1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
|
#
# # object <- readModels(file.choose())
# semPaths.mplus.model <- function(object,...)
# {
# invisible(semPaths(semPlotModel(object),...))
# }
readModels <- NULL
semPlotModel.mplus.model <- function (object,mplusStd=c("std", "stdy", "stdyx"),...)
{
mplusStd <- match.arg(mplusStd)
# Check for mplusAutomation:
if (!requireNamespace("MplusAutomation")) stop("'MplusAutomation' package must be installed to read Mplus output.")
addInteractions <- FALSE
if (is.character(object))
{
modfile <- object
object <- MplusAutomation::readModels(object)
Lambda <- NULL
Beta <- NULL
Psi <- NULL
Theta <- NULL
mod <- readLines(modfile)
# Find XWITH:
xs <- grep("XWITH",mod)
if (length(xs)>0)
{
# Split:
spl <- strsplit(mod[xs],split="\\|")
# Find vars that interact:
vars <- lapply(spl,function(x)strsplit(x[2],split="XWITH")[[1]])
# Extract Vars
newvars <- sapply(spl,'[',1)
# sanitize:
newvars <- gsub("\\W","",newvars)
vars <- lapply(vars,gsub,pattern="\\W",replacement="")
addInteractions <- TRUE
}
} else warning("Interactions are ommited. Use semPlotModel.mplus.model on the path to mplus output file for semPlot to attempt to find assigned interactions.")
if (length(object$parameters)==0) stop("No parameters detected in mplus output.")
parsUS <- object$parameters$unstandardized
if (is.null(parsUS$Group)) parsUS$Group <- ""
if (is.null(parsUS$BetweenWithin)) parsUS$BetweenWithin <- ""
if (any(grepl("\\|",parsUS$paramHeader)))
{
parsUS$paramHeader <- gsub("\\|", "BY", parsUS$paramHeader)
warning("'|' operator replaced by BY operator.")
}
if (any(grepl("New.Additional.Parameters",parsUS$paramHeader)))
{
parsUS <- parsUS[!grepl("New.Additional.Parameters",parsUS$paramHeader),]
warning("'New.Additional.Parameters' is not yet supported by semPlot. Parameters will not be shown and unexpected results might occur.")
}
noPars <- FALSE
# Temporary fix for EFA:
if (is.null(parsUS$est))
{
if (!is.null(parsUS$average))
{
parsUS$est <- parsUS$average
parsUS$se <- parsUS$average_se
} else
{
parsUS$est <- 0
parsUS$se <- 0
noPars <- TRUE
}
}
# Only find fixed if SE is present:
if (!is.null(parsUS$se)){
fixed <- parsUS$se==0
} else {
fixed <- FALSE
}
# Define Pars:
Pars <- data.frame(
label = "",
lhs = "",
edge = "--",
rhs = parsUS$param,
est = parsUS$est,
std = NA,
group = parsUS$Group,
fixed = fixed,
par = 0,
BetweenWithin = parsUS$BetweenWithin,
stringsAsFactors=FALSE)
# This code will check if parameters are equal. Check on as many of these columns as possible:
checkCols <- c("est","se", "posterior_sd" ,"pval","lower_2.5ci","upper_2.5ci" )
checkCols <- checkCols[checkCols %in% names(parsUS)]
if (!noPars)
{
parNums <- dlply(cbind(sapply(parsUS[checkCols],function(x)round(as.numeric(x),10)),data.frame(num=1:nrow(parsUS))),checkCols,'[[',"num")
for (i in 1:length(parNums)) Pars$par[parNums[[i]]] <- i
Pars$par[Pars$fixed] <- 0
} else Pars$par <- 1:nrow(Pars)
#
# c <- 1
# for (i in 1:nrow(Pars))
# {
# if (!isTRUE(Pars$fixed[i]) & Pars$par[i]==0)
# {
# par <- sapply(1:nrow(parsUS),function(j)isTRUE(all.equal(unlist(parsUS[j,c("est","se","est_se","pval")]),unlist(parsUS[i,c("est","se","est_se","pval")]))))
# Pars$par[par] <- c
# c <- c+1
# }
# }
#Standardization
#mplusStd <- modelOpts$mplusStd
#Call args from semPaths()
# if (!is.null(object$parameters$std.standardized) &
# (grepl("stand",sys.call(which =1)[3])|grepl("std",sys.call(which =1)[3])) & sys.call(3)$mplusStd=="std")
# {
# Pars$std <- object$parameters$std.standardized$est
# warning("Mplus std parameters will be plotted. To change that, use the modelOpts argument and set mplusStd to stdy, or stdyx parameters.")
# }else if (!is.null(object$parameters$stdy.standardized) & sys.call(3)$mplusStd=="stdy"){
# Pars$std <- object$parameters$stdy.standardized$est
# }else if (!is.null(object$parameters$stdyx.standardized) & sys.call(3)$mplusStd=="stdyx"){
# Pars$std <- object$parameters$stdyx.standardized$est
# }
if (!is.null(object$parameters$std.standardized) && mplusStd == "std")
{
Pars$std <- object$parameters$std.standardized$est
# warning("Mplus std parameters will be plotted. To change that, use the modelOpts argument and set mplusStd to stdy, or stdyx parameters.")
