Estimation statistics for categorical comparisons on a phyloseq object
Source:R/estim_pq.R
estim_diff_pq.RdComputes diversity metrics (Hill numbers by default) per sample and compares them across groups defined by a categorical variable using estimation statistics (effect sizes + bootstrap confidence intervals) via the dabestr package.
This approach replaces traditional p-value-based hypothesis testing with Gardner-Altman or Cumming estimation plots, following the estimation statistics framework (Ho et al. 2019).
Usage
estim_diff_pq(
physeq,
fact,
hill_scales = c(0, 1, 2),
custom_fn = NULL,
effect_type = "cohens_d",
idx = NULL,
ci = 95,
resamples = 5000,
na_remove = TRUE,
...
)Arguments
- physeq
(phyloseq, required) A phyloseq object.
- fact
(character, required) The name of a categorical column in
sample_datato use as the grouping factor.- hill_scales
(numeric vector, default
c(0, 1, 2)) The q values for Hill number computation: 0 = richness, 1 = Shannon exponential, 2 = inverse Simpson.- custom_fn
(function, default NULL) An optional custom diversity function. Must take a phyloseq object and return a named numeric vector (names = sample names) or a data.frame with one row per sample. If provided,
hill_scalesis ignored.- effect_type
(character, default
"mean_diff") The type of effect size to compute. One of:"mean_diff","median_diff","cohens_d","hedges_g","cliffs_delta".- idx
(list or character vector, default NULL) The group ordering for comparisons. If NULL, uses factor levels with first level as control. For 2 groups:
c("Control", "Treatment"). For 3+ groups:list(c("Ctrl", "T1", "T2")).- ci
(numeric, default 95) Confidence interval level (0-100).
- resamples
(integer, default 5000) Number of bootstrap resamples.
- na_remove
(logical, default TRUE) If TRUE, samples with NA in
factare removed before analysis.- ...
Additional arguments passed to dabestr plotting functions.
Value
A list of class "estim_diff_pq_result" with components:
- data
The diversity data.frame used for analysis
- dabest_objects
A named list of dabestr objects (one per metric)
- plots
A named list of dabestr plots (one per metric)
- summary
A tibble summarizing all effect sizes and CIs with columns:
metric,comparison,effect_size,ci_lower,ci_upper,pvalue_permtest,pvalue_welch,pvalue_mann_whitney- effect_type
The effect size type used
Details
The function uses the dabestr package to produce estimation
plots. For two groups, Gardner-Altman plots are produced
(float_contrast = TRUE). For three or more groups, Cumming plots are
used (float_contrast = FALSE).
References
Ho, J., Tumkaya, T., Aryal, S., Choi, H., & Claridge-Chang, A. (2019). Moving beyond P values: data analysis with estimation graphics. Nature Methods, 16(7), 565-566.
Examples
library(phyloseq)
data("data_fungi", package = "MiscMetabar")
pq <- subset_samples(data_fungi, !is.na(Height))
pq <- clean_pq(pq)
#> Cleaning suppress 144 taxa and 0 samples.
res <- estim_diff_pq(pq, fact = "Height")
res
#> $data
#> Hill_0 Hill_1 Hill_2
#> A10-005-B_S188_MERGED.fastq.gz 67 7.967879 3.177791
#> A10-005-H_S189_MERGED.fastq.gz 70 2.701628 1.908759
#> A10-005-M_S190_MERGED.fastq.gz 54 18.735415 13.172882
#> A12-007-B_S2_MERGED.fastq.gz 47 8.918381 5.224328
#> AB29-ABMX-H_S6_MERGED.fastq.gz 70 10.225479 5.504729
#> AD26-005-B_S9_MERGED.fastq.gz 150 8.934307 3.358402
#> AD26-005-H_S10_MERGED.fastq.gz 110 4.931153 2.385448
#> AD26-005-M_S11_MERGED.fastq.gz 125 27.640250 16.450947
#> AD30-ABMX-M_S12_MERGED.fastq.gz 61 8.148864 4.476903
#> AD32-007-M_S13_MERGED.fastq.gz 101 8.391872 3.323816
#> ADABM30X-B_S14_MERGED.fastq.gz 90 15.230481 10.761130
#> ADABM30X-H_S15_MERGED.fastq.gz 132 17.895618 10.730501
#> ADABM30X-M_S16_MERGED.fastq.gz 63 11.336162 6.831980
#> B18-006-B_S19_MERGED.fastq.gz 30 4.579201 2.462089
#> BA17-050-B_S21_MERGED.fastq.gz 162 14.968563 7.461988
#> BB19-006-H_S22_MERGED.fastq.gz 131 8.238795 4.533925
#> BB6-019-B_S23_MERGED.fastq.gz 88 6.009367 3.163064
#> BB6-019-H_S24_MERGED.fastq.gz 119 7.119430 2.622819
#> BB6-019-M_S25_MERGED.fastq.gz 88 25.769213 15.059862
#> BE9-006-B_S27_MERGED.fastq.gz 17 5.795489 3.344332
