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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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 ...
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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 ...
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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, ...
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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 ...
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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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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 ...
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Sequences comparison metrics
I know about Edit distance, Longest Common Subsequence and their normalized versions to measure the similarity between sequences But do we have any similarity measures other than the above ones?
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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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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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Dealing with the order of features (sequences)?
Assume we have following sequence database that is subsequently converted with one-hot encoding:
1 2 3 4
0 A B C D
1 B A D NA
2 A D C NA
One-hot encoded:
<...
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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. ...
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Clustering customers by their orders sequence patterns
I have dataset with clients orders. Example:
...
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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' ...
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Sequence prediction: ambiguity in training set
There is a set of sequences (train set), where each element is one or multiple tags:
A, B -- A -- Z -- Z, A
B -- A -- Z -- D
...
Given a new sequence:
...
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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 ...
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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 ...
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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 ...
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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, ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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:
...
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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")
...
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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?
...
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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 ...
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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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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 ...
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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)....
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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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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|...
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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)...
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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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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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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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"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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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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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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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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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)...
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