runMod1G: Run a biometric model based on 1 generation of anchestors

In espenmei/Bio1G: Fits biometric models in OpenMx

Description

Run a biometric model based on 1 generation of anchestors

Usage

runMod1G(vrs = NULL, Alist = NULL, Tlist = NULL, Elist = NULL,
  Mlist = NULL, D_M = NULL, D_F = NULL, D_P = NULL, D_C = NULL)

Arguments

vrs	string vector with name of variables
Alist	list of OpenMx components for additive genetic model
Tlist	list of OpenMx components for twin/pregnancy environmental model
Elist	list of OpenMx components for unique environmental model
D_M	dataframe with mother identifiers
D_F	dataframe with father identifiers
D_P	dataframe with pregnancy identifiers and mz dummy
D_C	dataframe with pregnancy identifiers, mz dummy, covariates and variables to be analyzed

Examples

library(OpenMx)

data(D_5var) # Load example dataframe

nv = 5
vrs = paste0("Y", 1:nv)

D_C = D_5var[, c(vrs, "Pid", "mz", "female")]
D_P = D_5var %>%
group_by(Pid) %>%
summarise(Mid = unique(Mid),
          Fid = unique(Fid),
          mz = unique(mz)) %>%
ungroup() %>%
data.frame()
D_M = data.frame(Mid = unique(D_P$Mid))
D_F = data.frame(Fid = unique(D_P$Fid))

# Specify an "independent pathway" model

# Additive genetic model
lCA = mxMatrix("Full", nv, 1, T, 0.5, labF("lCA", nv, 1), name = "lCA")
lSA = mxMatrix("Diag", nv, nv, T, 0.5, labD("lSA", nv), name = "lSA")
VA = mxAlgebra(lCA%*%t(lCA) + lSA%*%t(lSA), name = "VA")
# Twin specific environmental model
lCT = mxMatrix("Full", nv, 1, T, 0.5, labF("lCT", nv, 1), name = "lCT")
lST = mxMatrix("Diag", nv, nv, T, 0.5, labD("lST", nv), name = "lST")
VT = mxAlgebra(lCT%*%t(lCT) + lST%*%t(lST), name = "VT")
# Unique environmental model
lCE = mxMatrix("Full", nv, 1, T, 0.5, labF("lCE", nv, 1), name = "lCE")
lSE = mxMatrix("Diag", nv, nv, T, 0.5, labD("lSE", nv), name = "lSE")
VE = mxAlgebra(lCE%*%t(lCE) + lSE%*%t(lSE), name = "VE")
# Mean model
B = mxMatrix("Full", nv, 2, T, 0, labF("b", nv, 2), name = "B")
X = mxMatrix("Full", 2, 1, F, 1, c("x1", "data.female"), name = "X")
My = mxAlgebra(B%*%X, name = "My")

Apars = list(lCA, lSA, VA)
Tpars = list(lCT, lST, VT)
Epars = list(lCE, lSE, VE)
Mpars = list(B, X, My)
fit = runMod1G(vrs, Apars, Tpars, Epars, Mpars, D_M, D_F, D_P, D_C)
summary(fit)

espenmei/Bio1G documentation built on May 25, 2019, 5:21 p.m.