#> BE9-006-H_S28_MERGED.fastq.gz 11 5.501697 3.711273
#> BE9-006-M_S29_MERGED.fastq.gz 22 11.412889 8.606762
#> BG7-010-B_S30_MERGED.fastq.gz 39 15.258149 6.577062
#> BG7-010-H_S31_MERGED.fastq.gz 86 11.098284 4.417107
#> BG7-010-M_S32_MERGED.fastq.gz 52 15.365859 6.605331
#> BJ17-007-M_S34_MERGED.fastq.gz 158 10.857994 5.787965
#> BL7-006-B_S36_MERGED.fastq.gz 63 18.708521 6.979186
#> BL7-006-H_S37_MERGED.fastq.gz 50 22.572352 10.972762
#> BL7-006-M_S38_MERGED.fastq.gz 36 16.925041 9.666779
#> BP11-001-B_S43_MERGED.fastq.gz 84 6.626587 3.173056
#> BP11-001-H_S44_MERGED.fastq.gz 119 8.063167 2.946433
#> BP11-001-M_S45_MERGED.fastq.gz 73 3.914861 1.957519
#> BP12-025-B_S46_MERGED.fastq.gz 56 7.776651 4.052291
#> BQ4-018-B_S49_MERGED.fastq.gz 163 7.997291 4.608135
#> BQ4-018-H_S50_MERGED.fastq.gz 72 9.181735 4.824880
#> BQ4-018-M_S51_MERGED.fastq.gz 156 16.097605 8.275389
#> BT-006-M_S55_MERGED.fastq.gz 61 9.672663 5.999040
#> BV11-002-B_S57_MERGED.fastq.gz 98 6.944072 4.873753
#> BV11-002-H_S58_MERGED.fastq.gz 179 13.800674 5.592337
#> BV11-002-M_S59_MERGED.fastq.gz 76 11.799149 7.391348
#> C21-NV1-B_S62_MERGED.fastq.gz 35 11.286637 5.932252
#> C21-NV1-H_S63_MERGED.fastq.gz 73 6.527443 2.620203
#> C21-NV1-M_S64_MERGED.fastq.gz 8 2.866495 1.772771
#> CB8-019-B_S69_MERGED.fastq.gz 16 11.706178 8.812950
#> CB8-019-H_S70_MERGED.fastq.gz 33 1.397644 1.109174
#> CB8-019-M_S71_MERGED.fastq.gz 20 3.894227 2.051775
#> D18-003-B_S78_MERGED.fastq.gz 66 9.631651 5.428374
#> D18-003-H_S79_MERGED.fastq.gz 87 2.659561 1.478776
#> D18-003-M_S80_MERGED.fastq.gz 88 9.906082 4.506529
#> D61-010-B_S82_MERGED.fastq.gz 21 1.524569 1.214513
#> D9-027-B_S83_MERGED.fastq.gz 99 19.433579 7.589108
#> D9-027-H_S84_MERGED.fastq.gz 84 12.646257 6.675085
#> D9-027-M_S85_MERGED.fastq.gz 111 24.089806 9.609966
#> DJ2-008-B_S87_MERGED.fastq.gz 29 7.607661 4.461234
#> DJ2-008-H_S88_MERGED.fastq.gz 34 16.691044 11.587030
#> DJ2-008-M_S89_MERGED.fastq.gz 50 5.454623 2.292853
#> DS1-ABM002-B_S91_MERGED.fastq.gz 77 7.417789 3.083001
#> DS1-ABM002-H_S92_MERGED.fastq.gz 43 3.466204 2.269978
#> DS1-ABM002-M_S93_MERGED.fastq.gz 132 18.528548 10.705628
#> DU3-045-B_S94_MERGED.fastq.gz 134 15.427321 7.151758
#> DY5-004-B_S96_MERGED.fastq.gz 61 7.040679 3.558646
#> DY5-004-H_S97_MERGED.fastq.gz 27 2.638123 1.663783
#> DY5-004-M_S98_MERGED.fastq.gz 19 4.699036 2.188861
#> E9-009-B_S100_MERGED.fastq.gz 21 17.723121 15.144144
#> E9-009-H_S101_MERGED.fastq.gz 20 14.639441 12.096774
#> E9-009-M_S102_MERGED.fastq.gz 25 2.707789 1.585136
#> EC2-013-B_S104_MERGED.fastq.gz 89 2.935296 1.535002
#> F7-015-M_S106_MERGED.fastq.gz 52 6.853456 3.521697
#> FOMES19-H_S108_MERGED.fastq.gz 23 1.558617 1.197679
#> FOMES19-M_S109_MERGED.fastq.gz 21 1.480968 1.160913
#> H10-018-M_S110_MERGED.fastq.gz 4 1.016264 1.003876
#> H24-NVABM1-H_S111_MERGED.fastq.gz 62 14.250086 6.975467
#> J18-004-B_S114_MERGED.fastq.gz 21 13.693906 10.157100
#> J18-004-H_S115_MERGED.fastq.gz 47 5.330861 3.285425
#> J18-004-M_S116_MERGED.fastq.gz 34 14.097513 8.876414
#> K18-002-H_S117_MERGED.fastq.gz 74 1.635048 1.171398
#> L19X-B_S119_MERGED.fastq.gz 46 19.456407 12.677086
#> L19X-H_S120_MERGED.fastq.gz 93 13.777911 7.445490
#> L19X-M_S121_MERGED.fastq.gz 84 9.310051 5.264056
#> L23-002-B_S122_MERGED.fastq.gz 147 17.929015 6.462027
#> L23-002-H_S123_MERGED.fastq.gz 55 10.557775 6.035842
#> L23-002-M_S124_MERGED.fastq.gz 27 3.268428 2.469693
#> N19X-B_S126_MERGED.fastq.gz 34 14.626454 7.827476
#> N19X-H_S127_MERGED.fastq.gz 194 18.968399 7.731261
#> N19X-M_S128_MERGED.fastq.gz 113 22.360256 11.184175
#> N22-001-B_S129_MERGED.fastq.gz 4 2.790604 2.314286
#> N23-002-B_S130_MERGED.fastq.gz 135 1.667228 1.165840
#> N23-002-H_S131_MERGED.fastq.gz 74 13.579320 7.933936
#> N23-002-M_S132_MERGED.fastq.gz 3 2.021246 1.750455
#> NVABM-0163-H_S135_MERGED.fastq.gz 79 9.891670 3.980326
#> X
#> A10-005-B_S188_MERGED.fastq.gz A10-005-B_S188_MERGED.fastq.gz
#> A10-005-H_S189_MERGED.fastq.gz A10-005-H_S189_MERGED.fastq.gz
#> A10-005-M_S190_MERGED.fastq.gz A10-005-M_S190_MERGED.fastq.gz
#> A12-007-B_S2_MERGED.fastq.gz A12-007-B_S2_MERGED.fastq.gz
