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 ...

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1answer
16 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: ...
2
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1answer
21 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") ...
1
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1answer
19 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 ...
1
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1answer
20 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? ...
1
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1answer
23 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 ...
1
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1answer
34 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 ...
3
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0answers
56 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 ...
2
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1answer
25 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 ...
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0answers
24 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 ...
3
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2answers
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 ...
4
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2answers
405 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, ...
4
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1answer
68 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 ...
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0answers
39 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 ...
1
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1answer
84 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 ...
1
vote
1answer
61 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 ...
3
votes
2answers
70 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 ...
2
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1answer
135 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 ...
3
votes
2answers
237 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 $N$ ...
1
vote
1answer
295 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 ...
3
votes
1answer
456 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 ...
3
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1answer
109 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.
1
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1answer
94 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 ...
2
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1answer
384 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 ...
4
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2answers
465 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
votes
1answer
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 ...
4
votes
2answers
104 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 ...
3
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1answer
326 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 ...
3
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2answers
308 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. ...
2
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1answer
154 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 ...
3
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0answers
225 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 ...
4
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1answer
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 ...
3
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1answer
68 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 ...
3
votes
2answers
293 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 ...
3
votes
1answer
455 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 ...
7
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1answer
411 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 ...
3
votes
1answer
219 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 ...
3
votes
1answer
124 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 ...
3
votes
1answer
78 views

Dummycoding based on clustering from OM distances

I'm using TraMineR to determine a certain clustering based on Optimal Matching distances: ...
1
vote
1answer
258 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, ...
0
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0answers
146 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: ...
5
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1answer
612 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 ...
4
votes
2answers
275 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, ...
6
votes
2answers
392 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 ...
3
votes
1answer
119 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 ...
8
votes
1answer
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). ...
3
votes
1answer
81 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 ...
3
votes
1answer
223 views

Legend and TraMiner seqplot.tentrop function

I have a problem with the legend of a TraMineR graph. I have computed the 4 different entropies for the 4 cohorts that I'm analyzing and I would like to plot them in the same graph using the ...
4
votes
2answers
153 views

TraMineR seqLLCS and seqdist reference sequence issue

When comparing the same string sequences in the example below, why does the first call return 0 instead of 7? LCS.ex1[3,] is "S-U-M-S-SC-UC-MC" and LCS.ex2[1,] is also "S-U-M-S-SC-UC-MC". Does one ...
1
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0answers
62 views

how to keep covariates when creating a sequence object from a SPELL data

I have a SPELL data in which there are many covariates together with the basic variables (i.e., "id", "begin", "end", and "status"). When I define the SPELL data as a sequence object by "seqdef", it ...
4
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2answers
180 views

Modifying the time granularity of a state sequence

I created a sequence object from my SPELL-formatted data set. The sequence length of the sequence object is 1440 (i.e., 1-min intervals for a day). Is there any easy way for TraMineR to convert the ...