library(tidyverse) ## data manipulation
library(phyloseq) ## analysis of microbiome census data
library(phyloseq.extended)
library(ape) ## for tree manipulation
library(vegan) ## for community ecology analyses16S Metagenomics - Ravel dataset analysis
metabarcoding
FROGS
R
Introduction
This vignette is a re-analysis of the data set from Ravel et al. (2011), as suggested in the Homeworks section of the slides. Note that this is only one of many analyses that could be done on the data.
Analysis
Setup
We first setup our environment by loading a few packages
Data import
We then load the data from the Ravel et al. (2011) dataset. We assume that they are located in the data/ravel folder. A quick look at the folder content show that all files are plain text files in tsv format. We import them in the proper format (matrix for the abundances and the taxonomy, data.frame for the covariates)
otu <- read.table("ravel_data/counts.tsv") %>% as.matrix()
tax <- read.table("ravel_data/taxonomy.tsv") %>% as.matrix()
map <- read.table("ravel_data/metadata.tsv")The count table is in the taxa \(\times\) samples format, so we build our phyloseq object as follows:
ravel <- phyloseq(otu_table(otu, taxa_are_rows = TRUE),
tax_table(tax),
sample_data(map))
ravelphyloseq-class experiment-level object
otu_table() OTU Table: [ 247 taxa and 394 samples ]
sample_data() Sample Data: [ 394 samples by 8 sample variables ]
tax_table() Taxonomy Table: [ 247 taxa by 7 taxonomic ranks ]The data consists of 394 samples of the vaginal microbiome of women of reproductive ages and the original studies focused on the link between microbial composition and vaginosis. Each sample is associated to several covariates:
- ID: Woman unique ID
- Ethnic_Group: Ethnic group of the woman (in Asian, Black, Hispanic and White)
- pH: pH in the vagina
- Nugent_Score: Nugent score, a score of bacterial vaginosis on scale from 0 to 10
- Nugent_Cat: Nugent category, derived from the Nugent score. Can be either low (score in 0-3), intermediate (score in 4-6) or high (score in 7-10)
- CST: Community State Type, more on that later.
We can navigate through the metadata
Before moving on to elaborate statistics, we’ll look at the taxonomic composition of our samples
Taxonomic Composition
We then look at the community composition at the phylum level. In order to highlight the structure of the data, we split the samples according to each covariates in turn. We show several figures, corresponding to different taxonomic levels, for the Nugent Categry but only a phylum-level one for other covariates.
We can see right away that samples with low scores are dominated by Firmicutes and other phyla become more prevalent as the score increases.
plot_composition(ravel, "Kingdom", "Bacteria", "Phylum", fill = "Phylum") +
facet_grid(~Nugent_Cat, scales = "free_x", space = "free_x")Problematic taxa
taxa Kingdom Phylum rank
Bacteria_4 Bacteria_4 Bacteria Unknown 7
We have access to the following taxonimic ranks:
rank_names(ravel)[1] "Kingdom" "Phylum" "Class" "Order" "Family" "Genus" "Species"Given the importance of Firmicutes, we can zoom in within that phylum and investigate the composition at the genus level.
plot_composition(ravel, "Phylum", "Firmicutes", "Genus", fill = "Genus", numberOfTaxa = 5) +
facet_grid(~Nugent_Cat, scales = "free_x", space = "free_x")Problematic taxa
taxa Kingdom Phylum Class
Lachnospiraceae_8 Lachnospiraceae_8 Bacteria Firmicutes Clostridia
Order Family Genus rank
Lachnospiraceae_8 Clostridiales Lachnospiraceae Unknown 4
We see that most samples are dominated by the sole lactobacillus genus. Unfortunately, we don’t have access to species level affiliation and can zoom no further.
plot_composition(ravel, "Genus", "Lactobacillus", "Species", fill = "Species", numberOfTaxa = 7) +
facet_grid(~Nugent_Cat, scales = "free_x", space = "free_x")Problematic taxa
taxa Kingdom Phylum Class Order Family
L. iners L. iners Bacteria Firmicutes Bacilli Lactobacillales Lactobacillaceae
Genus Species rank
L. iners Lactobacillus Unknown 1
We can also organize, as suggested in the slides, the communities in terms of Nugent Category, CST and pH to examine their impact on community composition. For each of these covariates, we only examine the phylum-level composition:
The communities become more diverse as the nugent score increases.
plot_composition(ravel, "Kingdom", "Bacteria", "Phylum", fill = "Phylum") +
facet_grid(~Nugent_Score, scales = "free_x", space = "free_x")Problematic taxa
taxa Kingdom Phylum rank
Bacteria_4 Bacteria_4 Bacteria Unknown 7
Communities from CST I-III and V are dominated Firmicutes and have low diversity whereas communities from CST iV are more diverse.
plot_composition(ravel, "Kingdom", "Bacteria", "Phylum", fill = "Phylum") +
facet_grid(~CST, scales = "free_x", space = "free_x")Problematic taxa
taxa Kingdom Phylum rank
Bacteria_4 Bacteria_4 Bacteria Unknown 7
Ethnic group seems to be a structuring factor.
plot_composition(ravel, "Kingdom", "Bacteria", "Phylum", fill = "Phylum") +
facet_grid(~Ethnic_Group, scales = "free_x", space = "free_x")Problematic taxa
taxa Kingdom Phylum rank
Bacteria_4 Bacteria_4 Bacteria Unknown 7
but only because ethnic groups have a very contrasted score distributions:
ggplot(sample_data(ravel), aes(x = Ethnic_Group, group = Nugent_Cat, fill = Nugent_Cat)) +
geom_bar(stat = "count") +
scale_fill_brewer(type = "seq", palette = "Reds")
We will seldom use the Ethnic Group in downstream analyses.
Splitting by pH is a bit more involved as pH is not discrete by nature. We could to order the sample by pH using the x = argument.
plot_composition(ravel, "Kingdom", "Bacteria", "Phylum", x = "pH", fill = "Phylum")Problematic taxa
taxa Kingdom Phylum rank
Bacteria_4 Bacteria_4 Bacteria Unknown 7
but we end up with an ugly graph as several samples have exactly the same pH. In this case, there are not that many pH values and we therefore treat it as discrete variable. We observe that the diversity increases with the pH.
plot_composition(ravel, "Kingdom", "Bacteria", "Phylum", fill = "Phylum") +
facet_grid(~pH, scales = "free_x", space = "free_x")Problematic taxa
taxa Kingdom Phylum rank
Bacteria_4 Bacteria_4 Bacteria Unknown 7
Alpha-diversity
The samples have very different sampling depths:
sample_sums(ravel) %>% range()[1] 693 7361We thus rarefy them before computing alpha-diversities:
ravel_rare <- rarefy_even_depth(ravel, rngseed = 20190124)Graphics
We first explore the impact of each covariates on \(\alpha\)-diversities.
All measures confirm that diversity increases with Nugent Scores.
plot_richness(ravel_rare, x = "Nugent_Score", measures = c("Observed", "Shannon", "InvSimpson")) +
geom_boxplot(aes(group = Nugent_Score)) ## add one boxplot per Nugent Score values
Low ph correspond to low diversity, although the relationship between pH and diversity breaks down at high pH.
plot_richness(ravel_rare, x = "pH", measures = c("Observed", "Shannon", "InvSimpson")) +
geom_boxplot(aes(group = pH)) ## add one boxplot per pH value
All CST have extremely low effective diversity except for CST IV.
plot_richness(ravel_rare, x = "CST", measures = c("Observed", "Shannon", "InvSimpson")) +
geom_boxplot(aes(group = CST)) ## add one boxplot per CST score
Anova
We can quantify the previous claims by performing an ANOVA of the diversity against the covariates of interest. For the sake of brevity, we focus here on the effective number of species as measured by the InvSimpson measures. We first build a data.frame with both covariates and diversity indices.
div_data <- cbind(estimate_richness(ravel_rare, measures = "InvSimpson"), ## diversity indices
sample_data(ravel_rare) ## covariates
)Nugent Category has a significant impact on diversity…
model <- aov(InvSimpson ~ 0 + Nugent_Cat, data = div_data)
anova(model)Analysis of Variance Table
Response: InvSimpson
Df Sum Sq Mean Sq F value Pr(>F)
Nugent_Cat 3 3149.21 1049.74 545.63 < 2.2e-16 ***
Residuals 391 752.25 1.92
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1with three times the number of effective species in high samples compared to low ones.
coef(model) Nugent_Cathigh Nugent_Catintermediate Nugent_Catlow
4.878522 2.355929 1.514241 A post-hoc test reveals that all categories have different diversities:
TukeyHSD(model) Tukey multiple comparisons of means
95% family-wise confidence level
Fit: aov(formula = InvSimpson ~ 0 + Nugent_Cat, data = div_data)
$Nugent_Cat
diff lwr upr p adj
intermediate-high -2.5225936 -3.094529 -1.9506580 0.0000000
low-high -3.3642811 -3.755079 -2.9734830 0.0000000
low-intermediate -0.8416874 -1.351850 -0.3315244 0.0003577pH has a significant impact on diversity…
model <- lm(InvSimpson ~ pH, data = div_data)
anova(model)Analysis of Variance Table
Response: InvSimpson
Df Sum Sq Mean Sq F value Pr(>F)
pH 1 481.85 481.85 178.18 < 2.2e-16 ***
Residuals 392 1060.07 2.70
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1by increasing it
coef(model)(Intercept) pH
-5.279626 1.658691 CST has a significant impact on diversity…
model <- aov(InvSimpson ~ 0 + CST, data = div_data)
anova(model)Analysis of Variance Table
Response: InvSimpson
Df Sum Sq Mean Sq F value Pr(>F)
CST 5 3404.9 680.98 533.47 < 2.2e-16 ***
Residuals 389 496.6 1.28
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1with CST IV having much more diversity than other CST.
coef(model) CSTI CSTII CSTIII CSTIV CSTV
1.488067 1.574007 1.363830 5.095042 1.629058 A post-hoc test reveals that all CST are comparable except for CST IV.
