Table 1.

Simulation results comparing the various methods for estimating proportions of variance and 95% confidence intervals. HE is the Haseman-Elston regression with the proposed procedure for obtaining confidence intervals. HE-meta is the implementation of the meta-analysis procedure when the data set is randomly divided into multiple studies. In this case there are correlation individuals between the studies, while the meta-analysis procedures ignores these correlations. GENESIS is an R package that implements an average-information REML procedure. GENESIS-asymp provides confidence intervals (CIs) based on asymptotic normality. When these CIs contained inadmissible values, they were truncated to include only admissible values. The size of the confidence intervals for GENESIS-asypm was calculated using only simulations that had non-zero estimate of the variance component. GENESIS-ALBI provides confidence intervals calculated in a parametric bootstrap procedure implemented in the ALBI package. ‘P heritability’ is the R package ‘heritability’ implementation of the REML procedure. CIs are based on asymptotic normality. When ‘log’ is specified, the asymptotic normality is calculated on the log transformed variance components, and 0 value is assumed when an estimate is smaller than 0.001. Note that the ‘P heritability’ had convergence problems in the large sample size, null scenario, so that a small number of simulations was used to calculate parameters.

	3 correlation matrices						Only kinship matrix
	Large sample			Small sample			Large sample		Smalle sample
	Community (2/157)	HH (15/157)	kinship (40/157)	Community (2/157)	HH (15/157)	kinship (40/157)	kinship (0/140)	kinship (40/140)	kinship (0/140)	kinship (40/140)
					RMSE
HE	0.004	0.016	0.030	0.016	0.092	0.180	0.015	0.028	0.132	0.182
HE - meta							0.054	0.153
GENESIS	0.004	0.014	0.026	0.016	0.089	0.180	0.015	0.025	0.134	0.181
P heritability							0.026	0.025	0.140	0.177
					Coverage
HE	0.92	0.96	0.95	0.98	0.98	0.99	0.98	0.94	0.97	1.00
HE - meta							0.95	0.96
GENESIS asymp	0.94	0.96	0.95	0.72	0.78	0.86	0.98	0.95	0.98	0.91
GENESIS - ALBI							0.95	0.96	1.00	0.96
P heritability							0.92	0.96	0.98	0.97
P heritability - log							0.79	0.96	0.79	0.99
					Width
HE	0.02	0.06	0.12	0.06	0.32	0.63	0.05	0.11	0.46	0.68
HE - meta							0.14	0.21
GENESIS asymp	0.01	0.06	0.10	0.06	0.32	0.64	0.06	0.10	0.52	0.64
GENESIS - ALBI							0.05	0.10	0.55	0.57
P heritability							0.06	0.10	0.48	0.63
P heritability - log							0.42	0.10	0.90	0.73