DEPRECATED syntax in many of these models now, use internal model library to mrgsolve or other references!
A package of models in mrgsolve format.
devtools::install_github("metrumresearchgroup/modmrg", subdir="rdev")modmrg depends on mrgsolve. NOTE: we are still working out the necessary policies to make sure that modmrg is compatible with mrgsolve. For now, it is best to use the latest dev versions of both packages.
-
PK: 1, 2, 3 compartment
- All with dual-absorption and linear + non-linear elimination pathways
-
PD (all with 2-cmt PK):
- Indirect response type 1, 2, 3, 4
- Direct EMAX model
- Effect compartment model
-
TMDD
-
Viral dynamic 1- and 2-strain models
?modmrglibrary(modmrg). Loading required package: mrgsolve
. mrgsolve: Community Edition
. www.github.com/metrumresearchgroup
.
. Attaching package: 'modmrg'
. The following object is masked from 'package:mrgsolve':
.
. pkmodel
mod <- pk2cmt()
mod.
.
. -------- mrgsolve model object (unix) --------
. Project: /Users/kyleb/Rlibs/lib/modmrg/project
. source: pk2cmt.cpp
. shared object: modmrg (loaded)
.
. compile date: 05/02 10:26
. Time: start: 0 end: 24 delta: 1
. > add: <none>
. > tscale: 1
.
. Compartments: EV1 CENT PERIPH EV2 [4]
. Parameters: CL VC KA1 KA2 Q VP
. > VMAX KM [8]
. Omega: 0x0
. Sigma: 0x0
.
. Solver: atol: 1e-08 rtol: 1e-08
. > maxsteps: 2000 hmin: 0 hmax: 0
param(mod).
. Model parameters (N=8):
. name value . name value
. CL 1 | Q 2
. KA1 1 | VC 10
. KA2 1 | VMAX 0
. KM 2 | VP 10
init(mod).
. Model initial conditions (N=4):
. name value . name value
. CENT (2) 0 | EV2 (4) 0
. EV1 (1) 0 | PERIPH (3) 0
mod %>%
ev(amt=250, ii=48, addl=10) %>%
mrgsim(end=1000 )%>%
plot
mod <- irm1()
see(mod).
. Model file: irm1.cpp
. $PARAM
. CL=1, VC=10, KA1=0.5, KA2=0.5
. Q = 0, VP=10
. KIN = 10, KOUT=2, IC50 = 2, IMAX=1
. VMAX = 0, KM=2, n=1
.
. $INIT EV1 = 0, CENT= 0, PERIPH = 0, RESP = 5, EV2=0
.
.
. $GLOBAL
. #define CP (CENT/VC)
. #define CT (PERIPH/VP)
. #define CLNL (VMAX/(KM+CP))
. #define INH (IMAX*pow(CP,n)/(pow(IC50,n)+pow(CP,n)))
.
. $MAIN
. RESP_0 = KIN/KOUT;
.
. $ODE
. dxdt_EV1 = -KA1*EV1;
. dxdt_EV2 = -KA2*EV2;
. dxdt_CENT = KA1*EV1 + KA2*EV2 - (CL+CLNL+Q)*CP + Q*CT;
. dxdt_PERIPH = Q*CP - Q*CT;
. dxdt_RESP = KIN*(1-INH) - KOUT*RESP;
.
. $TABLE
. table(CP)=CP;
mod %>%
param(CL=0.5, n=2.5, IMAX=0.85) %>%
ev(amt=750) %>%
Req(RESP) %>%
knobs(IC50=seq(5,55,10), delta=0.1, end=96) %>%
plot
mod <- modmrg::pkmodel(ncmt=2) %>% param(Q=1, V2=8) %>% Req(CP)
mod %>% ev(amt=1000,rate=1000/100) %>% mrgsim(end=336) %>% plot
mod <- viral2()
modmrg:::code(mod). [1] "$PARAM"
. [2] "p= 25, fit=0.75, c = 8"
. [3] "delta=0.4, s=0, d=1/300, beta=5.5E-8"
. [4] "N = 6.5E6, shift=10, AUC=0, IC50=2"
. [5] "mu=6.14E-5, Tmax = 1.3E7, rho = 1.25"
. [6] ""
. [7] "$INIT"
. [8] "expos=0, T = 1126801, I = 1126801, V = 8148974"
. [9] "VM = 87.8, IM = 12.1"
. [10] ""
. [11] "$SET delta=0.2"
. [12] ""
. [13] "$GLOBAL"
. [14] "#define a (s + rho*T_0*(1-((T_0+N)/Tmax)) - d*T_0)"
. [15] "#define b (beta*T_0 * ((1-fit)/(1-mu-fit)) * (1+(rho*T_0)/(delta*Tmax)))"
. [16] "#define eps (expos/(IC50+expos))"
. [17] "#define epsm (expos/(IC50*shift+expos))"
. [18] ""
. [19] "$MAIN"
. [20] "T_0 = c*delta/((1-mu)*beta*p);"
. [21] "V_0 = a/b;"
. [22] "I_0 = (beta/delta)*V_0 * T_0;"
. [23] "VM_0 = V_0*(mu)/(1-mu-fit);"
. [24] "IM_0 = (beta/delta) * VM_0 * T_0;"
. [25] "expos_0 = AUC;"
. [26] ""
. [27] ""
. [28] "$ODE"
. [29] "dxdt_T = s+rho*T*(1-((T+I+IM+N)/Tmax)) - d*T - beta*V*T - beta*VM*T;"
. [30] "dxdt_I = beta*V*T - delta*I;"
. [31] "dxdt_V = (1-mu)*(1-eps)*p*I - c*V;"
. [32] "dxdt_IM = beta*VM*T - delta*IM;"
. [33] "dxdt_VM = mu*(1-eps)*p*I + (1-epsm)*fit*p*IM - c*VM;"
. [34] "dxdt_expos = 0;"
. [35] ""
. [36] "$TABLE"
. [37] "table(logVT) = log10(V+VM);"
. [38] "table(logV) = log10(V);"
. [39] "table(logVM) = log10(VM);"
. [40] "table(logIT) = log10(IM+I);"
. [41] "table(logChange) = log10(VM+V) - log10(VM_0 + V_0);"
. [42] ""