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size analysis update
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@SamGurr
SamGurr committed Sep 6, 2024
1 parent 1185d35 commit 8528131
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13 changes: 13 additions & 0 deletions RAnalysis/Output/1_Survival_Growth/size_growth/Experiment2_Length_MeanSE.csv
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"","Age","Larvae_pCO2","N","Length","sd","se","ci"
"1",2,"Low pCO2",5,96.812,1.82158447512049,0.814637342625539,2.26179586244402
"2",2,"Moderate pCO2",4,94.6225,0.830436632139986,0.415218316069993,1.32140999586307
"3",2,"High pCO2",4,70.605,4.43110595675617,2.21555297837808,7.05087839019965
"4",4,"Low pCO2",5,107.82,1.6290027624286,0.728512182465057,2.02267408308207
"5",4,"Moderate pCO2",4,103.5475,1.83545407642541,0.917727038212705,2.92061702201898
"6",4,"High pCO2",4,77.695,5.73481473109638,2.86740736554819,9.12536997623212
"7",8,"Low pCO2",5,164.264,10.5462543113657,4.71642830964279,13.094904294324
"8",8,"Moderate pCO2",5,157.718,7.40985627390977,3.31378846639311,9.20055176717805
"9",8,"High pCO2",5,98.226,13.0421117921907,5.83260970749801,16.193920672912
"10",10,"Low pCO2",5,182.32,7.21540366161173,3.22682661449294,8.9591069591309
"11",10,"Moderate pCO2",5,169.334,8.81216658943759,3.94092070460699,10.9417500002787
"12",10,"High pCO2",5,104.922,23.4121906279613,10.470249949261,29.0700742218232
6 changes: 3 additions & 3 deletions .../size_growth/Experiment4/Metamorphosis/Experiment4_Length_metamorphosis_Ttest_LowvMod.doc
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Two Sample t-test

data: Exp4_metamorphosis$Length by as.factor(Exp4_metamorphosis$Larvae_pCO2)
t = 3.8372, df = 4, p-value = 0.0185
t = 4.4838, df = 4, p-value = 0.01096
alternative hypothesis: true difference in means between group Low pCO2 and group Moderate pCO2 is not equal to 0
95 percent confidence interval:
2.128631 13.271369
4.175876 17.757458
sample estimates:
mean in group Low pCO2 mean in group Moderate pCO2
203.6 195.9
186.0333 175.0667

12 changes: 6 additions & 6 deletions ...wth/size_growth/Experiment4/Metamorphosis/Experiment4_MeanLength_metamorphosisLowvMod.csv
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"","ID","Larvae_pCO2","Age","Length"
"1","1","Low pCO2","14",201.1
"2","2","Low pCO2","14",206.6
"3","3","Low pCO2","14",203.1
"4","10","Moderate pCO2","14",194.6
"5","11","Moderate pCO2","14",194.8
"6","12","Moderate pCO2","14",198.3
"1","1","Low pCO2","12",181.6
"2","2","Low pCO2","12",187.7
"3","3","Low pCO2","12",188.8
"4","10","Moderate pCO2","12",175.2
"5","11","Moderate pCO2","12",173.3
"6","12","Moderate pCO2","12",176.7
Binary file added RAnalysis/Output/1_Survival_Growth/size_growth/MeanSE_2dpf_8dpf_Metamorph.pdf
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18 changes: 9 additions & 9 deletions ...tamorphosis/Experiment2_Experiment4_Low_v_Mod/Experiments2&4_Survival_CoxRegMixed_ADD.doc
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Cox mixed-effects model fit by maximum likelihood
Data: binary_Exp2_Exp4_all
events, n = 168055, 191196
Iterations= 10 42
Iterations= 9 38
NULL Integrated Fitted
Log-likelihood -1875749 -1873804 -1873784
Log-likelihood -1869472 -1868097 -1868079

Chisq df p AIC BIC
Integrated loglik 3890.26 3.00 0 3884.26 3854.16
Penalized loglik 3929.32 12.71 0 3903.90 3776.45
Chisq df p AIC BIC
Integrated loglik 2750.81 3.0 0 2744.81 2714.71
Penalized loglik 2786.18 12.2 0 2761.77 2639.33

