Nothing
R/umx-package.R
In umx: Structural Equation Modeling and Twin Modeling in R
Defines functions
.onAttach
# Copyright 2007-2022 Timothy C. Bates
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# An institution is the lengthened shadow of one man. Emerson.
# Plays to watch: "Copenhagen" (Michael Frein); "The chemistry between them" (Dorothy Hodgkin)
.onAttach <- function(libname, pkgname){
# umx_set_condensed_slots(FALSE)
umx_set_plot_format('DiagrammeR')
umx_set_dollar_symbol(umx.dollar.symbol = "$") # \u00A3 = GBP
umx_set_plot_file_suffix(umx.plot.suffix = "gv")
umx_set_silent(FALSE)
# if(is.null(getOption('knitr.table.format'))){
# umx_set_table_format('markdown')
# options('knitr.table.format' = "markdown")
# }
umx_set_auto_plot(TRUE)
umx_set_auto_run(TRUE)
umx_set_data_variance_check(minVar = .1, maxVarRatio = 1000)
umx_set_separator(umx_default_separator = ",")
umx_set_silent(FALSE)
umx_set_table_format("markdown")
umx_complete_dollar()
packageStartupMessage("For an overview type '?umx'")
# Soft note when OpenMx is stock/CRAN (not GenomicMx-capable). Never block attach.
startupNote = getOption("umx.genomicMx.startup")
if (is.null(startupNote)) {
startupNote = interactive()
}
if (isTRUE(startupNote) && isTRUE(getOption("umx.warned_openmx_engine")) != TRUE) {
st = tryCatch(xmu_openmx_engine_status(), error = function(e) NULL)
if (!is.null(st) && !isTRUE(st$ok)) {
packageStartupMessage(
"Note: OpenMx on this machine appears to be a stock/legacy build. ",
"For umx WLS/GSEM (SB fit, stacked multigroup Jacobian), install the GenomicMx OpenMx binary: ",
"install.OpenMx(\"GenomicMx\"). ",
"Silence with options(umx.genomicMx.startup = FALSE)."
)
options(umx.warned_openmx_engine = TRUE)
}
}
}
# Forgettable functions
# MASS mvrnorm # Used in umx_make_TwinData
# nlme intervals # Used in umxAPA
# polycor hetcor # Used in umxHetCor
# xtable xtable # Used in umxCompare
# methods::setClass is called during build not package source code.
#' @importFrom cowplot draw_label plot_grid ggdraw
#' @importFrom DiagrammeR grViz
#' @importFrom DiagrammeR DiagrammeR
#' @importFrom ggplot2 ggplot qplot ggtitle ylab xlab labs
#' @importFrom ggplot2 scale_x_continuous scale_x_continuous scale_y_continuous theme
#' @importFrom ggplot2 geom_abline geom_bar geom_curve geom_errorbar geom_hline geom_jitter geom_line
#' @importFrom ggplot2 geom_point geom_ribbon geom_segment geom_smooth geom_vline geom_histogram
#' @importFrom ggplot2 aes .data annotate coord_cartesian element_blank element_text arrow unit
#' @importFrom ggplot2 ggtitle xlab ylab scale_fill_hue expand_limits position_dodge
#' @importFrom ggplot2 theme_bw theme_gray theme_minimal
#' @importFrom graphics plot abline hist par
#' @importFrom kableExtra kbl add_footnote column_spec footnote
#' @importFrom kableExtra kable_classic kable_classic_2 kable_minimal kable_material kable_material_dark kable_paper
#' @importFrom knitr kable
#' @importFrom methods as getSlots is slotNames setClass .hasSlot
#' @importFrom MASS mvrnorm
#' @importFrom Matrix nearPD
#' @importFrom nlme intervals lme
#' @importFrom polycor hetcor
#' @importFrom quantmod Cl
#' @importFrom scales dollar
#' @importFrom stats AIC C aggregate as.formula coef complete.cases glm
