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MarcLavielle / mlxR

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Getting a syntax error #11

Open Anathawa opened 7 years ago

Anathawa commented 7 years ago

"> project.file <- 'C:/Users/lolsen/lixoft/monolix/monolix433/demos/theophylline/theophylline_project.mlxtran'

res1 <- simulx(project = project.file) [ERROR]: Lixoft Exception id:lixoft:Exception source:lixoft::LixoftObject message:[Delayed exceptions] [Delayed exception] id:lixoft:Exception source:lixoft::translator::MlxProjectToMlxtran message:Only MLXTRAN is managed file:........\mlx432\projects\lixoftLanguageTranslators\src\MlxProjectToMlxtran.cpp line:165

file:..........\mlx432\projects\commons\core\mlxUseful\src\LixoftObject.cpp line:68

Error in simulxunit(model = model, lv = lv, settings = settings, out.trt = out.trt) : MLXTRAN met a syntax error.

Parsing ... Incomplete match for: , lexer reached line 4. This error is reported for the actual MLXTRAN syntax and could be inaccurate for a deprecated syntax.

"

I'm trying to run the example on the Simulx website userguide, usng both my own Project data and the Theophyllin projréct, and get this error.

Anathawa commented 7 years ago

R 3.3.3, and R Studio downloaded today, Version 1.0.136 Monolix is the 433 version. mlrX downloaded into R Studio using the first option on the used guide. Testing the others, since that made a difference on my other pc:

This version has the same error: "library("devtools") install_github("MarcLavielle/mlxR") library("mlxR") "

Running this on a Windows laptop

MarcLavielle commented 7 years ago

dear Anna,

you should download the mlxR demo examples http://simulx.webpopix.org/simulx/mlxR310_demos.zip

and run for instance the script /userGuide/simulx/monolix1.R which is described here http://simulx.webpopix.org/userguide/monolix1/

best, Marc

2017-04-17 22:15 GMT+02:00 Anna Olsén notifications@github.com:

"> project.file <- 'C:/Users/lolsen/lixoft/monolix/monolix433/demos/ theophylline/theophylline_project.mlxtran'

res1 <- simulx(project = project.file) [ERROR]: Lixoft Exception id:lixoft:Exception source:lixoft::LixoftObject message:[Delayed exceptions] [Delayed exception] id:lixoft:Exception source:lixoft::translator::MlxProjectToMlxtran message:Only MLXTRAN is managed file:........\mlx432\projects\lixoftLanguageTranslators\src\ MlxProjectToMlxtran.cpp line:165

file:..........\mlx432\projects\commons\core\ mlxUseful\src\LixoftObject.cpp line:68

Error in simulxunit(model = model, lv = lv, settings = settings, out.trt = out.trt) : MLXTRAN met a syntax error.

Parsing ... Incomplete match for: , lexer reached line 4. This error is reported for the actual MLXTRAN syntax and could be inaccurate for a deprecated syntax.

"

I'm trying to run the example on the Simulx website userguide, usng both my own Project data and the Theophyllin projréct, and get this error.

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--

Marc Lavielle

CMAP, Ecole Polytechnique91128 Palaiseau Cedex

France Tel: (33) 1 69 33 46 00 (33) 6 37 31 93 05

Marc.Lavielle@inria.fr http://www.cmap.polytechnique.fr/~lavielle

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""

Anathawa commented 7 years ago

Working on it, just want to report that there is unfortunately a problem with the website to get to the downloads: image

MarcLavielle commented 7 years ago

it works on my side....

[image: Images intégrées 1]

2017-04-20 15:12 GMT+02:00 Anna Olsén notifications@github.com:

Working on it, just want to report that there is unfortunately a problem with the website to get to the downloads: [image: image] https://cloud.githubusercontent.com/assets/10557682/25232467/b0ec5622-25db-11e7-9d4a-d01c1c2c78f6.png

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Anathawa commented 7 years ago

I'm able to download the examples via your link, I just can not open it from the link on the website itself. Thank you for the prompt replies, I'm really happy to have found your programs, they will make life so much easier. :)

Anathawa commented 7 years ago

I'm still unable to get past the first step of using simulx. Using the script monolix1.R, it still gives me a reading error:

project.file <-

  • '~/Lena/Programvaror/Simulix_mlxR/mlxR310_demos/userGuide/simulx/monolixRuns/theophylline_project.mlxtran' res1 <- simulx(project = project.file) [ERROR]: Lixoft Exception id:lixoft:Exception source:lixoft::translator::MlxProjectToXMLX message:Source file '~/Lena/Programvaror/Simulix_mlxR/mlxR310_demos/userGuide/simulx/monolixRuns/theophylline_project.mlxtran' does not exist or is not a file or is not readable file:..........\mlxsuite44\projects\lixoftLanguageTranslators\src\LanguageTranslator.cpp line:42

Error: XML content does not seem to be XML: 'C:/Users/bjorn/OneDrive/Dokument/Lena/Programvaror/Simulix_mlxR/mlxR310_demos/userGuide/simulx/monolixRuns/theophylline_project_tr.xmlx'

This last sentence seems to be the key. There is no file named "theophylline_project_tr.xmlx" anywhere in the library. (I´m setting the wd manually, since I get an error running the first line)

MarcLavielle commented 7 years ago

it seems that you have an issue with the path.

