single_factor_association()

single_factor_association() tests whether group membership explains part of the discrepancy among sequences, as measured by a pairwise dissimilarity matrix. It runs a pseudo-ANOVA on distances and can attach permutation p-values for TraMineR-compatible statistics.

Function Usage

single_factor_association(
    distance_matrix,
    group,
    weights=None,
    R=1000,
    weight_permutation=None,
    squared=False
)

TraMineR Parameter Mapping

• distance_matrix -> TraMineR diss
• group -> TraMineR group / fac
• weights -> TraMineR weights
• R -> TraMineR R
• weight_permutation -> TraMineR weight.perm
• squared -> TraMineR squared

Entry Parameters

Parameter	Required	Type	Description
distance_matrix	✓	np.ndarray / pd.DataFrame	Square symmetric distance matrix with shape (n, n).
group	✓	array-like	Group label for each sequence. One value per row of the distance matrix. Missing labels are dropped together with the corresponding rows and columns.
weights	✗	np.ndarray	Optional sequence weights with shape (n,). If omitted, all sequences receive equal weight and permutations use "none".
R	✗	int	Number of permutations. Use R <= 1 to compute point estimates only. Default: 1000.
weight_permutation	✗	str / None	How weights enter permutation sampling: "replicate", "diss", "group", or "none". Default: None (resolved to "none" without weights, otherwise "replicate").
squared	✗	bool	If True, use exponent v = 2 on dissimilarities before analysis. Default: False (v = 1).

What It Returns

A dictionary with the main association summaries and supporting tables.

Key	Type	Description
pseudo_f	float	Pseudo F statistic.
pseudo_fbf	float	Brown-Forsythe-type pseudo F included for TraMineR compatibility; useful as a cautious companion statistic when within-group discrepancies differ.
pseudo_r2	float	Pseudo R², the share of total discrepancy explained by groups.
bartlett	float	Legacy discrepancy-homogeneity statistic; use cautiously, especially with weights.
levene	float	Generalized Levene statistic based on distances to group centers.
pseudo_f_pval	float	Permutation p-value for pseudo F.
stat	pd.DataFrame	Table of the five statistics with observed values and p-values.
groups	pd.DataFrame	Weighted group size and group discrepancy for each level, plus a Total row.
anova_table	pd.DataFrame	Explained, residual, and total sums of squares with degrees of freedom and mean squares.
R	int	Number of permutations used.
weight_permutation	str	Permutation mode actually used.

Examples

Step 1: Build a distance matrix

from sequenzo import SequenceData, load_dataset
from sequenzo.dissimilarity_measures import get_distance_matrix

df = load_dataset("mvad")
time_list = [c for c in df.columns if str(c).isdigit()]
seqdata = SequenceData(df, time=time_list, states=sorted(df[time_list].stack().unique()))

dist = get_distance_matrix(seqdata=seqdata, method="OM", norm="auto")

Step 2: Run the association test

from sequenzo.discrepancy_analysis import single_factor_association

group = df["male"].values  # example binary grouping variable

result = single_factor_association(
    distance_matrix=dist,
    group=group,
    R=1000,
)

Step 3: Run a weighted test with survey weights

weights = df["weight"].values

result_weighted = single_factor_association(
    distance_matrix=dist,
    group=group,
    weights=weights,
    R=1000,
    weight_permutation="diss",
)

Step 4: Read the main results

print(result["pseudo_r2"])
print(result["pseudo_f_pval"])
print(result["stat"])
print(result["groups"])

R Counterpart

• Closest R function: dissassoc
• Mapping note: Sequenzo returns the five-statistic setup used in TraMineR's weighted permutation workflow, including pseudo F, pseudo Fbf, pseudo R², Bartlett, and Levene.

Notes

• Import from sequenzo.discrepancy_analysis, not from internal subfolders.
• If weights is omitted, Sequenzo resolves weight_permutation to "none".
• If weights is supplied and weight_permutation is omitted, Sequenzo resolves to "replicate", matching TraMineR dissassoc().
• For survey or calibration weights, pass weight_permutation="diss" explicitly, as recommended by Studer et al. (2011).
• Use weight_permutation="replicate" only when weights are integer frequency counts from aggregated cases.
• By default, Sequenzo follows Studer et al. (2011) and uses nonsquared dissimilarities (v = 1). Set squared=True mainly when the dissimilarity is Euclidean, or as a sensitivity check. Squaring can break the triangle inequality for some sequence distances and change discrepancy contributions.
• Pseudo R² is a descriptive effect-size summary. Use the permutation p-values when you need inferential guidance.
• Rows with missing group labels are removed before the analysis.

Authors

Code: Sequenzo contributors

Documentation: Yuqi Liang

References

Studer, M., Ritschard, G., Gabadinho, A., & Müller, N. S. (2011). Discrepancy analysis of state sequences. Sociological Methods & Research, 40(3), 471–510.

McArdle, B. H., & Anderson, M. J. (2001). Fitting multivariate models to community data: A comment on distance-based redundancy analysis. Ecology, 82(1), 290–297.

Mielke, P. W., & Berry, K. J. (2007). Permutation Methods: A Distance Function Approach (2nd ed.). Springer.

Anderson, M. J. (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecology, 26, 32–46.