Model: Surv(Prop_time_metamophosis, Count_dead) ~ Generation + Larvae_pCO2 + (1 | ID)
Fixed coefficients
coef exp(coef) se(coef) z p
Generation2 0.30148192 1.351861 0.01270568 23.73 0.00000
Larvae_pCO2Moderate pCO2 0.04795042 1.049119 0.01239666 3.87 0.00011
coef exp(coef) se(coef) z p
Generation2 -0.27355089 0.7606736 0.01160190 -23.58 0.0e+00
Larvae_pCO2Moderate pCO2 0.04379186 1.0447649 0.01121469 3.90 9.4e-05

Random effects
Group Variable Std Dev Variance
ID Intercept 0.0225085800 0.0005066362
ID Intercept 0.0198799844 0.0003952138
4 changes: 2 additions & 2 deletions ...orphosis/Experiment2_Experiment4_Low_v_Mod/Experiments2&4_Survival_CoxRegMixed_ADD_HR.csv
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"","**Characteristic**","**exp(Beta)**","**95% CI**","**p-value**"
"1","Generation2","1.35","1.32, 1.39","<0.001"
"2","Larvae_pCO2Moderate pCO2","1.05","1.02, 1.07","<0.001"
"1","Generation2","0.76","0.74, 0.78","<0.001"
"2","Larvae_pCO2Moderate pCO2","1.04","1.02, 1.07","<0.001"
18 changes: 9 additions & 9 deletions ...tamorphosis/Experiment2_Experiment4_Low_v_Mod/Experiments2&4_Survival_CoxRegMixed_INT.doc
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Cox mixed-effects model fit by maximum likelihood
Data: binary_Exp2_Exp4_all
events, n = 168055, 191196
Iterations= 17 70
Iterations= 10 42
NULL Integrated Fitted
Log-likelihood -1875749 -1873801 -1873785
Log-likelihood -1869472 -1868094 -1868081

Chisq df p AIC BIC
Integrated loglik 3896.32 4.00 0 3888.32 3848.19
Penalized loglik 3927.43 11.73 0 3903.97 3786.33
Integrated loglik 2757.17 4.00 0 2749.17 2709.04
Penalized loglik 2783.74 10.91 0 2761.92 2652.45

Model: Surv(Prop_time_metamophosis, Count_dead) ~ Gen_pCO2 + (1 | ID)
Fixed coefficients
coef exp(coef) se(coef) z p
Gen_pCO21_Moderate pCO2 0.07012547 1.072643 0.01291994 5.43 5.7e-08
Gen_pCO22_Low pCO2 0.33047338 1.391627 0.01473747 22.42 0.0e+00
Gen_pCO22_Moderate pCO2 0.34436121 1.411088 0.01405660 24.50 0.0e+00
coef exp(coef) se(coef) z p
Gen_pCO21_Moderate pCO2 0.06440029 1.0665192 0.01160112 5.55 2.8e-08
Gen_pCO22_Low pCO2 -0.24672335 0.7813568 0.01329980 -18.55 0.0e+00
Gen_pCO22_Moderate pCO2 -0.23401546 0.7913496 0.01254748 -18.65 0.0e+00

Random effects
Group Variable Std Dev Variance
ID Intercept 0.0170230459 0.0002897841
ID Intercept 0.0144552913 0.0002089554
6 changes: 3 additions & 3 deletions ...orphosis/Experiment2_Experiment4_Low_v_Mod/Experiments2&4_Survival_CoxRegMixed_INT_HR.csv
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"","**Characteristic**","**exp(Beta)**","**95% CI**","**p-value**"
"1","Gen_pCO21_Moderate pCO2","1.07","1.05, 1.10","<0.001"
"2","Gen_pCO22_Low pCO2","1.39","1.35, 1.43","<0.001"
"3","Gen_pCO22_Moderate pCO2","1.41","1.37, 1.45","<0.001"
"1","Gen_pCO21_Moderate pCO2","1.07","1.04, 1.09","<0.001"
"2","Gen_pCO22_Low pCO2","0.78","0.76, 0.80","<0.001"
"3","Gen_pCO22_Moderate pCO2","0.79","0.77, 0.81","<0.001"
Binary file added .../Output/1_Survival_Growth/survival/embryo_to_metamorphosis/Experiments2&4_KaplanMeier.pdf
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Binary file added ...1_Survival_Growth/survival/embryo_to_metamorphosis/Experiments2&4_KaplanMeier_LowpCO2.pdf
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Binary file added ...vival_Growth/survival/embryo_to_metamorphosis/Experiments2&4_KaplanMeier_ModeratepCO2.pdf
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