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Data and libraries
Load Libraries
library(kableExtra)
library(tidyverse)
library(data.table)
library(metan)
library(ggthemes)
library(GGally)
library(furrr)
theme_set(theme_bw())Import and prepare dataset:
Genotype-environment analysis by mixed-effect models
Define a function to obtain the BLUPs and other model parameters:
BLUPS_par_mmer <- function(model, trait, teste_LRT) {
# log likelihood of the model, AIC, convergence T/F
modelfit <- summary(model)$logo
# number of groups for factors, could be used to compute DF
groups <- summary(model)$groups
# variance components
varcomp <- summary(model)$varcomp
# variance components
Vg <- model$sigma$Clone %>% as.vector()
Ve <- model$sigma$units %>% as.vector()
# Narrow-sense heritability
H2_narrow <- Vg / (Vg + Ve)
# Broad-sense heritability
Va <- model$sigma$`Ano:Clone` %>% as.vector()
Ve <- model$sigma$units %>% as.vector()
n.ano <- length(model$U$Ano[[trait]])
H2_Broad <- (Vg) / (Vg + (Va / n.ano) + (Ve / (2 * n.ano)))
# Extract the BLUPs and PEVs, compute Reliability (REL),
# de-regressed BLUPs and weights for downstream analysis
blups <- model$U$Clone %>%
unlist() %>%
tibble(Clone = names(.), BLUP = .) %>%
mutate(
Clone = gsub("Clone", "", Clone),
PEV = diag(as.matrix(model$PevU$Clone[[1]])),
# prediction error variance
REL = 1 - PEV / Vg,
# Reliability
drgBLUP = BLUP / REL,
# De-regressed BLUP
WT = (1 - H2_narrow) / ((0.1 + (1 - REL) / REL) * H2_narrow) # weight for downstream
)
# Combine all outputs into one object the function can return()
out <- list(
Trait = trait,
H2_Broad = H2_Broad,
H2_narrow = H2_narrow,
model = model,
modelfit = list(modelfit),
groups = list(groups),
blups = list(blups),
varcomp = list(varcomp),
teste_LRT = teste_LRT
)
return(out)
}
save(BLUPS_par_mmer, file = "output/BLUPS_par_mmer.Rdata")Convert trait columns to numeric and calculate the mean for each trait:
traits <- colnames(pheno)[6:ncol(pheno)]
pheno <- pheno %>%
mutate_at(traits, as.numeric)
mean_pheno <- pheno %>%
summarise(across(where(is.numeric), \(x) mean(x, na.rm = TRUE))) %>%
as.data.frame()
write.csv(mean_pheno, "output/mean_pheno.csv", row.names = FALSE)Set up parallel processing. Define and run multiple models to get the BLUPs: ATTENTION: This process is time-consuming.
# Função para rodar os modelos e coletar os resultados
run_models <- function(trait, pheno) {
# Selecionar apenas as colunas necessárias no início
data <- pheno %>%
select(1:5, all_of(trait)) %>%
na.omit() %>%
droplevels() %>%
as.data.table()
formula <- as.formula(paste(trait, "~ Ano:Bloco"))
formulas_random <- list(
as.formula("~ Clone + Ano + Ano:Clone + row + col"),
as.formula("~ Clone + Ano + row + col"),
as.formula("~ Clone + Ano:Clone + row + col"),
as.formula("~ Ano + Ano:Clone + row + col"),
as.formula("~ Clone + Ano + Ano:Clone + col"),
as.formula("~ Clone + Ano + Ano:Clone + row")
)
model <- function(formulas_random) {
sommer::mmer(
fixed = formula,
random = formulas_random,
rcov = ~ units,
data = data,
verbose = TRUE
)
}
models <-
map(formulas_random, model)
# Nomear os modelos
names(models) <-
c("Complete", "Clone:Year", "Year", "Clone", "row", "col")
# Calcular os testes ANOVA para todos os modelos
anova_tests <-
list(
sommer::anova.mmer(models$Complete, models$`Clone:Year`),
sommer::anova.mmer(models$Complete, models$Year),
sommer::anova.mmer(models$Complete, models$Clone),
sommer::anova.mmer(models$Complete, models$row),
sommer::anova.mmer(models$Complete, models$col)
)
teste_LRT <- do.call(bind_rows, anova_tests) %>%
distinct()
rownames(teste_LRT) <-
c("Complete", "Clone:Year", "Year", "Clone", "row", "col")
BLUPS_par_mmer(models$Complete, trait, teste_LRT)
}Run models in paralel for each trait
# Definir o plano para execução paralela
plan(multisession)
results <- future_map(traits, run_models, pheno = pheno)iteration LogLik wall cpu(sec) restrained
1 -394.699 13:44:3 142 0
2 -315.517 13:46:24 283 0
3 -290.671 13:48:41 420 0
4 -284.172 13:50:58 557 1
5 -283.035 13:53:17 696 1
6 -283.032 13:55:42 841 1
7 -283.032 13:58:5 984 1
iteration LogLik wall cpu(sec) restrained
1 -473.011 14:1:7 122 0
2 -353.738 14:3:10 245 0
3 -320.891 14:5:24 379 0
4 -313.841 14:7:30 505 0
5 -312.73 14:9:39 634 1
6 -312.632 14:11:47 762 1
7 -312.632 14:14:1 896 1
iteration LogLik wall cpu(sec) restrained
1 -394.699 14:16:44 143 0
2 -315.517 14:19:9 288 0
3 -290.671 14:21:27 426 0
4 -284.172 14:23:46 565 1
5 -283.035 14:26:4 703 1
6 -283.032 14:28:21 840 1
7 -283.032 14:30:42 981 1
iteration LogLik wall cpu(sec) restrained
1 -510.615 14:34:8 136 0
2 -363.489 14:36:25 273 0
3 -320.95 14:38:42 410 0
4 -312.27 14:40:58 546 1
5 -311.339 14:43:16 684 1
6 -311.335 14:45:32 820 1
7 -311.335 14:47:35 943 1
iteration LogLik wall cpu(sec) restrained
1 -371.879 14:50:35 123 0
2 -302.334 14:52:38 246 0
3 -285.188 14:54:43 371 0
4 -283.089 14:56:44 492 0
5 -283.034 14:58:44 612 0
6 -283.032 15:0:34 722 0
7 -283.032 15:2:21 829 0
iteration LogLik wall cpu(sec) restrained
1 -384.654 15:5:9 111 0
2 -315.719 15:7:2 224 0
3 -296.24 15:8:54 336 0
4 -290.797 15:10:44 446 1
5 -289.762 15:12:25 547 1
6 -289.761 15:14:6 648 1
Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 598.0635 687.4686 -283.0317
mod2 53 657.2635 746.6685 -312.6317 59.19997 1 1.42436244665181e-14 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 598.0635 687.4686 -283.0317
mod2 53 598.0635 687.4686 -283.0317 0 1 1
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 598.0635 687.4686 -283.0317
mod2 53 654.6696 744.0747 -311.3348 56.60615 1 5.32450566461941e-14 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 598.0635 687.4686 -283.0317
mod2 53 598.0635 687.4686 -283.0317 0 1 0.99903
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 598.0635 687.4686 -283.0317
mod2 53 611.5227 700.9277 -289.7613 13.45919 1 0.00024 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1iteration LogLik wall cpu(sec) restrained
1 -535.378 15:16:29 96 0
