# Tagged Questions

The R TraMineR library is a toolkit for exploring and rendering categorical sequence data such as sequences describing family life trajectories or professional careers. This CV "traminer" tag is intended for conceptual questions about the analyses that can be done with the library as well as more ...

18 views

### what is the appropriate one-class classifier for sequenced categorical data?

Can someone suggest an algorithm for an outlier detection system? My requirements are: it supposed to be a one class classifier, where on training phase, it only fed 'normal' data however the normal ...
13 views

### How the total pseudo R2 is calculated with the “dissmfac” function in TraMineR?

I am using the discrepancy analysis in TraMineR. I performed univariate analysis with "dissassoc" to measure the effect of each variable. Then, I did a multi-factors analysis using "dissmfac" to ...
28 views

### Why does the row order of the sequences in TraMineR influence clustering results (Wards method)?

We have a large sample (44,933 sequences each of potential length 35) with 9 states. We create a standard dissimilarity matrix: ...
27 views

### Optimal matching distances

If I have two sequences: 1: A-B-C-D 1: X-A-B-C-D and I do: library(TraMineR) seqdist(sequence1, sequence2, method = "OM") ...
23 views

### Normalizing the Turbulence index to match other indices

I calculated the index of complexity, longitudinal entropy, and turbulence for my data. The first two indicators vary from 0 to 1, whereas turbulence varies between 1 and 16 for one dataset and ...
25 views

### How to count the number of transitions between states in TraMineR?

Is there any way of getting a matrix with the count of transitions between states?. Something similar to the "seqtrate()" but containing the number of transitions instead of just the transitions rate? ...
27 views

### Length-dependent indel costs in OMA algorithm?

I re-read this article after a long time (this time paying attention to the fine print) and noticed that they use indel costs that depend on sequence length in their OMA. They argue that it is done to ...
38 views

### Residual/explained variance TraMineR

I'm sorry, if this question is already asked, but can someone explain to me, how the explained/residual variance from the dissassoc command is computed? I tried to add up the variance within using the ...
61 views

### Analyzing Sankey diagrams statistically?

Sankey diagrams are helpful for visualizing multiple, interacting processes: Are there any statistical tools available that can analyze the interactions of multiple processes? I'm aware of sequence ...
31 views

### Maximum cost in Optimal Matching in TraMineR

Sorry if this question was already asked. I'm new to sequence analysis, I'm using TraMineR to analyze some sequences with the Optimal Matching. But I need to know the maximum possible cost that can ...
26 views

### Mining sequential associations using entropy measures

Assume I have a sequence that looks like this: A-A-A-B-A-A-C-A-A-B-C Let's say I want to predict to use the sequences of letter that occur between one letter and ...
46 views

### Position-dependent substitution cost matrix for sequence alignment

Many sequence alignment algorithms and those which measure similarity between sequences require specification of a cost matrix defined on the sequence alphabet. However, the cost incurred does not ...
514 views

### similarity measure between two different ordered sequences

I know we can quantify the similarity between two sequences with the same length and same elements by rank order correlation. But how to measure similarity between two sequences of different length, ...
81 views

### Sequence analysis - Clusters quality - Time Use

I am trying to run sequence clustering on time use data but I fail to have "acceptable" clustering solution according to Studer (2010). The sequences have 76 episodes of 15 minutes slots (12 states)....
43 views

### How to force a division in tree and locate covariates that explain the variable in TraMineR?

my goal here is simple: I have a bunch of sequences, and a few sequences of interest (that do contain a certain subsequence). I want to force that division and use a tree method (either CART or CHAID)...
102 views

### How to do distance calculation and clustering for event sequences in TraMineR?

I've been using TraMineR for a while now, even though I consider myself a begginer user. The same goes for R language. Yet, I've been able to successfully perform a few optimal matching analysis. Now ...
65 views

### How to use cost of matching with substitution-cost matrix in OM TraMiner?

I have a little complicated alphabet. I have for example: 1. A1|B1 2. A1|B2 3. A2|B3 So, dissimilarity between A1|B1 and A2|B3 =1, but dissimilarity between A1|...
76 views

### How to interpret p-values in output of seqecmpgroup()?

The seqecmpgroup() function returns a table that, among other things, include p-values for each identified subsequence. How should these be interpreted? I can see ...
142 views

### How to do centroid clustering of sequences?

I want to cluster sequences using centroids. In the hclust package it is noted that "Method "centroid" is typically meant to be used with squared Euclidean ...
261 views

### Mining patterns in continuous sequence

I have data in form of $N$ sequences $s_j=(t_i, e_i)_{i\in\{1,\ldots,n_j\}}$ with $n_j$ data-points each, where $t_i$ is a time-stamp and $e_i$ is a categorial event, say $e_i\in\{A,B,C,D\}$. The $N$ ...
333 views

### Comparing two sequence objects?

Using TraMineR, is it possible to compare two sequence objects to calculate the discrepancy between them? By this I mean not comparing two sequences but two sets of ...
481 views

### What's the algorithm for finding sequences used by TraMineR?

I'm working an analysis about finding frequent sequences in a event-state dataset using the R package TraMineR (and ...
114 views

### How to measure multichannel distances between “event” sequences?

In TraMineR, seqdistmc is used to measure multichannel distances between "state" sequences. I am wondering if there is a function to measure multichannel distances between "event" sequences.
95 views