TukeyHSD(model) Tukey multiple comparisons of means
95% family-wise confidence level
Fit: aov(formula = InvSimpson ~ 0 + CST, data = div_data)
$CST
diff lwr upr p adj
II-I 0.08593971 -0.6031387 0.7750182 0.9970577
III-I -0.12423726 -0.5271451 0.2786706 0.9162924
IV-I 3.60697485 3.1826046 4.0313451 0.0000000
V-I 0.14099054 -0.5991985 0.8811795 0.9851071
III-II -0.21017698 -0.8843708 0.4640168 0.9131592
IV-II 3.52103513 2.8337996 4.2082706 0.0000000
V-II 0.05505082 -0.8615092 0.9716109 0.9998349
IV-III 3.73121211 3.3314644 4.1309599 0.0000000
V-III 0.26522780 -0.4611247 0.9915803 0.8549592
V-IV -3.46598431 -4.2044579 -2.7275107 0.0000000Beta diversities
We don’t have access to a phylogenetic, we’ll thus stick to jaccard and bray-curtis distances. As explained during the workshop, those distances are only meaningful when computed on rarefied data:
dist.jac <- distance(ravel_rare, method = "cc")
dist.bc <- distance(ravel_rare, method = "bray")Unconstrained ordination
We first perform unconstrained ordination on Jaccard and Bray-Curtis distances and color samples according to covariates to highlight the structure.
Jaccard distance induce a nice linear gradient of samples along the first axis which corresponds to the pH. The structure displayed in the first plance of the MDS is less easy to interpret when using the Bray distance but also capture a much higher fraction of the diversity.
p.jac <- plot_ordination(ravel_rare,
ordinate(ravel_rare, method = "MDS", distance = dist.jac),
color = "pH") + ggtitle("Jaccard")
p.bc <- plot_ordination(ravel_rare,
ordinate(ravel_rare, method = "MDS", distance = dist.bc),
color = "pH") + ggtitle("Bray-Curtis")
gridExtra::grid.arrange(p.jac, p.bc, ncol = 2)
Just like the pH, to which it is highly correlated, Nugent is a strong structuring factor of the communities.
p.jac <- plot_ordination(ravel_rare,
ordinate(ravel_rare, method = "MDS", distance = dist.jac),
color = "Nugent_Score") + ggtitle("Jaccard")
p.bc <- plot_ordination(ravel_rare,
ordinate(ravel_rare, method = "MDS", distance = dist.bc),
color = "Nugent_Score") + ggtitle("Bray-Curtis")
gridExtra::grid.arrange(p.jac, p.bc, ncol = 2)
CST are much better separated using the Bray distance than the Jaccard one. This means that although communities from different CST may have highly redudant microbial repertoire, they rarely have the same abundant taxa.
p.jac <- plot_ordination(ravel_rare,
ordinate(ravel_rare, method = "MDS", distance = dist.jac),
color = "CST") + ggtitle("Jaccard")
p.bc <- plot_ordination(ravel_rare,
ordinate(ravel_rare, method = "MDS", distance = dist.bc),
color = "CST") + ggtitle("Bray-Curtis")
gridExtra::grid.arrange(p.jac, p.bc, ncol = 2)
Constrained Ordination
Constrained ordination (not covered during the workshop) is similar to unconstrained ordination with the following difference:
- unconstrained ordination tries to capture the whole diversity, no matter where it comes from
- constrained ordination tries to capture only the fraction of diversity that can be explained by some covariates (which can be much smaller that the whole)
To perform constrained ordination, you should change the method argument to CAP (short for Constrained Analysis of Proximities) and specify a formula argument to tell the method what covariates can be used to explain the diversity. For instance, if we focus on the Ethnic Group
ord <- ordinate(ravel_rare, method = "CAP", distance = dist.bc, formula = ~ Ethnic_Group)
p12 <- plot_ordination(ravel_rare, ord, color = "Ethnic_Group", axes = c(1:2))
p23 <- plot_ordination(ravel_rare, ord, color = "Ethnic_Group", axes = c(2:3))
gridExtra::grid.arrange(p12, p23, nrow = 1)
Note that the CAP analysis kind of separates the samples according to their ethnic group. This is expected as we considered only the fraction of variance explained by those group. Note also there are only 3 constrained axes as we started with 4 groups (and hence 3 degrees of freedom). Finally, have a look at the percentages of variability: they are all extremely low, revealing that Ethnic group does not explain much.
We can add more covariates in the model to explain a larger fraction of the diversity (this is a bit counter-intuitive at first, but the more covariates you add to the model, the more degrees of freedom you have to explain the diversity and the less constrained is the analysis). Note that results of the full model are remarkably similar to results of the unconstrained analysis (but with smaller percentages of variance explained)
ord <- ordinate(ravel_rare, method = "CAP", distance = dist.bc, formula = ~ pH + Nugent_Cat + CST + Ethnic_Group)
p12 <- plot_ordination(ravel_rare, ord, color = "CST", axes = c(1:2))
p23 <- plot_ordination(ravel_rare, ord, color = "CST", axes = c(2:3))
gridExtra::grid.arrange(p12, p23, nrow = 1)
Hierarchical clustering
The hierarchical clustering of Bray-Curtis distances using the Ward linkage function (to produce spherical clusters) show a perfect separation of samples along CST. The CST were indeed defined almost exactly that way. The original study considered Jensen-Shannon Divergences (JSD) instead of Bray-Curtis distances but the result is essentially the same.
Careful readers could also argue that CST IV is quite diverse compared to other CST (the root node of CST-IV is quite high compared to the root node of other CSTs). They would be right as follow-up studies suggested to refine CST IV into subtypes IV-a and IV-b.
par(mar = c(1, 0, 2, 0))
plot_clust(ravel_rare, dist = "bray", method = "ward.D2", color = "CST",
title = "Clustering of samples (Bray-Curtis + Ward)\nsamples colored by CST")
PERMANOVA
We use the Bray-Curtis distance to assess which covariates have a structuring effect on the communities.
metadata <- sample_data(ravel_rare) %>% as("data.frame")
model <- vegan::adonis(dist.bc ~ pH + Nugent_Cat + CST + Ethnic_Group, data = metadata, permutations = 999)
Expand To view the content of model
model$aov.tab
Permutation: free
Number of permutations: 999
Terms added sequentially (first to last)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
pH 1 16.213 16.2134 178.039 0.12027 0.001 ***
Nugent_Cat 2 11.939 5.9695 65.551 0.08856 0.001 ***
CST 4 70.956 17.7389 194.791 0.52633 0.001 ***
Ethnic_Group 3 0.825 0.2749 3.019 0.00612 0.001 ***
Residuals 383 34.878 0.0911 0.25872
Total 393 134.811 1.00000
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
$call
vegan::adonis(formula = dist.bc ~ pH + Nugent_Cat + CST + Ethnic_Group,
data = metadata, permutations = 999)
$coefficients
NULL
$coef.sites
[,1] [,2] [,3] [,4] [,5]
(Intercept) 0.722594616 0.734802390 0.714325930 0.7602715473 0.885088947
pH 0.017819609 0.013190839 0.007745846 0.0156076310 -0.011132627
Nugent_Cat1 0.011311519 0.009449591 0.025387775 0.0157672483 -0.130503713
Nugent_Cat2 0.004327509 -0.001648870 0.001770643 0.0025889266 0.044054493
CST1 -0.605440684 0.184173321 0.160182234 -0.6355786922 0.044961295
CST2 0.189478551 -0.609440754 0.238232695 0.1678961681 0.073375462
CST3 0.102572499 0.183270618 -0.466923334 0.1602907778 0.016803315
CST4 0.129852277 0.179557183 0.158647444 0.1288256423 -0.190025499
