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Genomic-Selection-for-Drought-Tolerance-Using-Genome-Wide-SNPs-in-Casava/
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To peRKHSorm the analyses, we will need the following packages:
We can also use the eigenvalues of the G covariance matrix Gaussian Kernel (GK) to perform the analyses. But first, we have to build GK.
For this purpose, we will use the sommer package [@Covarrubias-Pazaran_2014]. In the code below, y is for the vector with the means, GK is G covariance matrix Gaussian Kernel for the random effects, which will be and identity matrix by default; and X is a design matrix for the fixed effects, which will be a vector of ones (1) by default. Note that we are returning to the “1, 0, -1” codification in the SNPs matrix. This is a requirement of the sommer package.
dist <- as.matrix(dist(scale(geno, center = TRUE, scale = TRUE))) ^ 2
GK <- exp(-dist / median(dist))
GK[1:5,1:5] Alagoana363.250437472 Arari424.250437476 BGM_2042
Alagoana363.250437472 1.0000000 0.4278287 0.3892939
Arari424.250437476 0.4278287 1.0000000 0.3832281
BGM_2042 0.3892939 0.3832281 1.0000000
BGM0290.250581760 0.3548060 0.3448635 0.3622436
BGM0368.250437186 0.3195954 0.3273520 0.3875223
BGM0290.250581760 BGM0368.250437186
Alagoana363.250437472 0.3548060 0.3195954
Arari424.250437476 0.3448635 0.3273520
BGM_2042 0.3622436 0.3875223
BGM0290.250581760 1.0000000 0.3404986
BGM0368.250437186 0.3404986 1.0000000To prove that the prediction is accurate, we should peRKHSorm a cross-validation (CV) scheme. For this purpose, we divide the data into a training set and a validation set.
First we separate the data into k folds. Then, we attribute NA for one fold and try to predict the data from this fold based on the others. When selecting the number of folds, one must prioritize the balance between the number of observations in each fold.
In addition, this process should be repeated for further validation. The step-by-step below will guide the CV in the data we are analysing.
Since we defined 5 folds, our data will be divided into 5 parts with 83 observations each.
The order is decreasing or increasing (numeric or alphabetical) regarding the name of the genotypes.
pheno <- pheno[order(pheno$ID_Clone, decreasing = F),]
geno <- geno[order(row.names(geno)),]
all(rownames(geno) == pheno$ID_Clone)[1] TRUEThis will be useful to assign each observation for a fold, which will be the next step.
In this step, we will assign each observation to a fold. Bear in mind that for each repetition, the folds will comprise different observations. The purpose of the repetition is to make sure of the randomness of the assignment step.
In this step, we will use the cvTools package [@cvTools]
For better peRKHSormance, we included this step in the loop of the next step.
The next step is the very CV. Here, we will define the linear predictor and the lists that will be useful in the loop. The first list, here called results_cv_RKHS and, contains the results for each fold assignation that we built in the previous step. The second GEBVS_RKHS contains the GEBVs.
Then, we will construct the loop. Each iteration will assign NA for a different fold, and we will use the other folds to predict the missing values. Note that the folds vary for each repetition and trait.
Set up parallel processing. Define and run multiple models to get the GEBVs ATTENTION: This process is time-consuming.
# Planejar o processamento em várias sessões para paralelização
plan(multisession)
# Iniciar uma lista para armazenar os resultados
results_list <-
future_map(traits, .options = furrr_options(seed = 100), function(j) {
# Pré-processamento dos dados
pheno2 <- pheno %>%
select(ID_Clone, all_of(j)) %>%
na.omit() %>%
ungroup() %>%
filter(ID_Clone %in% rownames(GK)) %>%
mutate(ID = factor(1:nrow(.))) %>%
droplevels()
# Filtrar as linhas de Z com base em pheno2$ID_Clone
GK1 <-
GK[rownames(GK) %in% pheno2$ID_Clone, rownames(GK) %in% pheno2$ID_Clone]
#Semente para reprodução
set.seed(100)
# Listas das folds
fold.list <- lapply(1:nrept, function(a) {
folds <- cvFolds(nlevels(pheno2$ID),
type = "random",
K = nfolds)
split(folds$subsets, f = folds$which)
})
# Usar future_map_dfr para criar dobras cruzadas em paralelo
future_map_dfr(1:length(fold.list), function(z) {
for (i in 1:nfolds) {
# Conjunto de treinamento
train_data <- pheno2
# Conjunto de validação
train_data[train_data$ID %in% fold.list[[z]][[i]], j] <- NA
# Fitting model
fixed <- formula(paste(j, " ~ 1"))
RKHS <-
sommer::mmer(
fixed,
random = ~ sommer::vsr(ID_Clone, Gu = GK1),
data = train_data,
rcov = ~ units
)
# GETGV
Pred <-
data.frame(
Yhat = RKHS$U$`u:ID_Clone`[[j]],
ID = train_data$ID,
ID_Clone = train_data$ID_Clone
) %>%
filter(ID %in% fold.list[[z]][[i]])
result1 <-
tibble(
GEBV = Pred$Yhat,
ID = Pred$ID,
ID_Clone = Pred$ID_Clone,
Trait = j,
rep = z,
fold = i
)
# Resultados da previsão
if (i == 1) {
result <- result1
} else {
result <- rbind(result, result1)
}
}
#Ordenando os resultados de acordo com o ID
result <- result[order(result$ID, decreasing = F),]
# Resultados da validação cruzada
result_cv <- tibble(
Trait = j,
rep = z,
Log = all(result$ID == pheno2$ID),
Ac = round(cor(result$GEBV, pheno2[[j]], use = "na.or.complete"), 3),
MSPE = round(mean((
result$GEBV - pheno2[[j]]
) ^ 2, na.rm = TRUE), 3),
result = list(result)
)
})
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4 -145.091 14:52:2 0 0
5 -145.075 14:52:2 0 0
6 -145.074 14:52:2 0 0
7 -145.074 14:52:2 0 0
iteration LogLik wall cpu(sec) restrained
1 -153.974 14:52:3 1 0
2 -147.867 14:52:3 1 0
3 -144.189 14:52:3 1 0
4 -142.891 14:52:3 1 0
5 -142.71 14:52:3 1 0
6 -142.689 14:52:3 1 0
7 -142.687 14:52:3 1 0
8 -142.687 14:52:3 1 0
iteration LogLik wall cpu(sec) restrained
1 -151.466 14:52:4 1 0
2 -145.723 14:52:4 1 0
3 -144.453 14:52:4 1 0
4 -144.313 14:52:4 1 0
5 -144.309 14:52:4 1 0
6 -144.309 14:52:4 1 0
iteration LogLik wall cpu(sec) restrained
1 -158.439 14:51:0 0 0
2 -156.437 14:51:0 0 0
3 -155.338 14:51:0 0 0
4 -154.893 14:51:1 1 0
5 -154.79 14:51:1 1 0
6 -154.767 14:51:1 1 0
7 -154.762 14:51:1 1 0
8 -154.761 14:51:1 1 0
9 -154.76 14:51:2 2 0
iteration LogLik wall cpu(sec) restrained
1 -150.888 14:51:2 0 0
2 -143.671 14:51:2 0 0
3 -142.49 14:51:2 0 0
4 -142.398 14:51:3 1 0
5 -142.398 14:51:3 1 0
iteration LogLik wall cpu(sec) restrained
1 -155.25 14:51:3 0 0
2 -151.296 14:51:4 1 0
3 -149.495 14:51:4 1 0
4 -148.882 14:51:4 1 0
5 -148.775 14:51:4 1 0
6 -148.757 14:51:4 1 0
7 -148.754 14:51:5 2 0
8 -148.753 14:51:5 2 0
iteration LogLik wall cpu(sec) restrained
1 -156.805 14:51:5 0 0
2 -153.479 14:51:5 0 0
3 -152.063 14:51:6 1 0
4 -151.627 14:51:6 1 0
5 -151.558 14:51:6 1 0
6 -151.548 14:51:6 1 0
7 -151.546 14:51:6 1 0
8 -151.546 14:51:7 2 0
iteration LogLik wall cpu(sec) restrained
1 -154.492 14:51:7 0 0
2 -148.761 14:51:7 0 0
3 -145.488 14:51:8 1 0
4 -143.912 14:51:8 1 0
5 -143.507 14:51:8 1 0