2 -470.687 15:18:6 193 0
3 -450.476 15:19:43 290 0
4 -447.928 15:21:22 389 0
5 -447.795 15:22:57 484 0
6 -447.769 15:24:29 576 0
7 -447.762 15:25:50 657 0
8 -447.761 15:27:8 735 0
9 -447.76 15:28:27 814 0
iteration LogLik wall cpu(sec) restrained
1 -614.03 15:30:11 69 0
2 -534.113 15:31:27 145 0
3 -515.081 15:32:38 216 0
4 -512.744 15:33:54 292 0
5 -512.512 15:35:12 370 0
6 -512.449 15:36:25 443 0
7 -512.429 15:37:20 498 0
8 -512.422 15:38:7 545 0
9 -512.42 15:38:55 593 0
10 -512.419 15:39:43 641 0
iteration LogLik wall cpu(sec) restrained
1 -535.378 15:40:36 46 0
2 -470.687 15:41:24 94 0
3 -450.476 15:42:10 140 0
4 -447.928 15:42:56 186 0
5 -447.795 15:43:40 230 0
6 -447.769 15:44:26 276 0
7 -447.762 15:45:11 321 0
8 -447.761 15:45:55 365 0
9 -447.76 15:46:39 409 0
iteration LogLik wall cpu(sec) restrained
1 -641.454 15:47:38 40 0
2 -507.57 15:48:19 81 0
3 -469.431 15:48:59 121 0
4 -465.32 15:49:41 163 0
5 -465.161 15:50:23 205 0
6 -465.13 15:51:3 245 0
7 -465.122 15:51:45 287 0
8 -465.12 15:52:30 332 0
9 -465.119 15:53:14 376 0
iteration LogLik wall cpu(sec) restrained
1 -529.4 15:54:15 42 0
2 -470.667 15:54:55 82 0
3 -453.266 15:55:36 123 0
4 -451.512 15:56:20 167 0
5 -451.499 15:57:1 208 0
6 -451.498 15:57:41 248 0
iteration LogLik wall cpu(sec) restrained
1 -528.449 15:58:42 41 0
2 -475.26 15:59:22 81 0
3 -460.44 16:0:6 125 0
4 -458.458 16:0:47 166 0
5 -458.31 16:1:30 209 0
6 -458.279 16:2:15 254 0
7 -458.271 16:2:57 296 0
8 -458.269 16:3:37 336 0
9 -458.268 16:4:17 376 0
Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 927.5204 1016.820 -447.7602
mod2 53 1056.8375 1146.137 -512.4187 129.31702 1 5.7807213084901e-30 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 927.5204 1016.82 -447.7602
mod2 53 927.5204 1016.82 -447.7602 0 1 1
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 927.5204 1016.820 -447.7602
mod2 53 962.2390 1051.538 -465.1195 34.71854 1 3.80986092686306e-09 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 927.5204 1016.820 -447.7602
mod2 53 934.9968 1024.296 -451.4984 7.47637 1 0.00625 **
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 927.5204 1016.820 -447.7602
mod2 53 948.5361 1037.835 -458.2681 21.01567 1 4.55542957069547e-06 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1iteration LogLik wall cpu(sec) restrained
1 15.6647 13:44:28 166 0
2 117.749 13:47:16 334 0
3 148.727 13:50:0 498 0
4 152.611 13:52:44 662 0
5 152.749 13:55:34 832 0
6 152.764 13:58:21 999 0
7 152.767 14:1:5 1163 0
8 152.767 14:3:56 1334 0
iteration LogLik wall cpu(sec) restrained
1 -80.7959 14:7:44 150 0
2 69.6931 14:10:14 300 0
3 116.347 14:12:48 454 0
4 121.918 14:15:33 619 0
5 122.156 14:18:29 795 0
6 122.185 14:21:11 957 0
7 122.19 14:23:52 1118 0
8 122.192 14:26:34 1280 0
9 122.192 14:29:13 1439 0
iteration LogLik wall cpu(sec) restrained
1 15.6647 14:32:23 166 0
2 117.749 14:35:3 326 0
3 148.727 14:37:41 484 0
4 152.611 14:40:26 649 0
5 152.749 14:43:8 811 0
6 152.764 14:45:45 968 0
7 152.767 14:48:11 1114 0
8 152.767 14:50:36 1259 0
iteration LogLik wall cpu(sec) restrained
1 -106.064 14:54:8 143 0
2 72.0855 14:56:32 287 0
3 122.696 14:58:53 428 0
4 128.271 15:1:2 557 0
5 128.41 15:3:11 686 0
6 128.431 15:5:21 816 0
7 128.435 15:7:30 945 0
8 128.436 15:9:43 1078 0
iteration LogLik wall cpu(sec) restrained
1 11.8319 15:12:40 118 0
2 108.707 15:14:39 237 0
3 137.44 15:16:19 337 0
4 140.756 15:17:59 437 0
5 140.832 15:19:40 538 0
6 140.835 15:21:23 641 0
7 140.835 15:23:2 740 0
iteration LogLik wall cpu(sec) restrained
1 35.4468 15:25:21 93 0
2 123.571 15:26:42 174 0
3 145.252 15:28:7 259 0
4 147.553 15:29:28 340 0
5 147.675 15:30:59 431 0
6 147.691 15:32:24 516 0
7 147.695 15:33:54 606 0
8 147.695 15:35:26 698 0
Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 -273.5348 -183.2544 152.7674
mod2 53 -212.3835 -122.1031 122.1918 61.15126 1 5.28539028651048e-15 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 -273.5348 -183.2544 152.7674
mod2 53 -273.5348 -183.2544 152.7674 0 1 1
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 -273.5348 -183.2544 152.7674
mod2 53 -224.8719 -134.5916 128.4360 48.66283 1 3.03973677890998e-12 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 -273.5348 -183.2544 152.7674
mod2 53 -249.6705 -159.3901 140.8352 23.86428 1 1.03372377017493e-06 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 -273.5348 -183.2544 152.7674
mod2 53 -263.3904 -173.1100 147.6952 10.14439 1 0.00145 **
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1iteration LogLik wall cpu(sec) restrained
1 -162.21 13:42:20 38 0
2 -104.964 13:43:6 84 0
3 -88.985 13:43:51 129 0
4 -86.9112 13:44:32 170 0
5 -86.8145 13:45:15 213 0
6 -86.808 13:45:59 257 0
7 -86.8074 13:46:41 299 0
iteration LogLik wall cpu(sec) restrained
1 -219.749 13:47:33 36 0
2 -130.556 13:48:9 72 0
3 -103.442 13:48:46 109 0
4 -100.333 13:49:23 146 0
5 -100.263 13:50:1 184 0
6 -100.261 13:50:36 219 0
7 -100.261 13:51:13 256 0
iteration LogLik wall cpu(sec) restrained
1 -162.21 13:51:55 37 0
2 -104.964 13:52:33 75 0
3 -88.985 13:53:10 112 0
4 -86.9112 13:53:46 148 0
5 -86.8145 13:54:25 187 0
6 -86.808 13:55:5 227 0
7 -86.8074 13:55:42 264 0
iteration LogLik wall cpu(sec) restrained
1 -230.556 13:56:34 38 0
2 -128.304 13:57:13 77 0
3 -100.681 13:57:52 116 0
4 -97.7205 13:58:28 152 0
5 -97.636 13:59:3 187 0
6 -97.6332 13:59:40 224 0
7 -97.6331 14:0:19 263 0
iteration LogLik wall cpu(sec) restrained
1 -165.592 14:1:9 35 0
2 -113.859 14:1:46 72 0
3 -100.718 14:2:24 110 0
4 -99.4108 14:3:3 149 0
5 -99.3575 14:3:43 189 0
6 -99.3527 14:4:24 230 0
7 -99.3523 14:5:8 274 0
iteration LogLik wall cpu(sec) restrained
1 -168.972 14:6:4 40 0
2 -119.657 14:6:44 80 0
3 -105.653 14:7:23 119 0
4 -103.829 14:8:0 156 0
5 -103.751 14:8:41 197 0
6 -103.747 14:9:21 237 0
7 -103.746 14:9:58 274 0
Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 197.6149 259.9120 -86.80744
mod2 41 224.5228 286.8199 -100.26138 26.90789 1 2.13386444379736e-07 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 197.6149 259.912 -86.80744