Ethnic_Group1 -0.002249168 0.007441758 0.016387048 -0.0064111491 0.038683580
Ethnic_Group2 0.003754876 -0.011610406 -0.015877694 0.0082844727 -0.022661339
Ethnic_Group3 0.004607258 -0.003106960 -0.006508110 0.0009498337 -0.004655408
[,6] [,7] [,8] [,9]
(Intercept) 0.724296696 0.804312055 0.947203659 6.760775e-01
pH 0.013739141 -0.007688265 -0.021916686 2.466291e-02
Nugent_Cat1 0.012010798 -0.005352422 -0.097405159 2.002773e-02
Nugent_Cat2 0.001791398 -0.003265274 0.036234176 1.706412e-02
CST1 -0.564318420 0.153360733 0.045889605 1.616148e-01
CST2 0.194574262 -0.408144703 0.068617707 2.031792e-01
CST3 0.079990649 0.057800468 0.012994790 -6.323258e-01
CST4 0.127879208 0.086479108 -0.187074841 1.188117e-01
Ethnic_Group1 0.001502731 0.004940693 0.031433647 5.096392e-03
Ethnic_Group2 0.003219285 -0.008929319 -0.012389142 9.261258e-06
Ethnic_Group3 0.006297239 0.004878317 -0.004698177 -1.163684e-02
[,10] [,11] [,12] [,13]
(Intercept) 0.6703214268 0.6704188855 0.81931728 0.6701782390
pH 0.0166661946 0.0236952321 -0.00199069 0.0249078890
Nugent_Cat1 0.0181667283 0.0229417706 -0.10157736 0.0214709148
Nugent_Cat2 -0.0008541267 0.0127814318 0.03698728 0.0156901934
CST1 -0.2893933784 0.1378220232 0.05212798 0.1547874879
CST2 0.2414743472 0.2112156692 0.09872172 0.2063713071
CST3 -0.2579233546 -0.6205122507 -0.09665440 -0.6297598601
CST4 0.1529493242 0.1190297895 -0.09194219 0.1200614779
Ethnic_Group1 0.0119479852 0.0066946293 0.03711725 0.0063588333
Ethnic_Group2 -0.0100738320 -0.0002803065 -0.04015542 -0.0003847355
Ethnic_Group3 -0.0010733044 -0.0110632992 0.01436770 -0.0114451280
[,14] [,15] [,16] [,17] [,18]
(Intercept) 0.768500691 0.710093832 0.757943031 0.794264144 0.752960437
pH 0.007896900 0.015699120 -0.002465777 -0.006937940 0.016430242
Nugent_Cat1 0.003891648 0.013587469 0.013073458 0.003064513 0.016428404
Nugent_Cat2 -0.004642192 0.001387423 0.001196690 0.001029120 0.002396099
CST1 0.175861891 -0.546445100 0.146834013 0.135015431 -0.634828494
CST2 -0.648924419 0.195983595 0.214899816 0.197749875 0.168266509
CST3 0.178696268 0.049337975 -0.521885817 -0.544206561 0.160068250
CST4 0.158829278 0.134586196 0.114598566 0.076037875 0.131011562
Ethnic_Group1 0.004241343 0.002547350 0.014840985 0.011222535 -0.005205843
Ethnic_Group2 -0.009090207 0.001141723 -0.009082550 -0.007251018 0.007759757
Ethnic_Group3 -0.005653302 0.006287648 -0.006094207 -0.007159183 0.001165776
[,19] [,20] [,21] [,22] [,23]
(Intercept) 0.696355573 0.698842909 0.761255476 0.916733087 1.08051108
pH 0.010162387 0.010453685 0.010640439 -0.018138567 -0.03186244
Nugent_Cat1 0.020695040 0.023099516 0.004683523 0.023482265 -0.05115223
Nugent_Cat2 0.001182359 0.001571072 -0.002239501 -0.011842304 0.02247202
CST1 0.159342134 0.159856942 0.176528480 0.134169908 0.01589654
CST2 0.233838098 0.242013214 -0.655445850 0.127765306 0.02465513
CST3 -0.353532177 -0.426172125 0.178726232 0.118699345 0.02291410
CST4 0.168661597 0.164338338 0.163340209 0.060240394 -0.08161316
Ethnic_Group1 0.020712465 0.018413953 0.004750832 -0.004217435 0.01744453
Ethnic_Group2 -0.022889437 -0.019036048 -0.010913618 -0.001508069 -0.01176248
Ethnic_Group3 -0.004399559 -0.005786980 -0.005072452 0.008131498 -0.00495727
[,24] [,25] [,26] [,27]
(Intercept) 0.6789049451 0.819653552 0.7581477062 0.7587576176
pH 0.0131122844 -0.001815464 0.0163024434 0.0162024391
Nugent_Cat1 0.0094613538 -0.080128143 0.0157419723 0.0156843984
Nugent_Cat2 -0.0006998876 0.027205857 0.0026899728 0.0027334851
CST1 0.1679539102 0.061478401 -0.6347547377 -0.6347223621
CST2 -0.1477836871 0.113220820 0.1678245902 0.1677792514
CST3 -0.3329394633 -0.115424064 0.1597755707 0.1598645827
CST4 0.1833022696 -0.125528442 0.1289710519 0.1289494558
Ethnic_Group1 0.0187933165 0.031991139 -0.0063326368 -0.0064355625
Ethnic_Group2 -0.0201612696 -0.024770463 0.0078016509 0.0078187207
Ethnic_Group3 -0.0066506401 -0.005353182 0.0008921849 0.0008203062
[,28] [,29] [,30] [,31] [,32]
(Intercept) 0.962514536 0.739868681 0.93451496 0.8622978265 0.756862788
pH -0.006738622 0.014146197 -0.01749469 -0.0042440043 0.015616547
Nugent_Cat1 0.026846461 0.023294191 -0.13009419 -0.1291422152 0.016770340
Nugent_Cat2 -0.023208221 -0.003076846 0.04583507 0.0413282813 0.001964205
CST1 0.040536437 -0.560330123 0.04246852 0.0367643015 -0.631237552
CST2 -0.143830285 0.097677276 0.05807892 0.0627782659 0.161547398
CST3 0.055725691 0.174389254 0.05068528 0.0009973057 0.161457545
CST4 0.023208140 0.147063196 -0.19930859 -0.1451228522 0.130295156
Ethnic_Group1 0.001692643 -0.003329884 0.03960841 0.0317489573 -0.005847380
Ethnic_Group2 -0.007756164 0.006021188 -0.02219887 -0.0233224295 0.007607304
Ethnic_Group3 0.004964852 0.006003270 -0.01003826 -0.0010688386 0.001129191
[,33] [,34] [,35] [,36]
(Intercept) 6.755361e-01 0.7590354529 1.033004476 0.791466992
pH 2.472290e-02 0.0161877732 -0.022672126 0.006397875
Nugent_Cat1 1.996429e-02 0.0156046749 0.043460728 0.009228797
Nugent_Cat2 1.699799e-02 0.0027350889 -0.022030433 0.001466317
CST1 1.617066e-01 -0.6339065693 0.069313069 -0.601118409
CST2 2.035672e-01 0.1675401771 -0.003079197 0.165281816
CST3 -6.339206e-01 0.1596429958 0.064319698 0.156244756
CST4 1.188527e-01 0.1288913664 -0.173886031 0.103887237
Ethnic_Group1 4.981160e-03 -0.0063943376 -0.019655382 -0.004706429
Ethnic_Group2 -3.292183e-05 0.0077944796 0.014007163 0.007486861
Ethnic_Group3 -1.149614e-02 0.0007466509 0.007938202 0.003998329
[,37] [,38] [,39] [,40] [,41]
(Intercept) 0.753757670 0.719025498 0.95241429 0.675835761 0.6806123795
pH 0.015055838 0.014232328 -0.01605017 0.023461491 0.0164173087
Nugent_Cat1 0.017661947 -0.084022383 -0.10458271 0.019177709 0.0277858310
Nugent_Cat2 0.001477058 0.023261591 0.04246441 0.016007611 -0.0003453985
CST1 -0.628979817 0.064934687 0.03228467 0.161753313 -0.0663019781
CST2 0.167587880 0.154124685 0.04479009 0.202071311 0.2352745788
CST3 0.161320775 -0.271884074 0.02825520 -0.630910518 -0.4637298970
CST4 0.131839854 -0.008603957 -0.14292596 0.119417326 0.1374697642
Ethnic_Group1 -0.004002976 0.039028259 0.03529412 0.006820382 0.0109782041
Ethnic_Group2 0.007588917 -0.023948062 -0.01385531 -0.001153520 -0.0055889117
Ethnic_Group3 0.002170293 -0.017677013 -0.01672929 -0.011442062 -0.0046235139
[,42] [,43] [,44] [,45] [,46]
(Intercept) 1.059661214 0.702837506 0.777555543 0.786949498 0.671521384
pH -0.025191768 0.009132911 0.002589826 0.001398514 0.019848864
Nugent_Cat1 -0.008295672 0.011047147 -0.100371331 -0.100237511 0.028175425
Nugent_Cat2 -0.007614500 0.003550189 0.039723960 0.039391403 0.003647328
CST1 0.018668298 0.164182110 0.065589387 0.059325099 0.030978941
CST2 0.004778048 0.239843890 0.135845074 0.132726274 0.230188259
CST3 0.022578699 -0.185249625 -0.201511844 -0.186120298 -0.550814758
CST4 -0.062953559 0.176027533 -0.059734382 -0.063430071 0.129211170
Ethnic_Group1 -0.008387056 0.018567075 0.047240592 0.046781092 0.007930897
Ethnic_Group2 0.013197593 -0.023321804 -0.027412727 -0.027556370 -0.002542328
Ethnic_Group3 -0.002900966 -0.001989862 -0.018192342 -0.018629728 -0.006335725
[,47] [,48] [,49] [,50] [,51]