} else if (!is.null(object$parameters$stdy.standardized) && mplusStd == "stdy")
{
Pars$std <- object$parameters$stdy.standardized$est
} else if (!is.null(object$parameters$stdyx.standardized) && mplusStd == "stdyx")
{
Pars$std <- object$parameters$stdyx.standardized$est
} else if (!is.null(object$parameters$standardized))
{
Pars$std <- object$parameters$standardized$est
}
Pars$lhs[grepl(".BY$",parsUS$paramHeader)] <- gsub("\\.BY$","",parsUS$paramHeader[grepl(".BY$",parsUS$paramHeader)])
Pars$edge[grepl(".BY$",parsUS$paramHeader)] <- "->"
Pars$lhs[grepl(".ON$",parsUS$paramHeader)] <- gsub("\\.ON$","",parsUS$paramHeader[grepl(".ON$",parsUS$paramHeader)])
Pars$edge[grepl(".ON$",parsUS$paramHeader)] <- "~>"
Pars[grepl(".ON$",parsUS$paramHeader),c("lhs","rhs")] <- Pars[grepl(".ON$",parsUS$paramHeader),c("rhs","lhs")]
Pars$lhs[grepl(".WITH$",parsUS$paramHeader)] <- gsub("\\.WITH$","",parsUS$paramHeader[grepl(".WITH$",parsUS$paramHeader)])
Pars$edge[grepl(".WITH$",parsUS$paramHeader)] <- "<->"
Pars$lhs[grepl("Variances",parsUS$paramHeader)] <- Pars$rhs[grepl("Variances",parsUS$paramHeader)]
Pars$edge[grepl("Variances",parsUS$paramHeader)] <- "<->"
Pars$edge[grepl("Means|Intercepts",parsUS$paramHeader)] <- "int"
# Extract threshold model:
Thresh <- Pars[grepl("Thresholds",parsUS$paramHeader),-(3:4)]
Thresh$lhs <- gsub("\\$.*","",Pars$rhs[grepl("Thresholds",parsUS$paramHeader)])
Thresh$BetweenWithin[Thresh$BetweenWithin == "Between"] <- "Within"
Pars <- Pars[!grepl("Thresholds",parsUS$paramHeader),]
# Detect latent/manifest:
Latents <- unique(gsub("\\.BY$","",parsUS$paramHeader[grepl(".BY$",parsUS$paramHeader)]))
var <- unique(unlist(Pars[c("lhs","rhs")]))
var <- var[var!=""]
# Variable dataframe:
Vars <- data.frame(
name = var,
manifest = !var%in%Latents,
exogenous = NA,
stringsAsFactors=FALSE)
### Add interactions and remove dummy variables:
if (addInteractions)
{
Vars <- Vars[!tolower(Vars$name)%in%tolower(newvars),]
Pars$knot <- 0
k <- 1
for (i in rev(seq_along(newvars)))
{
varlocs <- which(tolower(Pars$lhs)==tolower(newvars[i])|tolower(Pars$rhs)==tolower(newvars[i]))
for (v in seq_along(varlocs))
{
for (j in 1:length(vars[[i]]))
{
Parsnew <- Pars[varlocs[v],]
Parsnew$lhs[tolower(Parsnew$lhs)==tolower(newvars[i])] <- Vars$name[match(tolower(vars[[i]][j]),tolower(Vars$name))]
Parsnew$rhs[tolower(Parsnew$rhs)==tolower(newvars[i])] <- Vars$name[match(tolower(vars[[i]][j]),tolower(Vars$name))]
if (Parsnew$knot==0)
{
Parsnew$knot <- k
}
Pars <- rbind(Pars,Parsnew)
}
if (any(Pars$knot==k)) k <- k + 1
}
Pars <- Pars[-varlocs,]
}
}
# Abbreviate names with more than 8 characters:
Pars$lhs <- substring(Pars$lhs,1,8)
Pars$rhs <- substring(Pars$rhs,1,8)
Vars$name <- substring(Vars$name,1,8)
Vars <- Vars[!duplicated(Vars),]
semModel <- new("semPlotModel")
semModel@Pars <- Pars
semModel@Vars <- Vars
semModel@Computed <- TRUE
semModel@Original <- list(object)
semModel@ObsCovs <- list()
semModel@Thresholds <- Thresh
ImpCovs <- semMatrixAlgebra(semModel, Lambda %*% Imin(Beta, TRUE) %*% Psi %*% t(Imin(Beta, TRUE)) %*% t(Lambda) + Theta,model = "mplus")
if (!is.list(ImpCovs)) ImpCovs <- list(ImpCovs)
semModel@ImpCovs <- ImpCovs
return(semModel)
}
|