mod2 41 197.6149 259.912 -86.80744 0 1 1
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 197.6149 259.9120 -86.80744
mod2 41 219.2662 281.5633 -97.63308 21.65128 1 3.26990929235941e-06 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 197.6149 259.9120 -86.80744
mod2 41 222.7045 285.0017 -99.35225 25.08963 1 5.47263978461532e-07 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 197.6149 259.9120 -86.80744
mod2 41 231.4926 293.7898 -103.74630 33.87773 1 5.868655151605e-09 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1iteration LogLik wall cpu(sec) restrained
1 -461.848 14:10:59 45 0
2 -435.948 14:11:45 91 0
3 -427.273 14:12:31 137 0
4 -425.817 14:13:18 184 0
5 -425.693 14:14:5 231 0
6 -425.676 14:14:54 280 0
7 -425.674 14:15:44 330 0
8 -425.673 14:16:36 382 0
iteration LogLik wall cpu(sec) restrained
1 -504.675 14:17:41 45 0
2 -470.459 14:18:26 90 0
3 -461.911 14:19:6 130 0
4 -460.668 14:19:49 173 0
5 -460.557 14:20:31 215 0
6 -460.543 14:21:9 253 0
7 -460.542 14:21:50 294 0
8 -460.541 14:22:33 337 0
iteration LogLik wall cpu(sec) restrained
1 -461.848 14:23:21 41 0
2 -435.948 14:24:1 81 0
3 -427.273 14:24:40 120 0
4 -425.817 14:25:24 164 0
5 -425.693 14:26:5 205 0
6 -425.676 14:26:44 244 0
7 -425.674 14:27:25 285 0
8 -425.673 14:28:8 328 0
iteration LogLik wall cpu(sec) restrained
1 -512.102 14:29:1 36 0
2 -451.936 14:29:45 80 0
3 -434.318 14:30:31 126 0
4 -431.948 14:31:12 167 0
5 -431.788 14:31:52 207 0
6 -431.767 14:32:34 249 0
7 -431.764 14:33:15 290 0
8 -431.763 14:33:57 332 0
iteration LogLik wall cpu(sec) restrained
1 -456.402 14:34:52 39 0
2 -434.7 14:35:34 81 0
3 -428.895 14:36:15 122 0
4 -428.399 14:36:55 162 0
5 -428.393 14:37:34 201 0
6 -428.393 14:38:17 244 0
iteration LogLik wall cpu(sec) restrained
1 -477.151 14:39:20 43 0
2 -456.703 14:40:1 84 0
3 -449.048 14:40:43 126 0
4 -447.556 14:41:23 166 0
5 -447.425 14:42:5 208 0
6 -447.407 14:42:47 250 0
7 -447.405 14:43:30 293 0
8 -447.404 14:44:11 334 0
Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 875.3465 937.5529 -425.6732
mod2 41 945.0826 1007.2891 -460.5413 69.73615 1 6.77920499480788e-17 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 875.3465 937.5529 -425.6732
mod2 41 875.3465 937.5529 -425.6732 0 1 1
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 875.3465 937.5529 -425.6732
mod2 41 887.5270 949.7334 -431.7635 12.18049 1 0.00048 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 875.3465 937.5529 -425.6732
mod2 41 880.7859 942.9924 -428.3930 5.43948 1 0.01969 *
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 875.3465 937.5529 -425.6732
mod2 41 918.8085 981.0149 -447.4042 43.46198 1 4.32276349277575e-11 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1iteration LogLik wall cpu(sec) restrained
1 -289.567 13:44:28 165 0
2 -261.843 13:47:13 330 0
3 -252.699 13:49:55 492 0
4 -251.439 13:52:36 653 0
5 -251.401 13:55:23 820 0
6 -251.4 13:58:8 985 0
7 -251.4 14:0:51 1148 0
iteration LogLik wall cpu(sec) restrained
1 -345.015 14:4:27 149 0
2 -291.708 14:7:3 305 0
3 -275.052 14:9:31 453 0
4 -272.831 14:12:0 602 0
5 -272.769 14:14:38 760 0
6 -272.767 14:17:23 925 0
7 -272.767 14:20:9 1091 0
iteration LogLik wall cpu(sec) restrained
1 -289.567 14:23:12 161 0
2 -261.843 14:25:52 321 0
3 -252.699 14:28:32 481 0
4 -251.439 14:31:14 643 0
5 -251.401 14:33:54 803 0
6 -251.4 14:36:31 960 0
7 -251.4 14:39:13 1122 0
iteration LogLik wall cpu(sec) restrained
1 -359.488 14:43:11 162 0
2 -289.428 14:45:46 317 0
3 -268.502 14:48:9 460 0
4 -265.908 14:50:33 604 0
5 -265.836 14:52:56 747 0
6 -265.833 14:55:21 892 0
7 -265.833 14:57:42 1033 0
iteration LogLik wall cpu(sec) restrained
1 -304.458 15:0:51 128 0
2 -280.074 15:2:57 254 0
3 -272.389 15:5:5 382 0
4 -271.408 15:7:15 512 0
5 -271.387 15:9:23 640 0
6 -271.387 15:11:25 762 0
iteration LogLik wall cpu(sec) restrained
1 -299.241 15:14:22 118 0
2 -277.023 15:16:2 218 0
3 -270.418 15:17:39 315 0
4 -269.617 15:19:21 417 0
5 -269.594 15:20:59 515 0
6 -269.593 15:22:39 615 0
7 -269.593 15:24:15 711 0
Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 534.7999 625.0111 -251.4000
mod2 53 577.5335 667.7446 -272.7667 42.73355 1 6.27272180767349e-11 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 534.7999 625.0111 -251.4
mod2 53 534.7999 625.0111 -251.4 0 1 1
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 534.7999 625.0111 -251.4000
mod2 53 563.6663 653.8775 -265.8331 28.86639 1 7.75470773833564e-08 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 534.7999 625.0111 -251.4000
mod2 53 574.7737 664.9849 -271.3868 39.97378 1 2.57395491088429e-10 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 534.7999 625.0111 -251.4000
mod2 53 571.1866 661.3978 -269.5933 36.3867 1 1.61803235320847e-09 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1iteration LogLik wall cpu(sec) restrained
1 -528.817 13:44:5 141 0
2 -448.392 13:46:21 277 0
3 -417.392 13:48:34 410 0
4 -412.854 13:50:49 545 0
5 -412.724 13:53:5 681 0
6 -412.72 13:55:27 823 0
7 -412.72 13:57:45 961 0
iteration LogLik wall cpu(sec) restrained
1 -613.879 14:0:45 121 0
2 -519.424 14:2:43 239 0
3 -487.898 14:4:56 372 0
4 -483.179 14:7:2 498 0
5 -483.063 14:9:6 622 0
6 -483.059 14:11:8 744 0
7 -483.059 14:13:20 876 0
iteration LogLik wall cpu(sec) restrained
1 -528.817 14:15:54 135 0
2 -448.392 14:18:21 282 0
3 -417.392 14:20:36 417 0
4 -412.854 14:22:51 552 0
5 -412.724 14:25:1 682 0
6 -412.72 14:27:16 817 0
7 -412.72 14:29:26 947 0
iteration LogLik wall cpu(sec) restrained
1 -631.878 14:32:56 134 0
2 -484.676 14:35:8 266 0
3 -432.856 14:37:19 397 0
4 -425.721 14:39:37 535 0
5 -425.545 14:41:49 667 0
6 -425.541 14:44:1 799 0
7 -425.541 14:46:4 922 0
iteration LogLik wall cpu(sec) restrained
1 -511.928 14:49:0 117 0
2 -441.538 14:50:59 236 0
3 -419.121 14:52:59 356 0
4 -416.045 14:55:1 478 0
5 -415.968 14:56:59 596 0
6 -415.966 14:58:55 712 0
7 -415.966 15:0:42 819 0
iteration LogLik wall cpu(sec) restrained