#' @importFrom stats confint cor cov cov.wt cov2cor df lm cor.test dnorm pnorm reshape
#' @importFrom stats logLik na.exclude na.omit pchisq pf qchisq predict
#' @importFrom stats qnorm quantile reformulate residuals rnorm runif sd
#' @importFrom stats setNames update var delete.response terms model.frame fitted
#' @importFrom utils combn data flush.console read.table txtProgressBar
#' @importFrom utils globalVariables write.table packageVersion
#' @importFrom utils browseURL install.packages str read.csv read.delim capture.output
#' @importFrom utils head tail adist download.file
#' @importFrom xtable xtable
#' @importFrom zoo index
# old
# #' @importFrom Base::charToRaw
# #' @importFrom DiagrammeRsvg export_svg
# #' @importFrom rsvg rsvg_png rsvg_pdf
utils::globalVariables(c(
# data
"anthro",
"daysToExpiry",
"extrinsicValue",
"position",
"labelText",
"spot",
"delta",
"gammaScaled",
## from Doc
"top.ManMean",
'top.bCov',
'top.meanT1',
'top.meanT2MZ',
'top.meanT2DZ',
'top.meanT2sib',
'psi_a',
'psi_c',
'psi_e',
'unitM',
'Mean',
'FacMean',
'B',
'lamba',
'solvBE',
'psi_a',
'psi_c',
'psi_e',
'filter',
'Ts_',
'K',
'CovMZ_',
## from main umx files
"xFamMean", "Bwithin",
"xDiff",
"yDiff",
'ci.lower',
'ci.upper',
'r',
'xLevel',
'N',
'x',
'xtable',
'M', 'S',
'A', 'E',
'a', 'c', 'e',
'Am', 'Cm', 'Em',
'am', "cm",'em',
'Af', 'Cf', 'Ef',
'af', 'cf', 'ef',
"as", 'cs', 'es',
'ai', 'ci', 'ei',
'a_cp', 'c_cp', 'e_cp',
'A_cp', 'C_cp', 'E_cp',
'ACE', 'AC', "ACf", "ACm", 'hAC', 'hACf', 'hACm',
'ACEf', "ACEm",
'A11', 'A12', 'A21', 'A22', 'E11', 'E22','C11', 'C12', 'C21', 'C22',
'ACE.Af', 'ACE.Am', 'ACE.Cf', 'ACE.Cm', 'ACE.Ef', 'ACE.Em',
"ACE.af", "ACE.am", "ACE.cf", "ACE.cm", "ACE.ef", "ACE.em",
'ACE.Vf', 'ACE.Vm',
'Amf', 'Cmf',
'Asm', 'Asf', 'Csm', 'Csf',
'asf', 'asm', 'csf', 'csm',
'rAf', 'rAm', 'rCf', 'rCm', 'rEf', 'rEm',
'top.betaLin', 'top.betaQuad',
'top.a', 'top.c', 'top.e',
'top.A', 'top.C', 'top.E',
'top.a_std', 'top.c_std', 'top.e_std',
'top.A', 'top.a', 'top.af', 'top.ai', 'top.am', 'top.as', 'top.a_cp',
'top.C', 'top.c', 'top.cf', 'top.ci', 'top.cm', 'top.cs', 'top.c_cp',
'top.E', 'top.e', 'top.ef', 'top.ei', 'top.em', 'top.es', 'top.e_cp',
'top.expCovDZ', 'top.expCovMZ', 'top.expMeanDZ', 'top.expMeanMZ',
'top.Means', 'top.nSib', 'top.nVar', 'top.cp_loadings',
'common_loadings','cp_loadings',
'CorMFa', 'CorMFc', 'covT1', 'covT2', 'Def1', 'Def2', 'Def1Rlin', 'Def1Rquad', 'Def2Rlin', 'Def2Rquad', 'L', 'diagL',
'DZ.covsT1DZ' , 'MZ.covsT1MZ' ,
'DZ.covsT2DZ' , 'MZ.covsT2MZ' ,
'DZ.objective' , 'MZ.objective' ,
'DZf.objective' , 'MZf.objective' ,
'DZff.objective', 'MZff.objective',
'DZm.objective' , 'MZm.objective' ,
'DZmm.objective', 'MZmm.objective',
'DZfm.objective',
'Mf', 'Mm',
'MZW', 'DZW',
'fmCOV','mfCOV',
'newLbound',
# from umxACEv
'InvSD',
# from umxACEcov
'varStarts',
'lowerB',
'lowerW',
'CovB',
'CovW',
'CovWB',
'bCovWBb',
'bCovBb',
'bCovWB',
'bCovB',
'CovWBb',
'CovBb',
# from umxACE_cov_fixed
'top.Intercepts',
'defCovT1',
'top.betas',
'defCovT2',
'defCovT1',
'defCovT2',
'top.Intercepts',
'top.betas',
'Iden',
'nDv',
'meanDZ', 'meanMZ',
'nFac_UnitCol', 'nFac_Iden', 'nVar', 'nVar2', 'nVarIdenMatrix', 'nVarUnit', 'betas',