6 -143.419 14:51:8 1 0
7 -143.402 14:51:8 1 0
8 -143.399 14:51:9 2 0
9 -143.398 14:51:9 2 0
iteration LogLik wall cpu(sec) restrained
1 -153.676 14:51:9 0 0
2 -146.892 14:51:10 1 0
3 -143.572 14:51:10 1 0
4 -142.535 14:51:10 1 0
5 -142.399 14:51:10 1 0
6 -142.383 14:51:11 2 0
7 -142.381 14:51:11 2 0
8 -142.381 14:51:11 2 0
iteration LogLik wall cpu(sec) restrained
1 -153.683 14:51:12 1 0
2 -148.98 14:51:12 1 0
3 -147.606 14:51:12 1 0
4 -147.321 14:51:12 1 0
5 -147.296 14:51:13 2 0
6 -147.294 14:51:13 2 0
7 -147.294 14:51:13 2 0
iteration LogLik wall cpu(sec) restrained
1 -154.769 14:51:14 1 0
2 -149.761 14:51:14 1 0
3 -147.653 14:51:14 1 0
4 -147.054 14:51:14 1 0
5 -146.981 14:51:14 1 0
6 -146.973 14:51:15 2 0
7 -146.973 14:51:15 2 0
iteration LogLik wall cpu(sec) restrained
1 -156.632 14:51:16 1 0
2 -153.831 14:51:16 1 0
3 -152.6 14:51:16 1 0
4 -152.142 14:51:16 1 0
5 -152.039 14:51:17 2 0
6 -152.016 14:51:17 2 0
7 -152.011 14:51:17 2 0
8 -152.01 14:51:17 2 0
9 -152.01 14:51:18 3 0
iteration LogLik wall cpu(sec) restrained
1 -157.259 14:51:18 0 0
2 -154.272 14:51:18 0 0
3 -152.825 14:51:18 0 0
4 -152.28 14:51:19 1 0
5 -152.162 14:51:19 1 0
6 -152.137 14:51:19 1 0
7 -152.132 14:51:19 1 0
8 -152.131 14:51:20 2 0
9 -152.131 14:51:20 2 0
iteration LogLik wall cpu(sec) restrained
1 -153.464 14:51:20 0 0
2 -147.13 14:51:20 0 0
3 -144.525 14:51:21 1 0
4 -143.926 14:51:21 1 0
5 -143.883 14:51:21 1 0
6 -143.88 14:51:21 1 0
7 -143.88 14:51:22 2 0
iteration LogLik wall cpu(sec) restrained
1 -153.784 14:51:22 0 0
2 -149.731 14:51:23 1 0
3 -148.541 14:51:23 1 0
4 -148.242 14:51:23 1 0
5 -148.201 14:51:23 1 0
6 -148.195 14:51:23 1 0
7 -148.194 14:51:24 2 0
iteration LogLik wall cpu(sec) restrained
1 -157.672 14:51:24 0 0
2 -154.653 14:51:24 0 0
3 -152.882 14:51:24 0 0
4 -152.19 14:51:25 1 0
5 -152.057 14:51:25 1 0
6 -152.034 14:51:25 1 0
7 -152.03 14:51:25 1 0
8 -152.03 14:51:25 1 0
iteration LogLik wall cpu(sec) restrained
1 -155.062 14:51:26 0 0
2 -150.687 14:51:26 0 0
3 -149.01 14:51:26 0 0
4 -148.487 14:51:26 0 0
5 -148.395 14:51:27 1 0
6 -148.378 14:51:27 1 0
7 -148.375 14:51:27 1 0
8 -148.375 14:51:27 1 0
iteration LogLik wall cpu(sec) restrained
1 -155.256 14:51:28 1 0
2 -150.211 14:51:28 1 0
3 -147.976 14:51:28 1 0
4 -147.389 14:51:28 1 0
5 -147.332 14:51:29 2 0
6 -147.327 14:51:29 2 0
7 -147.326 14:51:29 2 0
iteration LogLik wall cpu(sec) restrained
1 -151.611 14:51:29 0 0
2 -146.113 14:51:30 1 0
3 -145.14 14:51:30 1 0
4 -145.004 14:51:30 1 0
5 -144.997 14:51:30 1 0
6 -144.996 14:51:31 2 0
iteration LogLik wall cpu(sec) restrained
1 -157.411 14:51:31 0 0
2 -154.477 14:51:32 1 0
3 -152.729 14:51:32 1 0
4 -152.023 14:51:32 1 0
5 -151.882 14:51:32 1 0
6 -151.856 14:51:32 1 0
7 -151.852 14:51:33 2 0
8 -151.851 14:51:33 2 0
iteration LogLik wall cpu(sec) restrained
1 -155.257 14:51:33 0 0
2 -150.523 14:51:33 0 0
3 -147.998 14:51:34 1 0
4 -146.936 14:51:34 1 0
5 -146.697 14:51:34 1 0
6 -146.648 14:51:34 1 0
7 -146.639 14:51:34 1 0
8 -146.637 14:51:35 2 0
9 -146.637 14:51:35 2 0
iteration LogLik wall cpu(sec) restrained
1 -155.351 14:51:35 0 0
2 -149.857 14:51:35 0 0
3 -147.059 14:51:36 1 0
4 -146.147 14:51:36 1 0
5 -146.03 14:51:36 1 0
6 -146.017 14:51:36 1 0
7 -146.016 14:51:37 2 0
8 -146.016 14:51:37 2 0
iteration LogLik wall cpu(sec) restrained
1 -155.647 14:51:37 0 0
2 -151.987 14:51:37 0 0
3 -150.599 14:51:38 1 0
4 -150.246 14:51:38 1 0
5 -150.208 14:51:38 1 0
6 -150.204 14:51:38 1 0
7 -150.204 14:51:38 1 0
iteration LogLik wall cpu(sec) restrained
1 -154.137 14:51:39 0 0
2 -149.093 14:51:39 0 0
3 -146.995 14:51:39 0 0
4 -146.39 14:51:39 0 0
5 -146.313 14:51:39 0 0
6 -146.304 14:51:40 1 0
7 -146.303 14:51:40 1 0
8 -146.302 14:51:40 1 0
iteration LogLik wall cpu(sec) restrained
1 -153.032 14:51:40 0 0
2 -146.698 14:51:40 0 0
3 -143.894 14:51:41 1 0
4 -142.969 14:51:41 1 0
5 -142.831 14:51:41 1 0
6 -142.813 14:51:41 1 0
7 -142.811 14:51:41 1 0
8 -142.81 14:51:41 1 0
iteration LogLik wall cpu(sec) restrained
1 -154.656 14:51:42 0 0
2 -149.862 14:51:42 0 0
3 -147.997 14:51:42 0 0
4 -147.54 14:51:42 0 0
5 -147.497 14:51:43 1 0
6 -147.494 14:51:43 1 0
7 -147.493 14:51:43 1 0
iteration LogLik wall cpu(sec) restrained
1 -157.54 14:51:43 0 0
2 -154.181 14:51:43 0 0
3 -152.305 14:51:44 1 0
4 -151.621 14:51:44 1 0
5 -151.502 14:51:44 1 0
6 -151.483 14:51:44 1 0
7 -151.48 14:51:45 2 0
8 -151.48 14:51:45 2 0
iteration LogLik wall cpu(sec) restrained
1 -156.631 14:51:45 0 0
2 -153.977 14:51:45 0 0
3 -153.146 14:51:46 1 0
4 -152.925 14:51:46 1 0
5 -152.889 14:51:46 1 0
6 -152.882 14:51:46 1 0
7 -152.881 14:51:46 1 0
8 -152.881 14:51:46 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.911 14:51:0 0 0
2 -118.677 14:51:0 0 0
3 -118.224 14:51:0 0 0
4 -118.15 14:51:0 0 0
5 -118.146 14:51:0 0 0
6 -118.146 14:51:1 1 0
iteration LogLik wall cpu(sec) restrained
1 -120.036 14:51:1 0 0
2 -118.963 14:51:1 0 0
3 -118.519 14:51:1 0 0
4 -118.418 14:51:1 0 0
5 -118.408 14:51:1 0 0
6 -118.407 14:51:1 0 0
iteration LogLik wall cpu(sec) restrained
1 -118.109 14:51:1 0 0
2 -115.543 14:51:2 1 0
3 -114.736 14:51:2 1 0
4 -114.598 14:51:2 1 0
5 -114.591 14:51:2 1 0
6 -114.59 14:51:2 1 0
iteration LogLik wall cpu(sec) restrained
1 -120.408 14:51:2 0 0
2 -119.771 14:51:2 0 0
3 -119.554 14:51:2 0 0
4 -119.523 14:51:2 0 0
5 -119.522 14:51:3 1 0
6 -119.522 14:51:3 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.811 14:51:3 0 0
2 -118.093 14:51:3 0 0
3 -116.848 14:51:3 0 0
4 -116.221 14:51:3 0 0
5 -116.04 14:51:3 0 0
6 -115.991 14:51:3 0 0
7 -115.978 14:51:3 0 0
8 -115.975 14:51:3 0 0
9 -115.974 14:51:4 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.957 14:51:4 0 0
2 -119.35 14:51:4 0 0
3 -119.213 14:51:4 0 0
4 -119.202 14:51:4 0 0
5 -119.202 14:51:4 0 0
iteration LogLik wall cpu(sec) restrained
1 -119.975 14:51:4 0 0
2 -118.939 14:51:4 0 0
3 -118.533 14:51:5 1 0
4 -118.45 14:51:5 1 0
5 -118.443 14:51:5 1 0
6 -118.443 14:51:5 1 0
iteration LogLik wall cpu(sec) restrained
1 -120.132 14:51:5 0 0
2 -118.594 14:51:5 0 0
3 -117.622 14:51:5 0 0
4 -117.261 14:51:5 0 0
5 -117.198 14:51:5 0 0
6 -117.188 14:51:5 0 0
7 -117.186 14:51:5 0 0
8 -117.186 14:51:6 1 0
iteration LogLik wall cpu(sec) restrained
1 -118.484 14:51:6 0 0
2 -116.129 14:51:6 0 0
3 -115.183 14:51:6 0 0
4 -114.975 14:51:6 0 0
5 -114.956 14:51:6 0 0
6 -114.954 14:51:6 0 0
7 -114.954 14:51:6 0 0
iteration LogLik wall cpu(sec) restrained
1 -119.04 14:51:7 1 0
2 -116.914 14:51:7 1 0
3 -115.891 14:51:7 1 0
4 -115.528 14:51:7 1 0
5 -115.45 14:51:7 1 0
6 -115.432 14:51:7 1 0
7 -115.428 14:51:7 1 0
8 -115.427 14:51:7 1 0
iteration LogLik wall cpu(sec) restrained
1 -121.973 14:51:7 0 0
2 -121.868 14:51:7 0 0
3 -121.816 14:51:8 1 0
4 -121.802 14:51:8 1 0
5 -121.801 14:51:8 1 0
6 -121.801 14:51:8 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.459 14:51:8 0 0
2 -117.452 14:51:8 0 0
3 -116.241 14:51:8 0 0
4 -115.762 14:51:8 0 0
5 -115.662 14:51:8 0 0
6 -115.642 14:51:8 0 0
