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Is there a bug with write_fst() and read_fst() from library(fst) in R?
Writing and reading a large data.table (~800M rows, 15 variables, 92GB) alters the data and I don't understand why!
psc_all_old <- haven::read_sas("~/own/data/archive/psc_all_v_20250331....
2
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2
answers
297
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Handling larger than memory datasets in R
I'm working with 50 Parquet files (each file is of ~800MB with ~380000 rows and ~8 columns). I need to perform a grouped summarisation in R. Something like:
group_by(sample_id, gene1, gene2) %>%
...
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1
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Hi. I'm getting an error when using ADEGENET For Genetic Distance
I am trying to run genetic distance analysis using adegenet on RStudio and I keep getting an error that some individuals are missing the -5 SNPs. I've copied a section of the code and error below. ...
1
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1
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123
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Triangle heatmap of FST distance matrix with p-values [duplicate]
I am trying to create a triangle heatmap of my FST distance matrix:
NWAtl CIV SEN MRT MOR PRT ESP PAL LG JN TUN MLT MR AEG
NWAtl 0 0 0 0 0 0,00098 0,00586 0,01953 0,01465 0,01855 ...
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1
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459
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How to calculate basic.stats of each population using hierfstat in R
I would like to calculate some summary statistics such as FIS, FST, Ho, He for "each population" using a hierfstat object with 217 samples and 38,000 sites. Although the basic.stats() ...
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1
answer
221
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Deserializing byte array into Java object in a different JVM
I want to do the below, would it theoretically work? (I am working on coding it and checking but that is taking some time)
Serialize a Java object of Custom class C1 (convert into byte[]) using FST ...
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0
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114
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Pass string into map_dfr to filter using tidyfst
I'm reading data stored in several fst-files using tidyfst and purrr::map_dfr. The following example works as expected.
library(tidyverse)
library(fst)
library(tidyfst)
# get all fst files in current ...
4
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0
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39
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Load R data objects' attributes without loading object from file? [duplicate]
I am aware that this question was already posted before, but since it was asked more than eight years ago I was wondering if there is solution now. The suggested answers in that post do not provide a ...
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0
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711
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read.fst() crashes R : workaround needed to detect corrupted file before read.fst()
This is an issue already opened on fstpackage's github, but it seems the package author is no longer actively maintaining it.
Meanwhile, I need a workaround to this crash problem, which is repeatable ...
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0
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80
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union two FSA's with different symbol lists
I have two finite state acceptors, a.fst and b.fst. They are both unweighted, simply encoding sequences of words. Their symbol (word) lists have some overlap, but are not identical. Now I want a union ...
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1
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145
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How to understand this formula in Direct Construction of Minimal Acyclic Subsequential Transducers?
In this paper "Direct Construction of Minimal Acyclic Subsequential Transducers" https://citeseerx.ist.psu.edu/viewdoc/download;jsessionid=690EBF51DD6D52AB9160723AAE3A9541?doi=10.1.1.24.3698&...
1
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0
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344
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Does the R arrow package have anything like the random access capability of the fst package?
Our team is looking to integrate more of our R and python work. One part of this effort has been trying to move from fst files (using the package fst), which as far as I know cannot be read in python ...
0
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1
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88
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Saving and readings lubridate intervals to/from disk
I am having problems recovering lubridate::intervals when reading back from csv, and fst formats.
Does anyone have a suggestion for how to do this?
library(tidyverse)
library(fst)
library(lubridate)
...
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2
answers
79
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There is a set of pairs (set_pairs) and I want to create a set (set_fsts) of first elements of those pairs. How can I do this in Isabelle?
There is a set of pairs (set_pairs) and I want to create a set (set_fsts) of first elements of those pairs. I am writing it in the following way
definition "set_fsts = {f . p ∈ set_piars ∧ fst p ...
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1
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692
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Fastest way to search for a long list of patterns in a text
Given a "large" list of patterns and a "short" text, what is the best/fastest way to search/tag those patterns in the text, where we are trying to find the pattern as a substring ...