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Fixed covariance coverage subsection warning and NAs in the group observations from read.Models() #209

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Fixed covariance coverage subsection warning and NAs in the group observations from read.Models() #209

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911ff5d
Fix for mplus 8.11
jenniferdguay May 24, 2024
2e2a2ee
Fix reading of groups in number of observations in summary of analysis
jenniferdguay May 24, 2024
980a451
revert to original readModel.R because group labels are added to the …
jenniferdguay May 25, 2024
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4 changes: 2 additions & 2 deletions R/readModels.R
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@jenniferdguay jenniferdguay May 27, 2024 •
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If we specify group labels (e.g., G1 and G2) in “GROUPING =“ of the model syntax, mplus knows how to label the levels in the grouping variable of the dataset (e.g., G1 refers to 1 and G2 refers to 2). The output does not print group levels in parenthesis (e.g., the (1) in Group G1 (1)) and the original code from mplusAutomation works.

So if we specify the model syntax with group labels (e.g., G1 and G2) in "GROUPING =", for instance:

alignment.mdl2 <- mplusObject(
  TITLE =     "Run alignment with oblimin rotation;",
  VARIABLE =  "USEVARIABLES = group x1-x10; GROUPING =  group(1 = G1 2 = G2);",
  MODEL= "F1-F2 BY x1-x10(*1);",
  ANALYSIS =  "ROTATION = OBLIMIN; alignment = fixed",
  OUTPUT = "align tech1;",
  rdata = simout$data
)

The original code can be used:

if (isTRUE(length(obs) %% 2 == 0)) {
            Observations <- as.numeric(obs[seq(2, to = length(obs), by = 2)])
            names(Observations) <- obs[seq(1, to = length(obs), by = 2)]
            attr(summaries, "Observations") <- Observations
          }

Whereas if we do not specify group labels in "Grouping =", but specify the number of levels in the group variable:

alignment.mdl <- mplusObject(
  TITLE =     "Run alignment with oblimin rotation;",
  VARIABLE =  "USEVARIABLES = group x1-x10; GROUPING =  group(2);",
  MODEL= "F1-F2 BY x1-x10(*1);",
  ANALYSIS =  "ROTATION = OBLIMIN; alignment = fixed",
  OUTPUT = "align tech1;",
  rdata = simout$data
)

Then the original code produces an error because it does not account for the group levels in parenthesis (e.g., (1) and (2) that have been printed next to G1 and G2 in the output). In this case, the proposed changes work:

if (isTRUE(length(obs) %% 2 == 0)) {
            Observations <- as.numeric(obs[seq(3, to = length(obs), by = 3)])
            names(Observations) <- obs[seq(1, to = length(obs), by = 3)]
            attr(allFiles[[listID]]$summaries, "Observations") <- Observations
          }

Thus, it could be good to check if group labels have been added in “Grouping =” argument, so that the original code can be used to parse the output, otherwise the proposed changes can be used.

Original file line number Diff line number Diff line change
Expand Up @@ -177,8 +177,8 @@ readModels <- function(target=getwd(), recursive=FALSE, filefilter, what="all",
obs <- gsub("Group", "", obs)
obs <- unlist(strsplit(trimws(obs), "\\s+"))
if (isTRUE(length(obs) %% 2 == 0)) {
Observations <- as.numeric(obs[seq(2, to = length(obs), by = 2)])
names(Observations) <- obs[seq(1, to = length(obs), by = 2)]
Observations <- as.numeric(obs[seq(3, to = length(obs), by = 3)])
names(Observations) <- obs[seq(1, to = length(obs), by = 3)]
attr(allFiles[[listID]]$summaries, "Observations") <- Observations
}
}
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