7 -115.638 14:51:9 1 0
8 -115.637 14:51:9 1 0
iteration LogLik wall cpu(sec) restrained
1 -120.269 14:51:9 0 0
2 -119.249 14:51:9 0 0
3 -118.712 14:51:9 0 0
4 -118.546 14:51:9 0 0
5 -118.521 14:51:9 0 0
6 -118.517 14:51:9 0 0
7 -118.517 14:51:9 0 0
iteration LogLik wall cpu(sec) restrained
1 -118.435 14:51:10 0 0
2 -116.521 14:51:10 0 0
3 -116.031 14:51:10 0 0
4 -115.972 14:51:10 0 0
5 -115.97 14:51:10 0 0
6 -115.97 14:51:10 0 0
iteration LogLik wall cpu(sec) restrained
1 -116.796 14:51:10 0 0
2 -111.761 14:51:10 0 0
3 -109.224 14:51:10 0 0
4 -108.346 14:51:11 1 0
5 -108.204 14:51:11 1 0
6 -108.183 14:51:11 1 0
7 -108.18 14:51:11 1 0
8 -108.179 14:51:11 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.141 14:51:11 0 0
2 -117.572 14:51:11 0 0
3 -117.113 14:51:11 0 0
4 -117.056 14:51:12 1 0
5 -117.055 14:51:12 1 0
6 -117.055 14:51:12 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.03 14:51:12 0 0
2 -117.343 14:51:12 0 0
3 -116.698 14:51:12 0 0
4 -116.534 14:51:12 0 0
5 -116.512 14:51:12 0 0
6 -116.508 14:51:12 0 0
7 -116.508 14:51:12 0 0
iteration LogLik wall cpu(sec) restrained
1 -120.538 14:51:13 0 0
2 -119.672 14:51:13 0 0
3 -119.142 14:51:13 0 0
4 -118.937 14:51:13 0 0
5 -118.897 14:51:13 0 0
6 -118.889 14:51:13 0 0
7 -118.888 14:51:13 0 0
8 -118.887 14:51:13 0 0
iteration LogLik wall cpu(sec) restrained
1 -119.813 14:51:14 1 0
2 -118.278 14:51:14 1 0
3 -117.561 14:51:14 1 0
4 -117.379 14:51:14 1 0
5 -117.359 14:51:14 1 0
6 -117.357 14:51:14 1 0
7 -117.356 14:51:14 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.054 14:51:14 0 0
2 -117.523 14:51:14 0 0
3 -117.076 14:51:15 1 0
4 -117.026 14:51:15 1 0
5 -117.025 14:51:15 1 0
6 -117.025 14:51:15 1 0
iteration LogLik wall cpu(sec) restrained
1 -120.345 14:51:15 0 0
2 -119.385 14:51:15 0 0
3 -118.934 14:51:15 0 0
4 -118.819 14:51:15 0 0
5 -118.806 14:51:15 0 0
6 -118.804 14:51:16 1 0
7 -118.804 14:51:16 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.444 14:51:16 0 0
2 -117.941 14:51:16 0 0
3 -117.343 14:51:16 0 0
4 -117.211 14:51:16 0 0
5 -117.199 14:51:16 0 0
6 -117.197 14:51:16 0 0
7 -117.197 14:51:17 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.041 14:51:17 0 0
2 -116.746 14:51:17 0 0
3 -115.524 14:51:17 0 0
4 -115.142 14:51:17 0 0
5 -115.087 14:51:17 0 0
6 -115.08 14:51:17 0 0
7 -115.079 14:51:17 0 0
8 -115.079 14:51:17 0 0
iteration LogLik wall cpu(sec) restrained
1 -118.499 14:51:18 0 0
2 -115.856 14:51:18 0 0
3 -114.748 14:51:18 0 0
4 -114.497 14:51:18 0 0
5 -114.476 14:51:18 0 0
6 -114.474 14:51:18 0 0
7 -114.474 14:51:18 0 0
iteration LogLik wall cpu(sec) restrained
1 -120.581 14:51:18 0 0
2 -120.077 14:51:18 0 0
3 -119.896 14:51:19 1 0
4 -119.863 14:51:19 1 0
5 -119.861 14:51:19 1 0
6 -119.86 14:51:19 1 0
iteration LogLik wall cpu(sec) restrained
1 -116.128 14:51:19 0 0
2 -111.197 14:51:19 0 0
3 -108.736 14:51:19 0 0
4 -107.715 14:51:19 0 0
5 -107.485 14:51:19 0 0
6 -107.439 14:51:20 1 0
7 -107.431 14:51:20 1 0
8 -107.429 14:51:20 1 0
9 -107.429 14:51:20 1 0
iteration LogLik wall cpu(sec) restrained
1 -114.88 14:51:20 0 0
2 -108.228 14:51:20 0 0
3 -105.467 14:51:20 0 0
4 -104.687 14:51:20 0 0
5 -104.596 14:51:20 0 0
6 -104.587 14:51:20 0 0
7 -104.586 14:51:21 1 0
iteration LogLik wall cpu(sec) restrained
1 -116.332 14:51:21 0 0
2 -112.81 14:51:21 0 0
3 -112.061 14:51:21 0 0
4 -111.926 14:51:21 0 0
5 -111.913 14:51:21 0 0
6 -111.911 14:51:21 0 0
7 -111.911 14:51:21 0 0
iteration LogLik wall cpu(sec) restrained
1 -114.802 14:51:21 0 0
2 -109.396 14:51:22 1 0
3 -108.172 14:51:22 1 0
4 -107.999 14:51:22 1 0
5 -107.99 14:51:22 1 0
6 -107.989 14:51:22 1 0
iteration LogLik wall cpu(sec) restrained
1 -115.935 14:51:22 0 0
2 -110.564 14:51:22 0 0
3 -108.562 14:51:22 0 0
4 -108.047 14:51:22 0 0
5 -107.981 14:51:23 1 0
6 -107.973 14:51:23 1 0
7 -107.972 14:51:23 1 0
8 -107.972 14:51:23 1 0
iteration LogLik wall cpu(sec) restrained
1 -115.02 14:51:23 0 0
2 -110.371 14:51:23 0 0
3 -109.17 14:51:23 0 0
4 -108.888 14:51:23 0 0
5 -108.851 14:51:23 0 0
6 -108.846 14:51:23 0 0
7 -108.845 14:51:24 1 0
iteration LogLik wall cpu(sec) restrained
1 -114.776 14:51:24 0 0
2 -107.94 14:51:24 0 0
3 -105.138 14:51:24 0 0
4 -104.303 14:51:24 0 0
5 -104.192 14:51:24 0 0
6 -104.179 14:51:24 0 0
7 -104.177 14:51:24 0 0
8 -104.177 14:51:24 0 0
iteration LogLik wall cpu(sec) restrained
1 -116.198 14:51:25 1 0
2 -111.93 14:51:25 1 0
3 -110.722 14:51:25 1 0
4 -110.475 14:51:25 1 0
5 -110.45 14:51:25 1 0
6 -110.447 14:51:25 1 0
7 -110.446 14:51:25 1 0
iteration LogLik wall cpu(sec) restrained
1 -115.662 14:51:25 0 0
2 -110.826 14:51:25 0 0
3 -109.075 14:51:25 0 0
4 -108.551 14:51:25 0 0
5 -108.463 14:51:26 1 0
6 -108.448 14:51:26 1 0
7 -108.446 14:51:26 1 0
8 -108.445 14:51:26 1 0
iteration LogLik wall cpu(sec) restrained
1 -116.732 14:51:26 0 0
2 -111.516 14:51:26 0 0
3 -108.895 14:51:26 0 0
4 -107.982 14:51:26 0 0
5 -107.833 14:51:26 0 0
6 -107.811 14:51:26 0 0
7 -107.808 14:51:27 1 0
8 -107.808 14:51:27 1 0
iteration LogLik wall cpu(sec) restrained
1 -116.062 14:51:27 0 0
2 -111.277 14:51:27 0 0
3 -109.278 14:51:27 0 0
4 -108.625 14:51:27 0 0
5 -108.508 14:51:27 0 0
6 -108.487 14:51:27 0 0
7 -108.484 14:51:27 0 0
8 -108.483 14:51:27 0 0
iteration LogLik wall cpu(sec) restrained
1 -115.191 14:51:28 0 0
2 -108.857 14:51:28 0 0
3 -105.983 14:51:28 0 0
4 -104.96 14:51:28 0 0
5 -104.759 14:51:28 0 0
6 -104.722 14:51:28 0 0
7 -104.715 14:51:28 0 0
8 -104.714 14:51:28 0 0
9 -104.714 14:51:28 0 0
iteration LogLik wall cpu(sec) restrained
1 -116.163 14:51:29 1 0
2 -111.882 14:51:29 1 0
3 -110.391 14:51:29 1 0
4 -110.024 14:51:29 1 0
5 -109.979 14:51:29 1 0
6 -109.973 14:51:29 1 0
7 -109.972 14:51:29 1 0
iteration LogLik wall cpu(sec) restrained
1 -115.404 14:51:29 0 0
2 -110.133 14:51:29 0 0
3 -108.751 14:51:30 1 0
4 -108.535 14:51:30 1 0
5 -108.523 14:51:30 1 0
6 -108.523 14:51:30 1 0
iteration LogLik wall cpu(sec) restrained
1 -115.327 14:51:30 0 0
2 -110.005 14:51:30 0 0
3 -108.283 14:51:30 0 0
4 -107.762 14:51:30 0 0
5 -107.674 14:51:30 0 0
6 -107.659 14:51:31 1 0
7 -107.657 14:51:31 1 0
8 -107.657 14:51:31 1 0
iteration LogLik wall cpu(sec) restrained
1 -114.201 14:51:31 0 0
2 -108.108 14:51:31 0 0
3 -106.392 14:51:31 0 0
4 -105.971 14:51:31 0 0
5 -105.918 14:51:31 0 0
6 -105.911 14:51:32 1 0
7 -105.91 14:51:32 1 0
iteration LogLik wall cpu(sec) restrained
1 -116.455 14:51:32 0 0
2 -112.493 14:51:32 0 0
3 -111.071 14:51:32 0 0
4 -110.678 14:51:32 0 0
5 -110.614 14:51:32 0 0
6 -110.603 14:51:32 0 0
7 -110.601 14:51:32 0 0
8 -110.601 14:51:32 0 0
iteration LogLik wall cpu(sec) restrained
1 -115.177 14:51:33 0 0
2 -110.19 14:51:33 0 0
3 -109.19 14:51:33 0 0
4 -109.091 14:51:33 0 0
5 -109.089 14:51:33 0 0
6 -109.089 14:51:33 0 0
iteration LogLik wall cpu(sec) restrained
1 -113.855 14:51:33 0 0
2 -105.355 14:51:33 0 0
3 -101.893 14:51:33 0 0
4 -100.779 14:51:34 1 0
5 -100.629 14:51:34 1 0
6 -100.612 14:51:34 1 0
7 -100.61 14:51:34 1 0