1 -528.577 15:3:23 107 0
2 -455.357 15:5:10 214 0
3 -428.084 15:7:0 324 0
4 -424.43 15:8:48 432 0
5 -424.333 15:10:37 541 0
6 -424.33 15:12:15 639 0
7 -424.33 15:13:53 737 0
Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 857.4398 946.6902 -412.7199
mod2 53 998.1175 1087.3678 -483.0588 140.67766 1 1.89246206135505e-32 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 857.4398 946.6902 -412.7199
mod2 53 857.4398 946.6902 -412.7199 0 1 1
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 857.4398 946.6902 -412.7199
mod2 53 883.0813 972.3316 -425.5406 25.64142 1 4.11120223239732e-07 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 857.4398 946.6902 -412.7199
mod2 53 863.9312 953.1815 -415.9656 6.49137 1 0.01084 *
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 857.4398 946.6902 -412.7199
mod2 53 880.6592 969.9095 -424.3296 23.21936 1 1.44534923248465e-06 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1iteration LogLik wall cpu(sec) restrained
1 -158.286 13:42:23 39 0
2 -100.872 13:43:9 85 0
3 -84.9006 13:43:54 130 0
4 -82.8507 13:44:35 171 0
5 -82.7562 13:45:18 214 0
6 -82.7498 13:46:2 258 0
7 -82.7493 13:46:44 300 0
iteration LogLik wall cpu(sec) restrained
1 -215.958 13:47:35 35 0
2 -126.643 13:48:12 72 0
3 -99.5404 13:48:49 109 0
4 -96.4518 13:49:26 146 0
5 -96.384 13:50:4 184 0
6 -96.3825 13:50:39 219 0
7 -96.3825 13:51:15 255 0
iteration LogLik wall cpu(sec) restrained
1 -158.286 13:51:58 37 0
2 -100.872 13:52:36 75 0
3 -84.9006 13:53:12 111 0
4 -82.8507 13:53:49 148 0
5 -82.7562 13:54:28 187 0
6 -82.7498 13:55:8 227 0
7 -82.7493 13:55:44 263 0
iteration LogLik wall cpu(sec) restrained
1 -226.713 13:56:37 38 0
2 -124.162 13:57:16 77 0
3 -96.5196 13:57:54 115 0
4 -93.5881 13:58:30 151 0
5 -93.5067 13:59:6 187 0
6 -93.5041 13:59:43 224 0
7 -93.504 14:0:22 263 0
iteration LogLik wall cpu(sec) restrained
1 -161.587 14:1:13 36 0
2 -109.907 14:1:50 73 0
3 -96.816 14:2:27 110 0
4 -95.5212 14:3:5 148 0
5 -95.4687 14:3:47 190 0
6 -95.4639 14:4:27 230 0
7 -95.4635 14:5:11 274 0
iteration LogLik wall cpu(sec) restrained
1 -166.076 14:6:6 39 0
2 -116.645 14:6:46 79 0
3 -102.599 14:7:25 118 0
4 -100.777 14:8:2 155 0
5 -100.699 14:8:43 196 0
6 -100.694 14:9:23 236 0
7 -100.694 14:10:0 273 0
Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 189.4985 251.7957 -82.74926
mod2 41 216.7650 279.0621 -96.38249 27.26647 1 1.77258942847132e-07 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 189.4985 251.7957 -82.74926
mod2 41 189.4985 251.7957 -82.74926 0 1 1
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 189.4985 251.7957 -82.74926
mod2 41 211.0080 273.3051 -93.50400 21.50949 1 3.52082519764859e-06 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 189.4985 251.7957 -82.74926
mod2 41 214.9269 277.2241 -95.46346 25.4284 1 4.59109129196136e-07 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 189.4985 251.7957 -82.74926
mod2 41 225.3872 287.6843 -100.69358 35.88865 1 2.08922621245291e-09 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1iteration LogLik wall cpu(sec) restrained
1 -562.778 14:12:43 146 0
2 -547.208 14:15:23 306 0
3 -537.405 14:18:10 473 0
4 -535.015 14:20:46 629 0
5 -534.857 14:23:22 785 0
6 -534.837 14:25:56 939 0
7 -534.834 14:28:30 1093 0
8 -534.833 14:31:8 1251 0
iteration LogLik wall cpu(sec) restrained
1 -592.784 14:34:28 132 0
2 -563.979 14:36:42 266 0
3 -549.176 14:38:57 401 0
4 -545.856 14:41:9 533 0
5 -545.652 14:43:22 666 0
6 -545.625 14:45:33 797 0
7 -545.62 14:47:34 918 0
8 -545.619 14:49:32 1036 0
iteration LogLik wall cpu(sec) restrained
1 -562.778 14:51:48 120 0
2 -547.208 14:53:47 239 0
3 -537.405 14:55:47 359 0
4 -535.015 14:57:47 479 0
5 -534.857 14:59:38 590 0
6 -534.837 15:1:24 696 0
7 -534.834 15:3:11 803 0
8 -534.833 15:4:58 910 0
iteration LogLik wall cpu(sec) restrained
1 -602.519 15:7:38 106 0
2 -565.678 15:9:28 216 0
3 -549.257 15:11:13 321 0
4 -545.996 15:12:51 419 0
5 -545.805 15:14:30 518 0
6 -545.78 15:15:55 603 0
7 -545.776 15:17:14 682 0
8 -545.775 15:18:38 766 0
iteration LogLik wall cpu(sec) restrained
1 -558.087 15:20:44 84 0
2 -547.294 15:22:8 168 0
3 -540.355 15:23:28 248 0
4 -538.859 15:24:48 328 0
5 -538.832 15:25:55 395 0
6 -538.832 15:27:2 462 0
iteration LogLik wall cpu(sec) restrained
1 -551.481 15:28:46 67 0
2 -543.944 15:29:52 133 0
3 -539.714 15:31:10 211 0
4 -538.537 15:32:20 281 0
5 -538.407 15:33:36 357 0
6 -538.388 15:34:47 428 0
7 -538.385 15:36:6 507 0
8 -538.385 15:37:3 564 0
Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 1101.667 1190.934 -534.8335
mod2 53 1123.239 1212.506 -545.6195 21.57199 1 3.4079354505434e-06 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 1101.667 1190.934 -534.8335
mod2 53 1101.667 1190.934 -534.8335 0 1 1
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 1101.667 1190.934 -534.8335
mod2 53 1123.551 1212.817 -545.7753 21.88364 1 2.89692983267488e-06 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 1101.667 1190.934 -534.8335
mod2 53 1109.663 1198.930 -538.8316 7.99634 1 0.00469 **
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 1101.667 1190.934 -534.8335
mod2 53 1108.770 1198.037 -538.3850 7.10313 1 0.00769 **
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1iteration LogLik wall cpu(sec) restrained
1 -361.373 13:44:7 141 0
2 -331.894 13:46:22 276 0
3 -316.66 13:48:37 411 0
4 -314.616 13:50:51 545 0
5 -314.564 13:53:7 681 0
6 -314.563 13:55:30 824 0
7 -314.563 13:57:49 963 0
iteration LogLik wall cpu(sec) restrained
1 -406.497 14:0:49 121 0
2 -359.525 14:2:48 240 0
3 -339.983 14:4:59 371 0
4 -337.587 14:7:6 498 0
5 -337.545 14:9:11 623 0
6 -337.545 14:11:13 745 0
iteration LogLik wall cpu(sec) restrained
1 -361.373 14:13:42 132 0
2 -331.894 14:16:0 270 0
3 -316.66 14:18:23 413 0
4 -314.616 14:20:41 551 0
5 -314.564 14:22:56 686 0
6 -314.563 14:25:7 817 0
7 -314.563 14:27:20 950 0
iteration LogLik wall cpu(sec) restrained
1 -421.695 14:30:49 139 0
2 -357.221 14:33:1 271 0