(Intercept) 0.7227544248 0.838202293 0.72884831 0.6707359031 0.92957667
pH 0.0097823668 -0.007370710 0.01180603 0.0245126889 -0.01418635
Nugent_Cat1 -0.0783784131 -0.120065790 -0.10695439 0.0203647249 -0.11368843
Nugent_Cat2 0.0300252366 0.038236544 0.03335378 0.0160535584 0.03737975
CST1 0.0881865750 0.053386439 0.06274659 0.1594103685 0.04188319
CST2 0.1675375834 0.094488819 0.13588462 0.2046562395 0.05212673
CST3 -0.3710829749 -0.040481169 -0.21323435 -0.6300354098 0.04792197
CST4 0.0349832192 -0.169847204 -0.04485797 0.1226274106 -0.18945420
Ethnic_Group1 0.0347571922 0.039524407 0.03777070 0.0070701797 0.03456135
Ethnic_Group2 -0.0318704193 -0.021698025 -0.02527524 -0.0008044425 -0.01203099
Ethnic_Group3 0.0007224278 -0.009121783 -0.01193179 -0.0113818999 -0.01230225
[,52] [,53] [,54] [,55]
(Intercept) 0.758795821 0.915797673 0.669983830 0.7543467947
pH 0.011603722 -0.015859914 0.023269668 0.0165439060
Nugent_Cat1 0.002549751 -0.119543020 0.021207261 0.0164296005
Nugent_Cat2 -0.001654719 0.034743182 0.014641016 0.0022403409
CST1 0.177065863 0.038409016 0.160233948 -0.6329348506
CST2 -0.656659559 0.052613635 0.212022225 0.1645834681
CST3 0.178575719 0.028737395 -0.620223572 0.1598918200
CST4 0.164755842 -0.168857377 0.128216642 0.1304567247
Ethnic_Group1 0.004502593 0.027204168 0.009203232 -0.0052752856
Ethnic_Group2 -0.011290701 -0.016923263 -0.001889852 0.0077302582
Ethnic_Group3 -0.005315166 -0.001661466 -0.010881654 0.0009018202
[,56] [,57] [,58] [,59]
(Intercept) 0.7645810966 1.024875465 0.680855969 0.6773659164
pH 0.0140851875 -0.009038381 0.014663235 0.0237228622
Nugent_Cat1 0.0160112257 0.077533590 0.018776480 0.0198342390
Nugent_Cat2 0.0017875583 -0.028901660 -0.001776043 0.0165310184
CST1 -0.6333985330 0.036616766 -0.280113322 0.1618710361
CST2 0.1673254004 0.030954451 0.237967564 0.2035245962
CST3 0.1608566986 0.034311214 -0.253688016 -0.6323098716
CST4 0.1273683642 -0.106759938 0.146891160 0.1184489477
Ethnic_Group1 -0.0062549973 -0.022412224 0.010779947 0.0054244586
Ethnic_Group2 0.0086357218 0.021006729 -0.009192200 -0.0001789837
Ethnic_Group3 0.0009361744 0.003460531 -0.000744002 -0.0116239517
[,60] [,61] [,62] [,63] [,64]
(Intercept) 0.684166059 0.752749327 0.896976004 0.753807691 0.883556803
pH 0.016825360 0.014443502 -0.014760460 0.009412331 -0.006475512
Nugent_Cat1 0.023404216 0.005051851 -0.121621128 0.004278927 -0.127516522
Nugent_Cat2 0.007729137 -0.005012199 0.042748398 -0.002089027 0.040886555
CST1 0.158542737 0.162868194 0.042101844 0.173561843 0.038583731
CST2 0.225712874 -0.607254986 0.078880336 -0.558659472 0.058659783
CST3 -0.564812689 0.161770873 -0.002398809 0.173911838 0.043346289
CST4 0.145923005 0.154892925 -0.172347627 0.167605696 -0.188244039
Ethnic_Group1 0.012487907 0.005017865 0.041800215 0.004813710 0.038014888
Ethnic_Group2 -0.007301713 -0.009251840 -0.016350024 -0.008097077 -0.014057469
Ethnic_Group3 -0.008310689 -0.004793844 -0.020346050 -0.002452817 -0.018647893
[,65] [,66] [,67] [,68]
(Intercept) 0.7585083611 0.6794140766 0.7584762236 0.714591088
pH 0.0161506336 0.0161155221 0.0162320018 0.009672369
Nugent_Cat1 0.0159034916 0.0295864476 0.0157251491 0.002219264
Nugent_Cat2 0.0025336699 0.0004948901 0.0027171718 0.003789499
CST1 -0.6357562285 -0.0352807807 -0.6352463829 0.140293724
CST2 0.1680911131 0.2406714213 0.1679372336 0.209056309
CST3 0.1600360639 -0.4900074179 0.1599869462 -0.571382318
CST4 0.1289194863 0.1371964816 0.1290060411 0.094543509
Ethnic_Group1 -0.0064329103 0.0111076701 -0.0064558017 0.016667085
Ethnic_Group2 0.0082107145 -0.0053580977 0.0078638557 -0.006732229
Ethnic_Group3 0.0009383131 -0.0044498287 0.0008327569 -0.012250964
[,69] [,70] [,71] [,72] [,73]
(Intercept) 0.727249815 0.884727714 0.702455460 0.742201379 0.860573793
pH 0.009405793 -0.002577894 0.012550701 0.005356876 -0.001895536
Nugent_Cat1 0.019524442 -0.119801307 0.023927715 -0.106924715 -0.121724774
Nugent_Cat2 -0.006595046 0.043597522 0.004721121 0.034930522 0.033060525
CST1 -0.437790736 0.034774690 0.157540563 0.072107343 0.030964014
CST2 0.118634623 0.037046990 0.229749377 0.148040807 0.058079307
CST3 0.053439565 0.032067696 -0.540355357 -0.268326498 0.011036106
CST4 0.132581412 -0.135256173 0.150749263 -0.015528699 -0.140457554
Ethnic_Group1 0.002027700 0.032913967 0.013927081 0.037699966 0.029415396
Ethnic_Group2 -0.002217334 -0.039941175 -0.010549639 -0.033122308 -0.018511796
Ethnic_Group3 0.009268193 0.015436725 -0.007211210 -0.002920937 -0.005990960
[,74] [,75] [,76] [,77]
(Intercept) 0.762155659 0.6755033210 0.8902649351 0.671599583
pH 0.007751429 0.0245523331 -0.0159151108 0.021462131
Nugent_Cat1 0.034548151 0.0201370372 -0.0083782914 0.020740249
Nugent_Cat2 -0.005137294 0.0169431602 -0.0102423252 0.010382062
CST1 -0.445284659 0.1609509662 0.1315851719 0.154085627
CST2 0.192528405 0.2019419662 -0.4092590999 0.212361843
CST3 0.166918159 -0.6316313660 0.1376355719 -0.594158344
CST4 0.148716083 0.1191491865 0.0398619617 0.135485292
Ethnic_Group1 -0.001828641 0.0053921545 -0.0006248119 0.011076851
Ethnic_Group2 -0.001071874 -0.0001457328 0.0002885636 -0.003846022
Ethnic_Group3 0.008397243 -0.0115867917 0.0003262029 -0.008989354
[,78] [,79] [,80] [,81] [,82]
(Intercept) 0.718852069 0.748434107 0.717267199 0.698992539 0.752346024
pH 0.017759214 0.016185198 0.014666149 0.009628839 0.016566206
Nugent_Cat1 0.011363765 0.016532574 0.019179891 0.013457704 0.015712479
Nugent_Cat2 0.004100665 0.002461509 0.001355061 0.003073642 0.002741640
CST1 -0.595635878 -0.631297122 -0.519022580 0.161582774 -0.634352524
CST2 0.190804979 0.173879639 0.196877727 0.240467050 0.169367561
CST3 0.091868199 0.155027419 0.094939088 -0.238415539 0.157029724
CST4 0.130387420 0.131432732 0.140183570 0.174185427 0.130128757
Ethnic_Group1 -0.001633212 -0.004390353 0.002194177 0.019117315 -0.005485087
Ethnic_Group2 0.003603191 0.007297684 0.000706889 -0.023358583 0.007735377
Ethnic_Group3 0.005162127 0.002192335 0.007919084 -0.002355596 0.001189713
[,83] [,84] [,85] [,86]
(Intercept) 0.7913653496 0.742854193 0.966574160 0.7462244952
pH -0.0005067984 0.016054537 -0.022630462 0.0008151790
Nugent_Cat1 0.0233863701 0.016040857 -0.101200668 0.0107959955
Nugent_Cat2 -0.0090077579 0.002620053 0.036717442 -0.0021504817
CST1 0.1889847722 -0.624097798 0.039670191 0.1567347699
CST2 -0.0541251906 0.177964836 0.044347647 0.2170454531
CST3 0.1803696692 0.150538728 0.035666981 -0.0872781694
CST4 0.1785847254 0.132291631 -0.166188262 0.1523696690
Ethnic_Group1 0.0053703213 -0.002771256 0.029315164 0.0147589020
Ethnic_Group2 -0.0147224723 0.006616437 -0.021496965 -0.0203995897
Ethnic_Group3 0.0038363052 0.003226347 0.001047155 0.0008876371
[,87] [,88] [,89] [,90]
(Intercept) 0.757653438 0.6910215869 0.751036791 0.897097943
pH 0.014941018 0.0180262062 0.015506569 -0.006232422
Nugent_Cat1 0.014906354 0.0203224098 0.016902734 -0.108740091
Nugent_Cat2 0.002394688 0.0100405421 0.002046047 0.040057347
CST1 -0.633027281 0.1504585782 -0.627790540 0.048210780
CST2 0.168090576 0.2026843016 0.173523984 0.048495273
CST3 0.157646141 -0.6154630522 0.154021782 0.050363629
CST4 0.127845191 0.1169082134 0.130847506 -0.196133101