8 -100.61 14:51:34 1 0
iteration LogLik wall cpu(sec) restrained
1 -118.003 14:51:34 0 0
2 -114.904 14:51:34 0 0
3 -113.364 14:51:34 0 0
4 -112.799 14:51:34 0 0
5 -112.68 14:51:34 0 0
6 -112.656 14:51:34 0 0
7 -112.65 14:51:35 1 0
8 -112.649 14:51:35 1 0
9 -112.649 14:51:35 1 0
iteration LogLik wall cpu(sec) restrained
1 -115.398 14:51:35 0 0
2 -109.491 14:51:35 0 0
3 -106.652 14:51:35 0 0
4 -105.459 14:51:35 0 0
5 -105.18 14:51:35 0 0
6 -105.122 14:51:35 0 0
7 -105.111 14:51:35 0 0
8 -105.109 14:51:36 1 0
9 -105.109 14:51:36 1 0
iteration LogLik wall cpu(sec) restrained
1 -115.942 14:51:36 0 0
2 -111.183 14:51:36 0 0
3 -109.45 14:51:36 0 0
4 -109.014 14:51:36 0 0
5 -108.961 14:51:36 0 0
6 -108.954 14:51:36 0 0
7 -108.953 14:51:36 0 0
iteration LogLik wall cpu(sec) restrained
1 -114.388 14:51:37 0 0
2 -108.363 14:51:37 0 0
3 -106.997 14:51:37 0 0
4 -106.772 14:51:37 0 0
5 -106.758 14:51:37 0 0
6 -106.757 14:51:37 0 0
iteration LogLik wall cpu(sec) restrained
1 -115.684 14:51:37 0 0
2 -110.913 14:51:37 0 0
3 -109.169 14:51:37 0 0
4 -108.642 14:51:38 1 0
5 -108.553 14:51:38 1 0
6 -108.537 14:51:38 1 0
7 -108.535 14:51:38 1 0
8 -108.534 14:51:38 1 0
iteration LogLik wall cpu(sec) restrained
1 -117.5 14:51:38 0 0
2 -114.425 14:51:38 0 0
3 -113.43 14:51:38 0 0
4 -113.197 14:51:38 0 0
5 -113.168 14:51:38 0 0
6 -113.164 14:51:38 0 0
7 -113.163 14:51:39 1 0
iteration LogLik wall cpu(sec) restrained
1 -159.608 14:51:1 1 0
2 -158.548 14:51:1 1 0
3 -158.014 14:51:1 1 0
4 -157.842 14:51:1 1 0
5 -157.814 14:51:1 1 0
6 -157.81 14:51:2 2 0
7 -157.809 14:51:2 2 0
iteration LogLik wall cpu(sec) restrained
1 -157.155 14:51:2 0 0
2 -153.283 14:51:3 1 0
3 -151.453 14:51:3 1 0
4 -151.116 14:51:3 1 0
5 -151.104 14:51:3 1 0
6 -151.103 14:51:3 1 0
iteration LogLik wall cpu(sec) restrained
1 -158.613 14:51:4 0 0
2 -155.699 14:51:4 0 0
3 -153.819 14:51:4 0 0
4 -153.214 14:51:5 1 0
5 -153.15 14:51:5 1 0
6 -153.144 14:51:5 1 0
7 -153.144 14:51:5 1 0
iteration LogLik wall cpu(sec) restrained
1 -158.427 14:51:6 1 0
2 -155.556 14:51:6 1 0
3 -154.231 14:51:6 1 0
4 -153.925 14:51:6 1 0
5 -153.901 14:51:6 1 0
6 -153.899 14:51:7 2 0
7 -153.899 14:51:7 2 0
iteration LogLik wall cpu(sec) restrained
1 -158.616 14:51:7 0 0
2 -155.471 14:51:8 1 0
3 -153.362 14:51:8 1 0
4 -152.561 14:51:8 1 0
5 -152.435 14:51:8 1 0
6 -152.419 14:51:8 1 0
7 -152.416 14:51:9 2 0
8 -152.416 14:51:9 2 0
iteration LogLik wall cpu(sec) restrained
1 -158.277 14:51:9 0 0
2 -155.242 14:51:10 1 0
3 -153.214 14:51:10 1 0
4 -152.424 14:51:10 1 0
5 -152.292 14:51:10 1 0
6 -152.273 14:51:10 1 0
7 -152.27 14:51:11 2 0
8 -152.27 14:51:11 2 0
iteration LogLik wall cpu(sec) restrained
1 -159.085 14:51:11 0 0
2 -157.732 14:51:12 1 0
3 -157.122 14:51:12 1 0
4 -156.953 14:51:12 1 0
5 -156.932 14:51:12 1 0
6 -156.929 14:51:13 2 0
7 -156.928 14:51:13 2 0
iteration LogLik wall cpu(sec) restrained
1 -156.578 14:51:14 1 0
2 -151.66 14:51:14 1 0
3 -149.222 14:51:14 1 0
4 -148.725 14:51:14 1 0
5 -148.702 14:51:14 1 0
6 -148.701 14:51:15 2 0
iteration LogLik wall cpu(sec) restrained
1 -158.648 14:51:15 0 0
2 -155.261 14:51:15 0 0
3 -153.142 14:51:16 1 0
4 -152.6 14:51:16 1 0
5 -152.571 14:51:16 1 0
6 -152.57 14:51:17 2 0
7 -152.57 14:51:17 2 0
iteration LogLik wall cpu(sec) restrained
1 -161.352 14:51:17 0 0
2 -160.645 14:51:17 0 0
3 -160.21 14:51:18 1 0
4 -160.034 14:51:18 1 0
5 -159.996 14:51:18 1 0
6 -159.988 14:51:18 1 0
7 -159.986 14:51:19 2 0
8 -159.986 14:51:19 2 0
iteration LogLik wall cpu(sec) restrained
1 -156.675 14:51:19 0 0
2 -152.216 14:51:19 0 0
3 -149.81 14:51:20 1 0
4 -149.267 14:51:20 1 0
5 -149.239 14:51:20 1 0
6 -149.238 14:51:20 1 0
7 -149.238 14:51:20 1 0
iteration LogLik wall cpu(sec) restrained
1 -157.747 14:51:21 0 0
2 -155.031 14:51:21 0 0
3 -153.868 14:51:21 0 0
4 -153.651 14:51:22 1 0
5 -153.64 14:51:22 1 0
6 -153.64 14:51:22 1 0
iteration LogLik wall cpu(sec) restrained
1 -157.847 14:51:23 1 0
2 -153.678 14:51:23 1 0
3 -151.04 14:51:23 1 0
4 -150.306 14:51:23 1 0
5 -150.253 14:51:23 1 0
6 -150.25 14:51:24 2 0
7 -150.25 14:51:24 2 0
iteration LogLik wall cpu(sec) restrained
1 -160.191 14:51:24 0 0
2 -159.097 14:51:25 1 0
3 -158.487 14:51:25 1 0
4 -158.245 14:51:25 1 0
5 -158.19 14:51:25 1 0
6 -158.177 14:51:25 1 0
7 -158.174 14:51:26 2 0
8 -158.173 14:51:26 2 0
iteration LogLik wall cpu(sec) restrained
1 -161.179 14:51:26 0 0
2 -160.215 14:51:26 0 0
3 -159.531 14:51:27 1 0
4 -159.207 14:51:27 1 0
5 -159.126 14:51:27 1 0
6 -159.107 14:51:27 1 0
7 -159.103 14:51:27 1 0
8 -159.103 14:51:28 2 0
iteration LogLik wall cpu(sec) restrained
1 -159.317 14:51:28 0 0
2 -157.509 14:51:28 0 0
3 -156.329 14:51:28 0 0
4 -155.812 14:51:29 1 0
5 -155.696 14:51:29 1 0
6 -155.673 14:51:29 1 0
7 -155.668 14:51:29 1 0
8 -155.668 14:51:30 2 0
iteration LogLik wall cpu(sec) restrained
1 -157.748 14:51:30 0 0
2 -154.403 14:51:30 0 0
3 -152.331 14:51:30 0 0
4 -151.702 14:51:31 1 0
5 -151.644 14:51:31 1 0
6 -151.64 14:51:31 1 0
7 -151.64 14:51:31 1 0
iteration LogLik wall cpu(sec) restrained
1 -158.586 14:51:32 0 0
2 -156.598 14:51:32 0 0
3 -155.558 14:51:32 0 0
4 -155.203 14:51:33 1 0
5 -155.142 14:51:33 1 0
6 -155.132 14:51:33 1 0
7 -155.131 14:51:33 1 0
8 -155.13 14:51:33 1 0
iteration LogLik wall cpu(sec) restrained
1 -158.634 14:51:34 0 0
2 -155.418 14:51:34 0 0
3 -153.579 14:51:34 0 0
4 -153.124 14:51:34 0 0
5 -153.096 14:51:35 1 0
6 -153.095 14:51:35 1 0
7 -153.094 14:51:35 1 0
iteration LogLik wall cpu(sec) restrained
1 -159.662 14:51:36 1 0
2 -157.293 14:51:36 1 0
3 -155.871 14:51:36 1 0
4 -155.47 14:51:36 1 0
5 -155.435 14:51:36 1 0
6 -155.432 14:51:37 2 0
7 -155.432 14:51:37 2 0
iteration LogLik wall cpu(sec) restrained
1 -158.843 14:51:37 0 0
2 -156.199 14:51:38 1 0
3 -154.528 14:51:38 1 0
4 -153.989 14:51:38 1 0
5 -153.928 14:51:38 1 0
6 -153.922 14:51:38 1 0
7 -153.921 14:51:38 1 0
iteration LogLik wall cpu(sec) restrained
1 -157.147 14:51:39 0 0
2 -153.06 14:51:39 0 0
3 -150.567 14:51:39 0 0
4 -149.845 14:51:39 0 0
5 -149.785 14:51:40 1 0
6 -149.781 14:51:40 1 0
7 -149.781 14:51:40 1 0
iteration LogLik wall cpu(sec) restrained
1 -158.671 14:51:40 0 0
2 -156.078 14:51:41 1 0
3 -154.465 14:51:41 1 0
4 -153.956 14:51:41 1 0
5 -153.903 14:51:41 1 0
6 -153.899 14:51:41 1 0
7 -153.898 14:51:41 1 0
iteration LogLik wall cpu(sec) restrained
1 -159.283 14:51:42 0 0
2 -156.564 14:51:42 0 0
3 -154.868 14:51:42 0 0
4 -154.347 14:51:42 0 0
5 -154.294 14:51:42 0 0
6 -154.29 14:51:43 1 0
7 -154.289 14:51:43 1 0
iteration LogLik wall cpu(sec) restrained
1 -158.348 14:51:43 0 0
2 -156.322 14:51:43 0 0
3 -155.647 14:51:43 0 0
4 -155.529 14:51:44 1 0
5 -155.522 14:51:44 1 0
6 -155.522 14:51:44 1 0
iteration LogLik wall cpu(sec) restrained
1 -156.894 14:51:1 0 0
2 -154.812 14:51:1 0 0
3 -153.652 14:51:1 0 0
4 -153.349 14:51:2 1 0
5 -153.325 14:51:2 1 0
6 -153.323 14:51:2 1 0
7 -153.323 14:51:2 1 0
iteration LogLik wall cpu(sec) restrained
1 -158.803 14:51:3 1 0
2 -158.303 14:51:3 1 0
