. 2021 Mar 9;10:e56088. doi: 10.7554/eLife.56088

Table 1. Mixed effects model investigating changes in FNR density between total chloroplast sub-compartments of three individuals each of WT and fnr1 Arabidopsis.

Analysis of data presented in Figure 1. Fixed effects taking either label density in the stroma as the intercept or label density in the margins/lamellae as the intercept. Linear mixed model fit by REML. Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘’ 1.

Deletion test carried out using Satterthwaite’s method with the R package lmerTest (Kuznetsova, Brockhoff & Christensen 2017). The model is a mixed effects model with random intercepts. The square root of response is the response variable, tissue is the fixed effect, and individual the random effect.
Fixed effect deleted	Sum sq			Mean sq			Num DF		Den DF				F value		Pr (>F)
Sub-compartment	14.231			7.1153			2		295.58				7.4565		0.000693		***
Model summary:
Random effects:
Groups		Name				Variance				Std. Dev.
individual		(Intercept)				0.1896				0.4354
Residual						0.9542				0.9769
Number of obs: 306, groups: individual, 6
Fixed effects when fnr1 stroma is set as the intercept
			Estimate		Std. Error			DF			t value			Pr (>\|t\|)
(Intercept)			0.9165		0.2791			4.2686			3.283			0.0276		*
Grana			−0.3607		0.1714			295.5794			−2.105			0.0361		*
Margin/lamellae			2.2884		0.1714			295.5794			13.355			<2⁻¹⁶		***
Genotype comparison WT:fnr1			0.1230		0.4128			5.0375			0.298			0.7776
WT grana: fnr1 grana			0.6286		0.2845			295.5794			2.210			0.0279		*
WT margin/lamellae: fnr1 margin/lamellae			−0.4661		0.2845			295.5794			−1.638			0.1025

Fixed effects when fnr1 margin/lamellae is set as the intercept
		Estimate			Std. Error			DF				t value		Pr (>\|t\|)
(Intercept)				0.9165	0.2791			4.2686				11.482		0.000228		***
Grana				−2.6491	0.1714			295.5794				−15.460		<2⁻¹⁶		***
Stroma				−2.2884	0.1714			295.5794				−13.355		<2⁻¹⁶		***
Genotype comparison WT:fnr1				−0.3430	0.4128			5.0375				−0.831		0.443524
WT grana: fnr1 grana				1.0947	0.2845			295.5794				3.848		0.000146		***
WT stroma: fnr1 stroma				−0.4661	0.2845			295.5794				1.638		0.102459

Fixed effects when Wt stroma is set as the intercept
				Estimate	Std. Error			DF				t value		Pr (>\|t\|)
(Intercept)				1.0395	0.3041			5.8576				3.418		0.0147		*
Grana				0.2679	0.2271			295.5794				1.180		0.2391
Margin/lamellae				1.8223	0.2271			295.5794				8.024		2.43⁻¹⁴		***
Genotype comparison WT:fnr1				−0.1230	0.4128			5.0375				−0.298		0.7776
Wt grana: fnr1 grana				−0.6286	0.2845			295.5794				−2.210		0.0279		*
Wt margin/lamellae: fnr1 margin/lamellae				0.4661	0.2845			295.5794				1.638		0.1025

Fixed effects when Wt margin/lamellae is set as the intercept
				Estimate	Std. Error			DF				t value		Pr (>\|t\|)
(Intercept)				2.8618	0.3041			5.8576				9.411		9.41⁻⁰⁵		***
Grana				−1.5544	0.2271			295.5794				−6.844		4.44⁻¹¹		***
Stroma				−1.8223	0.2271			295.5794				−8.024		2.43⁻¹⁴		***
Genotype comparison WT:fnr1				0.343	0.4128			5.0375				0.831		0.443524
Wt grana: fnr1 grana				−1.0947	0.2845			295.5794				−3.848		0.000146		***
Wt stroma: fnr1 stroma				−0.4661	0.2845			295.5794				−1.638		0.102459