zhenkewu / baker Goto Github PK

Hi, Mr. Zhenke Wu,

I hope this message finds you well. I am currently utilizing the baker package for my research and have a specific question regarding the simultaneous analysis of bronze and silver standards.

My understanding is that the Y vector in the baker package specifies the grouping information for the bronze standard, with the assumption that the silver standard includes only cases without a control group by default.

Could you please clarify if it is mandatory for the same set of cases to undergo both bronze and silver standard tests? Specifically, does baker require that all cases included in the analysis have results from both bronze and silver standard tests, as opposed to some cases having only bronze standard results and others having only silver standard results?

Understanding this requirement is crucial for the accurate interpretation of my data and the correct application of the baker package in my analysis.

Thank you for your time and assistance.

Dear Dr. Zhenke Wu,

I hope this message finds you well.

I am encountering an issue with the baker package while performing NPLCM model analysis and would appreciate your assistance.

When running the NPLCM model, I received the following error message:

==[baker] Results stored in: ==
D:/microsoft download2024_05_10_no_reg/results
Error in init_latent_jags_multipleSS(MSS_list, likelihood$cause_list) :
==[baker] Case(s) The 3, 4, 5, 12, 13, 22, 25, 28, 31, 32, 33, 35, 38, 40, 42, 44, 45, 47, 52-th subject(s) have positive silver-standard
measurements on causative agent combinations that are not specified in the 'cause_list' of
'model_options$likelihood'! Please consider 1) deleting these cases,
or 2) adding these combinations into 'cause_list'.

My Findings
Upon examining the data, I found that all the cases mentioned in the error involve subjects who tested positive for two or more pathogens in the silver standard (MSS) tests. The cases that did not produce errors were those where only one pathogen was detected. After removing the cases mentioned in the error, the model ran successfully.

My Questions
Could you please explain the cause of this error?
Is it a requirement that in silver standard (MSS) testing, a subject can only test positive for a single pathogen? If so, how should cases with multiple pathogen detections be handled?

I would greatly appreciate your guidance and suggestions on this matter.

Thank you very much for your assistance!

Best regards,
Sun Binhuang
Fudan University

Hello,
I am trying to run your model using only the vignette code, and get the following error when trying to fit the model (using the function nplcm()):

Welcome to JAGS 4.3.1 (official binary) on Wed May 17 06:31:21 2023
JAGS is free software and comes with ABSOLUTELY NO WARRANTY
Loading module: basemod: ok
Loading module: bugs: ok
Deleting model
Clearing data table
Reading data file jagsdata.txt
Compiling model graph
Resolving undeclared variables
Deleting model
RUNTIME ERROR:
Compilation error on line 32.
Dimension mismatch in subset expression of MBS_1
Warning: cannot open file 'CODAindex.txt': No such file or directoryError in file(file, "rt") : cannot open the connection

Please advise how to resolve.