'oneTwinMeans', 'predMeanT1DZ', 'predMeanT1MZ', 'predMeanT2DZ', 'predMeanT2MZ',
'R', 'Ra', 'Raf', 'Ram', 'Rc', 'Rcf', 'Rcm', 'Ref', 'Rem',
'thresholdDeviations', 'totalVariance', 'UnitLower',
'V', 'Vf', 'Vm', 'Vtot',
"C", "logLik", "var", 'SD', 'StdDev',
'binLabels', 'Unit_nBinx1',
'correlatedA', 'minCor', 'pos1by6', 'varList', 'Im1', 'IZ', 'ZI', 'Z',
# umxDOC
"dzAr", "Vmz", "Vdz",
"FacLoadtw", "cause", "Diag1", "Ones",
"Asmz", "Asdz", "Cstw", "Estw",
"specCovMZ", "specCovDZ", "FacCovMZ", "FacCovDZ",
# Used in tmx_genotypic_effect
"x1", "y1", "y2", "dose", "value", "freq", "Frequency",
# Used in umxGxE
"DefT1", "DefT2", "top.betaCoTwin", "top.betaSelf",
# Used in umxGxEbiv
"mod1", "mod2",
"Adz", "Amz",
"PsAdz" , "PsAmz" , "PsC",
"top.PsAdz", "top.PsAmz", "top.PsC",
"chA", "chC", "chE",
"top.a11", "top.a21", "top.a22",
"top.c11", "top.c21", "top.c22",
"top.e11", "top.e21", "top.e22",
"top.aBeta1", "top.aBeta2", "top.eBeta1", "top.eBeta2", "top.cBeta1", "top.cBeta2",
# Used in umxSimplex
"at" , "ct" , "et",
"Iai", "Ici", "Iei",
"SigmaA" , "SigmaC" , "SigmaE",
"SigmaPh11", "SigmaPh21dz", "SigmaPh21mz",
# Used in poly funs
"minus2SatLogLik", "nCells", "diffchi",
# Used in xmu_lavaan_process_group
"constraintOps", "handledOps",
# Used in power.ACE.test
"zygosity",
# xmu_twin_add_WeightMatrices
"mzWeightMatrix",
"dzWeightMatrix",
# xmuTwinUpgradeMeansToCovariateModel
"top.intercept",
"top.meansBetas",
"T1DefVars",
"T2DefVars",
"T3DefVars",
#MRDoC2
'dzmu',
'BE',
'A_',
'C_',
'E_',
'SPh',
'Smz_',
# fin functions
'loanRatio',
'netGainLoss'
))
# ===================================================================
# = Define some class containers to allow specialised model objects =
# = plot, etc. can then operate on these =
# ===================================================================
methods::setClass("MxModelDoC" , contains = "MxModel")
methods::setClass("MxModelMRDoC" , contains = "MxModel")
methods::setClass("MxModelTwinMaker", contains = "MxModel")
methods::setClass("MxModelACE" , contains = "MxModel")
methods::setClass("MxModelACE_GLM", contains = "MxModel")
methods::setClass("MxModelACEv" , contains = "MxModelACE")
methods::setClass("MxModelACEcov" , contains = "MxModel")
methods::setClass("MxModelACE_DE" , contains = "MxModel")
methods::setClass("umx_double_entry_data", contains = "data.frame")
methods::setClass("MxModelIP" , contains = "MxModel")
methods::setClass("MxModelCP" , contains = "MxModel")
methods::setClass("MxModelGxE" , contains = "MxModel")
methods::setClass("MxModelGxEbiv" , contains = "MxModelGxE")
methods::setClass("MxModelSexLim" , contains = "MxModel")
methods::setClass("MxModelSimplex", contains = "MxModel")
methods::setClass("MxModelGSEM" , contains = "MxModel")
# umxGSEM builds via umxRAM (MxRAMModel). as() has no default RAM -> GSEM path
# when GSEM contains MxModel (new() + RAM init is the empty-name crash).
methods::setAs("MxRAMModel", "MxModelGSEM", function(from) {
class(from) = "MxModelGSEM"
from
})
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Defines functions .onAttach
# Copyright 2007-2022 Timothy C. Bates
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# An institution is the lengthened shadow of one man. Emerson.
