nonmem utility functions written in Go with an emphasis on full test coverage
This project has two main goals
- to support my use cases in nonmem, as well as those requested by collegues
- handle parsing of lst files for command line summaries and as JSON output to be pulled into other programs like R
- execute jobs and support nonmem 7.4's pre-compiled binary features
- manage run submissions 'globally' in that a single run submission should not lock out the shell if you don't want, and all runs should be aware of one-another as to not oversaturate resources, namely CPU.
- clean up and provide some helpers for managing output from PsN submitted jobs, namely more first class integration with git.
- provide simulation and re-estimation templating
- first class hooks to R for pre- and post- processing
- to learn and experiment with go.
By using go, this utility is nicely cross platform, and is distributed as a single binary.
** Currently the software is considered pre-alpha and documentation is non-existant **. However, go, being a statically typed language and simple in it's structures, makes it reasonably easy to look at the raw source to get a feel for what is going on.
Example output as of November 2016 (with new fields continually being added)
{
"RunDetails": {
"NMversion": "7.2.0",
"RunStart": "Tue Dec 17 18:10:55 2013",
"RunEnd": "Tue Dec 17 18:11:32 2013",
"EstimationTime": 6.84,
"CovarianceTime": 3.34,
"FunctionEvaluations": 352,
"SignificantDigits": 3.4
},
"FinalParameterEstimates": {
"Theta": [
"2.31E+00",
"4.25E+01",
"4.64E+02",
"-8.09E-02",
"4.14E+00"
],
"Omega": [
"1.23E-01",
"0.00E+00",
"1.54E-01"
],
"Sigma": [
"1.00E+00"
],
"OmegaCorr": [
"3.51E-01",
"0.00E+00",
"3.92E-01"
],
"SigmaCorr": [
"1.00E+00"
]
},
"FinalParameterStdErr": {
"Theta": [
"8.53E-02",
"2.90E+00",
"2.96E+01",
"5.55E-02",
"1.36E+00"
],
"Omega": [
"2.23E-02",
".........",
"2.67E-02"
],
"Sigma": [
"........."
],
"OmegaCorr": [
"3.18E-02",
".........",
"3.40E-02"
],
"SigmaCorr": [
"........."
]
},
"ParameterStructures": {
"Theta": 5,
"Omega": [
1,
0,
1
],
"Sigma": [
1
]
},
"ParameterNames": {
"Theta": [
"KA",
"CL",
"V2",
"RUVp",
"RUVa"
],
"Omega": [],
"Sigma": []
},
"OFV": 2643.561
}
With tabular outputs that look like:
+-----------+----------+-------------------+--------------+---------------------+
| Theta | Name | Estimate (SN) | Estimate | StdErr (RSE) |
+-----------+----------+-------------------+--------------+---------------------+
| TH 1 | KA | 2.31E+00 | 2.31 | 0.0862 (3.7 %) |
| TH 2 | CL | 5.50E+01 | 55 | 3.33 (6.1 %) |
| TH 3 | V2 | 4.65E+02 | 465 | 29.7 (6.4 %) |
| TH 4 | RUVp | -8.06E-02 | -0.0806 | 0.0555 (68.9 %) |
| TH 5 | RUVa | 4.13E+00 | 4.13 | 1.36 (32.9 %) |
+-----------+----------+-------------------+--------------+---------------------+
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