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Fix TODOs in umxDoC.R #259

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Fix TODOs in umxDoC.R #259

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36 changes: 31 additions & 5 deletions R/umxDoC.R
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Original file line number Diff line number Diff line change
Expand Up @@ -341,6 +341,12 @@ umxDiscTwin <- function(x, y, data, mzZygs = c("MZFF", "MZMM"), dzZygs = c("DZFF
#' }
umxDoC <- function(name = "DoC", var1Indicators, var2Indicators, mzData= NULL, dzData= NULL, sep = "_T", causal= TRUE, autoRun = getOption("umx_auto_run"), intervals = FALSE, tryHard = c("no", "yes", "ordinal", "search"), optimizer = NULL, data = NULL, zyg = "zygosity") {
# TODO: umxDoC add some name checking to avoid variables like "a1"
# Check for reserved names
reserved = c("a", "c", "e", "as", "cs", "es", "expMean", "a_cp", "c_cp", "e_cp")
if(any(c(var1Indicators, var2Indicators) %in% reserved)){
stop("Variable names cannot be any of: ", paste(reserved, collapse = ", "), ". These are reserved for internal matrices.")
}

if(name == "DoC"){name = ifelse(causal, "DoC", "Chol")}
tryHard = match.arg(tryHard)
umx_check(is.logical(causal), "stop", "causal must be TRUE or FALSE")
Expand Down Expand Up @@ -368,6 +374,20 @@ umxDoC <- function(name = "DoC", var1Indicators, var2Indicators, mzData= NULL, d
dzData = xmu_make_mxData(dzData, manifests = selVars)
xmu_twin_check(selDVs= c(var1Indicators,var2Indicators), sep = sep, dzData = dzData, mzData = mzData, enforceSep = TRUE, nSib = nSib, optimizer = optimizer)

# Calculate start means from data
obsData = mzData$observed
# only do this for raw data (mzData$type == "raw")
if(!is.null(obsData) && mzData$type == "raw"){
# obsData is a matrix or data.frame
# T1 is selVars[1:nVar], T2 is selVars[(nVar+1):(2*nVar)]
meansT1 = colMeans(obsData[, selVars[1:nVar], drop=FALSE], na.rm = TRUE)
meansT2 = colMeans(obsData[, selVars[(nVar+1):(2*nVar)], drop=FALSE], na.rm = TRUE)
startMeans = (meansT1 + meansT2)/2
startMeans[is.na(startMeans)] = 0 # Fallback
} else {
startMeans = 0
}

# ========================
# = Make Factor Loadings =
# ========================
Expand Down Expand Up @@ -429,8 +449,7 @@ umxDoC <- function(name = "DoC", var1Indicators, var2Indicators, mzData= NULL, d
mxAlgebra(name= "expCovDZ", FacCovDZ + specCovDZ, dimnames = list(selVars, selVars)),

# Means model
# TODO: Better starts for means... (easy)
umxMatrix(name= "Means", "Full", nrow= 1, ncol= nVar, free= TRUE, values= .1),
umxMatrix(name= "Means", "Full", nrow= 1, ncol= nVar, free= TRUE, values= startMeans),
mxAlgebra(name= "expMean", cbind(top.Means, top.Means))
# TODO Why not just make ncol = nCol*2 and allow label repeats the equate means? Alg might be more efficient?
)
Expand Down Expand Up @@ -656,7 +675,6 @@ umxSummaryDoC <- function(model, digits = 2, comparison = NULL, std = TRUE, show
message("Summary support for DoC models not complete yet. Feedback welcome at http://github.com/tbates/umx/issues if you are using this.")

# TODO: Allow "a2b" in place of causal to avoid the make/modify 2-step
# TODO: Detect value of DZ covariance, and if .25 set "C" to "D" in tables
report = match.arg(report)
commaSep = paste0(umx_set_separator(silent=TRUE), " ")

Expand Down Expand Up @@ -711,7 +729,11 @@ umxSummaryDoC <- function(model, digits = 2, comparison = NULL, std = TRUE, show
# Bind diags of a_cp, c and e columns into nFac-row matrix
commonACE = cbind(diag(a_cp), diag(c_cp), diag(e_cp))
commonACE = data.frame(commonACE, row.names = paste("Common.factor", 1:nFac, sep = "."), stringsAsFactors = FALSE);
names(commonACE) = c ("A", "C", "E")
commonACE_names = c("A", "C", "E")
if(!is.null(model$top$dzCr) && model$top$dzCr$values == .25){
commonACE_names = c("A", "D", "E")
}
names(commonACE) = commonACE_names
if(report == "html"){
umx_print(commonACE, digits = digits, zero.print = ".", file = "std_spec.html")
} else {
Expand Down Expand Up @@ -741,7 +763,11 @@ umxSummaryDoC <- function(model, digits = 2, comparison = NULL, std = TRUE, show
cs = model$top$cs$values
es = model$top$es$values

specifics = data.frame(row.names = paste0('Specific ', c('a', 'c', 'e')), stringsAsFactors = FALSE,
labList = c('a', 'c', 'e')
if(!is.null(model$top$dzCr) && model$top$dzCr$values == .25){
labList = c('a', 'd', 'e')
}
specifics = data.frame(row.names = paste0('Specific ', labList), stringsAsFactors = FALSE,
rbind(diag(as),
diag(cs),
diag(es))
Expand Down
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