# Plays to watch: "Copenhagen" (Michael Frein); "The chemistry between them" (Dorothy Hodgkin)
.onAttach <- function(libname, pkgname){
# umx_set_condensed_slots(FALSE)
umx_set_plot_format('DiagrammeR')
umx_set_dollar_symbol(umx.dollar.symbol = "$") # \u00A3 = GBP
umx_set_plot_file_suffix(umx.plot.suffix = "gv")
umx_set_silent(FALSE)
# if(is.null(getOption('knitr.table.format'))){
# umx_set_table_format('markdown')
# options('knitr.table.format' = "markdown")
# }
umx_set_auto_plot(TRUE)
umx_set_auto_run(TRUE)
umx_set_data_variance_check(minVar = .1, maxVarRatio = 1000)
umx_set_separator(umx_default_separator = ",")
umx_set_silent(FALSE)
umx_set_table_format("markdown")
umx_complete_dollar()
packageStartupMessage("For an overview type '?umx'")
# Soft note when OpenMx is stock/CRAN (not GenomicMx-capable). Never block attach.
startupNote = getOption("umx.genomicMx.startup")
if (is.null(startupNote)) {
startupNote = interactive()
}
if (isTRUE(startupNote) && isTRUE(getOption("umx.warned_openmx_engine")) != TRUE) {
st = tryCatch(xmu_openmx_engine_status(), error = function(e) NULL)
if (!is.null(st) && !isTRUE(st$ok)) {
packageStartupMessage(
"Note: OpenMx on this machine appears to be a stock/legacy build. ",
"For umx WLS/GSEM (SB fit, stacked multigroup Jacobian), install the GenomicMx OpenMx binary: ",
"install.OpenMx(\"GenomicMx\"). ",
"Silence with options(umx.genomicMx.startup = FALSE)."
)
options(umx.warned_openmx_engine = TRUE)
}
}
}
# Forgettable functions
# MASS mvrnorm # Used in umx_make_TwinData
# nlme intervals # Used in umxAPA
# polycor hetcor # Used in umxHetCor
# xtable xtable # Used in umxCompare
# methods::setClass is called during build not package source code.
#' @importFrom cowplot draw_label plot_grid ggdraw
#' @importFrom DiagrammeR grViz
#' @importFrom DiagrammeR DiagrammeR
#' @importFrom ggplot2 ggplot qplot ggtitle ylab xlab labs
#' @importFrom ggplot2 scale_x_continuous scale_x_continuous scale_y_continuous theme
#' @importFrom ggplot2 geom_abline geom_bar geom_curve geom_errorbar geom_hline geom_jitter geom_line
#' @importFrom ggplot2 geom_point geom_ribbon geom_segment geom_smooth geom_vline geom_histogram
#' @importFrom ggplot2 aes .data annotate coord_cartesian element_blank element_text arrow unit
#' @importFrom ggplot2 ggtitle xlab ylab scale_fill_hue expand_limits position_dodge
#' @importFrom ggplot2 theme_bw theme_gray theme_minimal
#' @importFrom graphics plot abline hist par
#' @importFrom kableExtra kbl add_footnote column_spec footnote
#' @importFrom kableExtra kable_classic kable_classic_2 kable_minimal kable_material kable_material_dark kable_paper
#' @importFrom knitr kable
#' @importFrom methods as getSlots is slotNames setClass .hasSlot
#' @importFrom MASS mvrnorm
#' @importFrom Matrix nearPD
#' @importFrom nlme intervals lme
#' @importFrom polycor hetcor
#' @importFrom quantmod Cl
#' @importFrom scales dollar
#' @importFrom stats AIC C aggregate as.formula coef complete.cases glm
#' @importFrom stats confint cor cov cov.wt cov2cor df lm cor.test dnorm pnorm reshape