3 -330.404 14:35:14 404 0
4 -326.633 14:37:25 535 0
5 -326.553 14:39:45 675 0
6 -326.551 14:41:58 808 0
7 -326.551 14:44:15 945 0
iteration LogLik wall cpu(sec) restrained
1 -369.406 14:47:15 119 0
2 -347.739 14:49:14 238 0
3 -336.137 14:51:12 356 0
4 -334.358 14:53:11 475 0
5 -334.318 14:55:13 597 0
6 -334.317 14:57:11 715 0
iteration LogLik wall cpu(sec) restrained
1 -346.626 14:59:59 107 0
2 -326.464 15:1:45 213 0
3 -318.912 15:3:31 319 0
4 -318.059 15:5:20 428 0
5 -318.043 15:7:9 537 0
6 -318.043 15:8:58 646 0
Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 661.1255 750.3922 -314.5627
mod2 53 707.0892 796.3559 -337.5446 45.96368 1 1.2046603370457e-11 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 661.1255 750.3922 -314.5627
mod2 53 661.1255 750.3922 -314.5627 0 1 1
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 661.1255 750.3922 -314.5627
mod2 53 685.1023 774.3689 -326.5511 23.97677 1 9.75052895926333e-07 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 661.1255 750.3922 -314.5627
mod2 53 700.6341 789.9008 -334.3170 39.50859 1 3.26620244912293e-10 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 661.1255 750.3922 -314.5627
mod2 53 668.0854 757.3521 -318.0427 6.95995 1 0.00834 **
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1iteration LogLik wall cpu(sec) restrained
1 -805.664 13:44:29 163 0
2 -784.384 13:47:14 328 0
3 -772.521 13:49:54 488 0
4 -770.251 13:52:36 650 0
5 -770.14 13:55:21 815 0
6 -770.129 13:58:5 979 0
7 -770.128 14:0:47 1141 0
8 -770.127 14:3:32 1306 0
iteration LogLik wall cpu(sec) restrained
1 -849.138 14:7:19 151 0
2 -815.256 14:9:45 297 0
3 -798.999 14:12:14 446 0
4 -795.924 14:14:54 606 0
5 -795.774 14:17:43 775 0
6 -795.757 14:20:28 940 0
7 -795.755 14:23:9 1101 0
8 -795.755 14:25:46 1258 0
iteration LogLik wall cpu(sec) restrained
1 -805.664 14:28:43 156 0
2 -784.384 14:31:25 318 0
3 -772.521 14:34:3 476 0
4 -770.251 14:36:38 631 0
5 -770.14 14:39:18 791 0
6 -770.129 14:41:56 949 0
7 -770.128 14:44:34 1107 0
8 -770.127 14:46:57 1250 0
iteration LogLik wall cpu(sec) restrained
1 -855.04 14:50:29 143 0
2 -804.801 14:52:51 285 0
3 -783.083 14:55:15 429 0
4 -779.144 14:57:35 569 0
5 -778.979 14:59:48 702 0
6 -778.964 15:1:53 827 0
7 -778.963 15:3:57 951 0
8 -778.962 15:6:5 1079 0
iteration LogLik wall cpu(sec) restrained
1 -797.541 15:9:11 128 0
2 -782.619 15:11:14 251 0
3 -774.976 15:13:10 367 0
4 -773.812 15:15:1 478 0
5 -773.799 15:16:38 575 0
6 -773.798 15:18:18 675 0
iteration LogLik wall cpu(sec) restrained
1 -802.88 15:20:47 100 0
2 -789.111 15:22:26 199 0
3 -782.559 15:24:1 294 0
4 -781.079 15:25:30 383 0
5 -780.963 15:26:48 461 0
6 -780.95 15:28:12 545 0
7 -780.949 15:29:32 625 0
8 -780.949 15:31:2 715 0
Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 1572.255 1662.435 -770.1274
mod2 53 1623.509 1713.690 -795.7547 51.25459 1 8.11307329704012e-13 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 1572.255 1662.435 -770.1274
mod2 53 1572.255 1662.435 -770.1274 0 1 1
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 1572.255 1662.435 -770.1274
mod2 53 1589.925 1680.105 -778.9624 17.67003 1 3e-05 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 1572.255 1662.435 -770.1274
mod2 53 1579.597 1669.777 -773.7984 7.34197 1 0.00674 **
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 54 1572.255 1662.435 -770.1274
mod2 53 1593.897 1684.078 -780.9486 21.64253 1 3.28486263381027e-06 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1iteration LogLik wall cpu(sec) restrained
1 -362.218 15:32:13 33 0
2 -332.02 15:32:46 66 0
3 -310.736 15:33:23 103 1
4 -306.197 15:33:56 136 2
5 -305.828 15:34:28 168 2
6 -305.828 15:35:7 207 2
iteration LogLik wall cpu(sec) restrained
1 -403.57 15:35:47 28 0
2 -363.974 15:36:19 60 0
3 -341.893 15:36:41 82 1
4 -336.72 15:37:4 105 1
5 -336.115 15:37:25 126 1
6 -336.007 15:37:44 145 2
7 -335.992 15:38:3 164 2
8 -335.992 15:38:22 183 2
iteration LogLik wall cpu(sec) restrained
1 -362.218 15:38:44 19 0
2 -332.02 15:39:3 38 0
3 -310.736 15:39:21 56 1
4 -306.197 15:39:42 77 2
5 -305.828 15:40:0 95 2
6 -305.828 15:40:18 113 2
iteration LogLik wall cpu(sec) restrained
1 -407.423 15:40:43 17 0
2 -346.71 15:41:3 37 0
3 -317.669 15:41:22 56 1
4 -311.539 15:41:41 75 2
5 -311.025 15:41:59 93 2
6 -311.025 15:42:17 111 2
iteration LogLik wall cpu(sec) restrained
1 -336.469 15:42:42 19 0
2 -318.793 15:43:0 37 0
3 -309.671 15:43:18 55 0
4 -306.216 15:43:36 73 0
5 -305.83 15:43:53 90 1
6 -305.828 15:44:12 109 1
7 -305.828 15:44:31 128 1
iteration LogLik wall cpu(sec) restrained
1 -347.932 15:44:56 19 0
2 -322.828 15:45:13 36 0
3 -307.526 15:45:30 53 1
4 -305.828 15:45:49 72 1
5 -305.828 15:46:6 89 1
Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 635.6560 698.9746 -305.8280
mod2 41 695.9839 759.3025 -335.9919 60.3279 1 8.03011934485854e-15 ***
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 635.656 698.9746 -305.828
mod2 41 635.656 698.9746 -305.828 0 1 1
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 635.6560 698.9746 -305.8280
mod2 41 646.0491 709.3678 -311.0246 10.39316 1 0.00126 **
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 635.6560 698.9746 -305.828
mod2 41 635.6559 698.9746 -305.828 3e-05 1 0.99558
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Likelihood ratio test for mixed models
==============================================================
Df AIC BIC loLik Chisq ChiDf PrChisq
mod1 42 635.656 698.9746 -305.828
mod2 41 635.656 698.9746 -305.828 1e-05 1 0.99784
==============================================================
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1names(results) <- traits
# Salvar os resultados em formato RDS
saveRDS(results, file = "output/result_sommer_row_col_random.RDS")Obtain Parameters
As “future_map” was used to run each stage 1 analysis in parallel, each trait is stored as a separate element in a list. We need to process the “results” object into a “data.frame” or “matrix” for further analysis.