3 -158.038 14:51:3 1 0
4 -157.957 14:51:3 1 0
5 -157.945 14:51:3 1 0
6 -157.943 14:51:4 2 0
7 -157.943 14:51:4 2 0
iteration LogLik wall cpu(sec) restrained
1 -154.709 14:51:4 0 0
2 -150.363 14:51:5 1 0
3 -148.293 14:51:5 1 0
4 -147.841 14:51:5 1 0
5 -147.811 14:51:5 1 0
6 -147.809 14:51:5 1 0
7 -147.809 14:51:6 2 0
iteration LogLik wall cpu(sec) restrained
1 -157.045 14:51:6 0 0
2 -154.111 14:51:6 0 0
3 -152.034 14:51:6 0 0
4 -151.236 14:51:7 1 0
5 -151.115 14:51:7 1 0
6 -151.1 14:51:7 1 0
7 -151.098 14:51:7 1 0
8 -151.098 14:51:7 1 0
iteration LogLik wall cpu(sec) restrained
1 -157.307 14:51:8 0 0
2 -155.257 14:51:8 0 0
3 -154.018 14:51:8 0 0
4 -153.588 14:51:8 0 0
5 -153.521 14:51:9 1 0
6 -153.512 14:51:9 1 0
7 -153.51 14:51:9 1 0
8 -153.51 14:51:9 1 0
iteration LogLik wall cpu(sec) restrained
1 -157.064 14:51:10 1 0
2 -155.527 14:51:10 1 0
3 -154.721 14:51:10 1 0
4 -154.484 14:51:10 1 0
5 -154.455 14:51:11 2 0
6 -154.452 14:51:11 2 0
7 -154.452 14:51:11 2 0
iteration LogLik wall cpu(sec) restrained
1 -155.883 14:51:12 1 0
2 -153.186 14:51:12 1 0
3 -152.054 14:51:12 1 0
4 -151.873 14:51:12 1 0
5 -151.867 14:51:12 1 0
6 -151.866 14:51:13 2 0
iteration LogLik wall cpu(sec) restrained
1 -157.135 14:51:13 0 0
2 -155.254 14:51:13 0 0
3 -154.372 14:51:13 0 0
4 -154.186 14:51:14 1 0
5 -154.175 14:51:14 1 0
6 -154.174 14:51:14 1 0
iteration LogLik wall cpu(sec) restrained
1 -156.075 14:51:15 1 0
2 -152.226 14:51:15 1 0
3 -149.146 14:51:15 1 0
4 -147.53 14:51:15 1 0
5 -147.149 14:51:15 1 0
6 -147.081 14:51:16 2 0
7 -147.071 14:51:16 2 0
8 -147.069 14:51:16 2 0
9 -147.069 14:51:17 3 0
iteration LogLik wall cpu(sec) restrained
1 -157.799 14:51:17 0 0
2 -156.033 14:51:17 0 0
3 -154.954 14:51:17 0 0
4 -154.605 14:51:18 1 0
5 -154.559 14:51:18 1 0
6 -154.554 14:51:18 1 0
7 -154.553 14:51:18 1 0
iteration LogLik wall cpu(sec) restrained
1 -155.526 14:51:19 0 0
2 -152.013 14:51:19 0 0
3 -150.114 14:51:19 0 0
4 -149.676 14:51:19 0 0
5 -149.649 14:51:20 1 0
6 -149.647 14:51:20 1 0
7 -149.647 14:51:20 1 0
iteration LogLik wall cpu(sec) restrained
1 -158.331 14:51:20 0 0
2 -157.487 14:51:21 1 0
3 -156.963 14:51:21 1 0
4 -156.769 14:51:21 1 0
5 -156.735 14:51:21 1 0
6 -156.729 14:51:21 1 0
7 -156.728 14:51:22 2 0
iteration LogLik wall cpu(sec) restrained
1 -157.213 14:51:22 0 0
2 -154.978 14:51:22 0 0
3 -153.716 14:51:23 1 0
4 -153.358 14:51:23 1 0
5 -153.321 14:51:23 1 0
6 -153.317 14:51:23 1 0
7 -153.317 14:51:23 1 0
iteration LogLik wall cpu(sec) restrained
1 -157.314 14:51:24 0 0
2 -155.4 14:51:24 0 0
3 -154.329 14:51:24 0 0
4 -153.986 14:51:24 0 0
5 -153.939 14:51:25 1 0
6 -153.933 14:51:25 1 0
7 -153.933 14:51:25 1 0
iteration LogLik wall cpu(sec) restrained
1 -156.387 14:51:25 0 0
2 -153.343 14:51:26 1 0
3 -151.448 14:51:26 1 0
4 -150.78 14:51:26 1 0
5 -150.679 14:51:26 1 0
6 -150.666 14:51:26 1 0
7 -150.664 14:51:27 2 0
8 -150.664 14:51:27 2 0
iteration LogLik wall cpu(sec) restrained
1 -157.261 14:51:27 0 0
2 -155.48 14:51:27 0 0
3 -154.424 14:51:28 1 0
4 -154.087 14:51:28 1 0
5 -154.043 14:51:28 1 0
6 -154.037 14:51:28 1 0
7 -154.037 14:51:28 1 0
iteration LogLik wall cpu(sec) restrained
1 -157.992 14:51:29 0 0
2 -156.914 14:51:29 0 0
3 -156.295 14:51:29 0 0
4 -156.097 14:51:30 1 0
5 -156.07 14:51:30 1 0
6 -156.067 14:51:30 1 0
7 -156.067 14:51:30 1 0
iteration LogLik wall cpu(sec) restrained
1 -155.835 14:51:31 0 0
2 -152.209 14:51:31 0 0
3 -149.955 14:51:31 0 0
4 -149.247 14:51:32 1 0
5 -149.169 14:51:32 1 0
6 -149.162 14:51:32 1 0
7 -149.161 14:51:32 1 0
iteration LogLik wall cpu(sec) restrained
1 -155.809 14:51:33 1 0
2 -152.753 14:51:33 1 0
3 -151.469 14:51:33 1 0
4 -151.226 14:51:33 1 0
5 -151.213 14:51:33 1 0
6 -151.212 14:51:34 2 0
iteration LogLik wall cpu(sec) restrained
1 -157.051 14:51:34 0 0
2 -154.733 14:51:34 0 0
3 -153.446 14:51:34 0 0
4 -153.057 14:51:35 1 0
5 -153.006 14:51:35 1 0
6 -153 14:51:35 1 0
7 -152.999 14:51:35 1 0
iteration LogLik wall cpu(sec) restrained
1 -156.338 14:51:36 1 0
2 -153.855 14:51:36 1 0
3 -152.43 14:51:36 1 0
4 -152.018 14:51:36 1 0
5 -151.975 14:51:36 1 0
6 -151.971 14:51:37 2 0
7 -151.971 14:51:37 2 0
iteration LogLik wall cpu(sec) restrained
1 -157.786 14:51:37 0 0
2 -156.715 14:51:37 0 0
3 -156.196 14:51:38 1 0
4 -156.077 14:51:38 1 0
5 -156.068 14:51:38 1 0
6 -156.067 14:51:38 1 0
iteration LogLik wall cpu(sec) restrained
1 -156.53 14:51:38 0 0
2 -154.52 14:51:39 1 0
3 -153.51 14:51:39 1 0
4 -153.208 14:51:39 1 0
5 -153.168 14:51:39 1 0
6 -153.163 14:51:39 1 0
7 -153.162 14:51:39 1 0
iteration LogLik wall cpu(sec) restrained
1 -156.205 14:51:40 0 0
2 -152.1 14:51:40 0 0
3 -149.062 14:51:40 0 0
4 -147.829 14:51:40 0 0
5 -147.632 14:51:40 0 0
6 -147.606 14:51:41 1 0
7 -147.603 14:51:41 1 0
8 -147.602 14:51:41 1 0
iteration LogLik wall cpu(sec) restrained
1 -156.246 14:51:41 0 0
2 -153.372 14:51:42 1 0
3 -152.119 14:51:42 1 0
4 -151.896 14:51:42 1 0
5 -151.886 14:51:42 1 0
6 -151.885 14:51:42 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.873 14:51:1 0 0
2 -118.619 14:51:1 0 0
3 -118.163 14:51:1 0 0
4 -118.089 14:51:1 0 0
5 -118.085 14:51:1 0 0
6 -118.085 14:51:2 1 0
iteration LogLik wall cpu(sec) restrained
1 -120.07 14:51:2 0 0
2 -119.023 14:51:2 0 0
3 -118.591 14:51:2 0 0
4 -118.494 14:51:2 0 0
5 -118.485 14:51:2 0 0
6 -118.484 14:51:2 0 0
iteration LogLik wall cpu(sec) restrained
1 -118.063 14:51:2 0 0
2 -115.473 14:51:2 0 0
3 -114.684 14:51:3 1 0
4 -114.555 14:51:3 1 0
5 -114.548 14:51:3 1 0
6 -114.548 14:51:3 1 0
iteration LogLik wall cpu(sec) restrained
1 -120.383 14:51:3 0 0
2 -119.734 14:51:3 0 0
3 -119.516 14:51:3 0 0
4 -119.487 14:51:3 0 0
5 -119.486 14:51:4 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.764 14:51:4 0 0
2 -118.02 14:51:4 0 0
3 -116.781 14:51:4 0 0
4 -116.173 14:51:4 0 0
5 -116.002 14:51:4 0 0
6 -115.956 14:51:4 0 0
7 -115.945 14:51:4 0 0
8 -115.942 14:51:4 0 0
9 -115.941 14:51:4 0 0
iteration LogLik wall cpu(sec) restrained
1 -119.982 14:51:5 0 0
2 -119.387 14:51:5 0 0
3 -119.252 14:51:5 0 0
4 -119.242 14:51:5 0 0
5 -119.242 14:51:5 0 0
iteration LogLik wall cpu(sec) restrained
1 -119.968 14:51:5 0 0
2 -118.934 14:51:5 0 0
3 -118.529 14:51:5 0 0
4 -118.447 14:51:5 0 0
5 -118.44 14:51:6 1 0
6 -118.44 14:51:6 1 0
iteration LogLik wall cpu(sec) restrained
1 -120.095 14:51:6 0 0
2 -118.532 14:51:6 0 0
3 -117.563 14:51:6 0 0
4 -117.213 14:51:6 0 0
5 -117.155 14:51:6 0 0
6 -117.146 14:51:6 0 0
7 -117.145 14:51:6 0 0
8 -117.144 14:51:6 0 0
iteration LogLik wall cpu(sec) restrained
1 -118.472 14:51:7 0 0
2 -116.124 14:51:7 0 0
3 -115.199 14:51:7 0 0
4 -115.002 14:51:7 0 0
5 -114.985 14:51:7 0 0
6 -114.983 14:51:7 0 0
7 -114.983 14:51:7 0 0
iteration LogLik wall cpu(sec) restrained
1 -119.017 14:51:7 0 0
2 -116.881 14:51:7 0 0
3 -115.87 14:51:8 1 0
4 -115.52 14:51:8 1 0
5 -115.447 14:51:8 1 0
6 -115.431 14:51:8 1 0
7 -115.427 14:51:8 1 0
8 -115.426 14:51:8 1 0
iteration LogLik wall cpu(sec) restrained
1 -121.964 14:51:8 0 0
