Questions tagged [traminer]

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 general questions about sequence analysis. For TraMineR coding questions use the "traminer" tag under StackOverflow.

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How do I approach this problem about the order of the events?

So let's imagine I have a dataset of children. For each of them a have a bunch of characteristics (generation, gender, race, class, urban/rural, religion, bmi, number of siblings etc..) and plus the ...
ADayWithoutRain's user avatar
1 vote
1 answer
126 views

Multichannel distance from a reference sequence

I am working with a large dataset and applying multichannel sequence analysis to two life course domains. I would like to adapt a solution suggested in the post below to multichannel sequences, but I ...
Léa Pessin's user avatar
1 vote
1 answer
109 views

Viewing automated cost matrix for DHD in TraMineR

I'm using social sequence analysis, and comparing between different distance methods for my data. I'm wondering if there is a way to view/call the automatic substitution cost matrix that the dynamic ...
Siobhan's user avatar
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0 votes
1 answer
75 views

What is the specific normalization chi2 in seqdist?

In the documentation for the seqdist() function it is noted that there is "...a specific normalization for"CHI2" and "EUCLID". See the Details section." (p.60). But in the details section there is no ...
Aaron Conway's user avatar
1 vote
1 answer
82 views

How does the TraMiner Package Calculate Standard Error Using Weighted Data?

The TraMiner Package includes an option to include sampling weights in the analysis. However, I haven't found any discussion in the package documentation (or associated user manual) of how standard ...
LTD's user avatar
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2 votes
1 answer
1k views

Aligning and clustering sequences of events

I have some data describing sequences of events. There are a number of different events (over 30), and the data records which event occurred in what order. There are no fixed number of events that ...
TJC's user avatar
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1 vote
1 answer
505 views

Handling missing data in Sequence Analysis (TraMineR) within the observation window

I´m using sequence analysis. I have a question about how to deal with missing data within the observation window. The starting point of the analysis is when respondents leave secondary school (t0). I ...
Robin's user avatar
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2 votes
1 answer
82 views

Hierarchy of states in TraMineR

I am considering using TraMineR to analyze my data. However, before I do, I would like to know if it can handle hierarchical states, and I could not find the answer to this question in the ...
Vincent Labatut's user avatar
2 votes
1 answer
88 views

Identifying discriminant event subsequences among 3 groups

I am using TraMineR to identifying discriminant event subsequences among 3 groups. In the user guide, it does not mention how to interpret p-value when 3 groups are compared. Here is a part of my ...
renakre's user avatar
  • 857
3 votes
1 answer
501 views

Detecting outlier sequences in clusters

My question is a general one: I have sequences of categorical variables (click stream) that I analyzed using TraMineR. I now want to conduct cluster analysis (CA) using the WeightedCluster package. ...
user3315563's user avatar
2 votes
1 answer
70 views

Method for discriminating power in seqecmpgroup()

In the document for function seqecmpgroup(): "subsequences are then ordered by decreasing discriminant power." Just wondering what is the method to compute the value? It looks like the 'statistic' ...
Elsa's user avatar
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3 votes
2 answers
206 views

Looking for distance metrics for trajectories of state sequences, based on nearness in time

I am working with data on individual trajectories, defined as a categorical state defined for each time period, using R's TraMineR package to visualize and calculate distances between each pair of ...
user12623's user avatar
3 votes
1 answer
387 views

TraMineR: predicting class membership of new sequences

Question summary This question pertains to analyzing dissimilarities between discrete state sequences (e.g., using TraMineR), more specifically to classifying new, ...
Maxim.K's user avatar
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1 vote
0 answers
397 views

Sequence analysis and clustering of multiple object

My data set are like this ...
Bloodstone Programmer's user avatar
1 vote
1 answer
46 views

concurrent states

I plan to use TraMineR for a research study on student course-taking patterns in secondary schools. For instance – Algebra, Geometry, Algebra II, etc. – where each course is a state. I wondered how to ...
Sharon Koon's user avatar
2 votes
1 answer
67 views

Testing pdist() for statistical significance

Using pdist() in the PST package, two probabilistic suffix trees (PSTs) can be compared to each other. The function will output ...
histelheim's user avatar
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0 votes
0 answers
102 views

Is there any sequence dissimilarity measure that has an intuitive interpretation like the dissimilarity index has?