Ethnic_Group1 -0.005352032 0.0079064707 -0.003800532 0.033586979
Ethnic_Group2 0.007786397 -0.0004796443 0.007497475 -0.020256531
Ethnic_Group3 0.001076614 -0.0106232333 0.003170176 0.001423644
[,91] [,92] [,93] [,94]
(Intercept) 0.6738604618 0.7548359801 0.832721658 0.689917282
pH 0.0242193107 0.0122614499 0.003802460 0.016297468
Nugent_Cat1 0.0205557456 0.0214355616 0.004138754 0.013485746
Nugent_Cat2 0.0159369662 0.0007207549 -0.013558375 0.002333808
CST1 0.1611757632 -0.5770830584 -0.417985557 -0.473457015
CST2 0.2013940105 0.1807144309 0.131558163 0.222342951
CST3 -0.6313796855 0.1633879224 0.110780625 -0.042099048
CST4 0.1206612246 0.1381091614 0.043435643 0.143299118
Ethnic_Group1 0.0062249536 -0.0032402269 -0.002514690 0.005908167
Ethnic_Group2 -0.0007291376 0.0072316963 0.010414999 -0.005510131
Ethnic_Group3 -0.0115470626 0.0056552876 -0.003954632 0.005777747
[,95] [,96] [,97] [,98]
(Intercept) 0.7568757202 0.7519340753 0.686652979 0.921440034
pH 0.0162693965 0.0118062623 0.015371525 -0.010337159
Nugent_Cat1 0.0153884748 -0.0008187635 0.013282179 0.048458912
Nugent_Cat2 0.0027657867 -0.0014337867 0.001529225 -0.018580135
CST1 -0.6339206245 0.1759861036 -0.414004848 0.120428420
CST2 0.1683003531 -0.6454403161 0.226773526 0.108115574
CST3 0.1584030418 0.1756701278 -0.128841913 0.100368839
CST4 0.1289389598 0.1567641975 0.147512540 0.043174008
Ethnic_Group1 -0.0061918414 0.0061601649 0.006751042 -0.011560246
Ethnic_Group2 0.0076767245 -0.0110474627 -0.008175563 0.003805527
Ethnic_Group3 0.0007892933 -0.0048189423 0.002714611 0.010393197
[,99] [,100] [,101] [,102]
(Intercept) 0.813401673 0.7076456191 6.792012e-01 0.8138929953
pH -0.001364964 0.0177307867 2.295372e-02 -0.0003287229
Nugent_Cat1 0.001244701 0.0108745295 1.896443e-02 -0.1138333731
Nugent_Cat2 -0.003531222 0.0035572152 1.636045e-02 0.0378975790
CST1 -0.559705504 -0.5651248100 1.619247e-01 -0.0536163322
CST2 0.160294921 0.2022813723 2.030369e-01 0.0951718500
CST3 0.151003780 0.0483161058 -6.311821e-01 0.0162098064
CST4 0.075881223 0.1334781408 1.175363e-01 -0.1338733968
Ethnic_Group1 -0.001001458 0.0005085565 5.713310e-03 0.0307069068
Ethnic_Group2 0.007747126 0.0012881749 3.003597e-05 -0.0301073832
Ethnic_Group3 0.003113622 0.0055470570 -1.166922e-02 0.0127786269
[,103] [,104] [,105] [,106] [,107]
(Intercept) 0.747200062 0.875783427 0.757847891 0.6813748232 0.752617070
pH 0.014862327 -0.001172446 0.001591484 0.0142365416 0.016142496
Nugent_Cat1 0.014941521 0.014027196 -0.115747143 0.0218183232 0.017282721
Nugent_Cat2 0.002081278 -0.005703534 0.036939250 -0.0004484756 0.002015834
CST1 -0.623569644 0.071062141 0.068884450 -0.3005182275 -0.629880215
CST2 0.177231803 0.112194260 0.136474768 0.2321389169 0.172993185
CST3 0.145914519 -0.032815876 -0.189098440 -0.1266757544 0.159404675
CST4 0.128399740 0.051060836 -0.082855750 0.1508462360 0.132270219
Ethnic_Group1 -0.003667775 0.012525477 0.043832363 0.0104001791 -0.004091036
Ethnic_Group2 0.006637306 -0.023928300 -0.034164921 -0.0117749960 0.007731706
Ethnic_Group3 0.003691919 0.010127215 -0.008454293 0.0032858002 0.002415854
[,108] [,109] [,110] [,111] [,112]
(Intercept) 0.7587576176 0.927544980 0.702979691 0.744404180 0.765343220
pH 0.0162024391 -0.015932866 0.013563895 0.015756517 0.010745805
Nugent_Cat1 0.0156843984 -0.105746413 0.013860121 0.018121832 0.021928828
Nugent_Cat2 0.0027334851 0.021453769 0.010440700 0.001109474 -0.001905485
CST1 -0.6347223621 0.033305973 0.153733156 -0.619561701 -0.579213710
CST2 0.1677792514 0.051928143 0.208251656 0.162441948 0.174842175
CST3 0.1598645827 0.043161570 -0.603195717 0.158958708 0.159864034
CST4 0.1289494558 -0.175791444 0.113683085 0.134935635 0.129172325
Ethnic_Group1 -0.0064355625 0.023998133 0.010555120 -0.003130200 -0.004260776
Ethnic_Group2 0.0078187207 -0.011861058 -0.002803097 0.006494854 0.009112648
Ethnic_Group3 0.0008203062 -0.008040308 -0.010043517 0.003465884 0.005802861
[,113] [,114] [,115] [,116] [,117]
(Intercept) 0.696333976 0.844895218 0.670696963 0.769055170 0.745968695
pH 0.010140203 -0.008994717 0.016477455 0.012384397 0.016771524
Nugent_Cat1 0.012975414 -0.125428112 0.022814100 0.014884060 0.014046849
Nugent_Cat2 0.003088048 0.041905569 -0.002252089 0.001240570 0.003314201
CST1 0.160109993 0.052352312 -0.210596681 -0.628736057 -0.630841806
CST2 0.242768964 0.092743682 0.238919559 0.166836443 0.173323271
CST3 -0.212502985 -0.041670379 -0.330046091 0.160113583 0.147716739
CST4 0.175378202 -0.164452963 0.147741487 0.123715097 0.128258981
Ethnic_Group1 0.019191883 0.040131799 0.012666258 -0.005539622 -0.004198448
Ethnic_Group2 -0.023287452 -0.022684631 -0.009549030 0.008780482 0.006875199
Ethnic_Group3 -0.002088650 -0.007351756 -0.001747363 0.001334882 0.002463164
[,118] [,119] [,120] [,121] [,122]
(Intercept) 0.755789884 0.699237408 0.732578417 0.8349420672 0.753804096
pH 0.013012102 0.010135034 0.016551522 -0.0006944347 0.015842061
Nugent_Cat1 0.007854519 0.022505230 0.014922143 0.0165867975 0.017090452
Nugent_Cat2 -0.001961317 0.001617313 0.003050489 -0.0032322843 0.002169729
CST1 0.170013797 0.161315308 -0.612219019 0.1543695099 -0.632486743
CST2 -0.654015705 0.240730367 0.183643943 0.1615279648 0.172487953
CST3 0.178767516 -0.401860956 0.131179453 0.1425348380 0.160772158
CST4 0.165944204 0.166773403 0.131912767 0.1478774428 0.132224190
Ethnic_Group1 0.003880606 0.019212724 -0.002208525 0.0036604454 -0.004771470
Ethnic_Group2 -0.010844779 -0.020572061 0.005442499 -0.0102315689 0.007634676
Ethnic_Group3 -0.005063997 -0.005296722 0.004769874 0.0003900314 0.001740491
[,123] [,124] [,125] [,126]
(Intercept) 0.728253254 0.7576144432 0.750987888 0.7581238628
pH 0.006512595 0.0158816240 0.016681790 0.0157334711
Nugent_Cat1 -0.088017083 0.0154892781 0.016665551 0.0153436672
Nugent_Cat2 0.032809158 0.0025840187 0.002132277 0.0026133792
CST1 0.089046054 -0.6345945729 -0.632897104 -0.6337781249
CST2 0.168074467 0.1680089852 0.172498380 0.1682197219
CST3 -0.341745594 0.1600663891 0.159414404 0.1593173399
CST4 0.003014273 0.1288853592 0.132260136 0.1287952291
Ethnic_Group1 0.039509091 -0.0059883266 -0.004629034 -0.0060923263
Ethnic_Group2 -0.035514837 0.0078836188 0.007694997 0.0080045032
Ethnic_Group3 -0.002132665 0.0009456165 0.001701659 0.0008664208
[,127] [,128] [,129] [,130]
(Intercept) 0.8373898858 0.7127028455 0.978964913 0.841151130
pH -0.0022605980 0.0168491502 -0.004008811 -0.001352043
Nugent_Cat1 0.0164990751 0.0128288884 -0.042569789 -0.131182703
Nugent_Cat2 -0.0039238222 0.0026106766 0.018847268 0.048734697
CST1 0.1548832188 -0.5711860889 0.010863769 0.043877006
CST2 0.1627110321 0.1981422204 0.008772990 0.067144434
CST3 0.1421680418 0.0706613182 0.015290199 -0.018799722
CST4 0.1450548114 0.1326028164 -0.044786928 -0.135336100
Ethnic_Group1 0.0049284874 0.0006457723 0.003884126 0.040789605
Ethnic_Group2 -0.0106436560 0.0026050256 0.002927517 -0.041772158
Ethnic_Group3 0.0005994122 0.0060751839 -0.008594285 0.010690589
[,131] [,132] [,133] [,134]
(Intercept) 0.6831739521 0.667800754 0.6741472082 0.998041617
pH 0.0159704749 0.020724647 0.0239419934 -0.027181235