2 -121.858 14:51:8 0 0
3 -121.806 14:51:8 0 0
4 -121.792 14:51:8 0 0
5 -121.791 14:51:9 1 0
6 -121.791 14:51:9 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.437 14:51:9 0 0
2 -117.415 14:51:9 0 0
3 -116.212 14:51:9 0 0
4 -115.748 14:51:9 0 0
5 -115.655 14:51:9 0 0
6 -115.637 14:51:9 0 0
7 -115.633 14:51:9 0 0
8 -115.633 14:51:9 0 0
iteration LogLik wall cpu(sec) restrained
1 -120.236 14:51:10 0 0
2 -119.206 14:51:10 0 0
3 -118.674 14:51:10 0 0
4 -118.514 14:51:10 0 0
5 -118.491 14:51:10 0 0
6 -118.488 14:51:10 0 0
7 -118.487 14:51:10 0 0
iteration LogLik wall cpu(sec) restrained
1 -118.443 14:51:11 1 0
2 -116.546 14:51:11 1 0
3 -116.068 14:51:11 1 0
4 -116.012 14:51:11 1 0
5 -116.01 14:51:11 1 0
6 -116.01 14:51:11 1 0
iteration LogLik wall cpu(sec) restrained
1 -116.768 14:51:11 0 0
2 -111.72 14:51:11 0 0
3 -109.206 14:51:11 0 0
4 -108.347 14:51:12 1 0
5 -108.21 14:51:12 1 0
6 -108.191 14:51:12 1 0
7 -108.188 14:51:12 1 0
8 -108.187 14:51:12 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.08 14:51:12 0 0
2 -117.461 14:51:12 0 0
3 -116.994 14:51:12 0 0
4 -116.938 14:51:12 0 0
5 -116.936 14:51:12 0 0
6 -116.936 14:51:13 1 0
iteration LogLik wall cpu(sec) restrained
1 -118.997 14:51:13 0 0
2 -117.302 14:51:13 0 0
3 -116.666 14:51:13 0 0
4 -116.508 14:51:13 0 0
5 -116.488 14:51:13 0 0
6 -116.485 14:51:13 0 0
7 -116.485 14:51:13 0 0
iteration LogLik wall cpu(sec) restrained
1 -120.538 14:51:13 0 0
2 -119.678 14:51:14 1 0
3 -119.155 14:51:14 1 0
4 -118.955 14:51:14 1 0
5 -118.916 14:51:14 1 0
6 -118.909 14:51:14 1 0
7 -118.908 14:51:14 1 0
8 -118.908 14:51:14 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.797 14:51:14 0 0
2 -118.27 14:51:14 0 0
3 -117.573 14:51:14 0 0
4 -117.401 14:51:15 1 0
5 -117.383 14:51:15 1 0
6 -117.381 14:51:15 1 0
7 -117.38 14:51:15 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.053 14:51:15 0 0
2 -117.523 14:51:15 0 0
3 -117.078 14:51:15 0 0
4 -117.029 14:51:15 0 0
5 -117.028 14:51:16 1 0
iteration LogLik wall cpu(sec) restrained
1 -120.341 14:51:16 0 0
2 -119.387 14:51:16 0 0
3 -118.944 14:51:16 0 0
4 -118.831 14:51:16 0 0
5 -118.819 14:51:16 0 0
6 -118.818 14:51:16 0 0
7 -118.818 14:51:17 1 0
iteration LogLik wall cpu(sec) restrained
1 -119.406 14:51:17 0 0
2 -117.87 14:51:17 0 0
3 -117.266 14:51:17 0 0
4 -117.136 14:51:17 0 0
5 -117.124 14:51:17 0 0
6 -117.122 14:51:17 0 0
7 -117.122 14:51:17 0 0
iteration LogLik wall cpu(sec) restrained
1 -119.012 14:51:18 1 0
2 -116.695 14:51:18 1 0
3 -115.473 14:51:18 1 0
4 -115.098 14:51:18 1 0
5 -115.045 14:51:18 1 0
6 -115.038 14:51:18 1 0
7 -115.037 14:51:18 1 0
iteration LogLik wall cpu(sec) restrained
1 -118.468 14:51:18 0 0
2 -115.803 14:51:18 0 0
3 -114.702 14:51:18 0 0
4 -114.458 14:51:19 1 0
5 -114.438 14:51:19 1 0
6 -114.437 14:51:19 1 0
7 -114.437 14:51:19 1 0
iteration LogLik wall cpu(sec) restrained
1 -120.531 14:51:19 0 0
2 -120.008 14:51:19 0 0
3 -119.824 14:51:19 0 0
4 -119.792 14:51:19 0 0
5 -119.79 14:51:19 0 0
6 -119.79 14:51:19 0 0
iteration LogLik wall cpu(sec) restrained
1 -153.217 14:51:20 0 0
2 -150.452 14:51:20 0 0
3 -149.932 14:51:20 0 0
4 -149.901 14:51:20 0 0
5 -149.901 14:51:21 1 0
iteration LogLik wall cpu(sec) restrained
1 -152.663 14:51:21 0 0
2 -148.823 14:51:21 0 0
3 -147.843 14:51:22 1 0
4 -147.751 14:51:22 1 0
5 -147.75 14:51:22 1 0
iteration LogLik wall cpu(sec) restrained
1 -148.676 14:51:23 1 0
2 -140.961 14:51:23 1 0
3 -139.642 14:51:23 1 0
4 -139.564 14:51:23 1 0
5 -139.564 14:51:23 1 0
iteration LogLik wall cpu(sec) restrained
1 -150.864 14:51:24 0 0
2 -146.074 14:51:24 0 0
3 -145.315 14:51:24 0 0
4 -145.271 14:51:24 0 0
5 -145.27 14:51:25 1 0
iteration LogLik wall cpu(sec) restrained
1 -150.755 14:51:25 0 0
2 -145.269 14:51:25 0 0
3 -143.775 14:51:25 0 0
4 -143.558 14:51:26 1 0
5 -143.55 14:51:26 1 0
6 -143.55 14:51:26 1 0
iteration LogLik wall cpu(sec) restrained
1 -149.234 14:51:27 1 0
2 -142.903 14:51:27 1 0
3 -141.684 14:51:27 1 0
4 -141.595 14:51:27 1 0
5 -141.595 14:51:27 1 0
iteration LogLik wall cpu(sec) restrained
1 -150.027 14:51:28 0 0
2 -143.626 14:51:28 0 0
3 -142.094 14:51:28 0 0
4 -141.922 14:51:28 0 0
5 -141.918 14:51:29 1 0
6 -141.918 14:51:29 1 0
iteration LogLik wall cpu(sec) restrained
1 -153.455 14:51:29 0 0
2 -151.022 14:51:30 1 0
3 -150.526 14:51:30 1 0
4 -150.478 14:51:30 1 0
5 -150.478 14:51:30 1 0
iteration LogLik wall cpu(sec) restrained
1 -152.171 14:51:31 1 0
2 -147.725 14:51:31 1 0
3 -146.496 14:51:31 1 0
4 -146.323 14:51:31 1 0
5 -146.317 14:51:32 2 0
6 -146.316 14:51:32 2 0
iteration LogLik wall cpu(sec) restrained
1 -152.046 14:51:32 0 0
2 -148.119 14:51:33 1 0
3 -147.372 14:51:33 1 0
4 -147.318 14:51:33 1 0
5 -147.318 14:51:33 1 0
iteration LogLik wall cpu(sec) restrained
1 -150.27 14:51:34 1 0
2 -144.248 14:51:34 1 0
3 -142.921 14:51:34 1 0
4 -142.826 14:51:34 1 0
5 -142.826 14:51:34 1 0
iteration LogLik wall cpu(sec) restrained
1 -149.932 14:51:35 0 0
2 -143.744 14:51:35 0 0
3 -142.331 14:51:35 0 0
4 -142.168 14:51:35 0 0
5 -142.164 14:51:36 1 0
6 -142.164 14:51:36 1 0
iteration LogLik wall cpu(sec) restrained
1 -152.794 14:51:36 0 0
2 -149.286 14:51:36 0 0
3 -148.391 14:51:37 1 0
4 -148.282 14:51:37 1 0
5 -148.279 14:51:37 1 0
6 -148.279 14:51:37 1 0
iteration LogLik wall cpu(sec) restrained
1 -152.153 14:51:38 1 0
2 -147.691 14:51:38 1 0
3 -146.538 14:51:38 1 0
4 -146.371 14:51:38 1 0
5 -146.364 14:51:38 1 0
6 -146.363 14:51:38 1 0
iteration LogLik wall cpu(sec) restrained
1 -151.649 14:51:39 0 0
2 -148.277 14:51:39 0 0
3 -147.861 14:51:39 0 0
4 -147.849 14:51:39 0 0
5 -147.849 14:51:39 0 0
iteration LogLik wall cpu(sec) restrained
1 -153.286 14:51:40 0 0
2 -150.338 14:51:40 0 0
3 -149.785 14:51:40 0 0
4 -149.754 14:51:40 0 0
5 -149.754 14:51:41 1 0
iteration LogLik wall cpu(sec) restrained
1 -150.586 14:51:41 0 0
2 -145.35 14:51:41 0 0
3 -144.264 14:51:41 0 0
4 -144.172 14:51:41 0 0
5 -144.171 14:51:42 1 0
iteration LogLik wall cpu(sec) restrained
1 -147.625 14:51:42 0 0
2 -138.067 14:51:42 0 0
3 -135.647 14:51:42 0 0
4 -135.347 14:51:42 0 0
5 -135.341 14:51:43 1 0
6 -135.341 14:51:43 1 0
iteration LogLik wall cpu(sec) restrained
1 -150.583 14:51:43 0 0
2 -144.726 14:51:43 0 0
3 -143.384 14:51:43 0 0
4 -143.239 14:51:44 1 0
5 -143.236 14:51:44 1 0
6 -143.236 14:51:44 1 0
iteration LogLik wall cpu(sec) restrained
1 -152.755 14:51:44 0 0
2 -149.612 14:51:45 1 0
3 -148.865 14:51:45 1 0
4 -148.784 14:51:45 1 0
5 -148.782 14:51:45 1 0
6 -148.782 14:51:45 1 0
iteration LogLik wall cpu(sec) restrained
1 -151.311 14:51:46 0 0
2 -146.583 14:51:46 0 0
3 -145.736 14:51:46 0 0
4 -145.69 14:51:46 0 0
5 -145.69 14:51:46 0 0
iteration LogLik wall cpu(sec) restrained
1 -151.515 14:51:47 0 0
2 -147.217 14:51:47 0 0
3 -146.226 14:51:47 0 0
4 -146.108 14:51:47 0 0
5 -146.105 14:51:47 0 0
6 -146.105 14:51:47 0 0
iteration LogLik wall cpu(sec) restrained
1 -147.138 14:51:48 0 0
2 -138.244 14:51:48 0 0
3 -136.448 14:51:48 0 0
4 -136.31 14:51:48 0 0
