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Standardize output #31

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wleoncio opened this issue Apr 21, 2022 · 4 comments
Closed

Standardize output #31

wleoncio opened this issue Apr 21, 2022 · 4 comments
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wleoncio commented Apr 21, 2022 •
edited

Not sure if fixing #27 will consequently solve this, but something could be done to standardize the output of similar functions. See, for example, how Wald_CI_1x2(X = 250, n = 533) outputs a vector whereas LR_CI_1x2(X = 13, n = 16) outputs a string.

Here's a list of remaining functions:

  • Adjusted_inv_sinh_CI_OR_2x2
  • Adjusted_inv_sinh_CI_ratio_2x2
  • Adjusted_log_CI_2x2
  • AgrestiCaffo_CI_2x2
  • AgrestiCoull_CI_1x2
  • BaptistaPike_exact_conditional_CI_2x2
  • BaptistaPike_midP_CI_2x2
  • Bhapkar_test_paired_cxc
  • Blaker_exact_CI_1x2
  • Blaker_exact_test_1x2
  • Blaker_midP_CI_1x2
  • Arcsine_CI_1x2
  • Blaker_midP_test_1x2
  • BonettPrice_hybrid_Wilson_score_CI_CC_paired_2x2
  • BonettPrice_hybrid_Wilson_score_CI_paired_2x2
  • Bonferroni_type_CIs_paired_cxc
  • Bonferroni_type_CIs_rxc
  • Brant_test_2xc
  • BreslowDay_homogeneity_test_stratified_2x2
  • Chacko_test_1xc
  • ClopperPearson_exact_CI_1x2_beta_version
  • ClopperPearson_exact_CI_1x2
  • ClopperPearson_midP_CI_1x2
  • Cochran_Q_test_stratified_2x2
  • CochranArmitage_CI_rx2
  • CochranArmitage_exact_cond_midP_tests_rx2
  • CochranArmitage_MH_tests_rx2
  • CochranMantelHaenszel_test_stratified_2x2
  • Cornfield_exact_conditional_CI_2x2
  • Cornfield_midP_CI_2x2
  • Cumulative_models_for_2xc
  • Cumulative_models_for_rxc
  • Exact_binomial_test_1x2
  • Exact_cond_midP_linear_rank_tests_2xc
  • Exact_cond_midP_tests_rxc
  • Exact_cond_midP_unspecific_ordering_rx2
  • Exact_multinomial_test_1xc(1:3, seq
  • Exact_unconditional_test_2x2
  • Fisher_exact_test_2x2
  • Exact_unconditional_test_2x2
  • Fisher_midP_test_2x2
  • FisherFreemanHalton_asymptotic_test_rxc
  • FleissEveritt_test_paired_cxc
  • FleissLevinPaik_test_paired_cxc
  • gamma_coefficient_rxc_bca
  • gamma_coefficient_rxc
  • Gart_adjusted_logit_CI_2x2
  • Gold_Wald_CIs_1xc
  • Goodman_Wald_CIs_1xc
  • Goodman_Wald_CIs_for_diffs_1xc
  • Goodman_Wilson_score_CIs_1xc
  • Independence_smoothed_logit_CI_2x2
  • Inv_sinh_CI_OR_2x2
  • Inv_sinh_CI_ratio_2x2
  • InverseVariance_estimate_stratified_2x2
  • Jeffreys_CI_1x2
  • JonckheereTerpstra_test_rxc
  • Katz_log_CI_2x2
  • Kendalls_tau_b_rxc_bca
  • Kendalls_tau_b_rxc
  • Koopman_asymptotic_score_CI_2x2
  • KruskalWallis_asymptotic_test_rxc
  • linear_by_linear_test_rxc
  • LR_CI_1x2
  • LR_test_1x2
  • LR_test_1xc
  • LR_test_2x2
  • MantelHaenszel_estimate_stratified_2x2
  • MantelHaenszel_test_2xc
  • McNemar_asymptotic_test_CC_paired_2x2
  • McNemar_asymptotic_test_paired_2x2
  • McNemar_exact_cond_test_paired_2x2
  • McNemar_exact_unconditional_test_paired_2x2