Nugent_Cat1 0.0282601852 0.021741279 0.0202256575 -0.022381305
Nugent_Cat2 -0.0001203751 0.007508623 0.0160696758 -0.009066379
CST1 -0.0841348076 0.160229243 0.1608258627 0.050242124
CST2 0.2423981725 0.153329264 0.2048953454 0.047927374
CST3 -0.4667025740 -0.577763038 -0.6317081912 0.060125935
CST4 0.1383046110 0.142508741 0.1206781817 -0.172878491
Ethnic_Group1 0.0092894926 0.010540179 0.0061465777 -0.001325196
Ethnic_Group2 -0.0049133739 -0.005150038 -0.0003717278 0.013713694
Ethnic_Group3 -0.0044986089 -0.009134526 -0.0114960680 -0.006693349
[,135] [,136] [,137] [,138]
(Intercept) 0.809732641 0.6880000913 0.876350858 0.936456119
pH -0.009871716 0.0209640196 -0.004060841 -0.015982180
Nugent_Cat1 0.014205886 0.0229653585 -0.122638252 -0.112432763
Nugent_Cat2 -0.006665116 0.0131357503 0.032322534 0.042847805
CST1 0.125736527 0.1620085107 0.036051173 0.046575624
CST2 0.190572926 0.2038727691 0.052577918 0.053281671
CST3 -0.492739607 -0.6249193311 0.042479678 0.051956045
CST4 0.069212856 0.1151588400 -0.174245186 -0.202415284
Ethnic_Group1 0.007196111 0.0045936058 0.033328768 0.038803427
Ethnic_Group2 -0.001781075 0.0006158253 -0.014436219 -0.018711420
Ethnic_Group3 -0.006682341 -0.0111793171 -0.012691457 -0.009325414
[,139] [,140] [,141] [,142] [,143]
(Intercept) 6.863781e-01 0.93462477 0.855120582 0.723980058 0.95419815
pH 1.384570e-02 -0.01769642 -0.004492165 0.008171321 -0.02292882
Nugent_Cat1 1.481396e-02 -0.12541973 -0.128963063 0.009860409 -0.11620239
Nugent_Cat2 4.896688e-06 0.04685083 0.038036627 0.007177049 0.03865675
CST1 -3.150723e-01 0.04457524 0.036133348 0.140463214 0.04333829
CST2 2.383595e-01 0.05357077 0.069822790 0.205015569 0.05803341
CST3 -2.310838e-01 0.05239633 0.011817413 -0.587160284 0.05078745
CST4 1.469949e-01 -0.20022698 -0.166630622 0.098642026 -0.20628658
Ethnic_Group1 9.312246e-03 0.03965245 0.039417762 0.010375067 0.03707905
Ethnic_Group2 -8.589886e-03 -0.01871273 -0.023205183 -0.003069359 -0.01135197
Ethnic_Group3 -8.075372e-04 -0.01091754 -0.010168020 -0.009725063 -0.01505294
[,144] [,145] [,146] [,147] [,148]
(Intercept) 0.95989584 1.0263906436 0.760792908 1.01688592 0.678444227
pH -0.02323747 -0.0302560178 0.011244066 -0.02747001 0.018086511
Nugent_Cat1 -0.11902082 -0.0034888305 0.004436047 -0.09077292 0.028490945
Nugent_Cat2 0.04287558 -0.0074430936 -0.003049376 0.03137388 0.002287886
CST1 0.03716407 -0.0243259857 0.176313533 0.02241551 -0.009222700
CST2 0.06200364 0.0284423476 -0.651670123 0.03959910 0.237105789
CST3 0.04462171 0.0632625513 0.176813488 0.03500465 -0.526759314
CST4 -0.19288164 -0.1394804748 0.164260813 -0.12898210 0.131917133
Ethnic_Group1 0.04031165 -0.0068450628 0.003989881 0.03063526 0.008369849
Ethnic_Group2 -0.01582407 0.0107896419 -0.010280858 -0.01031139 -0.003845106
Ethnic_Group3 -0.01892775 0.0006110958 -0.004527892 -0.01933090 -0.005952683
[,149] [,150] [,151] [,152] [,153]
(Intercept) 0.853806711 0.700678908 0.868576014 0.809858898 6.776523e-01
pH -0.016109123 0.016433346 0.012926528 -0.003459337 2.399741e-02
Nugent_Cat1 0.007549284 0.020112591 -0.078601299 -0.104193500 2.024661e-02
Nugent_Cat2 -0.009471051 0.008232970 0.019543997 0.023418817 1.662889e-02
CST1 0.095029666 0.155722883 0.013575170 0.045561018 1.618084e-01
CST2 0.175473161 0.198959598 0.024548245 0.095025047 2.032896e-01
CST3 -0.408621820 -0.610595812 0.008700194 -0.075672639 -6.330810e-01
CST4 0.055522221 0.113881951 -0.058269303 -0.125885237 1.186782e-01
Ethnic_Group1 0.011194073 0.007654506 0.020647718 0.036366630 4.855818e-03
Ethnic_Group2 -0.007956029 -0.000363797 -0.014309595 -0.025834150 8.168664e-05
Ethnic_Group3 -0.005910752 -0.011887844 -0.004799918 -0.006083416 -1.154026e-02
[,154] [,155] [,156] [,157]
(Intercept) 0.663010543 0.684697018 0.6751718966 0.708849469
pH 0.024576777 0.020516166 0.0246583139 0.009099329
Nugent_Cat1 0.022366689 0.009678227 0.0196666003 0.024716560
Nugent_Cat2 0.009818165 0.012011461 0.0170778327 0.002189147
CST1 0.125151841 0.152541514 0.1618013557 0.159800059
CST2 0.211955414 0.203432301 0.2033870860 0.236812670
CST3 -0.611672850 -0.611892380 -0.6330074966 -0.477606118
CST4 0.121365150 0.114044197 0.1187032037 0.159225816
Ethnic_Group1 0.007158635 0.008273734 0.0052650464 0.017147991
Ethnic_Group2 -0.001025376 -0.002893495 -0.0001362897 -0.015868837
Ethnic_Group3 -0.010222887 -0.010626235 -0.0116428965 -0.006841835
[,158] [,159] [,160] [,161]
(Intercept) 0.6983672641 1.011142415 1.0215500119 7.703556e-01
pH 0.0166462476 -0.024154309 -0.0297237063 3.103640e-04
Nugent_Cat1 0.0171632929 -0.025935745 -0.0270990131 1.930767e-02
Nugent_Cat2 0.0118519709 -0.003076588 -0.0006187464 -2.260910e-03
CST1 0.1589991821 0.049181079 0.0257265520 1.411402e-01
CST2 0.2034944963 0.027890019 0.0444081069 1.949827e-01
CST3 -0.6184853130 0.052583293 0.0118344484 -5.645369e-01
CST4 0.1122057642 -0.172976145 -0.1397136831 9.474539e-02
Ethnic_Group1 0.0074365976 -0.007219917 0.0060938021 6.101383e-03
Ethnic_Group2 -0.0002101181 0.014944214 -0.0009293895 7.088242e-05
Ethnic_Group3 -0.0116923782 0.001660460 -0.0017518088 -1.009824e-02
[,162] [,163] [,164] [,165]
(Intercept) 0.689214462 8.285927e-01 0.710965115 0.661222413
pH 0.019031615 6.804482e-04 0.008020465 0.023125548
Nugent_Cat1 0.016487270 1.747068e-02 0.025030138 0.024974267
Nugent_Cat2 0.012970451 -3.497849e-03 0.001020789 0.008892372
CST1 0.155442686 1.533647e-01 0.158813809 0.113392703
CST2 0.203257454 1.649760e-01 0.233462701 0.222220739
CST3 -0.619726715 1.404508e-01 -0.458679350 -0.592641110
CST4 0.112823404 1.490017e-01 0.160727579 0.129825470
Ethnic_Group1 0.008436459 4.297016e-03 0.017212005 0.008689904
Ethnic_Group2 -0.002107637 -1.044064e-02 -0.016854758 -0.001892660
Ethnic_Group3 -0.011077530 7.918082e-05 -0.006298667 -0.008438522
[,166] [,167] [,168] [,169]
(Intercept) 0.6731743551 0.6712845578 0.674366273 0.759304218
pH 0.0249248292 0.0249320471 0.016542972 0.011996323
Nugent_Cat1 0.0203072088 0.0206331880 0.022284504 0.003509701
Nugent_Cat2 0.0165802350 0.0159065799 -0.002120751 -0.001082760
CST1 0.1615669318 0.1608557117 -0.217551298 0.177225734
CST2 0.2039350844 0.1995805291 0.243318763 -0.656802074
CST3 -0.6336088659 -0.6297092429 -0.343449926 0.178744160
CST4 0.1196418745 0.1213587405 0.147217331 0.163629373
Ethnic_Group1 0.0054295544 0.0067773838 0.010869423 0.005016020
Ethnic_Group2 -0.0001376367 -0.0007890636 -0.008225865 -0.011454174
Ethnic_Group3 -0.0116600502 -0.0119669905 -0.002941881 -0.005316786
[,170] [,171] [,172] [,173] [,174]
(Intercept) 0.6752645286 0.6770856505 1.030358288 0.814440938 1.00121683
pH 0.0246554886 0.0235650744 -0.029976313 -0.001627743 -0.02814646
Nugent_Cat1 0.0198088859 0.0195022744 -0.082474543 0.026184952 -0.09562604
Nugent_Cat2 0.0167662979 0.0163614232 0.032301936 -0.009915287 0.03823580
CST1 0.1613929238 0.1615743985 0.026077622 0.172630451 0.03947982
CST2 0.2039765305 0.2037124404 0.035874700 0.071008691 0.05053880
CST3 -0.6335867069 -0.6324550473 0.040060676 0.162099405 0.05457464
CST4 0.1195633733 0.1182413663 -0.138591653 0.159374673 -0.19389799
Ethnic_Group1 0.0054675823 0.0056437117 0.024069140 0.002843944 0.02998787
