Model code is written to a readable, transport format. This transport format
can be useful for (1) breaking connection to NONMEM modeling outputs that
are imported by $NMXML or $NMEXT and (2) saving model updates (e.g.,
an updated parameter list). Models can be read back using mread_yaml() or
converted to mrgsolve cpp format with yaml_to_cpp().
Arguments
- x
a model object.
- file
output file name; if non-character (e.g.,
NULL), no output will be written to file.- digits
precision to use when writing outputs.
Value
A list containing data that was written out to the yaml file, with added
item file, is returned invisibly.
Details
Parameters and omega and sigma matrices that were imported via $NMXML
or $NMEXT will be written into the yaml file and the NONMEM import blocks
will be dropped. This allows the user to load a model based on a NONMEM run
without having a connection to that output (e.g., root.xml or root.ext).
Given that the connection to the NONMEM modeling outputs is broken when
writing to yaml, any update to the NONMEM run will only be propagated to
the yaml file when mwrite_yaml() is run again.
The yaml file does not currently have the ability to track
other external dependencies, such as user-defined header files or other
code that might be sourced in by the user when the model is loaded via
mread(). NONMEM xml and ext files imported by $NMXML or $NMEXT are
the only external dependencies that are accounted for in the yaml
transport file.
Examples
mod <- house()
temp1 <- tempfile(fileext = ".yaml")
x <- mwrite_yaml(mod, temp1)
readLines(temp1)
#> [1] "source: mrgsolve::mwrite"
#> [2] "mrgsolve: 1.5.1"
#> [3] "format: yaml"
#> [4] "version: 1.0"
#> [5] "model: housemodel"
#> [6] "prob:"
#> [7] "- '# `mrgsolve` housemodel'"
#> [8] "- This model is compiled with `mrgsolve`."
#> [9] "- ' - Author: Metrum Research Group, LLC'"
#> [10] "- ' - Description: Generic indirect response PK/PD model'"
#> [11] "- ' - Covariates: Weight, female sex'"
#> [12] "- ' - Random effects: CL, VC, KA, KOUT'"
#> [13] "- ' - Error model: exponential'"
#> [14] "- ''"
#> [15] "- '# Model Annotations: '"
#> [16] "- ''"
#> [17] "- 'block name descr unit '"
#> [18] "- '-------- ------ ------------------------- ---------'"
#> [19] "- 'PARAM CL Clearance L/hr '"
#> [20] "- 'PARAM VC Volume of distribution L '"
#> [21] "- 'PARAM KA Absorption rate constant 1/hr '"
#> [22] "- 'PARAM F1 Bioavailability fraction . '"
#> [23] "- 'PARAM D1 Infusion duration hr '"
#> [24] "- 'PARAM WTCL Exponent WT on CL . '"
#> [25] "- 'PARAM WTVC Exponent WT on VC . '"
#> [26] "- 'PARAM SEXCL Prop cov effect on CL . '"
#> [27] "- 'PARAM SEXVC Prop cov effect on VC . '"
#> [28] "- 'PARAM KIN Resp prod rate constant 1/hr '"
#> [29] "- 'PARAM KOUT Resp elim rate constant 1/hr '"
#> [30] "- 'PARAM IC50 Conc giving 50% max resp ng/ml '"