  • McNemar_midP_test_paired_2x2
  • McNemarBowker_test_paired_cxc
  • Mee_asymptotic_score_CI_2x2
  • MidP_binomial_test_1x2
  • MidP_multinomial_test_1xc
  • MiettinenNurminen_asymptotic_score_CI_difference_2x2
  • MiettinenNurminen_asymptotic_score_CI_OR_2x2
  • MiettinenNurminen_asymptotic_score_CI_ratio_2x2
  • ML_estimates_and_CIs_stratified_2x2
  • MOVER_R_Wilson_CI_OR_2x2
  • MOVER_R_Wilson_CI_ratio_2x2
  • MOVER_Wilson_score_CI_paired_2x2
  • Newcombe_hybrid_score_CI_2x2
  • Newcombe_square_and_add_CI_paired_2x2
  • Pearson_chi_squared_test_1xc(n, runif
  • Pearson_chi_squared_test_2x2
  • Pearson_chi_squared_test_CC_2x2
  • Pearson_correlation_coefficient_rxc_bca
  • Pearson_correlation_coefficient_rxc
  • Pearson_LR_homogeneity_test_stratified_2x2
  • Pearson_LR_test_common_effect_stratified_2x2
  • Pearson_LR_tests_cum_OR_2xc
  • Pearson_LR_tests_rxc
  • Pearson_LR_tests_unspecific_ordering_rx2
  • Pearson_residuals_rxc
  • Peto_homogeneity_test_stratified_2x2
  • Peto_OR_estimate_stratified_2x2
  • PriceBonett_approximate_Bayes_CI_2x2
  • QuesenberryHurst_Wilson_score_CIs_1xc
  • RBG_test_and_CI_stratified_2x2
  • Scheffe_type_CIs_paired_cxc
  • Scheffe_type_CIs_rxc
  • Score_test_1x2
  • Score_test_and_CI_marginal_mean_scores_paired_cxc
  • Score_test_CC_1x2
  • Score_test_for_effect_in_the_probit_model_2xc
  • Spearman_correlation_coefficient_rxc_bca
  • Spearman_correlation_coefficient_rxc
  • stratified_2x2_tables
  • Stuart_test_paired_cxc
  • Tang_asymptotic_score_CI_paired_2x2
  • Tango_asymptotic_score_CI_paired_2x2
  • the_1x2_table_CIs
  • the_1x2_table_tests
  • the_1xc_table_CIs
  • the_1xc_table_tests
  • the_2x2_table_CIs_difference
  • the_2x2_table_CIs_OR
  • the_2x2_table_CIs_ratio
  • the_2x2_table_tests
  • the_2xc_table
  • the_paired_2x2_table_CIs_difference
  • the_paired_2x2_table_CIs_OR
  • the_paired_2x2_table_CIs_ratio
  • the_paired_2x2_table_tests
  • the_paired_cxc_table_nominal
  • the_paired_cxc_table_ordinal
  • the_rx2_table
  • the_rxc_table
  • Transformed_Blaker_exact_CI_paired_2x2
  • Transformed_Clopper_Pearson_exact_CI_paired_2x2
  • Transformed_Clopper_Pearson_midP_CI_paired_2x2
  • Transformed_Wilson_score_CI_paired_2x2
  • Trend_estimate_CI_tests_rx2
  • Uncorrected_asymptotic_score_CI_2x2
  • Wald_CI_1x2
  • Wald_CI_2x2
  • Wald_CI_AgrestiMin_paired_2x2
  • Wald_CI_BonettPrice_paired_2x2
  • Wald_CI_CC_1x2
  • Wald_CI_CC_2x2
  • Wald_CI_diff_CC_paired_2x2
  • Wald_CI_diff_paired_2x2
  • Wald_CI_OR_Laplace_paired_2x2
  • Wald_CI_OR_paired_2x2
  • Wald_CI_ratio_paired_2x2
  • Wald_test_1x2
  • Wald_test_and_CI_common_diff_stratified_2x2
  • Wald_test_and_CI_common_ratio_stratified_2x2
  • Wald_test_and_CI_marginal_mean_ranks_paired_cxc
  • Wald_test_and_CI_marginal_mean_scores_paired_cxc
  • Wald_test_CC_1x2
  • Wilson_score_CI_1x2
  • Wilson_score_CI_CC_1x2
  • Woolf_logit_CI_2x2
  • Woolf_test_and_CI_stratified_2x2
  • Z_unpooled_test_2x2

