Questions tagged [cooccurrence]
The cooccurrence tag has no summary.
13 questions
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Correct use of "Log-transform + 1" for ecological data? [duplicate]
I am conducting an occupancy study using camera trap data with the camtrapR and unmarked packages in R.
I encountered convergence issues in my prey–predator co-occupancy model, so I calculated the ...
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Analyzing index-pair co-occurrence heatmaps from permutation-generating swap sequences
I'm trying to find a method to quickly generate all index-pair sequences for the following problem:
Given a sequence of N elements, find the shortest sequence of lazy pair swaps (i, j) — where each (...
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How to compute Mutual Information
I am absolutely new to MI (and just really bad at it too!) and was wondering if someone could explain to me how to resolve this question.
"Say word A occurs once per 1'000 words (i.e, Freq. (A)=0,...
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Accuracy of PMI (Pointwise Mutual Information) calculation from co-occurrence matrix
Background
When calculate PMI or PPMI from a co-occurrence matrix (COM), it sums each row (co-occurrences) of the COM e.g. 2 for pineapple as in the formula in the snapshot. For this question, it is ...
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Best way to visualize which few data points out of many occur together frequently
Problem statement
I am trying to construct a model that predicts stock price volatility on a given day based on data points represented as strings that may or may not be present on that day. My ...
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Measure like relative frequency that also weights the total [closed]
Background
I see a lot of publications mentioning relative frequencies to indicate the presence of certain genes in a specific area. For example:
...
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Fisher exact test for mutation co-occurence
I've a dataset of 492 samples, for each sample I've information regarding if gene X has a germline mutation and a somatic mutation. I would like to test co-occurence of germline and somatic mutation ...
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Comparing species correlations between species in two habitats
I have two community data sets (samples as rows, species as columns, populated with abundance). This data comes from two habitats/sites, with differing numbers of samples at each site.
What I want ...
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Entropy or co-occurrence matrix to compute the randomness of gray scale images?
I have an algorithm that outputs gray scale images (not normalized). These images often contain a lot of random noise and sometimes also contain spatial structures.
I would like to have some kind of ...
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Correlation Test for Non-Mutually-Exclusive Categorical Data
I have a table of 288 rows and 4 columns where each row corresponds to a tumour sample, and each column is a gene. All of the values are 0 or 1, to indicate whether there's a mutation in a particular ...
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Why the two conditional entropy are not comparable?
I am learning the basics of text mining. For finding the syntagmatic relations in the text like the word "technology" occurs whenever the word "information" occurs i.e co-occurrence of words "...
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"Normalising" join probability of n events, by taking n-th root
I have a group of events which I guess you could call a compound events.
Each event is something like:
$$A=A_1\cap A_2\cap...\cap A_{n_a}$$
I am estimating the probability of the over all event by ...
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Cross Co-occurrence between two corpora
I've looked around for a solution to this problem specifically in nltk, quite a bit but couldn't find much help either on SO or elsewhere.
My problem is as follows:
I have a set of aligned pairs of ...
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