#> AB29-ABMX-H_S6_MERGED.fastq.gz AB29-ABMX-H_S6_MERGED.fastq.gz
#> AD26-005-B_S9_MERGED.fastq.gz AD26-005-B_S9_MERGED.fastq.gz
#> AD26-005-H_S10_MERGED.fastq.gz AD26-005-H_S10_MERGED.fastq.gz
#> AD26-005-M_S11_MERGED.fastq.gz AD26-005-M_S11_MERGED.fastq.gz
#> AD30-ABMX-M_S12_MERGED.fastq.gz AD30-ABMX-M_S12_MERGED.fastq.gz
#> AD32-007-M_S13_MERGED.fastq.gz AD32-007-M_S13_MERGED.fastq.gz
#> ADABM30X-B_S14_MERGED.fastq.gz ADABM30X-B_S14_MERGED.fastq.gz
#> ADABM30X-H_S15_MERGED.fastq.gz ADABM30X-H_S15_MERGED.fastq.gz
#> ADABM30X-M_S16_MERGED.fastq.gz ADABM30X-M_S16_MERGED.fastq.gz
#> B18-006-B_S19_MERGED.fastq.gz B18-006-B_S19_MERGED.fastq.gz
#> BA17-050-B_S21_MERGED.fastq.gz BA17-050-B_S21_MERGED.fastq.gz
#> BB19-006-H_S22_MERGED.fastq.gz BB19-006-H_S22_MERGED.fastq.gz
#> BB6-019-B_S23_MERGED.fastq.gz BB6-019-B_S23_MERGED.fastq.gz
#> BB6-019-H_S24_MERGED.fastq.gz BB6-019-H_S24_MERGED.fastq.gz
#> BB6-019-M_S25_MERGED.fastq.gz BB6-019-M_S25_MERGED.fastq.gz
#> BE9-006-B_S27_MERGED.fastq.gz BE9-006-B_S27_MERGED.fastq.gz
#> BE9-006-H_S28_MERGED.fastq.gz BE9-006-H_S28_MERGED.fastq.gz
#> BE9-006-M_S29_MERGED.fastq.gz BE9-006-M_S29_MERGED.fastq.gz
#> BG7-010-B_S30_MERGED.fastq.gz BG7-010-B_S30_MERGED.fastq.gz
#> BG7-010-H_S31_MERGED.fastq.gz BG7-010-H_S31_MERGED.fastq.gz
#> BG7-010-M_S32_MERGED.fastq.gz BG7-010-M_S32_MERGED.fastq.gz
#> BJ17-007-M_S34_MERGED.fastq.gz BJ17-007-M_S34_MERGED.fastq.gz
#> BL7-006-B_S36_MERGED.fastq.gz BL7-006-B_S36_MERGED.fastq.gz
#> BL7-006-H_S37_MERGED.fastq.gz BL7-006-H_S37_MERGED.fastq.gz
#> BL7-006-M_S38_MERGED.fastq.gz BL7-006-M_S38_MERGED.fastq.gz
#> BP11-001-B_S43_MERGED.fastq.gz BP11-001-B_S43_MERGED.fastq.gz
#> BP11-001-H_S44_MERGED.fastq.gz BP11-001-H_S44_MERGED.fastq.gz
#> BP11-001-M_S45_MERGED.fastq.gz BP11-001-M_S45_MERGED.fastq.gz
#> BP12-025-B_S46_MERGED.fastq.gz BP12-025-B_S46_MERGED.fastq.gz
#> BQ4-018-B_S49_MERGED.fastq.gz BQ4-018-B_S49_MERGED.fastq.gz
#> BQ4-018-H_S50_MERGED.fastq.gz BQ4-018-H_S50_MERGED.fastq.gz
#> BQ4-018-M_S51_MERGED.fastq.gz BQ4-018-M_S51_MERGED.fastq.gz
#> BT-006-M_S55_MERGED.fastq.gz BT-006-M_S55_MERGED.fastq.gz
#> BV11-002-B_S57_MERGED.fastq.gz BV11-002-B_S57_MERGED.fastq.gz
#> BV11-002-H_S58_MERGED.fastq.gz BV11-002-H_S58_MERGED.fastq.gz
#> BV11-002-M_S59_MERGED.fastq.gz BV11-002-M_S59_MERGED.fastq.gz
#> C21-NV1-B_S62_MERGED.fastq.gz C21-NV1-B_S62_MERGED.fastq.gz
#> C21-NV1-H_S63_MERGED.fastq.gz C21-NV1-H_S63_MERGED.fastq.gz
#> C21-NV1-M_S64_MERGED.fastq.gz C21-NV1-M_S64_MERGED.fastq.gz
#> CB8-019-B_S69_MERGED.fastq.gz CB8-019-B_S69_MERGED.fastq.gz
#> CB8-019-H_S70_MERGED.fastq.gz CB8-019-H_S70_MERGED.fastq.gz
#> CB8-019-M_S71_MERGED.fastq.gz CB8-019-M_S71_MERGED.fastq.gz
#> D18-003-B_S78_MERGED.fastq.gz D18-003-B_S78_MERGED.fastq.gz
#> D18-003-H_S79_MERGED.fastq.gz D18-003-H_S79_MERGED.fastq.gz
#> D18-003-M_S80_MERGED.fastq.gz D18-003-M_S80_MERGED.fastq.gz
#> D61-010-B_S82_MERGED.fastq.gz D61-010-B_S82_MERGED.fastq.gz
#> D9-027-B_S83_MERGED.fastq.gz D9-027-B_S83_MERGED.fastq.gz
#> D9-027-H_S84_MERGED.fastq.gz D9-027-H_S84_MERGED.fastq.gz
#> D9-027-M_S85_MERGED.fastq.gz D9-027-M_S85_MERGED.fastq.gz
#> DJ2-008-B_S87_MERGED.fastq.gz DJ2-008-B_S87_MERGED.fastq.gz
#> DJ2-008-H_S88_MERGED.fastq.gz DJ2-008-H_S88_MERGED.fastq.gz
#> DJ2-008-M_S89_MERGED.fastq.gz DJ2-008-M_S89_MERGED.fastq.gz
#> DS1-ABM002-B_S91_MERGED.fastq.gz DS1-ABM002-B_S91_MERGED.fastq.gz
#> DS1-ABM002-H_S92_MERGED.fastq.gz DS1-ABM002-H_S92_MERGED.fastq.gz
#> DS1-ABM002-M_S93_MERGED.fastq.gz DS1-ABM002-M_S93_MERGED.fastq.gz
#> DU3-045-B_S94_MERGED.fastq.gz DU3-045-B_S94_MERGED.fastq.gz
#> DY5-004-B_S96_MERGED.fastq.gz DY5-004-B_S96_MERGED.fastq.gz
#> DY5-004-H_S97_MERGED.fastq.gz DY5-004-H_S97_MERGED.fastq.gz
#> DY5-004-M_S98_MERGED.fastq.gz DY5-004-M_S98_MERGED.fastq.gz
#> E9-009-B_S100_MERGED.fastq.gz E9-009-B_S100_MERGED.fastq.gz
#> E9-009-H_S101_MERGED.fastq.gz E9-009-H_S101_MERGED.fastq.gz
#> E9-009-M_S102_MERGED.fastq.gz E9-009-M_S102_MERGED.fastq.gz
#> EC2-013-B_S104_MERGED.fastq.gz EC2-013-B_S104_MERGED.fastq.gz
#> F7-015-M_S106_MERGED.fastq.gz F7-015-M_S106_MERGED.fastq.gz