5 -136.309 14:51:48 0 0
iteration LogLik wall cpu(sec) restrained
1 -153.571 14:51:49 1 0
2 -150.912 14:51:49 1 0
3 -150.486 14:51:49 1 0
4 -150.469 14:51:49 1 0
5 -150.469 14:51:49 1 0
iteration LogLik wall cpu(sec) restrained
1 -153.106 14:51:49 0 0
2 -149.357 14:51:49 0 0
3 -148.086 14:51:50 1 0
4 -147.818 14:51:50 1 0
5 -147.796 14:51:50 1 0
6 -147.794 14:51:50 1 0
7 -147.794 14:51:50 1 0
iteration LogLik wall cpu(sec) restrained
1 -155.556 14:51:2 1 0
2 -153.901 14:51:2 1 0
3 -153.442 14:51:2 1 0
4 -153.399 14:51:2 1 0
5 -153.399 14:51:2 1 0
iteration LogLik wall cpu(sec) restrained
1 -153.815 14:51:3 0 0
2 -150.402 14:51:3 0 0
3 -149.303 14:51:3 0 0
4 -149.14 14:51:3 0 0
5 -149.134 14:51:4 1 0
6 -149.134 14:51:4 1 0
iteration LogLik wall cpu(sec) restrained
1 -153.217 14:51:4 0 0
2 -149.912 14:51:5 1 0
3 -149.142 14:51:5 1 0
4 -149.074 14:51:5 1 0
5 -149.073 14:51:5 1 0
iteration LogLik wall cpu(sec) restrained
1 -154.641 14:51:6 1 0
2 -152.42 14:51:6 1 0
3 -151.874 14:51:6 1 0
4 -151.825 14:51:6 1 0
5 -151.824 14:51:6 1 0
iteration LogLik wall cpu(sec) restrained
1 -152.961 14:51:7 0 0
2 -148.714 14:51:7 0 0
3 -147.373 14:51:7 0 0
4 -147.207 14:51:7 0 0
5 -147.204 14:51:8 1 0
6 -147.204 14:51:8 1 0
iteration LogLik wall cpu(sec) restrained
1 -153.018 14:51:8 0 0
2 -149.178 14:51:8 0 0
3 -148.157 14:51:9 1 0
4 -148.084 14:51:9 1 0
5 -148.084 14:51:9 1 0
iteration LogLik wall cpu(sec) restrained
1 -153.952 14:51:10 1 0
2 -151.615 14:51:10 1 0
3 -151.158 14:51:10 1 0
4 -151.126 14:51:10 1 0
5 -151.125 14:51:10 1 0
iteration LogLik wall cpu(sec) restrained
1 -154.952 14:51:11 0 0
2 -151.934 14:51:11 0 0
3 -150.448 14:51:12 1 0
4 -150.045 14:51:12 1 0
5 -150.004 14:51:12 1 0
6 -150 14:51:12 1 0
7 -150 14:51:12 1 0
iteration LogLik wall cpu(sec) restrained
1 -154.328 14:51:13 0 0
2 -151.931 14:51:13 0 0
3 -151.369 14:51:13 0 0
4 -151.316 14:51:14 1 0
5 -151.315 14:51:14 1 0
iteration LogLik wall cpu(sec) restrained
1 -154.816 14:51:14 0 0
2 -152.544 14:51:14 0 0
3 -151.95 14:51:15 1 0
4 -151.893 14:51:15 1 0
5 -151.893 14:51:15 1 0
iteration LogLik wall cpu(sec) restrained
1 -153.694 14:51:16 1 0
2 -150.267 14:51:16 1 0
3 -149.168 14:51:16 1 0
4 -149.044 14:51:16 1 0
5 -149.042 14:51:17 2 0
6 -149.042 14:51:17 2 0
iteration LogLik wall cpu(sec) restrained
1 -154.736 14:51:17 0 0
2 -152.137 14:51:18 1 0
3 -151.076 14:51:18 1 0
4 -150.84 14:51:18 1 0
5 -150.821 14:51:18 1 0
6 -150.82 14:51:18 1 0
7 -150.82 14:51:19 2 0
iteration LogLik wall cpu(sec) restrained
1 -155.147 14:51:19 0 0
2 -153.128 14:51:19 0 0
3 -152.576 14:51:19 0 0
4 -152.513 14:51:20 1 0
5 -152.512 14:51:20 1 0
6 -152.512 14:51:20 1 0
iteration LogLik wall cpu(sec) restrained
1 -152.58 14:51:21 1 0
2 -148.666 14:51:21 1 0
3 -147.994 14:51:21 1 0
4 -147.962 14:51:21 1 0
5 -147.962 14:51:21 1 0
iteration LogLik wall cpu(sec) restrained
1 -154.436 14:51:22 0 0
2 -152.505 14:51:22 0 0
3 -152.083 14:51:22 0 0
4 -152.049 14:51:23 1 0
5 -152.049 14:51:23 1 0
iteration LogLik wall cpu(sec) restrained
1 -153.806 14:51:23 0 0
2 -151.087 14:51:23 0 0
3 -150.452 14:51:24 1 0
4 -150.403 14:51:24 1 0
5 -150.402 14:51:24 1 0
iteration LogLik wall cpu(sec) restrained
1 -152.501 14:51:24 0 0
2 -148.423 14:51:25 1 0
3 -147.644 14:51:25 1 0
4 -147.616 14:51:25 1 0
5 -147.616 14:51:25 1 0
iteration LogLik wall cpu(sec) restrained
1 -154.938 14:51:26 1 0
2 -152.684 14:51:26 1 0
3 -151.972 14:51:26 1 0
4 -151.876 14:51:26 1 0
5 -151.873 14:51:26 1 0
6 -151.873 14:51:26 1 0
iteration LogLik wall cpu(sec) restrained
1 -155.683 14:51:27 0 0
2 -153.462 14:51:27 0 0
3 -152.545 14:51:27 0 0
4 -152.355 14:51:28 1 0
5 -152.342 14:51:28 1 0
6 -152.341 14:51:28 1 0
iteration LogLik wall cpu(sec) restrained
1 -152.71 14:51:29 1 0
2 -149.109 14:51:29 1 0
3 -148.202 14:51:29 1 0
4 -148.097 14:51:29 1 0
5 -148.095 14:51:29 1 0
6 -148.095 14:51:30 2 0
iteration LogLik wall cpu(sec) restrained
1 -153.876 14:51:30 0 0
2 -150.748 14:51:30 0 0
3 -149.815 14:51:30 0 0
4 -149.693 14:51:31 1 0
5 -149.689 14:51:31 1 0
6 -149.689 14:51:31 1 0
iteration LogLik wall cpu(sec) restrained
1 -152.705 14:51:32 0 0
2 -148.292 14:51:32 0 0
3 -146.924 14:51:32 0 0
4 -146.737 14:51:32 0 0
5 -146.732 14:51:33 1 0
6 -146.732 14:51:33 1 0
iteration LogLik wall cpu(sec) restrained
1 -153.261 14:51:33 0 0
2 -150.476 14:51:33 0 0
3 -149.941 14:51:34 1 0
4 -149.914 14:51:34 1 0
5 -149.914 14:51:34 1 0
iteration LogLik wall cpu(sec) restrained
1 -155.952 14:51:34 0 0
2 -153.992 14:51:35 1 0
3 -153.285 14:51:35 1 0
4 -153.176 14:51:35 1 0
5 -153.172 14:51:35 1 0
6 -153.172 14:51:35 1 0
iteration LogLik wall cpu(sec) restrained
1 -153.529 14:51:36 0 0
2 -150.101 14:51:36 0 0
3 -149.09 14:51:36 0 0
4 -148.959 14:51:36 0 0
5 -148.956 14:51:37 1 0
6 -148.956 14:51:37 1 0
iteration LogLik wall cpu(sec) restrained
1 -158.156 14:51:2 0 0
2 -154.754 14:51:2 0 0
3 -152.667 14:51:2 0 0
4 -152.086 14:51:2 0 0
5 -152.045 14:51:3 1 0
6 -152.043 14:51:3 1 0
7 -152.043 14:51:3 1 0
iteration LogLik wall cpu(sec) restrained
1 -155.122 14:51:4 1 0
2 -148.869 14:51:4 1 0
3 -146.19 14:51:4 1 0
4 -145.713 14:51:4 1 0
5 -145.696 14:51:4 1 0
6 -145.695 14:51:5 2 0
iteration LogLik wall cpu(sec) restrained
1 -158.294 14:51:5 0 0
2 -154.457 14:51:5 0 0
3 -151.918 14:51:6 1 0
4 -151.216 14:51:6 1 0
5 -151.174 14:51:6 1 0
6 -151.173 14:51:6 1 0
7 -151.173 14:51:6 1 0
iteration LogLik wall cpu(sec) restrained
1 -158.385 14:51:7 0 0
2 -154.8 14:51:7 0 0
3 -152.893 14:51:7 0 0
4 -152.479 14:51:8 1 0
5 -152.46 14:51:8 1 0
6 -152.459 14:51:8 1 0
iteration LogLik wall cpu(sec) restrained
1 -156.39 14:51:8 0 0
2 -150.76 14:51:9 1 0
3 -147.389 14:51:9 1 0
4 -146.449 14:51:9 1 0
5 -146.382 14:51:9 1 0
6 -146.379 14:51:10 2 0
7 -146.379 14:51:10 2 0
iteration LogLik wall cpu(sec) restrained
1 -156.827 14:51:10 0 0
2 -153.363 14:51:11 1 0
3 -151.85 14:51:11 1 0
4 -151.519 14:51:11 1 0
5 -151.497 14:51:11 1 0
6 -151.496 14:51:12 2 0
7 -151.496 14:51:12 2 0
iteration LogLik wall cpu(sec) restrained
1 -159.153 14:51:12 0 0
2 -155.953 14:51:13 1 0
3 -153.726 14:51:13 1 0
4 -152.986 14:51:13 1 0
5 -152.916 14:51:13 1 0
6 -152.911 14:51:13 1 0
7 -152.91 14:51:14 2 0
iteration LogLik wall cpu(sec) restrained
1 -156.988 14:51:14 0 0
2 -150.52 14:51:14 0 0
3 -145.976 14:51:15 1 0
4 -144.911 14:51:15 1 0
5 -144.882 14:51:15 1 0
6 -144.882 14:51:15 1 0
iteration LogLik wall cpu(sec) restrained
1 -155.162 14:51:16 0 0
2 -149.084 14:51:16 0 0
3 -146.392 14:51:17 1 0
4 -145.917 14:51:17 1 0
5 -145.902 14:51:17 1 0
6 -145.901 14:51:17 1 0
iteration LogLik wall cpu(sec) restrained
1 -158.945 14:51:18 0 0
2 -155.9 14:51:18 0 0
3 -154.167 14:51:18 0 0
4 -153.741 14:51:18 0 0
5 -153.717 14:51:19 1 0
6 -153.716 14:51:19 1 0
7 -153.716 14:51:19 1 0
iteration LogLik wall cpu(sec) restrained
1 -157.581 14:51:20 1 0
2 -153.271 14:51:20 1 0
3 -151.028 14:51:20 1 0
4 -150.585 14:51:20 1 0
5 -150.57 14:51:20 1 0
6 -150.57 14:51:21 2 0
