Unexpected behavior of "by=group" in combination with chron()
Nobody has claimed this yet.
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
Research direction
Start by running the reproducible data.table and chron example from the issue and compare the grouped chron results with paste(). Trace the grouped evaluation path implicated by the verbose output. Done means each yyyy group produces chron timestamps using its own year, with a regression test covering the reported case.
Written by the indexing model from the issue text.
Description
First off, thank you so very much for the amazing data.table package, which I have been using almost daily for many years.
I searched data.table NEWS and stack overflow [data.table] for previous mentions of this issue and did not find any.
There appears to be a data.table bug related to the use of "by=group" in combination with chron() from the chron package. In the following reproducible example, data.table with "by=group" seems to call chron() in such a way that information from the first group is leaked to and used by subsequent groups, unlike the way it works for other functions (I used paste() in the example). I do not think this is a chron bug, because data from the first "by=group" should not be available to subsequent groups, correct?
Notes: The data.table foo contains time/date information encoded as seconds since the beginning of the year (time.s) and year (yyyy). Chron can assemble this information into a timestamp via chron(time.s/60/60/24,origin=c(1,1,yyyy[1])). With "group=yyyy", the chron origin and resulting timestamp should vary by yyyy group, but they do not. The desired behavior is for each timestamp to use the correct year, e.g.: (01/01/19 00:01:01) instead of (01/01/17 00:01:01).
I have tried many variants of this code (e.g., re-ordering the groups, grouping by a third variable, or omitting a subset of lines). In all cases, all chron timestamps wound up using the year from the first group, as if "by=yyyy" had been omitted, whereas paste(yyyy[1],time.s) works as desired and expected.
I got the same behavior on three different machines and R versions as far back as 3.6.1. The example session info is from an instance of RStudio Cloud.
Thanks for your help,
-Klaus Huebert
library(data.table)
library(chron)
options(datatable.verbose=TRUE)
foo<-data.table(time.s=59:62, yyyy=c(2017,2019,2018,2017))
foo
# time.s yyyy
# 1: 59 2017
# 2: 60 2019
# 3: 61 2018
# 4: 62 2017
foo[,.(paste=paste(yyyy[1], time.s), chron=chron(time.s/60/60/24, origin=c(1, 1, yyyy[1]))), by=yyyy]
# Detected that j uses these columns: time.s
# Finding groups using forderv ... forder.c received 4 rows and 1 columns
# 0.000s elapsed (0.000s cpu)
# Finding group sizes from the positions (can be avoided to save RAM) ... 0.000s elapsed (0.000s cpu)
# Getting back original order ... forder.c received a vector type 'integer' length 3
# 0.000s elapsed (0.000s cpu)
# lapply optimization is on, j unchanged as 'list(paste(yyyy[1], time.s), chron(time.s/60/60/24, origin = c(1, 1, yyyy[1])))'
# GForce is on, left j unchanged
# Old mean optimization is on, left j unchanged.
# Making each group and running j (GForce FALSE) ...
# collecting discontiguous groups took 0.000s for 3 groups
# eval(j) took 0.000s for 3 calls
# 0.000s elapsed (0.000s cpu)
# yyyy paste chron
# 1: 2017 2017 59 (01/01/17 00:00:59)
# 2: 2017 2017 62 (01/01/17 00:01:02)
# 3: 2019 2019 60 (01/01/17 00:01:00)
# 4: 2018 2018 61 (01/01/17 00:01:01)
sessionInfo()
# R version 4.2.1 (2022-06-23)
# Platform: x86_64-pc-linux-gnu (64-bit)
# Running under: Ubuntu 20.04.5 LTS
#
# Matrix products: default
# BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
# LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
#
# locale:
# [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8
# [5] LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 LC_PAPER=C.UTF-8 LC_NAME=C
# [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] chron_2.3-58 data.table_1.14.2
#
# loaded via a namespace (and not attached):
# [1] compiler_4.2.1 tools_4.2.1
- Dominant language
- R
- Stars
- 3.9k
- Forks
- 1.1k
- Avg merge
- 14h 4m
- Merged PRs (30d)
- 4
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
More from Rdatatable/data.table
-
as.data.table() recurses without end on a survival::Surv object (or any data.frame carrying one) Open
Difficulty 2/5 1-3 hours Newbie friendliness 88/100
Rdatatable/data.table#7887 ·
-
consistency tests
Difficulty 2/5 1-3 hours Newbie friendliness 68/100
Rdatatable/data.table#7853 · 3 comments ·
-
internals
Difficulty 2/5 1-3 hours Newbie friendliness 65/100
Rdatatable/data.table#6938 · 1 comment ·
-
encoding fread
Difficulty 2/5 1-3 hours Newbie friendliness 65/100
Rdatatable/data.table#5179 · 8 comments ·
-
documentation programming
Difficulty 2/5 1-3 hours Newbie friendliness 68/100
Rdatatable/data.table#3199 · 3 comments ·
All issues in Rdatatable/data.table
Similar issues
-
Difficulty 2/5 1-3 hours Newbie friendliness 82/100
r-lib/pkgdepends#485 · 3 comments ·
-
Difficulty 1/5 Under an hour Newbie friendliness 92/100
-
beginners blocker
Difficulty 2/5 1-3 hours Newbie friendliness 78/100
-
enviPathR OpenBuild Error Build OK Build Warning policies-accepted pre-review precheck-passed
Difficulty 1/5 Under an hour Newbie friendliness 84/100
Bioconductor/BiocContributions#207 · 6 comments ·
-
Difficulty 2/5 1-3 hours Newbie friendliness 74/100
datacarpentry/semester-biology#1255 ·