Estimates EGA using the lower-order solution of the Louvain
algorithm (`cluster_louvain`

)to identify the lower-order
dimensions and then uses factor or network loadings to estimate factor
or network scores, which are used to estimate the higher-order dimensions
(for more details, see Jiménez et al., 2023)

## Usage

```
hierEGA(
data,
loading.method = c("BRM", "experimental"),
rotation = NULL,
scores = c("factor", "network"),
loading.structure = c("simple", "full"),
impute = c("mean", "median", "none"),
corr = c("auto", "cor_auto", "pearson", "spearman"),
na.data = c("pairwise", "listwise"),
model = c("BGGM", "glasso", "TMFG"),
lower.algorithm = "louvain",
higher.algorithm = c("leiden", "louvain", "walktrap"),
uni.method = c("expand", "LE", "louvain"),
plot.EGA = TRUE,
verbose = FALSE,
...
)
```

## Arguments

- data
Matrix or data frame. Should consist only of variables to be used in the analysis (does not accept correlation matrices)

- loading.method
Character (length = 1). Sets network loading calculation based on implementation described in

`"BRM"`

(Christensen & Golino, 2021) or an`"experimental"`

implementation. Defaults to`"BRM"`

- rotation
Character. A rotation to use to obtain a simpler structure. For a list of rotations, see

`rotations`

for options. Defaults to`NULL`

or no rotation. By setting a rotation,`scores`

estimation will be based on the rotated loadings rather than unrotated loadings- scores
Character (length = 1). How should scores for the higher-order structure be estimated? Defaults to

`"network"`

for network scores computed using the`net.scores`

function. Set to`"factor"`

for factor scores computed using`fa`

. Factors scores will be based on**EFA**(as in Jiménez et al., 2023)*Factor scores use the number of communities from*`EGA`

. Estimated factor loadings may not align with these communities. The plots using factor scores will have higher order factors that may not completely map on to the lower order communities. Look at`$hierarchical$higher_order$lower_loadings`

to determine the composition of the lower order factors.- loading.structure
Character (length = 1). Whether simple structure or the saturated loading matrix should be used when computing scores (

`scores = "network"`

only). Defaults to`"simple"`

`"simple"`

structure more closely mirrors traditional hierarchical factor analytic methods such as CFA;`"full"`

structure more closely mirrors EFA methodsSimple structure is the more conservative (established) approach and is therefore the default. Treat

`"full"`

as experimental as proper vetting and validation has not been established- impute
Character (length = 1). If there are any missing data, then imputation can be implemented. Available options:

`"none"`

--- Default. No imputation is performed`"mean"`

--- The mean value of each variable is used to replace missing data for that variable`"median"`

--- The median value of each variable is used to replace missing data for that variable

- corr
Character (length = 1). Method to compute correlations. Defaults to

`"auto"`

. Available options:`"auto"`

--- Automatically computes appropriate correlations for the data using Pearson's for continuous, polychoric for ordinal, tetrachoric for binary, and polyserial/biserial for ordinal/binary with continuous. To change the number of categories that are considered ordinal, use`ordinal.categories`

(see`polychoric.matrix`

for more details)`"cor_auto"`

--- Uses`cor_auto`

to compute correlations. Arguments can be passed along to the function`"pearson"`

--- Pearson's correlation is computed for all variables regardless of categories`"spearman"`

--- Spearman's rank-order correlation is computed for all variables regardless of categories

For other similarity measures, compute them first and input them into

`data`

with the sample size (`n`

)- na.data
Character (length = 1). How should missing data be handled? Defaults to

`"pairwise"`

. Available options:`"pairwise"`

--- Computes correlation for all available cases between two variables`"listwise"`

--- Computes correlation for all complete cases in the dataset

- model
Character (length = 1). Defaults to

`"glasso"`

. Available options:`"BGGM"`

--- Computes the Bayesian Gaussian Graphical Model. Set argument`ordinal.categories`

to determine levels allowed for a variable to be considered ordinal. See`?BGGM::estimate`

for more details`"glasso"`

--- Computes the GLASSO with EBIC model selection. See`EBICglasso.qgraph`

for more details`"TMFG"`

--- Computes the TMFG method. See`TMFG`

for more details

- lower.algorithm
Character or

`igraph`

`cluster_*`

function (length = 1). Defaults to the lower order`"louvain"`

with most common consensus clustering (1000 iterations; see`community.consensus`

for more details)Louvain with consensus clustering is

*strongly*recommended. Using any other algorithm is considered*experimental*as they have not been designed to capture lower order communities- higher.algorithm
Character or