#> FOMES19-H_S108_MERGED.fastq.gz FOMES19-H_S108_MERGED.fastq.gz
#> FOMES19-M_S109_MERGED.fastq.gz FOMES19-M_S109_MERGED.fastq.gz
#> H10-018-M_S110_MERGED.fastq.gz H10-018-M_S110_MERGED.fastq.gz
#> H24-NVABM1-H_S111_MERGED.fastq.gz H24-NVABM1-H_S111_MERGED.fastq.gz
#> J18-004-B_S114_MERGED.fastq.gz J18-004-B_S114_MERGED.fastq.gz
#> J18-004-H_S115_MERGED.fastq.gz J18-004-H_S115_MERGED.fastq.gz
#> J18-004-M_S116_MERGED.fastq.gz J18-004-M_S116_MERGED.fastq.gz
#> K18-002-H_S117_MERGED.fastq.gz K18-002-H_S117_MERGED.fastq.gz
#> L19X-B_S119_MERGED.fastq.gz L19X-B_S119_MERGED.fastq.gz
#> L19X-H_S120_MERGED.fastq.gz L19X-H_S120_MERGED.fastq.gz
#> L19X-M_S121_MERGED.fastq.gz L19X-M_S121_MERGED.fastq.gz
#> L23-002-B_S122_MERGED.fastq.gz L23-002-B_S122_MERGED.fastq.gz
#> L23-002-H_S123_MERGED.fastq.gz L23-002-H_S123_MERGED.fastq.gz
#> L23-002-M_S124_MERGED.fastq.gz L23-002-M_S124_MERGED.fastq.gz
#> N19X-B_S126_MERGED.fastq.gz N19X-B_S126_MERGED.fastq.gz
#> N19X-H_S127_MERGED.fastq.gz N19X-H_S127_MERGED.fastq.gz
#> N19X-M_S128_MERGED.fastq.gz N19X-M_S128_MERGED.fastq.gz
#> N22-001-B_S129_MERGED.fastq.gz N22-001-B_S129_MERGED.fastq.gz
#> N23-002-B_S130_MERGED.fastq.gz N23-002-B_S130_MERGED.fastq.gz
#> N23-002-H_S131_MERGED.fastq.gz N23-002-H_S131_MERGED.fastq.gz
#> N23-002-M_S132_MERGED.fastq.gz N23-002-M_S132_MERGED.fastq.gz
#> NVABM-0163-H_S135_MERGED.fastq.gz NVABM-0163-H_S135_MERGED.fastq.gz
#> Sample_names Tree_name Sample_id
#> A10-005-B_S188_MERGED.fastq.gz A10-005-B_S188 A10-005 188
#> A10-005-H_S189_MERGED.fastq.gz A10-005-H_S189 A10-005 189
#> A10-005-M_S190_MERGED.fastq.gz A10-005-M_S190 A10-005 190
#> A12-007-B_S2_MERGED.fastq.gz A12-007-B_S2 A12-007 2
#> AB29-ABMX-H_S6_MERGED.fastq.gz AB29-ABMX-H_S6 AB29-abm-X 6
#> AD26-005-B_S9_MERGED.fastq.gz AD26-005-B_S9 AD26-005 9
#> AD26-005-H_S10_MERGED.fastq.gz AD26-005-H_S10 AD26-005 10
#> AD26-005-M_S11_MERGED.fastq.gz AD26-005-M_S11 AD26-005 11
#> AD30-ABMX-M_S12_MERGED.fastq.gz AD30-ABMX-M_S12 AD30-abm-X 12
#> AD32-007-M_S13_MERGED.fastq.gz AD32-007-M_S13 AD32-007 13
#> ADABM30X-B_S14_MERGED.fastq.gz ADABM30X-B_S14 AD30-abm-X 14
#> ADABM30X-H_S15_MERGED.fastq.gz ADABM30X-H_S15 AD30-abm-X 15
#> ADABM30X-M_S16_MERGED.fastq.gz ADABM30X-M_S16 AD30-abm-X 16
#> B18-006-B_S19_MERGED.fastq.gz B18-006-B_S19 B18-006 19
#> BA17-050-B_S21_MERGED.fastq.gz BA17-050-B_S21 BA17-050 21
#> BB19-006-H_S22_MERGED.fastq.gz BB19-006-H_S22 BB19-006 22
#> BB6-019-B_S23_MERGED.fastq.gz BB6-019-B_S23 BB6-019 23
#> BB6-019-H_S24_MERGED.fastq.gz BB6-019-H_S24 BB6-019 24
#> BB6-019-M_S25_MERGED.fastq.gz BB6-019-M_S25 BB6-019 25
#> BE9-006-B_S27_MERGED.fastq.gz BE9-006-B_S27 BE9-006 27
#> BE9-006-H_S28_MERGED.fastq.gz BE9-006-H_S28 BE9-006 28
#> BE9-006-M_S29_MERGED.fastq.gz BE9-006-M_S29 BE9-006 29
#> BG7-010-B_S30_MERGED.fastq.gz BG7-010-B_S30 BG7-010 30
#> BG7-010-H_S31_MERGED.fastq.gz BG7-010-H_S31 BG7-010 31
#> BG7-010-M_S32_MERGED.fastq.gz BG7-010-M_S32 BG7-010 32
#> BJ17-007-M_S34_MERGED.fastq.gz BJ17-007-M_S34 BJ17-007 34
#> BL7-006-B_S36_MERGED.fastq.gz BL7-006-B_S36 BL7-006 36
#> BL7-006-H_S37_MERGED.fastq.gz BL7-006-H_S37 BL7-006 37
#> BL7-006-M_S38_MERGED.fastq.gz BL7-006-M_S38 BL7-006 38
#> BP11-001-B_S43_MERGED.fastq.gz BP11-001-B_S43 BP11-001 43
#> BP11-001-H_S44_MERGED.fastq.gz BP11-001-H_S44 BP11-001 44
#> BP11-001-M_S45_MERGED.fastq.gz BP11-001-M_S45 BP11-001 45
#> BP12-025-B_S46_MERGED.fastq.gz BP12-025-B_S46 BP12-025 46
#> BQ4-018-B_S49_MERGED.fastq.gz BQ4-018-B_S49 BQ4-018 49
#> BQ4-018-H_S50_MERGED.fastq.gz BQ4-018-H_S50 BQ4-018 50
#> BQ4-018-M_S51_MERGED.fastq.gz BQ4-018-M_S51 BQ4-018 51
#> BT-006-M_S55_MERGED.fastq.gz BT-006-M_S55 BT7-006 55
#> BV11-002-B_S57_MERGED.fastq.gz BV11-002-B_S57 BU11-002 57
#> BV11-002-H_S58_MERGED.fastq.gz BV11-002-H_S58 BU11-002 58
#> BV11-002-M_S59_MERGED.fastq.gz BV11-002-M_S59 BU11-002 59
#> C21-NV1-B_S62_MERGED.fastq.gz C21-NV1-B_S62 C21-nv-1 62
#> C21-NV1-H_S63_MERGED.fastq.gz C21-NV1-H_S63 C21-nv-1 63
#> C21-NV1-M_S64_MERGED.fastq.gz C21-NV1-M_S64 C21-nv-1 64
#> CB8-019-B_S69_MERGED.fastq.gz CB8-019-B_S69 CB8-019 69
#> CB8-019-H_S70_MERGED.fastq.gz CB8-019-H_S70 CB8-019 70