Combine the results them into a single data frame for each parameter.
BLUPS <- map_dfr(results, function(res) {
data.frame(
trait = res$Trait,
Clone = res$blups[[1]]$Clone,
BLUP = res$blups[[1]]$BLUP,
BLUPS_mean = res$blups[[1]]$BLUP + mean_pheno[, res$Trait],
drgBLUP_mean = res$blups[[1]]$drgBLUP + mean_pheno[, res$Trait]
)
})
H2 <- map_dfr(results, function(res) {
data.frame(
trait = res$Trait,
H2_Broad = res$H2_Broad,
H2_narrow = res$H2_narrow
)
})
varcomp <- map_dfr(results, function(res) {
data.frame(
trait = res$Trait,
grp = c("Clone", "Ano", "Ano:Clone", "row", "col", "units"),
res$varcomp
)
})
teste_LRT <- map_dfr(results, function(res) {
data.frame(
trait = res$Trait,
model = c("Complete", "Clone:Year", "Year", "Clone", "row", "col"),
res$teste_LRT
)
})
# Function to extract residuals from each model and create a data frame
fitted_residual_data <- map_dfr(results, function(res) {
extract_res <- sommer::residuals.mmer(res$model)
df <- data.frame(residuals(res$model)[, c(1:5, 8, 15)], trait = res$Trait)
colnames(df)[6:7] <- c("fitted", "residuals")
return(df)
})Results
Variance components
Distribution of variance components
varcomp %>%
group_by(trait) %>%
mutate(freq_relat = VarComp / sum(VarComp)) %>%
mutate(freq_relat = round(freq_relat * 100, 2)) %>%
select(trait, grp, freq_relat) %>%
kbl(escape = F, align = 'c') %>%
kable_classic("hover", full_width = F, position = "center", fixed_thead = T)| trait | grp | freq_relat |
|---|---|---|
| N_Roots | Clone | 34.04 |
| N_Roots | Ano | 9.46 |
| N_Roots | Ano:Clone | 15.76 |
| N_Roots | row | 0.00 |
| N_Roots | col | 1.45 |
| N_Roots | units | 39.29 |
| FRY | Clone | 22.22 |
| FRY | Ano | 9.47 |
| FRY | Ano:Clone | 25.75 |
| FRY | row | 2.37 |
| FRY | col | 1.66 |
| FRY | units | 38.53 |
| ShY | Clone | 38.82 |
| ShY | Ano | 8.67 |
| ShY | Ano:Clone | 14.56 |
| ShY | row | 3.65 |
| ShY | col | 0.70 |
| ShY | units | 33.60 |
| DMC | Clone | 37.91 |
| DMC | Ano | 8.64 |
| DMC | Ano:Clone | 13.82 |
| DMC | row | 2.50 |
| DMC | col | 4.18 |
| DMC | units | 32.95 |
| StY | Clone | 15.90 |
| StY | Ano | 9.74 |
| StY | Ano:Clone | 25.73 |
| StY | row | 1.82 |
| StY | col | 4.83 |
| StY | units | 41.98 |
| Plant.Height | Clone | 23.32 |
| Plant.Height | Ano | 9.89 |
| Plant.Height | Ano:Clone | 15.06 |
| Plant.Height | row | 4.38 |
| Plant.Height | col | 3.32 |
| Plant.Height | units | 44.04 |
| HI | Clone | 23.65 |
| HI | Ano | 9.16 |
| HI | Ano:Clone | 28.91 |
| HI | row | 0.61 |
| HI | col | 1.92 |
| HI | units | 35.76 |
| StC | Clone | 37.81 |
| StC | Ano | 8.62 |
| StC | Ano:Clone | 13.90 |
| StC | row | 2.52 |
| StC | col | 4.29 |
| StC | units | 32.85 |
| Root.Le | Clone | 17.91 |
| Root.Le | Ano | 11.07 |
| Root.Le | Ano:Clone | 12.46 |
| Root.Le | row | 1.85 |
| Root.Le | col | 1.22 |
| Root.Le | units | 55.49 |
| Root.Di | Clone | 20.14 |
| Root.Di | Ano | 10.43 |
| Root.Di | Ano:Clone | 17.93 |
| Root.Di | row | 2.50 |
| Root.Di | col | 0.90 |
| Root.Di | units | 48.10 |
| Stem.D | Clone | 16.10 |
| Stem.D | Ano | 10.73 |
| Stem.D | Ano:Clone | 18.62 |
| Stem.D | row | 1.58 |
| Stem.D | col | 1.85 |
| Stem.D | units | 51.12 |
| Nstem.Plant | Clone | 14.52 |
| Nstem.Plant | Ano | 10.65 |
| Nstem.Plant | Ano:Clone | 24.66 |
| Nstem.Plant | row | 0.00 |
| Nstem.Plant | col | 0.00 |
| Nstem.Plant | units | 50.17 |
FIGURE 1 Distribution of variance components
varcomp %>%
mutate(
grp = recode(
grp,
"Ano" = "Year",
"Ano:Clone" = "Clone:Year",
"Clone" = "Clone",
"row" = "Row",
"col" = "Col",
.default = "Residual"
),
grp = fct_relevel(grp, c("Row", "Col", "Year", "Clone", "Clone:Year", "Residual"))
) %>%
ggplot(aes(x = trait, y = VarComp, fill = grp)) +
geom_col(position = "fill") +
labs(y = "Variance Component (%)", x = "Traits", fill = "Var. Comp.") +
scale_fill_gdocs() +
theme_minimal() +
theme(
text = element_text(size = 25, face = "bold"),
axis.text.x = element_text(size = 20, angle = 45, hjust = 1, vjust = 1)
)
Ploting BLUPS
Distribution of the BLUPs
BLUPS %>%
ggplot(aes(x = BLUPS_mean, fill = trait, color = trait)) +
geom_density(alpha = 0.8, show.legend = F) +
facet_wrap(~ trait, ncol = 4, scales = "free", strip.position = "bottom") +
scale_fill_gdocs() +
scale_color_gdocs() +
theme_bw() +
theme(
text = element_text(size = 20),
panel.spacing = unit(1, "lines"),
strip.background = element_blank(),
panel.background = element_blank(),
plot.background = element_blank(),
strip.placement = "outside"
) +
labs(x = "", y = "Density")
Residual Analisys
Residual distribution
fitted_residual_data %>%
ggplot(aes(x = residuals)) +
geom_histogram(aes(y = ..density..), bins = 10, fill = "lightblue", color = "black") +
geom_density(color = "red", size = 1) +
facet_wrap(~ trait, ncol = 4, scales = "free", strip.position = "bottom") +
