Read back models written to file using mwrite_yaml(). Function
yaml_to_cpp() is also provided to convert the yaml file to mrgsolve cpp
file format.
Arguments
- file
the yaml file name.
- model
a new model name to use when calling
mread_yaml().- project
the directory where the model should be built.
- update
TRUEif model settings should be written into the cpp file in a$SETblock.- ...
passed to
mread().
Details
Note that yaml_to_cpp() by default writes model settings into the cpp
file. mread_yaml() does not write model settings into the file but rather
update the model object directly with data read back from the yaml file.
Examples
mod <- house()
temp <- tempfile(fileext = ".yaml")
mwrite_yaml(mod, file = temp)
# Note: this model is not compiled
mod <- mread_yaml(temp, model = "new-house", compile = FALSE)
mod
#>
#>
#> -------------- source: new-house.mod --------------
#>
#> project: /private/var/fol.../T/RtmpF53bHU
#> shared object: new-house.mod-so-502e2c00b028 <not loaded>
#>
#> time: start: 0 end: 120 delta: 0.25
#> add: <none>
#>
#> compartments: GUT CENT RESP [3]
#> parameters: CL VC KA F1 D1 WTCL WTVC SEXCL SEXVC
#> KIN KOUT IC50 WT SEX [14]
#> captures: DV CP [2]
#> omega: 4x4
#> sigma: 1x1
#>
#> solver: atol: 1e-08 rtol: 1e-08 maxsteps: 20k
#> ------------------------------------------------------
cppfile <- yaml_to_cpp(temp, project = tempdir())
readLines(cppfile)
#> [1] "$PROB"
#> [2] "# `mrgsolve` housemodel"
#> [3] "This model is compiled with `mrgsolve`."
#> [4] " - Author: Metrum Research Group, LLC"
#> [5] " - Description: Generic indirect response PK/PD model"
#> [6] " - Covariates: Weight, female sex"
#> [7] " - Random effects: CL, VC, KA, KOUT"
#> [8] " - Error model: exponential"
#> [9] ""
#> [10] "# Model Annotations: "
#> [11] ""
#> [12] "block name descr unit "
#> [13] "-------- ------ ------------------------- ---------"
#> [14] "PARAM CL Clearance L/hr "
#> [15] "PARAM VC Volume of distribution L "
#> [16] "PARAM KA Absorption rate constant 1/hr "
#> [17] "PARAM F1 Bioavailability fraction . "
#> [18] "PARAM D1 Infusion duration hr "
#> [19] "PARAM WTCL Exponent WT on CL . "
#> [20] "PARAM WTVC Exponent WT on VC . "
#> [21] "PARAM SEXCL Prop cov effect on CL . "
#> [22] "PARAM SEXVC Prop cov effect on VC . "
#> [23] "PARAM KIN Resp prod rate constant 1/hr "
#> [24] "PARAM KOUT Resp elim rate constant 1/hr "
#> [25] "PARAM IC50 Conc giving 50% max resp ng/ml "
#> [26] "PARAM WT Weight kg "
#> [27] "PARAM SEX Covariate female sex . "
#> [28] "CMT GUT Dosing compartment mg "
#> [29] "CMT CENT Central compartment mg "
#> [30] "CMT RESP Response unitless "
#> [31] "CAPTURE DV Dependent variable ng/ml "
#> [32] "CAPTURE CP Plasma concentration ng/ml "
#> [33] ""
#> [34] "$PARAM"
#> [35] "CL = 1"
#> [36] "VC = 20"
#> [37] "KA = 1.2"
#> [38] "F1 = 1"
#> [39] "D1 = 2"
#> [40] "WTCL = 0.75"
#> [41] "WTVC = 1"
#> [42] "SEXCL = 0.7"
#> [43] "SEXVC = 0.85"
#> [44] "KIN = 100"
#> [45] "KOUT = 2"
#> [46] "IC50 = 10"
#> [47] "WT = 70"
#> [48] "SEX = 0"
#> [49] ""
#> [50] "$INIT"
#> [51] "GUT = 0"
#> [52] "CENT = 0"
#> [53] "RESP = 50"
#> [54] ""
#> [55] "$OMEGA"
#> [56] "@block"
#> [57] "@labels ECL EVC EKA EKOUT"
#> [58] "// row 1"
#> [59] "0"
#> [60] "// row 2"
#> [61] "0"
#> [62] "0"
#> [63] "// row 3"
#> [64] "0"
#> [65] "0"
#> [66] "0"
#> [67] "// row 4"
#> [68] "0"
#> [69] "0"
#> [70] "0"
#> [71] "0"
#> [72] ""
#> [73] "$SIGMA"
#> [74] "@block"
#> [75] "@labels EXPO"
#> [76] "// row 1"
#> [77] "0"
#> [78] ""
#> [79] "$PLUGIN"
#> [80] "base"
#> [81] " "
#> [82] "$GLOBAL"
#> [83] "#define CP (CENT/VCi)"
#> [84] "#define INH (CP/(IC50+CP))"
#> [85] "typedef double localdouble;"
#> [86] " "
#> [87] "$MAIN"
#> [88] "F_GUT = F1;"
#> [89] "D_CENT = D1;"
#> [90] "double CLi = exp(log(CL) + WTCL*log(WT/70) + log(SEXCL)*SEX + ECL);"
#> [91] "double VCi = exp(log(VC) + WTVC*log(WT/70) + log(SEXVC)*SEX + EVC);"
#> [92] "double KAi = exp(log(KA) + EKA);"
#> [93] "double KOUTi = exp(log(KOUT) + EKOUT);"
#> [94] "RESP_0 = KIN/KOUTi;"
#> [95] " "
#> [96] "$ODE"
#> [97] "dxdt_GUT = -KAi*GUT;"
#> [98] "dxdt_CENT = KAi*GUT - (CLi/VCi)*CENT;"
#> [99] "dxdt_RESP = KIN*(1-INH) - KOUTi*RESP;"
#> [100] " "
#> [101] "$TABLE"
#> [102] "double DV = CP*exp(EXPO);"
#> [103] " "
#> [104] "$CAPTURE"
#> [105] "DV"
#> [106] "CP"
#> [107] ""
#> [108] "$SET"
#> [109] "end = 120"
#> [110] "delta = 0.25"
#> [111] " "
#> [112] "start = 0"
#> [113] "end = 120"
#> [114] "delta = 0.25"
#> [115] "add = numeric(0)"
#> [116] "atol = 1e-08"
#> [117] "rtol = 1e-08"
#> [118] "ss_atol = 1e-08"
#> [119] "ss_rtol = 1e-08"
#> [120] "maxsteps = 20000"
#> [121] "hmax = 0"
#> [122] "hmin = 0"
#> [123] "mxhnil = 2"
#> [124] "ixpr = 0"
#> [125] "mindt = 2.22044605e-15"
#> [126] "digits = -1"
#> [127] "tscale = 1"
#> [128] "outvars = c(\"GUT\", \"CENT\", \"RESP\", \"DV\", \"CP\")"
#> [129] ""