#> CB8-019-M_S71_MERGED.fastq.gz CB8-019-M_S71 CB8-019 71
#> D18-003-B_S78_MERGED.fastq.gz D18-003-B_S78 D18-003 78
#> D18-003-H_S79_MERGED.fastq.gz D18-003-H_S79 D18-003 79
#> D18-003-M_S80_MERGED.fastq.gz D18-003-M_S80 D18-003 80
#> D61-010-B_S82_MERGED.fastq.gz D61-010-B_S82 DG1-010 82
#> D9-027-B_S83_MERGED.fastq.gz D9-027-B_S83 D9-027 83
#> D9-027-H_S84_MERGED.fastq.gz D9-027-H_S84 D9-027 84
#> D9-027-M_S85_MERGED.fastq.gz D9-027-M_S85 D9-027 85
#> DJ2-008-B_S87_MERGED.fastq.gz DJ2-008-B_S87 DJ2-008 87
#> DJ2-008-H_S88_MERGED.fastq.gz DJ2-008-H_S88 DJ2-008 88
#> DJ2-008-M_S89_MERGED.fastq.gz DJ2-008-M_S89 DJ2-008 89
#> DS1-ABM002-B_S91_MERGED.fastq.gz DS1-ABM002-B_S91 DS1abm002 91
#> DS1-ABM002-H_S92_MERGED.fastq.gz DS1-ABM002-H_S92 DS1abm002 92
#> DS1-ABM002-M_S93_MERGED.fastq.gz DS1-ABM002-M_S93 DS1abm002 93
#> DU3-045-B_S94_MERGED.fastq.gz DU3-045-B_S94 DU3-045 94
#> DY5-004-B_S96_MERGED.fastq.gz DY5-004-B_S96 DY5-004 96
#> DY5-004-H_S97_MERGED.fastq.gz DY5-004-H_S97 DY5-004 97
#> DY5-004-M_S98_MERGED.fastq.gz DY5-004-M_S98 DY5-004 98
#> E9-009-B_S100_MERGED.fastq.gz E9-009-B_S100 E9-009 100
#> E9-009-H_S101_MERGED.fastq.gz E9-009-H_S101 E9-009 101
#> E9-009-M_S102_MERGED.fastq.gz E9-009-M_S102 E9-009 102
#> EC2-013-B_S104_MERGED.fastq.gz EC2-013-B_S104 EC2-013 104
#> F7-015-M_S106_MERGED.fastq.gz F7-015-M_S106 F7-015 106
#> FOMES19-H_S108_MERGED.fastq.gz FOMES19-H_S108 FOMES19 108
#> FOMES19-M_S109_MERGED.fastq.gz FOMES19-M_S109 FOMES19 109
#> H10-018-M_S110_MERGED.fastq.gz H10-018-M_S110 H10-018 110
#> H24-NVABM1-H_S111_MERGED.fastq.gz H24-NVABM1-H_S111 H24-nvabm-1 111
#> J18-004-B_S114_MERGED.fastq.gz J18-004-B_S114 J18-004 114
#> J18-004-H_S115_MERGED.fastq.gz J18-004-H_S115 J18-004 115
#> J18-004-M_S116_MERGED.fastq.gz J18-004-M_S116 J18-004 116
#> K18-002-H_S117_MERGED.fastq.gz K18-002-H_S117 K18-002 117
#> L19X-B_S119_MERGED.fastq.gz L19X-B_S119 L19-X 119
#> L19X-H_S120_MERGED.fastq.gz L19X-H_S120 L19-X 120
#> L19X-M_S121_MERGED.fastq.gz L19X-M_S121 L19-X 121
#> L23-002-B_S122_MERGED.fastq.gz L23-002-B_S122 L23-002 122
#> L23-002-H_S123_MERGED.fastq.gz L23-002-H_S123 L23-002 123
#> L23-002-M_S124_MERGED.fastq.gz L23-002-M_S124 L23-002 124
#> N19X-B_S126_MERGED.fastq.gz N19X-B_S126 N19-X 126
#> N19X-H_S127_MERGED.fastq.gz N19X-H_S127 N19-X 127
#> N19X-M_S128_MERGED.fastq.gz N19X-M_S128 N19-X 128
#> N22-001-B_S129_MERGED.fastq.gz N22-001-B_S129 M22-001 129
#> N23-002-B_S130_MERGED.fastq.gz N23-002-B_S130 N23-002 130
#> N23-002-H_S131_MERGED.fastq.gz N23-002-H_S131 N23-002 131
#> N23-002-M_S132_MERGED.fastq.gz N23-002-M_S132 N23-002 132
#> NVABM-0163-H_S135_MERGED.fastq.gz NVABM-0163-H_S135 nvabm0163 135
#> Height Diameter Time
#> A10-005-B_S188_MERGED.fastq.gz Low 52 15
#> A10-005-H_S189_MERGED.fastq.gz High 52 15
#> A10-005-M_S190_MERGED.fastq.gz Middle 52 15
#> A12-007-B_S2_MERGED.fastq.gz Low 28,4 0
#> AB29-ABMX-H_S6_MERGED.fastq.gz High 99 5
#> AD26-005-B_S9_MERGED.fastq.gz Low 115,5 15
#> AD26-005-H_S10_MERGED.fastq.gz High 115,5 15
#> AD26-005-M_S11_MERGED.fastq.gz Middle 115,5 15
#> AD30-ABMX-M_S12_MERGED.fastq.gz Middle - 5
#> AD32-007-M_S13_MERGED.fastq.gz Middle 52 NA
#> ADABM30X-B_S14_MERGED.fastq.gz Low - 5
#> ADABM30X-H_S15_MERGED.fastq.gz High - 5
#> ADABM30X-M_S16_MERGED.fastq.gz Middle - 5
#> B18-006-B_S19_MERGED.fastq.gz Low 32,5 10
#> BA17-050-B_S21_MERGED.fastq.gz Low 30 10
#> BB19-006-H_S22_MERGED.fastq.gz High 37,5 15
#> BB6-019-B_S23_MERGED.fastq.gz Low 33,8 5
#> BB6-019-H_S24_MERGED.fastq.gz High 33,8 5
#> BB6-019-M_S25_MERGED.fastq.gz Middle 33,8 5
#> BE9-006-B_S27_MERGED.fastq.gz Low 23,1 0
#> BE9-006-H_S28_MERGED.fastq.gz High 23,1 0
#> BE9-006-M_S29_MERGED.fastq.gz Middle 23,1 0
#> BG7-010-B_S30_MERGED.fastq.gz Low 32 0
#> BG7-010-H_S31_MERGED.fastq.gz High 32 0
#> BG7-010-M_S32_MERGED.fastq.gz Middle 32 0
#> BJ17-007-M_S34_MERGED.fastq.gz Middle 32 5
#> BL7-006-B_S36_MERGED.fastq.gz Low 35,6 0
#> BL7-006-H_S37_MERGED.fastq.gz High 35,6 0
#> BL7-006-M_S38_MERGED.fastq.gz Middle 35,6 0
#> BP11-001-B_S43_MERGED.fastq.gz Low 47,5 15
#> BP11-001-H_S44_MERGED.fastq.gz High 47,5 15
#> BP11-001-M_S45_MERGED.fastq.gz Middle 47,5 15
