, LLC
> 1043 Heather Lane
> Wake Forest, NC 27587
> 240-644-8827 <(240)%20644-8827>
> acp...@gm...
>
> This communication, including any attachments, is intended only for the
> person or entity to which it is addressed and may contain confidential
> material. Any review, retransmission, distribution or other use of this
> information by persons or entities other than the intended recipient is
> prohibited. If you received this in error, please destroy any copies,
> contact the sender and delete the material from any computer. Thank you.
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> Xpose-general mailing list
> Xpo...@li...
> https://lists.sourceforge.net/lists/listinfo/xpose-general
>
>

[Xpose-general] error reading in files

[Al C. <acp...@gm...>]

Hi -

 

I'm getting the following error when trying to read NONMEM output files into
xpose4:

Error in (function (cl, name, valueClass)  : 

  assignment of an object of class "logical" is not valid for @'Data' in an
object of class "xpose.data"; is(value, "data.frame or NULL") is not TRUE

 

I'm running NONMEM 7.3.0 from the DOS command line, and am using R version
3.3.1 with Xpose 4.5.0.  The $TABLE statement used to generate the output
file follows:

$TABLE NOPRINT ONEHEADER NOTITLE FILE=sdtab1

       ID EVID MDV TIME

A copy of the output file is attached.

 

 

I tried searching the archive, but didn't find an answer for this;  any help
would be appreciated.

 

Thanks,

 

 

Al Corey, Principal
AC Pharmaco, LLC
1043 Heather Lane
Wake Forest, NC 27587
240-644-8827
 <mailto:acp...@gm...> acp...@gm...

This communication, including any attachments, is intended only for the
person or entity to which it is addressed and may contain confidential
material. Any review, retransmission, distribution or other use of this
information by persons or entities other than the intended recipient is
prohibited. If you received this in error, please destroy any copies,
contact the sender and delete the material from any computer. Thank you.

 

Re: [Xpose-general] Error runsum or tabulate.parameters

[Andrew H. <And...@fa...>]

Hi Krina

Not really sure.  Can you share table files with me and I can investigate?

Best regards,
Andrew

Andrew Hooker, Ph.D.
Associate Professor of Pharmacometrics
Dept. of Pharmaceutical Biosciences
Uppsala University
Box 591, 751 24, Uppsala, Sweden
Phone: +46 18 471 4355
Mobile: +46 768 000 725
www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>







On 27 Jan 2017, at 15:28 , Krina Mehta <kr...@gm...<mailto:kr...@gm...>> wrote:

Hello,

I have been trying to create parameters summary using runsum or tabulate.parameters command and am getting below mentioned error messages.

Any suggestions what I could be doing wrong?

thanks,
Krina

> tabulate.parameters(xpdb)
Error in if (sigma[[i]][j] == 0) next : argument is of length zero
> runsum(xpdb, dir = "../")
Error in if (sigma[[i]][j] == 0) next : argument is of length zero
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[Xpose-general] Error runsum or tabulate.parameters

[Krina M. <kr...@gm...>]

Hello,

I have been trying to create parameters summary using runsum or
tabulate.parameters command and am getting below mentioned error messages.

Any suggestions what I could be doing wrong?

thanks,
Krina

> tabulate.parameters(xpdb)
Error in if (sigma[[i]][j] == 0) next : argument is of length zero
> runsum(xpdb, dir = "../")
Error in if (sigma[[i]][j] == 0) next : argument is of length zero

Re: [Xpose-general] Error Reading NONMEM table file

[Krina M. <kr...@gm...>]

Thank you, Andrew.

I was having this issue while reading in table file for model ran through
PDxPop. However, table file was read fine later on when I ran model
directly through NONMEM.



On Mon, Oct 17, 2016 at 11:58 PM, Andrew Hooker <And...@fa...
> wrote:

> Hi Krina
>
> I do not know from the information you have given us.  It seems like the
> table is not able to be read in.  Are you sure formatting of the table is
> as it should be?
>
> Best regards,
> Andrew
>
> Andrew Hooker, Ph.D.
> Associate Professor of Pharmacometrics
> Dept. of Pharmaceutical Biosciences
> Uppsala University
> Box 591, 751 24, Uppsala, Sweden
> Phone: +46 18 471 4355
> Mobile: +46 768 000 725
> www.farmbio.uu.se/research/researchgroups/pharmacometrics/
>
>
>
>
>
>
>
> On 17 Oct 2016, at 20:05 , Krina Mehta <kr...@gm...> wrote:
>
> Hello,
>
> I am trying to read nonmem table file as an xpose data object and am
> getting below mentioned error message. Can you please suggest what could be
> causing this error and how can I correct it?
>
> DataObj14 <- xpose.data(runno = ".", table.names = "./mix14.tab",
> directory = getwd())
>
> Looking for NONMEM table files.
>     Reading D:/ARCHIVE/ECUvendorwork/Pharsight/aHUS_metaanalysis/aHUS
> Meta Report_Krina/pedsFACIT/Mix./mix14.tab.
> Error in (function (cl, name, valueClass)  :
>   assignment of an object of class “logical” is not valid for @‘Data’ in
> an object of class “xpose.data”; is(value, "data.frame or NULL") is not TRUE
>
> Thank you,
> Krina
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot______
> _________________________________________
> Xpose-general mailing list
> Xpo...@li...
> https://lists.sourceforge.net/lists/listinfo/xpose-general
>
>
>