`igraph`

`cluster_*`

function (length = 1). Defaults to`"walktrap"`

. Three options are listed below but all are available (see`community.detection`

for other options):`"leiden"`

--- See`cluster_leiden`

for more details`"louvain"`

--- By default,`"louvain"`

will implement the Louvain algorithm using the consensus clustering method (see`community.consensus`

for more information). This function will implement`consensus.method = "most_common"`

and`consensus.iter = 1000`

unless specified otherwise`"walktrap"`

--- See`cluster_walktrap`

for more details

Using

`algorithm`

will set only`higher.algorithm`

and`lower.algorithm`

will default to Louvain with most common consensus clustering (1000 iterations)- uni.method
Character (length = 1). What unidimensionality method should be used? Defaults to

`"louvain"`

. Available options:`"expand"`

--- Expands the correlation matrix with four variables correlated 0.50. If number of dimension returns 2 or less in check, then the data are unidimensional; otherwise, regular EGA with no matrix expansion is used. This method was used in the Golino et al.'s (2020)*Psychological Methods*simulation`"LE"`

--- Applies the Leading Eigenvector algorithm (`cluster_leading_eigen`

) on the empirical correlation matrix. If the number of dimensions is 1, then the Leading Eigenvector solution is used; otherwise, regular EGA is used. This method was used in the Christensen et al.'s (2023)*Behavior Research Methods*simulation`"louvain"`

--- Applies the Louvain algorithm (`cluster_louvain`

) on the empirical correlation matrix. If the number of dimensions is 1, then the Louvain solution is used; otherwise, regular EGA is used. This method was validated Christensen's (2022)*PsyArXiv*simulation. Consensus clustering can be used by specifying either`"consensus.method"`

or`"consensus.iter"`

- plot.EGA
Boolean. If

`TRUE`

, returns a plot of the network and its estimated dimensions. Defaults to`TRUE`

- verbose
Boolean (length = 1). Whether messages and (insignificant) warnings should be output. Defaults to

`FALSE`

(silent calls). Set to`TRUE`

to see all messages and warnings for every function call- ...
Additional arguments to be passed on to

`auto.correlate`

,`network.estimation`

,`community.detection`

,`community.consensus`

,`EGA`

, and`rotations`

## Value

Returns a list of lists containing:

- lower_order
`EGA`

results for the lower order structure- higher_order
`EGA`

results for the higher order structure- parameters
A list containing

`lower_loadings`

and`lower_scores`

that were used to estimate scores and the higher order`EGA`

results, respectively- dim.variables
A data frame with variable names and their lower and higher order assignments

- TEFI
Generalized TEFI using

`tefi`

- plot.hierEGA
Plot output if

`plot.EGA = TRUE`

## References

**Hierarchical EGA simulation**

Jiménez, M., Abad, F. J., Garcia-Garzon, E., Golino, H., Christensen, A. P., & Garrido, L. E. (2023).
Dimensionality assessment in bifactor structures with multiple general factors: A network psychometrics approach.
*Psychological Methods*.

**Conceptual implementation**

Golino, H., Thiyagarajan, J. A., Sadana, R., Teles, M., Christensen, A. P., & Boker, S. M. (2020).
Investigating the broad domains of intrinsic capacity, functional ability and
environment: An exploratory graph analysis approach for improving analytical
methodologies for measuring healthy aging.
*PsyArXiv*.

## See also

`plot.EGAnet`

for plot usage in `EGAnet`

## Author

Marcos Jiménez <marcosjnezhquez@gmailcom>, Francisco J. Abad <fjose.abad@uam.es>, Eduardo Garcia-Garzon <egarcia@ucjc.edu>, Hudson Golino <hfg9s@virginia.edu>, Alexander P. Christensen <alexpaulchristensen@gmail.com>, and Luis Eduardo Garrido <luisgarrido@pucmm.edu.do>

## Examples

```
# Example using network scores
opt.hier <- hierEGA(
data = optimism, scores = "network",
plot.EGA = FALSE # No plot for CRAN checks
)
#> Warning: This implementation of `hierEGA` is experimental.
#>
#> The underlying function and/or output may change until the results have been appropriately vetted and validated.
# \donttest{
# Plot multilevel plot
plot(opt.hier, plot.type = "multilevel")
# Plot multilevel plot with higher order
# border color matching the corresponding
# lower order color
plot(opt.hier, color.match = TRUE)
# Plot levels separately
plot(opt.hier, plot.type = "separate")# }
```