#> BP12-025-B_S46_MERGED.fastq.gz Low 64,5 10
#> BQ4-018-B_S49_MERGED.fastq.gz Low 34 0
#> BQ4-018-H_S50_MERGED.fastq.gz High 34 0
#> BQ4-018-M_S51_MERGED.fastq.gz Middle 34 0
#> BT-006-M_S55_MERGED.fastq.gz Middle 41 0
#> BV11-002-B_S57_MERGED.fastq.gz Low 33 5
#> BV11-002-H_S58_MERGED.fastq.gz High 33 5
#> BV11-002-M_S59_MERGED.fastq.gz Middle 33 5
#> C21-NV1-B_S62_MERGED.fastq.gz Low 30 0
#> C21-NV1-H_S63_MERGED.fastq.gz High 30 0
#> C21-NV1-M_S64_MERGED.fastq.gz Middle 30 0
#> CB8-019-B_S69_MERGED.fastq.gz Low 33,3 0
#> CB8-019-H_S70_MERGED.fastq.gz High 33,3 0
#> CB8-019-M_S71_MERGED.fastq.gz Middle 33,3 0
#> D18-003-B_S78_MERGED.fastq.gz Low 45,5 5
#> D18-003-H_S79_MERGED.fastq.gz High 45,5 5
#> D18-003-M_S80_MERGED.fastq.gz Middle 45,5 5
#> D61-010-B_S82_MERGED.fastq.gz Low 36,3 15
#> D9-027-B_S83_MERGED.fastq.gz Low 18,9 NA
#> D9-027-H_S84_MERGED.fastq.gz High 18,9 NA
#> D9-027-M_S85_MERGED.fastq.gz Middle 18,9 NA
#> DJ2-008-B_S87_MERGED.fastq.gz Low 76,4 0
#> DJ2-008-H_S88_MERGED.fastq.gz High 76,4 0
#> DJ2-008-M_S89_MERGED.fastq.gz Middle 76,4 0
#> DS1-ABM002-B_S91_MERGED.fastq.gz Low 25 15
#> DS1-ABM002-H_S92_MERGED.fastq.gz High 25 15
#> DS1-ABM002-M_S93_MERGED.fastq.gz Middle 25 15
#> DU3-045-B_S94_MERGED.fastq.gz Low 38 15
#> DY5-004-B_S96_MERGED.fastq.gz Low 60,4 0
#> DY5-004-H_S97_MERGED.fastq.gz High 60,4 0
#> DY5-004-M_S98_MERGED.fastq.gz Middle 60,4 0
#> E9-009-B_S100_MERGED.fastq.gz Low 29,5 0
#> E9-009-H_S101_MERGED.fastq.gz High 29,5 0
#> E9-009-M_S102_MERGED.fastq.gz Middle 29,5 0
#> EC2-013-B_S104_MERGED.fastq.gz Low 52 15
#> F7-015-M_S106_MERGED.fastq.gz Middle 50 10
#> FOMES19-H_S108_MERGED.fastq.gz High <NA> NA
#> FOMES19-M_S109_MERGED.fastq.gz Middle <NA> NA
#> H10-018-M_S110_MERGED.fastq.gz Middle 88,5 15
#> H24-NVABM1-H_S111_MERGED.fastq.gz High 30 5
#> J18-004-B_S114_MERGED.fastq.gz Low 27,6 0
#> J18-004-H_S115_MERGED.fastq.gz High 27,6 0
#> J18-004-M_S116_MERGED.fastq.gz Middle 27,6 0
#> K18-002-H_S117_MERGED.fastq.gz High 33,5 10
#> L19X-B_S119_MERGED.fastq.gz Low 30 NA
#> L19X-H_S120_MERGED.fastq.gz High 30 NA
#> L19X-M_S121_MERGED.fastq.gz Middle 30 NA
#> L23-002-B_S122_MERGED.fastq.gz Low 40,5 10
#> L23-002-H_S123_MERGED.fastq.gz High 40,5 10
#> L23-002-M_S124_MERGED.fastq.gz Middle 40,5 10
#> N19X-B_S126_MERGED.fastq.gz Low 33,5 NA
#> N19X-H_S127_MERGED.fastq.gz High 33,5 NA
#> N19X-M_S128_MERGED.fastq.gz Middle 33,5 NA
#> N22-001-B_S129_MERGED.fastq.gz Low 34 0
#> N23-002-B_S130_MERGED.fastq.gz Low 21,5 15
#> N23-002-H_S131_MERGED.fastq.gz High 21,5 15
#> N23-002-M_S132_MERGED.fastq.gz Middle 21,5 15
#> NVABM-0163-H_S135_MERGED.fastq.gz High 40 10
#> .sample_id
#> A10-005-B_S188_MERGED.fastq.gz A10-005-B_S188_MERGED.fastq.gz
#> A10-005-H_S189_MERGED.fastq.gz A10-005-H_S189_MERGED.fastq.gz
#> A10-005-M_S190_MERGED.fastq.gz A10-005-M_S190_MERGED.fastq.gz
#> A12-007-B_S2_MERGED.fastq.gz A12-007-B_S2_MERGED.fastq.gz
#> AB29-ABMX-H_S6_MERGED.fastq.gz AB29-ABMX-H_S6_MERGED.fastq.gz
#> AD26-005-B_S9_MERGED.fastq.gz AD26-005-B_S9_MERGED.fastq.gz
#> AD26-005-H_S10_MERGED.fastq.gz AD26-005-H_S10_MERGED.fastq.gz
#> AD26-005-M_S11_MERGED.fastq.gz AD26-005-M_S11_MERGED.fastq.gz
#> AD30-ABMX-M_S12_MERGED.fastq.gz AD30-ABMX-M_S12_MERGED.fastq.gz
#> AD32-007-M_S13_MERGED.fastq.gz AD32-007-M_S13_MERGED.fastq.gz
#> ADABM30X-B_S14_MERGED.fastq.gz ADABM30X-B_S14_MERGED.fastq.gz
#> ADABM30X-H_S15_MERGED.fastq.gz ADABM30X-H_S15_MERGED.fastq.gz
#> ADABM30X-M_S16_MERGED.fastq.gz ADABM30X-M_S16_MERGED.fastq.gz
#> B18-006-B_S19_MERGED.fastq.gz B18-006-B_S19_MERGED.fastq.gz
#> BA17-050-B_S21_MERGED.fastq.gz BA17-050-B_S21_MERGED.fastq.gz
#> BB19-006-H_S22_MERGED.fastq.gz BB19-006-H_S22_MERGED.fastq.gz
#> BB6-019-B_S23_MERGED.fastq.gz BB6-019-B_S23_MERGED.fastq.gz
#> BB6-019-H_S24_MERGED.fastq.gz BB6-019-H_S24_MERGED.fastq.gz
#> BB6-019-M_S25_MERGED.fastq.gz BB6-019-M_S25_MERGED.fastq.gz
#> BE9-006-B_S27_MERGED.fastq.gz BE9-006-B_S27_MERGED.fastq.gz
#> BE9-006-H_S28_MERGED.fastq.gz BE9-006-H_S28_MERGED.fastq.gz
#> BE9-006-M_S29_MERGED.fastq.gz BE9-006-M_S29_MERGED.fastq.gz
#> BG7-010-B_S30_MERGED.fastq.gz BG7-010-B_S30_MERGED.fastq.gz