labs(x = "Residuals", y = "Density") +
theme_bw() +
theme(
text = element_text(size = 20),
panel.spacing = unit(1, "lines"),
strip.background = element_blank(),
panel.background = element_blank(),
plot.background = element_blank(),
strip.placement = "outside"
)
Residuals vs fitted values
fitted_residual_data %>%
ggplot(aes(x = fitted, y = residuals)) +
geom_point(color = "blue", alpha = 0.7) +
facet_wrap(~ trait, ncol = 4, scales = "free", strip.position = "bottom") +
labs(x = "Fitted Values", y = "Residuals") +
theme_bw() +
theme(
text = element_text(size = 20),
panel.spacing = unit(1, "lines"),
strip.background = element_blank(),
panel.background = element_blank(),
plot.background = element_blank(),
strip.placement = "outside"
)
Models Analisys
LRT test for comparation of models
teste_LRT %>%
kbl(escape = F, align = 'c') %>%
kable_classic("hover", full_width = F, position = "center", fixed_thead = T)| trait | model | Df | AIC | BIC | loLik | Chisq | ChiDf | PrChisq |
|---|---|---|---|---|---|---|---|---|
| N_Roots | Complete | 54 | 598.0635 | 687.4686 | -283.03174 | NA | NA | |
| N_Roots | Clone:Year | 53 | 657.2635 | 746.6685 | -312.63173 | 59.19997 | 1 | 1.42436244665181e-14 *** |
| N_Roots | Year | 53 | 598.0635 | 687.4686 | -283.03174 | 0.00000 | 1 | 1 |
| N_Roots | Clone | 53 | 654.6696 | 744.0747 | -311.33482 | 56.60615 | 1 | 5.32450566461941e-14 *** |
| N_Roots | row | 53 | 598.0635 | 687.4686 | -283.03174 | 0.00000 | 1 | 0.99903 |
| N_Roots | col | 53 | 611.5227 | 700.9277 | -289.76134 | 13.45919 | 1 | 0.00024 *** |
| FRY | Complete | 54 | 927.5204 | 1016.8198 | -447.76022 | NA | NA | |
| FRY | Clone:Year | 53 | 1056.8375 | 1146.1368 | -512.41873 | 129.31702 | 1 | 5.7807213084901e-30 *** |
| FRY | Year | 53 | 927.5204 | 1016.8198 | -447.76022 | 0.00000 | 1 | 1 |
| FRY | Clone | 53 | 962.2390 | 1051.5383 | -465.11949 | 34.71854 | 1 | 3.80986092686306e-09 *** |
| FRY | row | 53 | 934.9968 | 1024.2962 | -451.49841 | 7.47637 | 1 | 0.00625 ** |
| FRY | col | 53 | 948.5361 | 1037.8355 | -458.26806 | 21.01567 | 1 | 4.55542957069547e-06 *** |
| ShY | Complete | 54 | -273.5348 | -183.2544 | 152.76738 | NA | NA | |
| ShY | Clone:Year | 53 | -212.3835 | -122.1031 | 122.19175 | 61.15126 | 1 | 5.28539028651048e-15 *** |
| ShY | Year | 53 | -273.5348 | -183.2544 | 152.76738 | 0.00000 | 1 | 1 |
| ShY | Clone | 53 | -224.8719 | -134.5916 | 128.43597 | 48.66283 | 1 | 3.03973677890998e-12 *** |
| ShY | row | 53 | -249.6705 | -159.3901 | 140.83525 | 23.86428 | 1 | 1.03372377017493e-06 *** |
| ShY | col | 53 | -263.3904 | -173.1100 | 147.69519 | 10.14439 | 1 | 0.00145 ** |
| DMC | Complete | 42 | 197.6149 | 259.9120 | -86.80744 | NA | NA | |
| DMC | Clone:Year | 41 | 224.5228 | 286.8199 | -100.26138 | 26.90789 | 1 | 2.13386444379736e-07 *** |
| DMC | Year | 41 | 197.6149 | 259.9120 | -86.80744 | 0.00000 | 1 | 1 |
| DMC | Clone | 41 | 219.2662 | 281.5633 | -97.63308 | 21.65128 | 1 | 3.26990929235941e-06 *** |
| DMC | row | 41 | 222.7045 | 285.0017 | -99.35225 | 25.08963 | 1 | 5.47263978461532e-07 *** |
| DMC | col | 41 | 231.4926 | 293.7898 | -103.74630 | 33.87773 | 1 | 5.868655151605e-09 *** |
| StY | Complete | 42 | 875.3465 | 937.5529 | -425.67323 | NA | NA | |
| StY | Clone:Year | 41 | 945.0826 | 1007.2891 | -460.54131 | 69.73615 | 1 | 6.77920499480788e-17 *** |
| StY | Year | 41 | 875.3465 | 937.5529 | -425.67323 | 0.00000 | 1 | 1 |
| StY | Clone | 41 | 887.5270 | 949.7334 | -431.76348 | 12.18049 | 1 | 0.00048 *** |
| StY | row | 41 | 880.7859 | 942.9924 | -428.39297 | 5.43948 | 1 | 0.01969 * |
| StY | col | 41 | 918.8085 | 981.0149 | -447.40423 | 43.46198 | 1 | 4.32276349277575e-11 *** |
| Plant.Height | Complete | 54 | 534.7999 | 625.0111 | -251.39996 | NA | NA | |
| Plant.Height | Clone:Year | 53 | 577.5335 | 667.7446 | -272.76673 | 42.73355 | 1 | 6.27272180767349e-11 *** |
| Plant.Height | Year | 53 | 534.7999 | 625.0111 | -251.39996 | 0.00000 | 1 | 1 |
| Plant.Height | Clone | 53 | 563.6663 | 653.8775 | -265.83315 | 28.86639 | 1 | 7.75470773833564e-08 *** |
| Plant.Height | row | 53 | 574.7737 | 664.9849 | -271.38684 | 39.97378 | 1 | 2.57395491088429e-10 *** |
| Plant.Height | col | 53 | 571.1866 | 661.3978 | -269.59331 | 36.38670 | 1 | 1.61803235320847e-09 *** |
| HI | Complete | 54 | 857.4398 | 946.6902 | -412.71992 | NA | NA | |
| HI | Clone:Year | 53 | 998.1175 | 1087.3678 | -483.05875 | 140.67766 | 1 | 1.89246206135505e-32 *** |
| HI | Year | 53 | 857.4398 | 946.6902 | -412.71992 | 0.00000 | 1 | 1 |
| HI | Clone | 53 | 883.0813 | 972.3316 | -425.54063 | 25.64142 | 1 | 4.11120223239732e-07 *** |
| HI | row | 53 | 863.9312 | 953.1815 | -415.96561 | 6.49137 | 1 | 0.01084 * |
