NEWS.md

In Upsilon: Another Test of Association for Count Data

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NEWS

Version 0.1.1

2026-03-07

1. Created version 0.1.1 from version 0.1.0
2. [MINOR CHANGE] Edited the vignette "Upsilon test by example".

Version 0.1.0 (First public release)

2025-12-20

1. [MINOR CHANGE] Commented out unnecessary print() and cat() function calls in R/telescoped.chisq.plot.R, R/telescoped.gtest.plot.R, and R/telescoped.upsilon.plot.R.
2. [MINOR CHANGE] Revised the package title to "Another Test of Association for Count Data" from "Test of Association for Count Data"
3. [IMPROVEMENT] The fast methods of tests now accept categorical variables in all basic vector types including character vector, integer vector, an numeric vector.

2025-12-14

1. [IMPROVEMENT] Updated documentation for upsilon.test() with more examples with visualizations.
2. [MAJOR CHANGE] Marked most functions in the package as internal, as they are under development. The three exported functions are thoroughly tested.
3. [MINOR CHANGE] Updated documentation for modified.chisq.test() and modified.gtest().
4. [MINOR CHANGE] Changed the package title to "Test of Association for Count Data" from "Upsilon Test of Association for Count Data" to deal with a complaint from CRAN check.

2025-12-13

1. [IMPROVEMENT] Revised the vignette of examples to make it accessible to the user. Renamed the vignette file name and title. Rewrote the text. Adjusted the plots.

2025-12-12

1. [IMPROVEMENT] Updated telescoped.* plotting functions to use plot_matrix() and return ggplot objects.
2. [IMPROVEMENT] Updated upsilon.gof.statistic() and upsilon.gof.test() with rescale.p parameter for probability normalization control.
3. [IMPROVEMENT] Refactored Vignettes to RMarkdown format with optimized 2x2 figure layouts.

2025-12-11

1. Created version 0.1.0 from version 0.0.4.8
2. [IMPROVEMENT] Added strict input validation (length checks, non-negative checks) to all statistical functions.
3. [NEW FEATURE] Introduced new function plot_matrix() for ggplot2-based balloon plots and heatmaps.

Version 0.0.4.8

2025-09-29

1. Added table_with_shapes function

Version 0.0.4.7

2024-11-12

1. Added table_with_circles function

Version 0.0.4.6

2024-10-01

1. Added Mutual Information in gtest

Version 0.0.4.5

2023-10-25

1. The second priority telescoped test order is from small to large focus 2023-10-24
2. Changed point plot

2023-09-04

1. Changed test_that test cases significant digits to 7.
2. Added No-NA Pearson's Chi-squared Test result for R and CPP
3. Added No-NA G-Test result for R and CPP

2023-09-03

1. Added telescoped.chisq.plot.R
2. Added telescoped.chisq.test.R
3. Added telescoped.data.R
4. Added telescoped.gtest.plot.R
5. Added telescoped.gtest.R
6. Added telescoped.upsilon.plot.R
7. Added telescoped.upsilon.test.R

2023-09-01

1. Changed function name upsilon() to fast.upsilon.test()
2. Changed function name chisq() to fast.chisq.test()
3. Changed function name gtest() to fast.gtest() 2023-08-25
4. Added gtest.R 2023-08-24
5. Added chisq.R

Version 0.0.4.4

2023-04-17

1. Updated document of upsilon()

Version 0.0.4.3

2023-04-09

1. Added if in upsilon.R

2023-04-06

1. Added upsilon() function condition in "upsilon_cpp.cpp"

2023-04-04

1. Added avg = n/(nrnc). Changed n/(nrnc) to "avg" and move "avg" outside of sum. From dividing by "avg" each time to dividing by "avg" only once when computing statistics.