Re: [Xpose-general] Error Reading NONMEM table file

[Andrew H. <And...@fa...>]

Hi Krina

I do not know from the information you have given us.  It seems like the table is not able to be read in.  Are you sure formatting of the table is as it should be?

Best regards,
Andrew

Andrew Hooker, Ph.D.
Associate Professor of Pharmacometrics
Dept. of Pharmaceutical Biosciences
Uppsala University
Box 591, 751 24, Uppsala, Sweden
Phone: +46 18 471 4355
Mobile: +46 768 000 725
www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>







On 17 Oct 2016, at 20:05 , Krina Mehta <kr...@gm...<mailto:kr...@gm...>> wrote:

Hello,

I am trying to read nonmem table file as an xpose data object and am getting below mentioned error message. Can you please suggest what could be causing this error and how can I correct it?

DataObj14 <- xpose.data(runno = ".", table.names = "./mix14.tab", directory = getwd())

Looking for NONMEM table files.
    Reading D:/ARCHIVE/ECUvendorwork/Pharsight/aHUS_metaanalysis/aHUS Meta Report_Krina/pedsFACIT/Mix./mix14.tab.
Error in (function (cl, name, valueClass)  :
  assignment of an object of class “logical” is not valid for @‘Data’ in an object of class “xpose.data”; is(value, "data.frame or NULL") is not TRUE

Thank you,
Krina
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[Xpose-general] Error Reading NONMEM table file

[Krina M. <kr...@gm...>]

Hello,

I am trying to read nonmem table file as an xpose data object and am
getting below mentioned error message. Can you please suggest what could be
causing this error and how can I correct it?

DataObj14 <- xpose.data(runno = ".", table.names = "./mix14.tab", directory
= getwd())

Looking for NONMEM table files.
    Reading D:/ARCHIVE/ECUvendorwork/Pharsight/aHUS_metaanalysis/aHUS Meta
Report_Krina/pedsFACIT/Mix./mix14.tab.
Error in (function (cl, name, valueClass)  :
  assignment of an object of class “logical” is not valid for @‘Data’ in an
object of class “xpose.data”; is(value, "data.frame or NULL") is not TRUE

Thank you,
Krina

[Xpose-general] Xpose install problem

[Phumprut G. <Phu...@st...>]

Hello, I'm graduate student from CU, Thailand

I would like to ask you some questions about Xpose installation
I installed Xpose last week and program show more "Loading required package:".
How can I resolve this problem

PS. I attach print screen of Xpose program that show install problem

Thank you
PHUMPRUT G

Re: [Xpose-general] xpose4 error_change covariates scope

[Andrew H. <And...@fa...>]

Hi Lorena,

I think that we need more information.  How do you know that only 3 of 7 covariates were considered?  How did you try to change the covariate scope?

Best regards,
Andrew

Andrew Hooker, Ph.D.
Associate Professor of Pharmacometrics
Dept. of Pharmaceutical Biosciences
Uppsala University
Box 591, 751 24, Uppsala, Sweden
Phone: +46 18 471 4355
Mobile: +46 768 000 725
www.farmbio.uu.se/research/researchgroups/pharmacometrics/<http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/>





On 19 May 2016, at 18:32 , Lorena Santulario <lor...@gm...<mailto:lor...@gm...>> wrote:

Dear all,

First of all, thank you for your help.
I am a new R user and I am trying to do some plots using xpose4.
My purpose is to get ETA vs. covariates plots. For that, I'm running a GAM, having 4 parameters (ETA1, ETA2, ETA3 and ETA4) and 7 covariates.

I only run the GAM for one ETA each time. However 3 of the 7 covariates are never considered in the different steps of the GAM.


Because of that, I tried to change covariate scope and put less covariates. After that, I get this error:

 Error in xvardef(v, object) :

trying to get slot "Prefs" from an object of a basic class ("function") with no slots


 Appreciate any comment. Thank you in advice

Lorena



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