I want to know how much the sequences in my sample differ from a given ideal-typical sequence. Is there any intuitive way of interpreting the dissimilarity measures for sequences? If it would be the ...
Kenji's user avatar
  • 858
2 votes
1 answer
159 views

Inter-rater reliability for sequential data

I have 20 sequences that were coded by 2 judges, for example: Sequence 1, Judge 1: A-B-C-A-B-E-F Sequence 1, Judge 2: A-B-E-C-A-B-F I want to check the inter-rater reliability. Any suggestions on how ...
user3315563's user avatar
2 votes
1 answer
202 views

How to get a distance matrix using "SVRspell"?

I am trying to compute a distance matrix using the method "SVRspell" (seqdistOO function). I want to use an exponential weight of spell length equal to 2 and I want to discard matching sub-sequences ...
Andres Felipe Castro Torres's user avatar
4 votes
1 answer
698 views

Why use K-medoids for sequence analysis?

In the package WeightedCluster there seems to be facilities for using K-medoids clustering (i.e. wcKMedoids()), but not the more ...
histelheim's user avatar
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2 votes
1 answer
139 views

TraMineR - dont print message of seqdef

Is there a possibility to disable the initial message (1) when creating a sequence with seqdef library(TraMineR) ? (1) this ...
giac's user avatar
  • 863
2 votes
1 answer
86 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 ...
Shab's user avatar
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2 votes
1 answer
103 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: ...
Larry's user avatar
  • 21
3 votes
1 answer
609 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") ...
histelheim's user avatar
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1 vote
1 answer
645 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? ...
GeorgeLBA's user avatar
  • 135
2 votes
1 answer
88 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 ...
Kenji's user avatar
  • 858
0 votes
1 answer
107 views

Residual / explained variance TraMineR

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 ...
user96982's user avatar
5 votes
1 answer
4k 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 ...
histelheim's user avatar
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2 votes
1 answer
179 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 ...
GeorgeLBA's user avatar
  • 135
4 votes
2 answers
225 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 ...
curryage's user avatar
  • 263
5 votes
1 answer
486 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)....
giac's user avatar
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1 vote
0 answers
106 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)...
Pedro Braz's user avatar
2 votes
1 answer
647 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 ...
Pedro Braz's user avatar
1 vote
1 answer
259 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|...
Alexandra's user avatar
4 votes
2 answers
258 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 ...
histelheim's user avatar
  • 2,983
3 votes
1 answer
342 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 ...
histelheim's user avatar
  • 2,983
4 votes
2 answers
1k 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 $N$ ...
thias's user avatar
  • 965
4 votes
1 answer
2k 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 ...
histelheim's user avatar
  • 2,983
6 votes
1 answer
1k 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 ...
Stefan's user avatar
  • 63
4 votes
1 answer
371 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.
POTENZA's user avatar
  • 361
2 votes
1 answer
240 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 ...
histelheim's user avatar
  • 2,983
4 votes
1 answer
1k 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 ...
Kenji's user avatar
  • 858
6 votes
2 answers
1k 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)...
histelheim's user avatar
  • 2,983
4 votes
1 answer
354 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 ...
histelheim's user avatar
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4 votes
2 answers
229 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 ...
Shawn's user avatar
  • 43
3 votes
1 answer
1k 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 ...
POD's user avatar
  • 229
4 votes
2 answers
734 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. ...
histelheim's user avatar
  • 2,983
2 votes
1 answer
610 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 ...
FERREIRA's user avatar
3 votes
0 answers
421 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 ...
Richard's user avatar
  • 135
5 votes
1 answer
59 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 ...
POTENZA's user avatar
  • 361