You should try to set the working directory to the source file location (.../mlxR310_demos/userGuide/simulx/) and set

project.file <- 'monolixRuns/theophylline_project.mlxtran'

then, try

d <- readDatamlx(project=project.file) names(d)

2017-04-20 16:01 GMT+02:00 Anna Olsén notifications@github.com:

I'm still unable to get past the first step of using simulx. Using the script monolix1.R, it still gives me a reading error:

project.file <-

  • '~/Lena/Programvaror/Simulix_mlxR/mlxR310_demos/userGuide/ simulx/monolixRuns/theophylline_project.mlxtran'

res1 <- simulx(project = project.file) [ERROR]: Lixoft Exception id:lixoft:Exception source:lixoft::translator::MlxProjectToXMLX message:Source file '~/Lena/Programvaror/Simulix_ mlxR/mlxR310_demos/userGuide/simulx/monolixRuns/theophylline_project.mlxtran' does not exist or is not a file or is not readable file:..........\mlxsuite44\projects\lixoftLanguageTranslators\src\ LanguageTranslator.cpp line:42

Error: XML content does not seem to be XML: 'C:/Users/bjorn/OneDrive/ Dokument/Lena/Programvaror/Simulix_mlxR/mlxR310_demos/ userGuide/simulx/monolixRuns/theophylline_project_tr.xmlx'

This last sentence seems to be the key. There is no file named "theophylline_project_tr.xmlx" anywhere in the library. (I´m setting the wd manually, since I get an error running the first line)

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Anathawa commented 7 years ago

I'm trying to read my actual data, and it doesn't like what it finds: "> project.file <-

Anathawa commented 7 years ago

Wow, that extra line actually made a sdifference! "d <- readDatamlx(project=project.file)" made it possible to use the command simulx() on the Theophylline dataset!

Thanks, trying to get it to work for my own data now. :)

Anathawa commented 7 years ago

The _model.txt that monolix generates does indeed not have a separate row "INPUT:" but it wont accept manual editing. This is what it looks like: "[COVARIATE] input = weight

[INDIVIDUAL] input = {V_pop, omega_V, Cl_pop, omega_Cl, Emax_pop, omega_Emax, EC50_pop, omega_EC50, S0_pop, omega_S0}

DEFINITION: V = {distribution=lognormal, typical=V_pop, sd=omega_V} Cl = {distribution=lognormal, typical=Cl_pop, sd=omega_Cl} Emax = {distribution=lognormal, typical=Emax_pop, sd=omega_Emax} EC50 = {distribution=lognormal, typical=EC50_pop, sd=omega_EC50} S0 = {distribution=lognormal, typical=S0_pop, sd=omega_S0}

[LONGITUDINAL] input = {a1, a2}

input = {V, Cl}

EQUATION: Cc = pkmodel(V, Cl)

OUTPUT: output = Cc

input = {Cc, Emax, EC50, S0} Cc = {use=regressor}

EQUATION: Cc_sat = max(Cc, 0) A = Emax*Cc_sat / (Cc_sat+EC50) S = S0 E = A + S

OUTPUT: output = E

DEFINITION: y1 = {distribution=normal, prediction=Cc, errorModel=constant(a1)}

y2 = {distribution=normal, prediction=E, errorModel=constant(a2)}

"

MarcLavielle commented 7 years ago

you should have a look at these examples:

http://simulx.webpopix.org/case-studies/workflow-pk1/ http://simulx.webpopix.org/case-studies/workflow-pkpd1/

Marc

2017-04-20 16:40 GMT+02:00 Anna Olsén notifications@github.com:

The _model.txt that monolix generates does indeed not have a separate row "INPUT:" but it wont accept manual editing. This is what it looks like: "[COVARIATE] input = weight

[INDIVIDUAL] input = {V_pop, omega_V, Cl_pop, omega_Cl, Emax_pop, omega_Emax, EC50_pop, omega_EC50, S0_pop, omega_S0}

DEFINITION: V = {distribution=lognormal, typical=V_pop, sd=omega_V} Cl = {distribution=lognormal, typical=Cl_pop, sd=omega_Cl} Emax = {distribution=lognormal, typical=Emax_pop, sd=omega_Emax} EC50 = {distribution=lognormal, typical=EC50_pop, sd=omega_EC50} S0 = {distribution=lognormal, typical=S0_pop, sd=omega_S0}

[LONGITUDINAL] input = {a1, a2}

input = {V, Cl}

EQUATION: Cc = pkmodel(V, Cl)

OUTPUT: output = Cc

input = {Cc, Emax, EC50, S0} Cc = {use=regressor}

EQUATION: Cc_sat = max(Cc, 0) A = Emax*Cc_sat / (Cc_sat+EC50) S = S0 E = A + S

OUTPUT: output = E

DEFINITION: y1 = {distribution=normal, prediction=Cc, errorModel=constant(a1)}

y2 = {distribution=normal, prediction=E, errorModel=constant(a2)}

"

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Anathawa commented 7 years ago

You were absolutely right, it was indeed all based on getting the directories right, All working now, thank you so much!

Angieraad15 commented 6 years ago

Hi ,

I m using the Monlix 2016R1 moonlix version and I have been facing some issues when trying to perform a hierarchical fit : The model is set of 6 ODE and I need to define different initial condition per patient per compartment ( the 6 compartment). Is there a way to get around that ? (I have tried to use the initial conditions as regressor and define that in the data file but it failed).

Thanks in Advance

Angie

MarcLavielle commented 6 years ago

Please contact the Lixoft support Marc

Le mer. 16 mai 2018 à 14:09, Angieraad15 notifications@github.com a écrit :

Hi ,

I m using the Monlix 2016R1 moonlix version and I have been facing some issues when trying to perform a hierarchical fit : The model is set of 6 ODE and I need to define different initial condition per patient per compartment ( the 6 compartment). Is there a way to get around that ? (I have tried to use the initial conditions as regressor and define that in the data file but it failed).

Thanks in Advance

Angie

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