#' @importFrom stats logLik na.exclude na.omit pchisq pf qchisq predict
#' @importFrom stats qnorm quantile reformulate residuals rnorm runif sd
#' @importFrom stats setNames update var delete.response terms model.frame fitted
#' @importFrom utils combn data flush.console read.table txtProgressBar
#' @importFrom utils globalVariables write.table packageVersion
#' @importFrom utils browseURL install.packages str read.csv read.delim capture.output
#' @importFrom utils head tail adist download.file
#' @importFrom xtable xtable
#' @importFrom zoo index
# old
# #' @importFrom Base::charToRaw
# #' @importFrom DiagrammeRsvg export_svg
# #' @importFrom rsvg rsvg_png rsvg_pdf
utils::globalVariables(c(
# data
"anthro",
"daysToExpiry",
"extrinsicValue",
"position",
"labelText",
"spot",
"delta",
"gammaScaled",
## from Doc
"top.ManMean",
'top.bCov',
'top.meanT1',
'top.meanT2MZ',
'top.meanT2DZ',
'top.meanT2sib',
'psi_a',
'psi_c',
'psi_e',
'unitM',
'Mean',
'FacMean',
'B',
'lamba',
'solvBE',
'psi_a',
'psi_c',
'psi_e',
'filter',
'Ts_',
'K',
'CovMZ_',
## from main umx files
"xFamMean", "Bwithin",
"xDiff",
"yDiff",
'ci.lower',
'ci.upper',
'r',
'xLevel',
'N',
'x',
'xtable',
'M', 'S',
'A', 'E',
'a', 'c', 'e',
'Am', 'Cm', 'Em',
'am', "cm",'em',
'Af', 'Cf', 'Ef',
'af', 'cf', 'ef',
"as", 'cs', 'es',
'ai', 'ci', 'ei',
'a_cp', 'c_cp', 'e_cp',
'A_cp', 'C_cp', 'E_cp',
'ACE', 'AC', "ACf", "ACm", 'hAC', 'hACf', 'hACm',
'ACEf', "ACEm",
'A11', 'A12', 'A21', 'A22', 'E11', 'E22','C11', 'C12', 'C21', 'C22',
'ACE.Af', 'ACE.Am', 'ACE.Cf', 'ACE.Cm', 'ACE.Ef', 'ACE.Em',
"ACE.af", "ACE.am", "ACE.cf", "ACE.cm", "ACE.ef", "ACE.em",
'ACE.Vf', 'ACE.Vm',
'Amf', 'Cmf',
'Asm', 'Asf', 'Csm', 'Csf',
'asf', 'asm', 'csf', 'csm',
'rAf', 'rAm', 'rCf', 'rCm', 'rEf', 'rEm',
'top.betaLin', 'top.betaQuad',
'top.a', 'top.c', 'top.e',
'top.A', 'top.C', 'top.E',
'top.a_std', 'top.c_std', 'top.e_std',
'top.A', 'top.a', 'top.af', 'top.ai', 'top.am', 'top.as', 'top.a_cp',
'top.C', 'top.c', 'top.cf', 'top.ci', 'top.cm', 'top.cs', 'top.c_cp',
'top.E', 'top.e', 'top.ef', 'top.ei', 'top.em', 'top.es', 'top.e_cp',
'top.expCovDZ', 'top.expCovMZ', 'top.expMeanDZ', 'top.expMeanMZ',
'top.Means', 'top.nSib', 'top.nVar', 'top.cp_loadings',
'common_loadings','cp_loadings',
'CorMFa', 'CorMFc', 'covT1', 'covT2', 'Def1', 'Def2', 'Def1Rlin', 'Def1Rquad', 'Def2Rlin', 'Def2Rquad', 'L', 'diagL',
'DZ.covsT1DZ' , 'MZ.covsT1MZ' ,
'DZ.covsT2DZ' , 'MZ.covsT2MZ' ,
'DZ.objective' , 'MZ.objective' ,
'DZf.objective' , 'MZf.objective' ,
'DZff.objective', 'MZff.objective',
'DZm.objective' , 'MZm.objective' ,
'DZmm.objective', 'MZmm.objective',
'DZfm.objective',
'Mf', 'Mm',
'MZW', 'DZW',
'fmCOV','mfCOV',
'newLbound',
# from umxACEv
'InvSD',
# from umxACEcov
'varStarts',
'lowerB',
'lowerW',
'CovB',
'CovW',
'CovWB',
'bCovWBb',
'bCovBb',
'bCovWB',
'bCovB',
'CovWBb',
'CovBb',
# from umxACE_cov_fixed
'top.Intercepts',
'defCovT1',
'top.betas',
'defCovT2',
'defCovT1',
'defCovT2',
'top.Intercepts',
'top.betas',
'Iden',
'nDv',
'meanDZ', 'meanMZ',
'nFac_UnitCol', 'nFac_Iden', 'nVar', 'nVar2', 'nVarIdenMatrix', 'nVarUnit', 'betas',