Ethnic_Group2 -0.0002583643 -0.0003898285 -0.006145157 -0.011046034 -0.01055159
Ethnic_Group3 -0.0116535561 -0.0115019161 -0.015859212 0.002046059 -0.01100993
[,175] [,176] [,177] [,178] [,179]
(Intercept) 0.864641062 1.049620852 0.962292537 0.990307202 1.135219257
pH -0.004251937 -0.020998966 -0.020809795 -0.025812618 -0.044889031
Nugent_Cat1 -0.125479965 0.060407658 -0.094323377 -0.092565147 -0.007051290
Nugent_Cat2 0.034140287 -0.041100433 0.031151673 0.028273874 -0.005257709
CST1 0.035302653 0.044898484 0.043043525 0.038832422 0.023395087
CST2 0.058291104 0.019809238 0.049983546 0.055968998 0.010921780
CST3 0.025071915 0.036204285 0.051299924 0.049660295 0.034197188
CST4 -0.162946552 -0.132357132 -0.197718626 -0.193685016 -0.101765958
Ethnic_Group1 0.034118973 -0.027986566 0.028341494 0.032699222 -0.007358188
Ethnic_Group2 -0.014855151 0.027763653 -0.004243288 -0.009376622 0.009895006
Ethnic_Group3 -0.013605618 0.003550471 -0.014212077 -0.015901458 -0.001748864
[,180] [,181] [,182] [,183]
(Intercept) 6.724989e-01 0.747348211 0.754704769 0.7643932389
pH 2.495172e-02 0.015634257 0.016457971 0.0031303897
Nugent_Cat1 2.044393e-02 0.014978603 0.016109075 0.0114942658
Nugent_Cat2 1.656911e-02 0.002297837 0.002638517 0.0008428242
CST1 1.591488e-01 -0.627439001 -0.635316914 0.1316285507
CST2 2.052987e-01 0.165778769 0.170217549 0.1976844312
CST3 -6.336289e-01 0.151939261 0.160170647 -0.5602337570
CST4 1.191793e-01 0.129595195 0.130556268 0.1016839370
Ethnic_Group1 5.418617e-03 -0.003849089 -0.005609751 0.0108014266
Ethnic_Group2 -4.289655e-05 0.006487899 0.008084266 -0.0034987463
Ethnic_Group3 -1.156976e-02 0.002601280 0.001287817 -0.0109349862
[,184] [,185] [,186] [,187] [,188]
(Intercept) 0.744996044 0.88192328 0.92005669 0.678909752 0.93868708
pH 0.014051547 -0.01425135 -0.01610384 0.022153424 -0.01816936
Nugent_Cat1 -0.002480307 -0.12590281 -0.08305564 0.016516160 -0.13017957
Nugent_Cat2 -0.001867355 0.04840270 0.01777162 0.013621778 0.04707346
CST1 0.174892725 0.04808919 0.03386640 0.157744446 0.04016829
CST2 -0.641364126 0.08970185 0.07020286 0.203646488 0.05381582
CST3 0.176098247 -0.01701364 -0.02375451 -0.625762665 0.04952610
CST4 0.153722143 -0.18270892 -0.12544943 0.119046302 -0.18702533
Ethnic_Group1 0.007885538 0.04400440 0.03017009 0.008437649 0.04179650
Ethnic_Group2 -0.012285667 -0.02264012 -0.00834591 -0.001832570 -0.02239237
Ethnic_Group3 -0.007040594 -0.01340336 -0.01683413 -0.011498482 -0.01227334
[,189] [,190] [,191] [,192]
(Intercept) 0.6737777770 0.7575161497 0.6836423045 0.97249839
pH 0.0243014024 0.0163361176 0.0152837587 -0.02278482
Nugent_Cat1 0.0207726877 0.0157986554 0.0151607353 -0.11150695
Nugent_Cat2 0.0161970318 0.0026829031 -0.0008092002 0.04667519
CST1 0.1610614634 -0.6357493420 -0.3647722498 0.03776547
CST2 0.2054241217 0.1678108930 0.2250814681 0.04667104
CST3 -0.6319170556 0.1600946538 -0.1592125076 0.04645257
CST4 0.1203639838 0.1292937150 0.1467017767 -0.17615928
Ethnic_Group1 0.0057999352 -0.0063609386 0.0079078736 0.03441422
Ethnic_Group2 -0.0002571698 0.0079708895 -0.0084745957 -0.01704702
Ethnic_Group3 -0.0114020366 0.0008590701 0.0027866106 -0.01166615
[,193] [,194] [,195] [,196] [,197]
(Intercept) 0.700762405 0.769767158 0.811249834 0.745866391 0.671805092
pH 0.016256942 0.004018860 -0.001081753 0.016615653 0.016893481
Nugent_Cat1 0.011635628 0.036804065 0.019316923 0.014569375 0.020991645
Nugent_Cat2 0.002330030 -0.011491215 -0.009036041 0.003159605 -0.001721885
CST1 -0.524972040 -0.340692131 0.166779305 -0.631010226 -0.219324857
CST2 0.209487372 0.099945738 0.087859754 0.174556024 0.241833436
CST3 0.017286906 0.161422892 0.158166787 0.147132983 -0.332607346
CST4 0.134966835 0.144631430 0.159325472 0.128655104 0.146614772
Ethnic_Group1 0.004421568 -0.002256805 0.005191888 -0.004406734 0.012106631
Ethnic_Group2 -0.001304993 -0.003681856 -0.013193961 0.006880820 -0.008604185
Ethnic_Group3 0.005635221 0.009349115 0.002470232 0.002421476 -0.002503685
[,198] [,199] [,200] [,201] [,202]
(Intercept) 0.749667790 0.75891432 0.6739696207 0.7061884373 0.90706356
pH 0.015980720 0.01855062 0.0248896916 0.0167035897 -0.01144337
Nugent_Cat1 0.018280281 -0.09687288 0.0200679400 0.0132142774 -0.11420959
Nugent_Cat2 0.002257041 0.03712031 0.0168521630 0.0021069835 0.04126003
CST1 -0.624614137 0.04287638 0.1619487735 -0.5432936814 0.02816020
CST2 0.176189685 0.09100772 0.2041559598 0.2051269806 0.07286084
CST3 0.161739120 -0.13458350 -0.6338342283 0.0446190980 -0.03342541
CST4 0.134885743 -0.03233155 0.1194638985 0.1350192395 -0.10359174
Ethnic_Group1 -0.003815043 0.03437181 0.0053174856 0.0025153186 0.03906116
Ethnic_Group2 0.007805842 -0.04540087 -0.0002136136 0.0008889753 -0.02356001
Ethnic_Group3 0.002814848 0.01523577 -0.0115806830 0.0062687466 -0.01220012
[,203] [,204] [,205] [,206]
(Intercept) 0.662958228 0.6792171669 0.6762200421 0.9766436349
pH 0.024833749 0.0166634846 0.0234726543 -0.0320806030
Nugent_Cat1 0.022946055 0.0296571531 0.0184013806 -0.0030770074
Nugent_Cat2 0.011230581 0.0004917689 0.0151604448 -0.0120467027
CST1 0.132953155 -0.0018287433 0.1608239432 0.1130618293
CST2 0.212689273 0.2303671011 0.2052381076 -0.3301459335
CST3 -0.617952593 -0.5116071004 -0.6320234759 0.1219548421
CST4 0.123615781 0.1363443833 0.1186714982 0.0006881916
Ethnic_Group1 0.008005717 0.0111426694 0.0066904782 -0.0007201461
Ethnic_Group2 -0.001708815 -0.0058050872 -0.0007549076 -0.0022158891
Ethnic_Group3 -0.009975175 -0.0046916903 -0.0112762687 0.0037093712
[,207] [,208] [,209] [,210] [,211]
(Intercept) 0.688365502 0.706035927 0.883211014 0.6923455672 0.762904985
pH 0.015214037 0.013403163 -0.005580007 0.0129954221 0.011773335
Nugent_Cat1 0.012729600 -0.057799501 -0.115440574 0.0159489584 0.004774590
Nugent_Cat2 0.001712557 0.021341668 0.046240541 -0.0015941657 -0.002349051
CST1 -0.433718417 0.102946518 0.045993703 -0.2815121375 0.170982141
CST2 0.227374121 0.182244389 0.056378427 0.2315938670 -0.632059887
CST3 -0.097355325 -0.456854033 0.017849471 -0.2384010429 0.169817909
CST4 0.144307255 0.073136029 -0.164419265 0.1384844498 0.159210622
Ethnic_Group1 0.006897637 0.027583219 0.034937640 0.0097371524 0.004859187
Ethnic_Group2 -0.007365052 -0.021516140 -0.039179798 -0.0083831109 -0.010102491
Ethnic_Group3 0.003914649 -0.005750951 0.015524384 0.0003058721 -0.003652751
[,212] [,213] [,214] [,215]
(Intercept) 0.7597084981 0.6778025857 0.690658353 0.744639673
pH 0.0151882247 0.0236221464 0.010623855 0.001725217
Nugent_Cat1 0.0176001890 0.0204992970 0.018472816 -0.104338325
Nugent_Cat2 -0.0003368857 0.0162061563 0.001159080 0.035206434
CST1 -0.6104756753 0.1608122317 0.150855054 0.081844687
CST2 0.1529282218 0.2039387251 0.230012883 0.159255775
CST3 0.1569534100 -0.6326891314 -0.315992656 -0.277972074
CST4 0.1270733169 0.1190746541 0.166697095 -0.036331103
Ethnic_Group1 -0.0049619978 0.0053048393 0.021267152 0.038442833
Ethnic_Group2 0.0078749953 -0.0001151667 -0.024197092 -0.033745140
Ethnic_Group3 0.0030989138 -0.0112373661 -0.002904316 -0.001180093
[,216] [,217] [,218] [,219] [,220]
(Intercept) 0.754128234 0.731325462 0.668628637 0.687115963 0.694000502
