Table 2.

Reporting scores by questionnaire section. Independent sample comparison p values are from Student’s t-tests, while paired samples’ ones are from paired t-tests. In the paired sample there were 32 preprints and 35 peer-reviewed articles with no applicable questions in the Drugs and Reagents section; thus, there were only 17 pairs available for the statistical comparison. 2-way ANOVA results are presented in individual lines below each comparison set. All values are presented as mean ± S.D. 95% C.I.; 95% confidence interval of the difference

Study stage	Subset	# of applicable questions	Score (preprints)	Score (peer-reviewed)	Difference [95% C.I.]	pvalue	Sample size
Independent samples	Title and abstract	1 ± 0	84.2 ± 36.7	93.4 ± 25.0	9.2 [−0.8, 19.3]	0.07	76
	Risk of bias	3.7 ± 0.5	39.3 ± 23.6	39.9 ± 20.2	0.6 [−6.4, 7.6]	0.87	76
	Drugs and reagents	1.2 ± 1.4	62.2 ± 36.0	78.5 ± 29.2	16.3 [0.6, 31.9]	0.04	31 (bioRxiv), 38 (PubMed)
	Data presentation	7.3 ± 0.9	75.1 ± 16.9	79.9 ± 12.7	4.8 [−0.02, 9.6]	0.05	76
	Data analysis	6 ± 0	83.6 ± 20.4	81.0 ± 19.4	−2.6 [−8.9, 3.9]	0.44	76
Group: F = 5.53, df = 1, p = 0.02; Section: F = 97.09, df = 4, p < 2 × 10−16; Interaction: F = 2.46, df = 4, p = 0.04
Paired sample	Title and abstract	1 ± 0	85.7 ± 35.3	83.9 ± 37.1	1.8 [−8.0, 4.4]	0.57	56
	Risk of bias	3.7 ± 0.5	39.7 ± 20.6	54.2 ± 17.4	14.6 [8.4, 20.8]	1.6 × 10−5	56
	Drugs and reagents	0.9 ± 1.3	66.4 ± 35.7	81.6 ± 26.8	15.2 [4.0, 26.4]	0.01	17
	Data presentation	7.3 ± 0.8	78.4 ± 12.5	80.9 ± 13.3	2.5 [−0.3, 5.4]	0.08	56
	Data analysis	6 ± 0	84.5 ± 16.2	88.1 ± 14.2	3.6 [−0.5, 7.6]	0.08	56
Group: F = 6.31, df = 1, p = 0.01; Section: F = 50.37, df = 4, p < 2 × 10−16; Interaction: F = 2.00, df = 4, p = 0.09