The R TraMineR library is a toolbox for exploring and rendering categorical sequence data such as sequences describing family life trajectories or professional careers. The "traminer" tag is intended for question regarding the library as well as any general questions about the analysis of ...

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16 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 ...
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1answer
20 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 ...
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1answer
42 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 ...
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2answers
41 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 ...
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1answer
63 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 ...
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2answers
112 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 $N$ ...
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1answer
101 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 ...
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1answer
216 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 ...
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1answer
80 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.
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1answer
56 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 ...
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1answer
176 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 ...
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2answers
295 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 ...
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1answer
61 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 ...
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2answers
76 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 ...
2
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1answer
169 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
236 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. ...
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1answer
95 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 ...
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165 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 ...
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1answer
44 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
54 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 ...
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2answers
212 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
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1answer
304 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 ...
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1answer
296 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 ...
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1answer
160 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
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1answer
105 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
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1answer
77 views

Dummycoding based on clustering from OM distances

I'm using TraMineR to determine a certain clustering based on Optimal Matching distances: ...
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1answer
179 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, ...
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110 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: ...
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1answer
462 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 ...
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2answers
194 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, ...
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2answers
327 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
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1answer
103 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 ...
6
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1answer
1k 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
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1answer
69 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
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1answer
150 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 ...
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2answers
137 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 ...
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55 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
152 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 ...
3
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2answers
137 views

how to randomly select 5% of the sample

The number of sequences in my sequence data is about 5,000, and the sequence length is 1440. In order to reduce computational time to obtain an optimal matching pairwise matrix, I want to randomly ...
4
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1answer
112 views

How to find the rows that meet some conditions in a sequence data set

Here is the summary of my sequence data generated in the SPELL format. All sequences are supposed to have the same length of 1440, but the summary tells me that they are not the same (see "min/max ...
4
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1answer
204 views

What is the relationship between substitution cost matrix and indel costs?

In TraMineR I might compute dissimilarities as such: ...
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0answers
59 views

extractSeqFromW function [closed]

I'm using R and the library TraMineR to do sequence analysis on social science data. I need to use the extractSeqFromW function, but I have problems opening the file even if they are exactly in that ...
5
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1answer
300 views

Problems with Groups in Traminer

I'm having a problem using the group function in TraMineR. I have a data set that contains SPELL data, so multiple rows per case. I also have demographic data per case, at one row per case. I merge ...
2
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1answer
224 views

Optimal matching distances as percentages?

I'm using R and the library TraMineR to do sequence analysis on social science data. I have computed an optimal matching (OM) distance matrix. ...
4
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1answer
418 views

How to describe multi-channel sequence objects in TraMineR?

I have created a multi-channel object here: https://github.com/aronlindberg/VOSS-Sequencing-Toolkit/blob/master/creating_multichannel_object.R However, when I try to use various functions to ...