### What is the role of log2 in Elzinga's turbulence measure?

Elzinga's turbulence measure (TraMineR User's Guide, p. 85) is the log2 of the number of "distinct subsequences that can be extracted from the distinct state sequence" multiplied by "the variance of ...
418 views

### Entropy of state distribution, complexity index and turbulence for sequences of varying length

I have a dataset of varying sequence lengths and want to calculate descriptive measured for it. The main cause of differing lengths is that some cases are right censored, and are dealt properly when ...
478 views

### Should normalization completely weed out correlation?

I have two variables: ordering & length. The former measures the ordering of a sequence (i.e. all permutations of A-B-C), and the former is the length of the sequence (i.e. A-B-C has a length of 3)...
87 views

### Sampling from sequence data

I work with 4 sequence datasets that I want to compare. The datasets range from roughly 150 to 2000 sequences. I've been able to use TraMineR on datasets up to 1000 sequences long, but when I try to ...
107 views

### minimum criteria for datasets used with TraMineR

I posted this to the TraMineR user list and it was suggested that it would be appropriate to post it here as well. Any suggestions as to how to determine the minimum dataset size and missingness ...
343 views

### Mean and Variance of a Set of Sequences

I am trying to find the probability distribution (like mean and variance) of a set of sequences which have different length. I came into different measurement models that quantify the distance between ...
320 views

### Comparing clustering of sequences in datasets with different N?

When doing sequence analysis using a package such as TraMineR, one can calculate a clustering based on Optimal Matching (OM) distances, and then plot it as a tree. ...
159 views

### Problem with big Data in TraMineR

I would like to analyse the trajectories of patients hospitalized for CVA (cerebrovascular accident) with the package TraMineR. I have a large dataset with around 25,000 trajectories observed during ...
231 views

### data-transformation for multi-state analysis using traminer/mstate

I am trying to estimate a multi-state model and am following the setup in the book by Mills (2011). The research units can go through different states a, b, c, and d. The research units can move ...
46 views

### Separate opening and extension penalties for indels

ClustalG, the social science version of ClustalX, can use different 'opening' and 'extension' penalties for indels, so that an indel operation can have more weight when it adds the first element for a ...
71 views

### Weightining using TraMineR

I have read some posts on weighting. However, I am still unclear on the sort of weights I need to use. I am using data from the Longitudinal Survey of Australian Youth (LSAY). This survey provides ...
309 views

### Measuring entropy for event sequences?

In TraMineR the function seqient() for calculating the entropy of a sequence object is not available for event sequences (as ...
477 views

### How to estimate the centroid of clustered sequences?

I have run a sequence analaysis using the Optimal Matching algorithm. Afterwards, I have clustered the resulting distance matrice using the Ward algorithm and calculated silhouettes as measures of ...
419 views

### When and how to use weights for sequence analysis in social science?

Weighting in sequence analysis So far, I have scarcely found papers that address the issue of weighting for sequence analysis (using for example the optimal matching algorithm). Sequence analysis ...
223 views

### Duration weighted Optimal Matching Algorithm using R

Besides the ado provided by Brendan Halpin for Stata, is there a way to pursue an Optimal Matching using the R-package TraMineR which weights OM’s elementary ...
129 views

### How to interpret TraMineRs results of disstreedisplay and seqtreedisplay?

I am not quite sure what the differences are between the outputs and results of disstreedisplay and seqtreedisplay. Maybe you ...
80 views

### Dummycoding based on clustering from OM distances

I'm using TraMineR to determine a certain clustering based on Optimal Matching distances: ...
270 views

### “NAs introduced by coercion” in seqecreate

I am using seqecreate to specify an event sequence object using TraMineR. The dataset has 1271 rows and 4 columns, an id, ...
152 views

### Questions about seqtreedisplay and GraphViz [closed]

After I installed Graphviz, I used the following command to plot a tree resulting from a tree-structured analysis of my sequences: ...
633 views

### Index plot for each cluster sorted by the silhouette

After a cluster analysis I´m trying to plot for each cluster the Index plot of the Silhouette value instead of for the complete dataset (like in the WeightedCluster Library Manual by Matthias Studer)....
287 views

### User Defined Substitution Cost Matrix

I have a 30x30 symmetric matrix that I would like to use as a substitution cost matrix in TraMineR to analyze sequences of length 10 with an alphabet of 30. When I try to perform OM with this matrix, ...
406 views

### Other substitution matrices for missing value state in sequence analysis with TraMineR?

We have a question about how to deal with missing values/gaps within sequences. We like to set up our own substitution-cost matrix for the Optimal Matching process. As far as we know, TraMiner allows ...
121 views

### How to calculate turbulence and similarity index with TraMineR?

I am new to sequence analysis and wondering whether TraMineR can calculate Elzinga's turbulence and similarity index or I should learn to use his CHESA software to do this? I appreciate any thoughts ...
2k views

### Do low silhouette widths mean the data has little underlying structure?

I am new to sequence analysis, and I was wondering how you react if the average silhouette widths (ASW) from cluster analyses of Optimal Matching-based dissimilarity matrices are low (around.25). ...
82 views

### Bootstrap the Complexity Index in (Ex)TraMineR?

I'm computing the Complexity Index using TraMineR. Does it make sense to use the bootstrap procedure in order to obtain the confidence intervals for the Complexity Indexes? In this case, is there a ...