#> BG7-010-H_S31_MERGED.fastq.gz BG7-010-H_S31_MERGED.fastq.gz
#> BG7-010-M_S32_MERGED.fastq.gz BG7-010-M_S32_MERGED.fastq.gz
#> BJ17-007-M_S34_MERGED.fastq.gz BJ17-007-M_S34_MERGED.fastq.gz
#> BL7-006-B_S36_MERGED.fastq.gz BL7-006-B_S36_MERGED.fastq.gz
#> BL7-006-H_S37_MERGED.fastq.gz BL7-006-H_S37_MERGED.fastq.gz
#> BL7-006-M_S38_MERGED.fastq.gz BL7-006-M_S38_MERGED.fastq.gz
#> BP11-001-B_S43_MERGED.fastq.gz BP11-001-B_S43_MERGED.fastq.gz
#> BP11-001-H_S44_MERGED.fastq.gz BP11-001-H_S44_MERGED.fastq.gz
#> BP11-001-M_S45_MERGED.fastq.gz BP11-001-M_S45_MERGED.fastq.gz
#> BP12-025-B_S46_MERGED.fastq.gz BP12-025-B_S46_MERGED.fastq.gz
#> BQ4-018-B_S49_MERGED.fastq.gz BQ4-018-B_S49_MERGED.fastq.gz
#> BQ4-018-H_S50_MERGED.fastq.gz BQ4-018-H_S50_MERGED.fastq.gz
#> BQ4-018-M_S51_MERGED.fastq.gz BQ4-018-M_S51_MERGED.fastq.gz
#> BT-006-M_S55_MERGED.fastq.gz BT-006-M_S55_MERGED.fastq.gz
#> BV11-002-B_S57_MERGED.fastq.gz BV11-002-B_S57_MERGED.fastq.gz
#> BV11-002-H_S58_MERGED.fastq.gz BV11-002-H_S58_MERGED.fastq.gz
#> BV11-002-M_S59_MERGED.fastq.gz BV11-002-M_S59_MERGED.fastq.gz
#> C21-NV1-B_S62_MERGED.fastq.gz C21-NV1-B_S62_MERGED.fastq.gz
#> C21-NV1-H_S63_MERGED.fastq.gz C21-NV1-H_S63_MERGED.fastq.gz
#> C21-NV1-M_S64_MERGED.fastq.gz C21-NV1-M_S64_MERGED.fastq.gz
#> CB8-019-B_S69_MERGED.fastq.gz CB8-019-B_S69_MERGED.fastq.gz
#> CB8-019-H_S70_MERGED.fastq.gz CB8-019-H_S70_MERGED.fastq.gz
#> CB8-019-M_S71_MERGED.fastq.gz CB8-019-M_S71_MERGED.fastq.gz
#> D18-003-B_S78_MERGED.fastq.gz D18-003-B_S78_MERGED.fastq.gz
#> D18-003-H_S79_MERGED.fastq.gz D18-003-H_S79_MERGED.fastq.gz
#> D18-003-M_S80_MERGED.fastq.gz D18-003-M_S80_MERGED.fastq.gz
#> D61-010-B_S82_MERGED.fastq.gz D61-010-B_S82_MERGED.fastq.gz
#> D9-027-B_S83_MERGED.fastq.gz D9-027-B_S83_MERGED.fastq.gz
#> D9-027-H_S84_MERGED.fastq.gz D9-027-H_S84_MERGED.fastq.gz
#> D9-027-M_S85_MERGED.fastq.gz D9-027-M_S85_MERGED.fastq.gz
#> DJ2-008-B_S87_MERGED.fastq.gz DJ2-008-B_S87_MERGED.fastq.gz
#> DJ2-008-H_S88_MERGED.fastq.gz DJ2-008-H_S88_MERGED.fastq.gz
#> DJ2-008-M_S89_MERGED.fastq.gz DJ2-008-M_S89_MERGED.fastq.gz
#> DS1-ABM002-B_S91_MERGED.fastq.gz DS1-ABM002-B_S91_MERGED.fastq.gz
#> DS1-ABM002-H_S92_MERGED.fastq.gz DS1-ABM002-H_S92_MERGED.fastq.gz
#> DS1-ABM002-M_S93_MERGED.fastq.gz DS1-ABM002-M_S93_MERGED.fastq.gz
#> DU3-045-B_S94_MERGED.fastq.gz DU3-045-B_S94_MERGED.fastq.gz
#> DY5-004-B_S96_MERGED.fastq.gz DY5-004-B_S96_MERGED.fastq.gz
#> DY5-004-H_S97_MERGED.fastq.gz DY5-004-H_S97_MERGED.fastq.gz
#> DY5-004-M_S98_MERGED.fastq.gz DY5-004-M_S98_MERGED.fastq.gz
#> E9-009-B_S100_MERGED.fastq.gz E9-009-B_S100_MERGED.fastq.gz
#> E9-009-H_S101_MERGED.fastq.gz E9-009-H_S101_MERGED.fastq.gz
#> E9-009-M_S102_MERGED.fastq.gz E9-009-M_S102_MERGED.fastq.gz
#> EC2-013-B_S104_MERGED.fastq.gz EC2-013-B_S104_MERGED.fastq.gz
#> F7-015-M_S106_MERGED.fastq.gz F7-015-M_S106_MERGED.fastq.gz
#> FOMES19-H_S108_MERGED.fastq.gz FOMES19-H_S108_MERGED.fastq.gz
#> FOMES19-M_S109_MERGED.fastq.gz FOMES19-M_S109_MERGED.fastq.gz
#> H10-018-M_S110_MERGED.fastq.gz H10-018-M_S110_MERGED.fastq.gz
#> H24-NVABM1-H_S111_MERGED.fastq.gz H24-NVABM1-H_S111_MERGED.fastq.gz
#> J18-004-B_S114_MERGED.fastq.gz J18-004-B_S114_MERGED.fastq.gz
#> J18-004-H_S115_MERGED.fastq.gz J18-004-H_S115_MERGED.fastq.gz
#> J18-004-M_S116_MERGED.fastq.gz J18-004-M_S116_MERGED.fastq.gz
#> K18-002-H_S117_MERGED.fastq.gz K18-002-H_S117_MERGED.fastq.gz
#> L19X-B_S119_MERGED.fastq.gz L19X-B_S119_MERGED.fastq.gz
#> L19X-H_S120_MERGED.fastq.gz L19X-H_S120_MERGED.fastq.gz
#> L19X-M_S121_MERGED.fastq.gz L19X-M_S121_MERGED.fastq.gz
#> L23-002-B_S122_MERGED.fastq.gz L23-002-B_S122_MERGED.fastq.gz
#> L23-002-H_S123_MERGED.fastq.gz L23-002-H_S123_MERGED.fastq.gz
#> L23-002-M_S124_MERGED.fastq.gz L23-002-M_S124_MERGED.fastq.gz
#> N19X-B_S126_MERGED.fastq.gz N19X-B_S126_MERGED.fastq.gz
#> N19X-H_S127_MERGED.fastq.gz N19X-H_S127_MERGED.fastq.gz
#> N19X-M_S128_MERGED.fastq.gz N19X-M_S128_MERGED.fastq.gz
#> N22-001-B_S129_MERGED.fastq.gz N22-001-B_S129_MERGED.fastq.gz
#> N23-002-B_S130_MERGED.fastq.gz N23-002-B_S130_MERGED.fastq.gz