#> [31] "- 'PARAM WT Weight kg '"
#> [32] "- 'PARAM SEX Covariate female sex . '"
#> [33] "- 'CMT GUT Dosing compartment mg '"
#> [34] "- 'CMT CENT Central compartment mg '"
#> [35] "- 'CMT RESP Response unitless '"
#> [36] "- 'CAPTURE DV Dependent variable ng/ml '"
#> [37] "- 'CAPTURE CP Plasma concentration ng/ml '"
#> [38] "param:"
#> [39] " CL: 1.0"
#> [40] " VC: 20.0"
#> [41] " KA: 1.2"
#> [42] " F1: 1.0"
#> [43] " D1: 2.0"
#> [44] " WTCL: 0.75"
#> [45] " WTVC: 1.0"
#> [46] " SEXCL: 0.7"
#> [47] " SEXVC: 0.85"
#> [48] " KIN: 100.0"
#> [49] " KOUT: 2.0"
#> [50] " IC50: 10.0"
#> [51] " WT: 70.0"
#> [52] " SEX: 0.0"
#> [53] "init:"
#> [54] " GUT: 0.0"
#> [55] " CENT: 0.0"
#> [56] " RESP: 50.0"
#> [57] "capture:"
#> [58] "- DV"
#> [59] "- CP"
#> [60] "omega:"
#> [61] " data:"
#> [62] " matrix1:"
#> [63] " row1: 0.0"
#> [64] " row2:"
#> [65] " - 0.0"
#> [66] " - 0.0"
#> [67] " row3:"
#> [68] " - 0.0"
#> [69] " - 0.0"
#> [70] " - 0.0"
#> [71] " row4:"
#> [72] " - 0.0"
#> [73] " - 0.0"
#> [74] " - 0.0"
#> [75] " - 0.0"
#> [76] " labels:"
#> [77] " matrix1:"
#> [78] " - ECL"
#> [79] " - EVC"
#> [80] " - EKA"
#> [81] " - EKOUT"
#> [82] " names: '...'"
#> [83] "sigma:"
#> [84] " data:"
#> [85] " matrix1:"
#> [86] " row1: 0.0"
#> [87] " labels:"
#> [88] " matrix1: EXPO"
#> [89] " names: '...'"
#> [90] "envir: []"
#> [91] "plugin: base"
#> [92] "update:"
#> [93] " start: 0.0"
#> [94] " end: 120.0"
#> [95] " delta: 0.25"
#> [96] " add: []"
#> [97] " atol: 1.0e-08"
#> [98] " rtol: 1.0e-08"
#> [99] " ss_atol: 1.0e-08"
#> [100] " ss_rtol: 1.0e-08"
#> [101] " maxsteps: 20000.0"
#> [102] " hmax: 0.0"
#> [103] " hmin: 0.0"
#> [104] " mxhnil: 2.0"
#> [105] " ixpr: 0.0"
#> [106] " mindt: 2.22044605e-15"
#> [107] " digits: -1.0"
#> [108] " tscale: 1.0"
#> [109] " outvars:"
#> [110] " - GUT"
#> [111] " - CENT"
#> [112] " - RESP"
#> [113] " - DV"
#> [114] " - CP"
#> [115] "set:"
#> [116] " end: 120.0"
#> [117] " delta: 0.25"
#> [118] "code:"
#> [119] "- $PLUGIN"
#> [120] "- base"
#> [121] "- ' '"
#> [122] "- $GLOBAL"
#> [123] "- '#define CP (CENT/VCi)'"
#> [124] "- '#define INH (CP/(IC50+CP))'"
#> [125] "- typedef double localdouble;"
#> [126] "- ' '"
#> [127] "- $MAIN"
#> [128] "- F_GUT = F1;"
#> [129] "- D_CENT = D1;"
#> [130] "- double CLi = exp(log(CL) + WTCL*log(WT/70) + log(SEXCL)*SEX + ECL);"
#> [131] "- double VCi = exp(log(VC) + WTVC*log(WT/70) + log(SEXVC)*SEX + EVC);"
#> [132] "- double KAi = exp(log(KA) + EKA);"
#> [133] "- double KOUTi = exp(log(KOUT) + EKOUT);"
#> [134] "- RESP_0 = KIN/KOUTi;"
#> [135] "- ' '"
#> [136] "- $ODE"
#> [137] "- dxdt_GUT = -KAi*GUT;"
#> [138] "- dxdt_CENT = KAi*GUT - (CLi/VCi)*CENT;"
#> [139] "- dxdt_RESP = KIN*(1-INH) - KOUTi*RESP;"
#> [140] "- ' '"
#> [141] "- $TABLE"
#> [142] "- double DV = CP*exp(EXPO);"
#> [143] "- ' '"