iteration LogLik wall cpu(sec) restrained
1 -159.105 14:51:21 0 0
2 -156.3 14:51:21 0 0
3 -154.317 14:51:22 1 0
4 -153.537 14:51:22 1 0
5 -153.426 14:51:22 1 0
6 -153.415 14:51:23 2 0
7 -153.413 14:51:23 2 0
8 -153.413 14:51:23 2 0
iteration LogLik wall cpu(sec) restrained
1 -157.96 14:51:23 0 0
2 -153.863 14:51:24 1 0
3 -150.97 14:51:24 1 0
4 -149.991 14:51:24 1 0
5 -149.901 14:51:24 1 0
6 -149.895 14:51:24 1 0
7 -149.895 14:51:25 2 0
iteration LogLik wall cpu(sec) restrained
1 -157.263 14:51:25 0 0
2 -153.071 14:51:25 0 0
3 -150.854 14:51:25 0 0
4 -150.396 14:51:26 1 0
5 -150.379 14:51:26 1 0
6 -150.379 14:51:26 1 0
iteration LogLik wall cpu(sec) restrained
1 -155.765 14:51:27 1 0
2 -149.819 14:51:27 1 0
3 -147.223 14:51:27 1 0
4 -146.788 14:51:27 1 0
5 -146.775 14:51:27 1 0
6 -146.775 14:51:28 2 0
iteration LogLik wall cpu(sec) restrained
1 -156.314 14:51:28 0 0
2 -152.858 14:51:28 0 0
3 -151.606 14:51:29 1 0
4 -151.377 14:51:29 1 0
5 -151.366 14:51:29 1 0
6 -151.365 14:51:29 1 0
iteration LogLik wall cpu(sec) restrained
1 -159.676 14:51:30 0 0
2 -157.344 14:51:30 0 0
3 -155.731 14:51:30 0 0
4 -155.221 14:51:30 0 0
5 -155.179 14:51:31 1 0
6 -155.176 14:51:31 1 0
7 -155.176 14:51:31 1 0
iteration LogLik wall cpu(sec) restrained
1 -157.767 14:51:32 0 0
2 -154.437 14:51:32 0 0
3 -152.849 14:51:32 0 0
4 -152.504 14:51:32 0 0
5 -152.485 14:51:33 1 0
6 -152.484 14:51:33 1 0
iteration LogLik wall cpu(sec) restrained
1 -155.521 14:51:33 0 0
2 -147.231 14:51:33 0 0
3 -141.852 14:51:34 1 0
4 -140.551 14:51:34 1 0
5 -140.495 14:51:34 1 0
6 -140.493 14:51:34 1 0
7 -140.493 14:51:34 1 0
iteration LogLik wall cpu(sec) restrained
1 -156.906 14:51:35 0 0
2 -150.738 14:51:35 0 0
3 -146.736 14:51:35 0 0
4 -145.563 14:51:36 1 0
5 -145.48 14:51:36 1 0
6 -145.476 14:51:36 1 0
7 -145.476 14:51:36 1 0
iteration LogLik wall cpu(sec) restrained
1 -157.817 14:51:37 1 0
2 -154.071 14:51:37 1 0
3 -151.818 14:51:37 1 0
4 -151.14 14:51:37 1 0
5 -151.076 14:51:37 1 0
6 -151.071 14:51:38 2 0
7 -151.07 14:51:38 2 0
iteration LogLik wall cpu(sec) restrained
1 -157.823 14:51:38 0 0
2 -152.987 14:51:38 0 0
3 -149.955 14:51:39 1 0
4 -149.252 14:51:39 1 0
5 -149.225 14:51:39 1 0
6 -149.224 14:51:39 1 0
iteration LogLik wall cpu(sec) restrained
1 -154.608 14:51:40 1 0
2 -147.21 14:51:40 1 0
3 -143.933 14:51:40 1 0
4 -143.44 14:51:40 1 0
5 -143.431 14:51:40 1 0
6 -143.431 14:51:40 1 0
iteration LogLik wall cpu(sec) restrained
1 -158.525 14:51:41 0 0
2 -155.904 14:51:41 0 0
3 -154.415 14:51:41 0 0
4 -153.968 14:51:41 0 0
5 -153.923 14:51:42 1 0
6 -153.919 14:51:42 1 0
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5 -119.951 14:51:55 0 0The object “GEBVS_RKHS” contains the GEBVs for each trait and clone. The table above shows the first five clones and their GEBVs for each trait.
GEBVS_RKHS |>
group_by(Trait, ID_Clone) |>
summarise(GEBV = mean(GEBV)) %>%
pivot_wider(names_from = Trait, values_from = GEBV) %>%
head() %>%
kbl(escape = F, align = 'c') |>
kable_classic("hover", full_width = F, position = "center", fixed_thead = T)`summarise()` has grouped output by 'Trait'. You can override using the
`.groups` argument.| ID_Clone | DMC | FRY | HI | N_Roots | Nstem.Plant | Plant.Height | Root.Di | Root.Le | ShY | StC | StY | Stem.D |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BGM_2042 | 0.8851626 | 1.3775816 | 1.3504393 | 0.6349606 | 0.2436677 | 0.0377981 | 0.5743877 | 1.3658880 | 2.5388808 | 0.8840124 | 0.3752536 | 0.0794001 |
| BGM0368.250437186 | 1.0559030 | -0.3675476 | 0.3446849 | 0.2653845 | 0.0682762 | 0.0043035 | -0.3011155 | -0.2631986 | -2.2886017 | 1.0532570 | -0.0273292 | -0.0151872 |
| BGM0424.250437187 | 0.3769805 | -0.0584124 | -0.6649231 | 0.0488446 | 0.0440244 | 0.0168310 | -0.1650248 | -0.0106796 | -0.4532117 | 0.3828497 | 0.0125693 | 0.0170974 |
| BGM0611.250437190 | -0.3807381 | 0.0447070 | -0.3671337 | 0.2625928 | 0.0984610 | -0.0341276 | 0.2121542 | 0.5576522 | -0.0286580 | -0.3846556 | -0.0397691 | -0.0440015 |
| BGM0652.250437861 | 0.3289363 | 0.1283697 | -0.5251662 | 0.1961288 | 0.1018050 | 0.0031698 | -0.0252586 | 0.5300556 | 0.8376198 | 0.3238434 | 0.0160116 | 0.0235057 |
| BGM0699.250437199 | 0.1243751 | -0.1788720 | -1.0288358 | -0.0047164 | 0.0343550 | 0.0108437 | -0.0565137 | 0.2842844 | 0.2205706 | 0.1122764 | -0.0277006 | 0.0437123 |
Acuracy and MSPE for each trait and repetition:
results_cv_RKHS[-6] |>
group_by(Trait) %>%
summarise_all(mean) %>%
arrange(desc(Ac), MSPE) %>%
kbl(escape = F, align = 'c') |>
kable_classic("hover", full_width = F, position = "center", fixed_thead = T)| Trait | rep | Log | Ac | MSPE |
|---|---|---|---|---|
| Root.Le | 3 | 1 | 0.3714 | 1.9894 |
| Stem.D | 3 | 1 | 0.3512 | 0.0084 |
| ShY | 3 | 1 | 0.3288 | 13.2408 |
| FRY | 3 | 1 | 0.3280 | 1.1972 |
| Root.Di | 3 | 1 | 0.3170 | 3.3912 |
| StY | 3 | 1 | 0.3090 | 0.0724 |
| Plant.Height | 3 | 1 | 0.3032 | 0.0080 |
| HI | 3 | 1 | 0.2640 | 11.7624 |
| Nstem.Plant | 3 | 1 | 0.2600 | 0.0330 |
| N_Roots | 3 | 1 | 0.2484 | 0.9312 |
| StC | 3 | 1 | 0.1908 | 6.0810 |
| DMC | 3 | 1 | 0.1900 | 6.1150 |
The object “result_cv” is divided by repetition. In the “result_cv” objects for each repetition, “Rep” is the number of the repetition, “Log” is a diagnostic indicating if the order of the predicted breeding values matches the order of the adjusted means, “Ac” is the prediction accuracy (correlation between the GEBV and adjusted means), and “MSPE” is the mean square prediction error (the lower, the better).
Let’s now move on to processing each model. Since this can be time-consuming, I’ve separated it into parallel processing and each model into each script:
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] kableExtra_1.4.0 cvTools_0.3.3 robustbase_0.99-4-1
[4] lattice_0.22-6 lubridate_1.9.4 forcats_1.0.0
[7] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[10] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[13] ggplot2_3.5.1 tidyverse_2.0.0 furrr_0.3.1
[16] future_1.34.0
loaded via a namespace (and not attached):
[1] gtable_0.3.6 xfun_0.50 bslib_0.8.0 tzdb_0.4.0
[5] vctrs_0.6.5 tools_4.3.3 generics_0.1.3 parallel_4.3.3
[9] DEoptimR_1.1-3-1 pkgconfig_2.0.3 lifecycle_1.0.4 compiler_4.3.3
[13] git2r_0.35.0 munsell_0.5.1 codetools_0.2-20 httpuv_1.6.15
[17] htmltools_0.5.8.1 sass_0.4.9 yaml_2.3.10 later_1.4.1
[21] pillar_1.10.1 jquerylib_0.1.4 cachem_1.1.0 parallelly_1.41.0
[25] tidyselect_1.2.1 digest_0.6.37 stringi_1.8.4 listenv_0.9.1
[29] rprojroot_2.0.4 fastmap_1.2.0 grid_4.3.3 colorspace_2.1-1
[33] cli_3.6.3 magrittr_2.0.3 withr_3.0.2 scales_1.3.0
[37] promises_1.3.2 timechange_0.3.0 rmarkdown_2.29 globals_0.16.3
[41] workflowr_1.7.1 hms_1.1.3 evaluate_1.0.3 knitr_1.49
[45] viridisLite_0.4.2 rlang_1.1.4 Rcpp_1.0.14 glue_1.8.0
[49] xml2_1.3.6 svglite_2.1.3 rstudioapi_0.17.1 jsonlite_1.8.9
[53] R6_2.5.1 systemfonts_1.1.0 fs_1.6.5 Weverton Gomes da Costa, Pós-Doutorando, Embrapa Mandioca e Fruticultura, wevertonufv@gmail.com↩︎