'oneTwinMeans', 'predMeanT1DZ', 'predMeanT1MZ', 'predMeanT2DZ', 'predMeanT2MZ',
'R', 'Ra', 'Raf', 'Ram', 'Rc', 'Rcf', 'Rcm', 'Ref', 'Rem',
'thresholdDeviations', 'totalVariance', 'UnitLower',
'V', 'Vf', 'Vm', 'Vtot',
"C", "logLik", "var", 'SD', 'StdDev',
'binLabels', 'Unit_nBinx1',
'correlatedA', 'minCor', 'pos1by6', 'varList', 'Im1', 'IZ', 'ZI', 'Z',
# umxDOC
"dzAr", "Vmz", "Vdz",
"FacLoadtw", "cause", "Diag1", "Ones",
"Asmz", "Asdz", "Cstw", "Estw",
"specCovMZ", "specCovDZ", "FacCovMZ", "FacCovDZ",
# Used in tmx_genotypic_effect
"x1", "y1", "y2", "dose", "value", "freq", "Frequency",
# Used in umxGxE
"DefT1", "DefT2", "top.betaCoTwin", "top.betaSelf",
# Used in umxGxEbiv
"mod1", "mod2",
"Adz", "Amz",
"PsAdz" , "PsAmz" , "PsC",
"top.PsAdz", "top.PsAmz", "top.PsC",
"chA", "chC", "chE",
"top.a11", "top.a21", "top.a22",
"top.c11", "top.c21", "top.c22",
"top.e11", "top.e21", "top.e22",
"top.aBeta1", "top.aBeta2", "top.eBeta1", "top.eBeta2", "top.cBeta1", "top.cBeta2",
# Used in umxSimplex
"at" , "ct" , "et",
"Iai", "Ici", "Iei",
"SigmaA" , "SigmaC" , "SigmaE",
"SigmaPh11", "SigmaPh21dz", "SigmaPh21mz",
# Used in poly funs
"minus2SatLogLik", "nCells", "diffchi",
# Used in xmu_lavaan_process_group
"constraintOps", "handledOps",
# Used in power.ACE.test
"zygosity",
# xmu_twin_add_WeightMatrices
"mzWeightMatrix",
"dzWeightMatrix",
# xmuTwinUpgradeMeansToCovariateModel
"top.intercept",
"top.meansBetas",
"T1DefVars",
"T2DefVars",
"T3DefVars",
#MRDoC2
'dzmu',
'BE',
'A_',
'C_',
'E_',
'SPh',
'Smz_',
# fin functions
'loanRatio',
'netGainLoss'
))
# ===================================================================
# = Define some class containers to allow specialised model objects =
# = plot, etc. can then operate on these =
# ===================================================================
methods::setClass("MxModelDoC" , contains = "MxModel")
methods::setClass("MxModelMRDoC" , contains = "MxModel")
methods::setClass("MxModelTwinMaker", contains = "MxModel")
methods::setClass("MxModelACE" , contains = "MxModel")
methods::setClass("MxModelACE_GLM", contains = "MxModel")
methods::setClass("MxModelACEv" , contains = "MxModelACE")
methods::setClass("MxModelACEcov" , contains = "MxModel")
methods::setClass("MxModelACE_DE" , contains = "MxModel")
methods::setClass("umx_double_entry_data", contains = "data.frame")
methods::setClass("MxModelIP" , contains = "MxModel")
methods::setClass("MxModelCP" , contains = "MxModel")
methods::setClass("MxModelGxE" , contains = "MxModel")
methods::setClass("MxModelGxEbiv" , contains = "MxModelGxE")
methods::setClass("MxModelSexLim" , contains = "MxModel")
methods::setClass("MxModelSimplex", contains = "MxModel")
methods::setClass("MxModelGSEM" , contains = "MxModel")
# umxGSEM builds via umxRAM (MxRAMModel). as() has no default RAM -> GSEM path
# when GSEM contains MxModel (new() + RAM init is the empty-name crash).
methods::setAs("MxRAMModel", "MxModelGSEM", function(from) {
class(from) = "MxModelGSEM"
from
})
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