Table 3. Mixed effects model investigating changes in FNR density between different the chloroplast sub-compartments of WT Arabidopsis following dark adaptation or light adaptation of leaves.

Analysis performed using the data in Figure 6. 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	0.30184				0.10061			3			12				2.3613			0.1227
Model summary:
Random effects:
Groups		Name					Variance					Std. Dev.
Individual		(Intercept)					0.1073					0.3276
Residual							0.04261					0.2064
Number of obs: 24, groups: individual, 6
Fixed effects when dark adapted stroma is set as the intercept::
				Estimate		Std. Error			DF				t value				Pr (>|t|)
(Intercept)				1.1743		0.2235			6.3067				5.253				0.00164			**
Grana				0.3104		0.1685			12				1.842				0.09033			.
Lamellae				1.4748		0.1685			12				8.75				1.48−06			***
Margins				1.3736		0.1685			12				8.15				3.11−06			***
Light:dark comparison				0.4157		0.3161			6.3067				1.315				0.23427
Light:dark grana				0.1421		0.2384			12				0.596				0.5622
Light:dark lamellae				0.1482		0.2384			12				0.622				0.54562
Light:dark margins				0.5963		0.2384			12				2.502				0.02782			*
Fixed effects when dark adapted lamellae is set as the intercept::
		Estimate				Std. Error			DF					t value			Pr (>|t|)
(Intercept)				2.64913		0.223542			6.306738					11.851			1.52−05			***
Grana				−1.16437		0.168543			12.000001					−6.908			1.63−05			***
Margins				−0.101175		0.168543			12.000001					−0.6			0.5595
Stroma				−1.474807		0.168543			12.000001					−8.75			1.48−06			***
Light:dark comparison				0.563988		0.316136			6.306738					1.784			0.1223
Light:dark grana				−0.006164		0.238356			12.000001					−0.026			0.9798
Light:dark margins				0.44808		0.238356			12.000001					1.88			0.0846			.
Light:dark stroma				−0.148241		0.238356			12.000001					−0.622			0.5456
Fixed effects when light acclimated stroma is set as the intercept:
					Estimate	Std. Error			DF					t value			Pr (>|t|)
(Intercept)					1.5901	0.2235			6.3067					7.113			0.00031			***
Grana					0.4525	0.1685			12					2.685			0.01986			*
Lamellae					1.623	0.1685			12					9.63			5.37−07			***
Margins					1.97	0.1685			12					11.688			6.48−08			***
Dark:light comparison					−0.4157	0.3161			6.3067					−1.315			0.23427
Dark:light grana					−0.1421	0.2384			12					−0.596			0.5622
Dark:light lamellae					−0.1482	0.2384			12					−0.622			0.54562
Dark:light margins					−0.5963	0.2384			12					−2.502			0.02782			*
Fixed effects when light acclimated lamellae is set as the intercept:
					Estimate	Std. Error			DF					t value			Pr (>|t|)
(Intercept)			3.213118			0.223542			6.306738					14.374			4.68−06			***
Grana			−1.170535			0.168543			12.000001					−6.945			1.55−05			***
Margins			0.346905			0.168543			12.000001					2.058			0.062			.
Stroma			−1.623048			0.168543			12.000001					−9.63			5.37−07			***
Dark:light comparison			−0.563988			0.316136			6.306738					−1.784			0.1223
Dark:light grana			0.006164			0.238356			12.000001					0.026			0.9798
Dark:light margins			−0.44808			0.238356			12.000001					−1.88			0.0846			.
Dark:light stroma			0.148241			0.238356			12.000001					0.622			0.5456