A convenient way to work through the list is by using the https://github.com/ocbe-uio/contingencytables/blob/b0acdc14fd27c3616bf37d55ffab33d9b110c89b/tests/testthat/test-outputFormat.R file.
@wleoncio wleoncio added this to the MVP for 1.1.0 milestone Apr 21, 2022
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The test starting on this line hows the different outputs to be reduced.

contingencytables/tests/testthat/test-outputFormat.R

Line 17 in 475b52b

test_that("Output classes are the expected", {

@wleoncio wleoncio mentioned this issue Jun 14, 2022
Closed
wleoncio added a commit that referenced this issue Aug 24, 2022
@wleoncio
Renamed internal .print() to my_sprintf()
35e0465 
For descriptiveness sake; may also reduce confusion when #31 is worked on
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wleoncio commented Aug 24, 2022 •
edited

  • Change output of all functions to their own class
  • Create a print() method for this class, remember to output with invisible()
  • Supersede printresults argument

@wleoncio wleoncio self-assigned this Sep 1, 2022
wleoncio added a commit that referenced this issue Sep 1, 2022
@wleoncio
Improved output parsing on some functions (#31)
9bec466 
Functions now output an object of class contingencytables_output, a
method of which is created for `print()`. Unit tests are adapted
accordingly.
wleoncio added a commit that referenced this issue Sep 1, 2022
@wleoncio
Wrapping tests with print()
0b447dd 
Planning ahead for unit test breakage caused by further development of #31.
wleoncio added a commit that referenced this issue Sep 2, 2022
@wleoncio
Changed contingencytables_output structure (#31)
c4bf5c7 
This should accommodate different sets of output, since the class is defined (as best as S3 can, that is) as a list of `name` and `statistics`.
wleoncio added a commit that referenced this issue Sep 2, 2022
@wleoncio
Refactoring, test adjustments (#31)
1f90956
wleoncio added a commit that referenced this issue Sep 2, 2022
@wleoncio
Converted more function output classes (#31)
ca6e83a
wleoncio added a commit that referenced this issue Sep 2, 2022
@wleoncio
Added more tests for #31
e5b8f05
wleoncio added a commit that referenced this issue Sep 19, 2022
@wleoncio
Converted more function output classes (#31)
34023e1
wleoncio added a commit that referenced this issue Oct 28, 2022
@wleoncio
Added some more tests for #31
f96f972
wleoncio added a commit that referenced this issue Jan 18, 2023
@wleoncio
Changed superclass name (#31)
83e86b7 
In preparation for creation of subclasses to better organize printing methods
wleoncio added a commit that referenced this issue Jan 18, 2023
@wleoncio
Changing superclass into independent class (#31)
ed94bef 
On second though, it may be better to just have the two subclasses as their own thing. They can be grouped into a superclass if it makes sense, in the future.
wleoncio added a commit that referenced this issue Jan 18, 2023
@wleoncio
Created print method for *_multipletests class (#31)
f35a577
wleoncio added a commit that referenced this issue Jan 18, 2023
@wleoncio
Removed printresults from Cumulative_models_for_2xc (#31)
fe99333
wleoncio added a commit that referenced this issue Jan 18, 2023
@wleoncio
Replacing print() with cat() (#31)
08d6070
wleoncio added a commit that referenced this issue Jan 18, 2023
@wleoncio
Improved output of Cumulative_models_for_rxc (#31)
7cc9995
wleoncio added a commit that referenced this issue Jan 18, 2023
@wleoncio
Improved output of Exact_binomial_test_1x2 (#31)
11e4c60
wleoncio added a commit that referenced this issue Jan 19, 2023
@wleoncio
Improved output of Exact_cond_midP_linear_rank_tests_2xc() (#31)
3dd334b
wleoncio added a commit that referenced this issue Jan 19, 2023
@wleoncio
Fixed print method (#31)
44c43c6
wleoncio added a commit that referenced this issue Jan 19, 2023
@wleoncio
Added generator for package classes (#31)
233fd9a
wleoncio added a commit that referenced this issue Jan 19, 2023
@wleoncio
Adding default and shortened class_name (#31)
6ff5439
wleoncio added a commit that referenced this issue Jan 19, 2023
@wleoncio
Using class instantiator in functions (#31)
f70bbaa 
Saves one line per function, so around 160 lines in gross (120 net)
total.
wleoncio added a commit that referenced this issue Jan 19, 2023
@wleoncio
Improved output of Exact_cond_midP_tests_rxc (#31)
881cfda
wleoncio added a commit that referenced this issue Jan 19, 2023
@wleoncio
Improved output of Exact_cond_midP_unspecific_ordering_rx2 (#31)
d7b316d
wleoncio added a commit that referenced this issue Jan 19, 2023
@wleoncio
Improved output of Exact_cond_midP_unspecific_ordering_rx2 (#31)
5e37191 
New idea: giving the instantiator the same name as the class.
wleoncio added a commit that referenced this issue Jan 19, 2023
@wleoncio
Replacing _multiple class with _result (#31)
68bfcf4
wleoncio added a commit that referenced this issue Jan 19, 2023
@wleoncio
Replacing _single class with _result (#31)
00c60d5
wleoncio added a commit that referenced this issue Jan 20, 2023
@wleoncio
Removed superseded class, updated tests (#31)
3e5480f
@wleoncio wleoncio mentioned this issue Jan 20, 2023
Closed
wleoncio added a commit that referenced this issue Jan 20, 2023
@wleoncio
Removed legacy printresult args (#31)
8aadea4
wleoncio added a commit that referenced this issue Jan 20, 2023
@wleoncio
Standardized output of several functions (#31)
11c50c6 
Improved output of Exact_unconditional_test_2x2 (#31)

