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UUPharmacometrics / xpose

Graphical diagnostics for pharmacometric models
https://uupharmacometrics.github.io/xpose
GNU Lesser General Public License v3.0
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Parameters read in as na #203

Closed AdamD-Mirati closed 2 years ago

AdamD-Mirati commented 2 years ago

list_vars(xpdb_001)

List of available variables for problem no. 1 
 - Subject identifier (id)               : ID
 - Dependent variable (dv)               : DV
 - Independent variable (idv)            : TIME
 - Event identifier (evid)               : EVID
 - Missing dependent variable (mdv)      : MDV
 - Model typical predictions (pred)      : PRED
 - Model individual predictions (ipred)  : IPRED
 - Residuals (res)                       : IWRES, CWRES, RES, WRES
 - Not attributed (na)                   : CL, V, KA

Is there a way to ensure that the parameters are read in properly?

bguiastr commented 2 years ago

Hi,

Sorry for the delay on my answer. Yes to have your parameters read as parameters by default simply use the $TABLE FILENAME=patab<runno> naming convention from xpose4. The same goes for the categorical (catab) and continuous covariates (cotab).

However you do not have to rerun anything you could simply declare these to be parameters to xpose as follows: (Please note that DOSE and CPRED are not paramters but it was for the sake of the example)

library(xpose)
#> Loading required package: ggplot2
#> 
#> Attaching package: 'xpose'
#> The following object is masked from 'package:stats':
#> 
#>     filter

## Check the variable assigment
list_vars(xpdb_ex_pk, .problem = 1)
#> 
#> List of available variables for problem no. 1 
#>  - Subject identifier (id)               : ID
#>  - Dependent variable (dv)               : DV
#>  - Independent variable (idv)            : TIME
#>  - Dose amount (amt)                     : AMT
#>  - Event identifier (evid)               : EVID
#>  - Model typical predictions (pred)      : PRED
#>  - Model individual predictions (ipred)  : IPRED
#>  - Model parameter (param)               : KA, CL, V, ALAG1
#>  - Eta (eta)                             : ETA1, ETA2, ETA3
#>  - Residuals (res)                       : CWRES, IWRES, RES, WRES
#>  - Categorical covariates (catcov)       : SEX, MED1, MED2
#>  - Continuous covariates (contcov)       : CLCR, AGE, WT
#>  - Compartment amounts (a)               : A1, A2
#>  - Not attributed (na)                   : DOSE, SS, II, TAD, CPRED

## Re-assign DOSE and CPRED as model parameters
xpdb_2 <- set_var_types(xpdb_ex_pk, .problem = 1, param = c("DOSE", "CPRED"))

## Check that it worked
list_vars(xpdb_2, .problem = 1)
#> 
#> List of available variables for problem no. 1 
#>  - Subject identifier (id)               : ID
#>  - Dependent variable (dv)               : DV
#>  - Independent variable (idv)            : TIME
#>  - Dose amount (amt)                     : AMT
#>  - Event identifier (evid)               : EVID
#>  - Model typical predictions (pred)      : PRED
#>  - Model individual predictions (ipred)  : IPRED
#>  - Model parameter (param)               : DOSE, CPRED, KA, CL, V, ALAG1
#>  - Eta (eta)                             : ETA1, ETA2, ETA3
#>  - Residuals (res)                       : CWRES, IWRES, RES, WRES
#>  - Categorical covariates (catcov)       : SEX, MED1, MED2
#>  - Continuous covariates (contcov)       : CLCR, AGE, WT
#>  - Compartment amounts (a)               : A1, A2
#>  - Not attributed (na)                   : SS, II, TAD

Created on 2022-10-21 with reprex v2.0.2

AdamD-Mirati commented 2 years ago

Hi Ben,

Thanks for the reply! I talked to my boss and I actually figured out that it was due to the fact I was capitalizing my table files (ie, PATAB vs patab). I have since revised my table file names and have been able to generate the various parameter plots.

Sincerely, Adam

Adam Dickinson, PharmD Senior Scientist, Clinical Pharmacology | Mirati Therapeutics, Inc. Mobile: 717-254-3022 | Direct: 619-937-2625 Email: @.**@.> Location: Durham, North Carolina (EST)

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From: Benjamin @.> Sent: Friday, October 21, 2022 8:51 AM To: UUPharmacometrics/xpose @.> Cc: Adam Dickinson @.>; Author @.> Subject: Re: [UUPharmacometrics/xpose] Parameters read in as na (Issue #203)

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Hi,

Sorry for the delay on my answer. Yes to have your parameters read as parameters by default simply use the $TABLE FILENAME=patab naming convention from xpose4. The same goes for the categorical (catab) and continuous covariates (cotab).

However you do not have to rerun anything you could simply declare these to be parameters to xpose as follows: (Please note that DOSE and CPRED are not paramters but it was for the sake of the example)

library(xpose)

> Loading required package: ggplot2

>

> Attaching package: 'xpose'

> The following object is masked from 'package:stats':

>

> filter

Check the variable assigment

list_vars(xpdb_ex_pk, .problem = 1)

>

> List of available variables for problem no. 1

> - Subject identifier (id) : ID

> - Dependent variable (dv) : DV

> - Independent variable (idv) : TIME

> - Dose amount (amt) : AMT

> - Event identifier (evid) : EVID

> - Model typical predictions (pred) : PRED

> - Model individual predictions (ipred) : IPRED

> - Model parameter (param) : KA, CL, V, ALAG1

> - Eta (eta) : ETA1, ETA2, ETA3

> - Residuals (res) : CWRES, IWRES, RES, WRES

> - Categorical covariates (catcov) : SEX, MED1, MED2

> - Continuous covariates (contcov) : CLCR, AGE, WT

> - Compartment amounts (a) : A1, A2

> - Not attributed (na) : DOSE, SS, II, TAD, CPRED

Re-assign DOSE and CPRED as model parameters

xpdb_2 <- set_var_types(xpdb_ex_pk, .problem = 1, param = c("DOSE", "CPRED"))

Check that it worked

list_vars(xpdb_2, .problem = 1)

>

> List of available variables for problem no. 1

> - Subject identifier (id) : ID

> - Dependent variable (dv) : DV

> - Independent variable (idv) : TIME

> - Dose amount (amt) : AMT

> - Event identifier (evid) : EVID

> - Model typical predictions (pred) : PRED

> - Model individual predictions (ipred) : IPRED

> - Model parameter (param) : DOSE, CPRED, KA, CL, V, ALAG1

> - Eta (eta) : ETA1, ETA2, ETA3

> - Residuals (res) : CWRES, IWRES, RES, WRES

> - Categorical covariates (catcov) : SEX, MED1, MED2

> - Continuous covariates (contcov) : CLCR, AGE, WT

> - Compartment amounts (a) : A1, A2

> - Not attributed (na) : SS, II, TAD

Created on 2022-10-21 with reprex v2.0.2https://reprex.tidyverse.org

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bguiastr commented 2 years ago

Glad to hear you were able to figure it out !