2023-04-02

1. Fixed Warning message: In n * nr * nc : NAs produced by integer overflow in "upsilon.test.R"
2. Changed some codes to make the layout more concise and beautiful in "upsilon.test.R", "upsilon.gof.test.R", "modified.chisq.test.R", and "modified.GTest.R".
3. Added the following line // [[Rcpp::interfaces(r, cpp)]] in "modified_chisq_statistic_cpp.cpp" and "upsilon_gof_statistic_cpp.cpp".
4. Switched row-by-row to column-by-column traverse in modified_chisq_statistic_cpp().
5. Changed line 64 names(ESTIMATE) = "Cramér's V" to names(ESTIMATE) = "Cram\uE9r's V" in "modified.chisq.test.R"

2023-03-23

1. The upsilon_statistic_cpp() has been optimized to speed up by a factor of two. In traversing an Rcpp NumericMatrix, accessing elements column wise can be much faster than row wise. We saw 2 times speedup on 10,000x10,000 matrix after we switched row-by-row to column-by-column traverse.

2023-03-09

1. Added the following line // [[Rcpp::interfaces(r, cpp)]] in "upsilon_statistic_cpp.cpp" to export the upsilon_statistic_cpp() C++ function to other packages.

2023-02-28

1. Added conclusions in Table 7（according to the author）in vignette "upsilon_test.Rmd".

2023-02-22

1. Added legend for stars_pval() in vignette "upsilon_test.Rmd".
2. Interpreted the conclusions in Table 7.
3. Placed the tables(1-5) below the description.

2023-02-20

1. Added test cases using testthat (requested 2023-02-18)
2. Deleted the "doc" folder, which seems to contain another old copy of the vignette. (requested 2023-02-18)
3. Revised the note under 2023-02-14. (requested 2023-02-19)

2023-02-19

1. Updated the vignette "NEWS.md"
2. Updated DESCRIPTION, REFERENCES.bib.
3. Updated R manual inside "upsilon.test.R"

2023-02-18

1. Updated the vignette "upsilon_test.Rmd"
2. Updated DESCRIPTION, REFERENCES.bib.
3. Updated the R manual for all R functions.

2023-02-14

1. Effect size changed (From (Upsilon statistic/max Upsilon statistic) to sqrt(Upsilon statistic/max Upsilon statistic)). The reason for taking the square root is to normalize the Upsilon statistic so that it falls between 0 and 1, which makes it easier to interpret the strength of the association between the variables. When the except value are all same in a 2x2 table, the Upsilon statistic is as same as Pearson's chisq-test, the effect size is also same.

2. Added Table 6 and Table 7 in vignette "upsilon_test.Rmd".

2023-02-07

1. Added comparisons with Fisher’s exact test in vignette "upsilon_test.Rmd".

2023-02-02

1. Removed compare.results from vignettes.

Version 0.0.4.2

2022-07-01

1. Corrected the residual matrix calculation for the upsilon.test().

2022-06-29

1. Added effect size as the estimate in the return of the Upsilon test. MS.

2022-06-16

1. Created version 0.0.4.2 from 0.0.4.1.
2. Renamed statistic.cpp() to upsilon.statistic(). (Requested 2022-06-16)
3. Added function modified.chisq.statistic(). (Requested 2022-06-16)

Version 0.0.4.1

2022-06-16

1. Changed the return of statistic.cpp() and gof.statistic.cpp() from a list to a numeric.
2. Updated the tests due to the changes in 1.

2022-06-15

1. Created version 0.0.4.1
2. For the modified.chisq.test function changed the estimate to be the Cramer's V. The current implementation is V^2. (Requested 2022-06-01)
3. Moved the comparison with other methods to vignettes (compare.results.R, auc.plot ) (Requested 2022-06-08)
4. Moved the non-essential packages in the "Imports:" field to "Suggests:" field in DESCRIPTION. (Requested 2022-06-08)
5. Deleted "test.cpp" from the src folder. (Requested 2022-06-08)

Version 0.0.4

2022-04-06

1. Created version 0.0.4.

Version 0.0.3

2022-01-06

1. Created version 0.0.3.

Version 0.0.2

2021-12-23

1. Created version 0.0.2.

Version 0.0.1

2021-03-27

1. Created version 0.0.1.

Version 0.0.0

2021-03-11

1. Created version 0.0.0.

Upsilon documentation built on March 7, 2026, 5:07 p.m.