Improved output of Fisher exact and midP (#31)

Improved output of FisherFreemanHalton_asymptotic_test_rxc (#31)

Improved output of FleissEveritt_test_paired_cxc (#31)

Improved output of gamma_coefficient_rxc_bca (#31)

Improved output of gamma_coefficient_rxc (#31)

Improved output of Gart_adjusted_logit_CI_2x2 (#31)

Improved output of Gold_Wald_CIs_1xc (#31)

Improved output of Goodman_Wald_CIs_1xc (#31)

Improved output of Goodman_Wald_CIs_for_diffs_1xc (#31)

Improved output of Goodman_Wilson_score_CIs_1xc (#31)
@wleoncio wleoncio mentioned this issue Jan 20, 2023
Closed
wleoncio added a commit that referenced this issue Feb 20, 2023
@wleoncio
Standardized output of more functions (#31)
ca805f5
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We should try having the print format be an attribute. This way, we could retain backwards-compatibility because the statistics elements could be moved up I've level. As a bonus, the print format stays hidden (user doesn't care about it anyway).

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One potential issue to the above would be that we would end up with a class with a dynamic amount of attributes instead of the current standard in development. Might not be such a big deal, but something to briefly consider.

wleoncio added a commit that referenced this issue Feb 23, 2023
@wleoncio
Added new class (#31, #42)
4e91fc5 
Should supersede the previous one once things are a bit more mature. As
a proof-of-concept, applies the new class to a function. Working through the functions alfabetically will automatically resolve issue #42.
wleoncio added a commit that referenced this issue Feb 23, 2023
@wleoncio
Converted more functions to the newest class (#31, #42)
f5953f1
wleoncio added a commit that referenced this issue Feb 23, 2023
@wleoncio
Converted more function to the newest class (#31)
7c27b7d
wleoncio added a commit that referenced this issue Feb 24, 2023
@wleoncio
Migrated to newest class (#31)
42fc298
wleoncio added a commit that referenced this issue Feb 24, 2023
@wleoncio
Removed older class (#31)
d3e02f3
wleoncio added a commit that referenced this issue Apr 14, 2023
@wleoncio
Replaced my_sprintf() with cat() on aggregated tables (#31)
f767191
wleoncio added a commit that referenced this issue Apr 14, 2023
@wleoncio
Converted more functions to the newest class (#31)
40c2577
wleoncio added a commit that referenced this issue Apr 14, 2023
@wleoncio
Converted remaining functions to the newest class (#31)
dabc435
wleoncio added a commit that referenced this issue Apr 14, 2023
@wleoncio
Merge branch 'issue-31' into develop (solves #31)
ddd29ad
wleoncio added a commit that referenced this issue May 10, 2023
@wleoncio
Superseding fetch_print_format() (#31)
721570b
wleoncio added a commit that referenced this issue May 10, 2023
@wleoncio
Removed fetch_print_format() (#31)
4fe396b
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