| HI | col | 53 | 880.6592 | 969.9095 | -424.32960 | 23.21936 | 1 | 1.44534923248465e-06 *** |
| StC | Complete | 42 | 189.4985 | 251.7957 | -82.74926 | NA | NA | |
| StC | Clone:Year | 41 | 216.7650 | 279.0621 | -96.38249 | 27.26647 | 1 | 1.77258942847132e-07 *** |
| StC | Year | 41 | 189.4985 | 251.7957 | -82.74926 | 0.00000 | 1 | 1 |
| StC | Clone | 41 | 211.0080 | 273.3051 | -93.50400 | 21.50949 | 1 | 3.52082519764859e-06 *** |
| StC | row | 41 | 214.9269 | 277.2241 | -95.46346 | 25.42840 | 1 | 4.59109129196136e-07 *** |
| StC | col | 41 | 225.3872 | 287.6843 | -100.69358 | 35.88865 | 1 | 2.08922621245291e-09 *** |
| Root.Le | Complete | 54 | 1101.6669 | 1190.9336 | -534.83346 | NA | NA | |
| Root.Le | Clone:Year | 53 | 1123.2389 | 1212.5056 | -545.61945 | 21.57199 | 1 | 3.4079354505434e-06 *** |
| Root.Le | Year | 53 | 1101.6669 | 1190.9336 | -534.83346 | 0.00000 | 1 | 1 |
| Root.Le | Clone | 53 | 1123.5506 | 1212.8173 | -545.77528 | 21.88364 | 1 | 2.89692983267488e-06 *** |
| Root.Le | row | 53 | 1109.6633 | 1198.9300 | -538.83163 | 7.99634 | 1 | 0.00469 ** |
| Root.Le | col | 53 | 1108.7701 | 1198.0367 | -538.38503 | 7.10313 | 1 | 0.00769 ** |
| Root.Di | Complete | 54 | 661.1255 | 750.3922 | -314.56275 | NA | NA | |
| Root.Di | Clone:Year | 53 | 707.0892 | 796.3559 | -337.54458 | 45.96368 | 1 | 1.2046603370457e-11 *** |
| Root.Di | Year | 53 | 661.1255 | 750.3922 | -314.56275 | 0.00000 | 1 | 1 |
| Root.Di | Clone | 53 | 685.1023 | 774.3689 | -326.55113 | 23.97677 | 1 | 9.75052895926333e-07 *** |
| Root.Di | row | 53 | 700.6341 | 789.9008 | -334.31704 | 39.50859 | 1 | 3.26620244912293e-10 *** |
| Root.Di | col | 53 | 668.0854 | 757.3521 | -318.04272 | 6.95995 | 1 | 0.00834 ** |
| Stem.D | Complete | 54 | 1572.2548 | 1662.4351 | -770.12738 | NA | NA | |
| Stem.D | Clone:Year | 53 | 1623.5093 | 1713.6897 | -795.75467 | 51.25459 | 1 | 8.11307329704012e-13 *** |
| Stem.D | Year | 53 | 1572.2548 | 1662.4351 | -770.12738 | 0.00000 | 1 | 1 |
| Stem.D | Clone | 53 | 1589.9248 | 1680.1051 | -778.96239 | 17.67003 | 1 | 3e-05 *** |
| Stem.D | row | 53 | 1579.5967 | 1669.7770 | -773.79836 | 7.34197 | 1 | 0.00674 ** |
| Stem.D | col | 53 | 1593.8973 | 1684.0776 | -780.94864 | 21.64253 | 1 | 3.28486263381027e-06 *** |
| Nstem.Plant | Complete | 42 | 635.6560 | 698.9746 | -305.82798 | NA | NA | |
| Nstem.Plant | Clone:Year | 41 | 695.9839 | 759.3025 | -335.99193 | 60.32790 | 1 | 8.03011934485854e-15 *** |
| Nstem.Plant | Year | 41 | 635.6560 | 698.9746 | -305.82798 | 0.00000 | 1 | 1 |
| Nstem.Plant | Clone | 41 | 646.0491 | 709.3678 | -311.02456 | 10.39316 | 1 | 0.00126 ** |
| Nstem.Plant | row | 41 | 635.6559 | 698.9746 | -305.82797 | 0.00003 | 1 | 0.99558 |
| Nstem.Plant | col | 41 | 635.6560 | 698.9746 | -305.82799 | 0.00001 | 1 | 0.99784 |
Then, now we go to execute the Genomic Wide Selection script: GWS.Rmd
R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=Portuguese_Brazil.utf8 LC_CTYPE=Portuguese_Brazil.utf8
[3] LC_MONETARY=Portuguese_Brazil.utf8 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Brazil.utf8
time zone: America/Sao_Paulo
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] furrr_0.3.1 future_1.34.0 GGally_2.2.1 ggthemes_5.1.0
[5] metan_1.19.0 data.table_1.16.4 lubridate_1.9.4 forcats_1.0.0
[9] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2 readr_2.1.5
[13] tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
[17] kableExtra_1.4.0
loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 viridisLite_0.4.2 farver_2.1.2
[4] fastmap_1.2.0 tweenr_2.0.3 mathjaxr_1.6-0
[7] promises_1.3.2 digest_0.6.37 timechange_0.3.0
[10] lifecycle_1.0.4 magrittr_2.0.3 compiler_4.3.3
[13] rlang_1.1.4 sass_0.4.9 tools_4.3.3
[16] yaml_2.3.10 knitr_1.49 labeling_0.4.3
[19] plyr_1.8.9 xml2_1.3.6 RColorBrewer_1.1-3
[22] workflowr_1.7.1 withr_3.0.2 numDeriv_2016.8-1.1
[25] grid_4.3.3 polyclip_1.10-7 git2r_0.35.0
[28] colorspace_2.1-1 globals_0.16.3 scales_1.3.0
[31] MASS_7.3-60.0.1 cli_3.6.3 crayon_1.5.3
[34] rmarkdown_2.29 ragg_1.3.3 reformulas_0.4.0
[37] generics_0.1.3 rstudioapi_0.17.1 tzdb_0.4.0
[40] minqa_1.2.8 cachem_1.1.0 ggforce_0.4.2
[43] splines_4.3.3 parallel_4.3.3 vctrs_0.6.5
[46] boot_1.3-31 Matrix_1.6-1 jsonlite_1.8.9
[49] sommer_4.3.6 hms_1.1.3 patchwork_1.3.0
[52] ggrepel_0.9.6 listenv_0.9.1 systemfonts_1.1.0
[55] jquerylib_0.1.4 parallelly_1.41.0 glue_1.8.0
[58] nloptr_2.1.1 ggstats_0.8.0 codetools_0.2-20
[61] stringi_1.8.4 gtable_0.3.6 later_1.4.1
[64] lme4_1.1-36 lmerTest_3.1-3 munsell_0.5.1
[67] pillar_1.10.1 htmltools_0.5.8.1 R6_2.5.1
[70] textshaping_0.4.1 Rdpack_2.6.2 rprojroot_2.0.4
[73] evaluate_1.0.3 lattice_0.22-6 rbibutils_2.3
[76] httpuv_1.6.15 bslib_0.8.0 Rcpp_1.0.14
[79] svglite_2.1.3 nlme_3.1-166 whisker_0.4.1
[82] xfun_0.50 fs_1.6.5 pkgconfig_2.0.3