Tagged Questions

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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2
votes
1answer
118 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 ...
1
vote
1answer
47 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
vote
1answer
45 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 ...
1
vote
1answer
96 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
votes
2answers
127 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
49 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 ...
3
votes
2answers
64 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
votes
1answer
95 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
votes
2answers
178 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
votes
1answer
65 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
votes
0answers
118 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
votes
1answer
41 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
votes
1answer
49 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 ...
2
votes
2answers
157 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
183 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 ...
6
votes
1answer
231 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 ...
2
votes
1answer
120 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
85 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 ...
2
votes
1answer
76 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
106 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
votes
0answers
77 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
votes
1answer
359 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 ...
3
votes
2answers
150 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
240 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
91 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 ...
5
votes
1answer
937 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
57 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
113 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
114 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
vote
0answers
52 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
votes
2answers
136 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
votes
2answers
125 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
votes
1answer
96 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
votes
1answer
155 views

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

In TraMineR I might compute dissimilarities as such: ...
1
vote
0answers
46 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
votes
1answer
219 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
votes
1answer
194 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
votes
1answer
336 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 ...