#> N23-002-H_S131_MERGED.fastq.gz N23-002-H_S131_MERGED.fastq.gz
#> N23-002-M_S132_MERGED.fastq.gz N23-002-M_S132_MERGED.fastq.gz
#> NVABM-0163-H_S135_MERGED.fastq.gz NVABM-0163-H_S135_MERGED.fastq.gz
#> [ reached 'max' / getOption("max.print") -- omitted 41 rows ]
#>
#> $dabest_objects
#> $dabest_objects$Hill_0
#> DABESTR v2025.3.15
#> ==================
#>
#> Good afternoon!
#> The current time is 14:36 PM on Friday March 13, 2026.
#>
#> The character(0) Cohen's d between Low and High is -0.12 [95%CI -0.56, 0.309].
#> The p-value of the two-sided permutation t-test is 0.5813, calculated for legacy purposes only.
#>
#> The character(0) Cohen's d between Middle and High is -0.187 [95%CI -0.617, 0.232].
#> The p-value of the two-sided permutation t-test is 0.3911, calculated for legacy purposes only.
#>
#> 5000 bootstrap samples were taken; the confidence interval is bias-corrected and accelerated.
#> Any p-value reported is the probability of observing the effect size (or greater),
#> assuming the null hypothesis of zero difference is true.
#> For each p-value, 5000 reshuffles of the control and test labels were performed.
#>
#>
#> $dabest_objects$Hill_1
#> DABESTR v2025.3.15
#> ==================
#>
#> Good afternoon!
#> The current time is 14:36 PM on Friday March 13, 2026.
#>
#> The character(0) Cohen's d between Low and High is -0.016 [95%CI -0.434, 0.418].
#> The p-value of the two-sided permutation t-test is 0.9417, calculated for legacy purposes only.
#>
#> The character(0) Cohen's d between Middle and High is 0.163 [95%CI -0.254, 0.585].
#> The p-value of the two-sided permutation t-test is 0.4475, calculated for legacy purposes only.
#>
#> 5000 bootstrap samples were taken; the confidence interval is bias-corrected and accelerated.
#> Any p-value reported is the probability of observing the effect size (or greater),
#> assuming the null hypothesis of zero difference is true.
#> For each p-value, 5000 reshuffles of the control and test labels were performed.
#>
#>
#> $dabest_objects$Hill_2
#> DABESTR v2025.3.15
#> ==================
#>
#> Good afternoon!
#> The current time is 14:36 PM on Friday March 13, 2026.
#>
#> The character(0) Cohen's d between Low and High is -0.039 [95%CI -0.47, 0.387].
#> The p-value of the two-sided permutation t-test is 0.8581, calculated for legacy purposes only.
#>
#> The character(0) Cohen's d between Middle and High is 0.187 [95%CI -0.23, 0.592].
#> The p-value of the two-sided permutation t-test is 0.3828, calculated for legacy purposes only.
#>
#> 5000 bootstrap samples were taken; the confidence interval is bias-corrected and accelerated.
#> Any p-value reported is the probability of observing the effect size (or greater),
#> assuming the null hypothesis of zero difference is true.
#> For each p-value, 5000 reshuffles of the control and test labels were performed.
#>
#>
#>
#> $plots
#> $plots$Hill_0
#>
#> $plots$Hill_1
#>
#> $plots$Hill_2
#>
#>
#> $summary
#> # A tibble: 6 × 8
#> metric comparison effect_size ci_lower ci_upper pvalue_permtest pvalue_welch
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Hill_0 High vs Low -0.120 -0.560 0.309 0.577 0.581
#> 2 Hill_0 High vs Mid… -0.187 -0.617 0.232 0.386 0.391
#> 3 Hill_1 High vs Low -0.0158 -0.434 0.418 0.942 0.942
#> 4 Hill_1 High vs Mid… 0.163 -0.254 0.585 0.454 0.448
#> 5 Hill_2 High vs Low -0.0387 -0.470 0.387 0.869 0.858
#> 6 Hill_2 High vs Mid… 0.187 -0.230 0.592 0.396 0.383
#> # ℹ 1 more variable: pvalue_mann_whitney <dbl>
#>
#> $effect_type
#> [1] "cohens_d"
#>
#> attr(,"class")
#> [1] "estim_diff_pq_result"
res$plots$Hill_0
res$summary
#> # A tibble: 6 × 8
#> metric comparison effect_size ci_lower ci_upper pvalue_permtest pvalue_welch
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 Hill_0 High vs Low -0.120 -0.560 0.309 0.577 0.581
#> 2 Hill_0 High vs Mid… -0.187 -0.617 0.232 0.386 0.391
#> 3 Hill_1 High vs Low -0.0158 -0.434 0.418 0.942 0.942
#> 4 Hill_1 High vs Mid… 0.163 -0.254 0.585 0.454 0.448
#> 5 Hill_2 High vs Low -0.0387 -0.470 0.387 0.869 0.858
#> 6 Hill_2 High vs Mid… 0.187 -0.230 0.592 0.396 0.383
#> # ℹ 1 more variable: pvalue_mann_whitney <dbl>