pH 0.013361711 0.004784078 0.022081149 0.016921521 0.017068792
Nugent_Cat1 0.012968986 -0.029718152 0.021339911 0.016093845 0.014491965
Nugent_Cat2 0.001747485 0.016222481 0.011724251 0.004108619 0.010721010
CST1 -0.622850241 0.135538604 0.159915505 0.084852124 0.153239486
CST2 0.172532791 0.205711721 0.213155803 0.219326533 0.205203784
CST3 0.145385256 -0.544349249 -0.608302552 -0.563455084 -0.616187213
CST4 0.124220437 0.072576993 0.133705822 0.117009727 0.112506801
Ethnic_Group1 -0.004205670 0.023374985 0.010561871 0.011816259 0.008965801
Ethnic_Group2 0.006661516 -0.017163376 -0.003336468 -0.005273023 -0.001805951
Ethnic_Group3 0.003426585 -0.007468816 -0.009824975 -0.006249266 -0.010501025
[,221] [,222] [,223] [,224] [,225]
(Intercept) 0.689699200 0.753940426 0.683105843 0.9984549697 0.795778100
pH 0.020570783 0.016355621 0.021737153 -0.0123720560 0.003084693
Nugent_Cat1 0.018940104 0.015135676 0.020044726 0.0028126394 0.032457843
Nugent_Cat2 0.011862202 0.002896507 0.009252076 -0.0007376737 -0.010167534
CST1 0.155084810 -0.635293128 0.141908765 -0.0568363881 -0.124561712
CST2 0.199323745 0.170086076 0.202136066 0.0260482123 0.002348447
CST3 -0.618519861 0.156365982 -0.608326340 0.0110406280 0.090173203
CST4 0.120314608 0.129033123 0.121494177 0.0005331439 0.102832200
Ethnic_Group1 0.007215040 -0.005682752 0.007958962 0.0051236408 0.003961294
Ethnic_Group2 -0.001559392 0.007658992 -0.002249179 0.0027616284 -0.005473210
Ethnic_Group3 -0.010419838 0.001218049 -0.009147207 0.0099387150 0.012823460
[,226] [,227] [,228] [,229] [,230]
(Intercept) 0.817365213 0.665960963 0.712245204 0.985653590 0.823342232
pH 0.005909493 0.023903759 0.010058823 -0.024016130 -0.006263563
Nugent_Cat1 0.019372066 0.021437409 -0.022413240 -0.105145047 -0.001645989
Nugent_Cat2 -0.003943912 0.011351342 0.008465757 0.044421135 -0.006690170
CST1 -0.488664557 0.139474616 0.089031436 0.041723914 0.168852659
CST2 0.134081126 0.212700071 0.202396783 0.047983919 -0.581189437
CST3 0.119610290 -0.619044773 -0.478488141 0.049867620 0.168179070
CST4 0.100845781 0.121476527 0.078614357 -0.181842405 0.114860914
Ethnic_Group1 -0.002096297 0.008173806 0.028680711 0.033382389 0.002058555
Ethnic_Group2 0.006229864 -0.001808326 -0.018755219 -0.021343604 -0.006879841
Ethnic_Group3 0.010018104 -0.010071342 -0.008049025 -0.001200955 -0.002846436
[,231] [,232] [,233] [,234] [,235]
(Intercept) 0.741298856 0.709803626 0.750540743 0.684067352 0.6750041109
pH 0.007969434 0.013655841 0.016071794 0.022315001 0.0246065385
Nugent_Cat1 0.019669747 0.015671722 0.014371578 0.019105693 0.0193554931
Nugent_Cat2 -0.010321010 -0.001531869 0.002658696 0.014448956 0.0157417733
CST1 -0.240737179 -0.397319618 -0.625327542 0.157373977 0.1595743690
CST2 -0.171383038 0.214322147 0.171807157 0.203076131 0.2037322631
CST3 0.170950855 -0.053807411 0.151412729 -0.625461068 -0.6316834622
CST4 0.132285508 0.130110037 0.126897988 0.119506375 0.1204911033
Ethnic_Group1 0.005629788 0.005216989 -0.004060302 0.007761115 0.0064929745
Ethnic_Group2 -0.004670677 -0.006001141 0.007204484 -0.002779408 -0.0009616898
Ethnic_Group3 0.002986461 0.008398944 0.003266885 -0.010440705 -0.0114176868
[,236] [,237] [,238] [,239]
(Intercept) 0.7407830831 0.6753157795 0.6917026594 0.893579968
pH 0.0141952181 0.0244751087 0.0160015224 -0.007325750
Nugent_Cat1 0.0163883470 0.0195917195 0.0259537231 -0.121369179
Nugent_Cat2 0.0009058897 0.0167513733 0.0002407673 0.040580255
CST1 -0.5920970018 0.1617448289 0.0064215675 0.041270641
CST2 0.1677102826 0.2034887363 0.2266769533 0.052838651
CST3 0.1238814532 -0.6338961066 -0.5085223654 0.044791544
CST4 0.1247284070 0.1189445479 0.1265148233 -0.183207715
Ethnic_Group1 -0.0038703122 0.0053702102 0.0105536920 0.037130150
Ethnic_Group2 0.0060394558 -0.0004219238 -0.0061675154 -0.030543730
Ethnic_Group3 0.0056834057 -0.0113819203 -0.0038025141 0.001390851
[,240] [,241] [,242] [,243]
(Intercept) 0.7629678298 0.6745636717 0.772253392 0.91274183
pH 0.0139360369 0.0242900510 -0.002433028 -0.01434793
Nugent_Cat1 0.0155700699 0.0194085903 -0.005348302 -0.11603172
Nugent_Cat2 0.0003073105 0.0163419807 0.007265342 0.02914777
CST1 -0.5934419785 0.1612459929 0.136994475 0.03786778
CST2 0.1645750690 0.2045337901 0.199290297 0.05646764
CST3 0.1374331194 -0.6334602014 -0.539682192 0.03787903
CST4 0.1186902472 0.1195701647 0.078730142 -0.18303256
Ethnic_Group1 -0.0039092442 0.0060154357 0.016572546 0.02774298
Ethnic_Group2 0.0077944855 -0.0005149711 -0.012183480 -0.01390503
Ethnic_Group3 0.0061996646 -0.0114433325 -0.005825293 -0.00543282
[,244] [,245] [,246] [,247]
(Intercept) 0.8566567175 0.669594956 0.860983253 0.758053886
pH -0.0003306667 0.016747580 -0.011416424 0.013144545
Nugent_Cat1 -0.1040491610 0.024638919 0.007104194 0.018932120
Nugent_Cat2 0.0380065970 -0.001708858 -0.004335184 0.001103491
CST1 0.0393202683 -0.177077397 0.155182967 -0.613992887
CST2 0.0581577320 0.246383674 0.160674086 0.175038445
CST3 -0.0292661100 -0.348196336 0.143380691 0.161075508
CST4 -0.1031971322 0.147039300 0.117035092 0.132138613
Ethnic_Group1 0.0327313798 0.013492264 0.006985469 -0.003816611
Ethnic_Group2 -0.0411916682 -0.008707694 -0.010864260 0.007961307
Ethnic_Group3 0.0165724856 -0.002123258 0.001791425 0.003864609
[,248] [,249] [,250] [,251]
(Intercept) 0.7521950903 0.669078781 0.787946253 0.7609857856
pH 0.0001067375 0.024654814 0.001484199 0.0118395637
Nugent_Cat1 -0.0595446550 0.020024993 -0.105760421 0.0054876868
Nugent_Cat2 0.0173783404 0.015490136 0.031274483 -0.0007106417
CST1 0.1002982576 0.159914795 0.053041101 0.1778579379
CST2 0.1830016140 0.208044924 0.120472417 -0.6572938372
CST3 -0.3872847944 -0.630305529 -0.173082438 0.1783360752
CST4 0.0028691225 0.123137998 -0.054901702 0.1654086266
Ethnic_Group1 0.0362279244 0.007639492 0.031608998 0.0044273017
Ethnic_Group2 -0.0289418433 -0.001086271 -0.028669240 -0.0113163007
Ethnic_Group3 -0.0102380939 -0.011366140 -0.001159257 -0.0051957708
[,252] [,253] [,254] [,255] [,256]
(Intercept) 0.682777537 0.871205704 0.704618442 1.03506569 0.758025583
pH 0.021309947 -0.007737657 0.015048544 -0.03261708 0.015791583
Nugent_Cat1 0.018550552 -0.115304366 0.014399078 -0.09311610 0.015585420
Nugent_Cat2 0.014568811 0.040405566 0.010283949 0.03581207 0.002153457
CST1 0.159153269 0.046898996 0.155346510 0.02955380 -0.632767256
CST2 0.204399036 0.076730692 0.203238050 0.04381487 0.167928511
CST3 -0.625340391 0.012978811 -0.613392992 0.04287133 0.159248129
CST4 0.114507805 -0.196531835 0.111046554 -0.15325282 0.128025096
Ethnic_Group1 0.007274579 0.038478669 0.008584294 0.03018964 -0.005456614
Ethnic_Group2 -0.001289976 -0.016269617 -0.001125168 -0.01483809 0.008023911
Ethnic_Group3 -0.011322429 -0.010640134 -0.011610233 -0.01232956 0.001585704
[,257] [,258] [,259] [,260] [,261]
(Intercept) 0.669604497 0.859329234 0.874122022 6.743108e-01 0.93845912
pH 0.022893573 -0.010075092 -0.017986783 2.474584e-02 -0.01572762
Nugent_Cat1 0.018611341 0.010841828 -0.114531489 1.970900e-02 -0.10657508
Nugent_Cat2 0.012972323 -0.005230527 0.041702416 1.693971e-02 0.03748349
CST1 0.164530957 0.154970429 0.056990313 1.609737e-01 0.03665349
CST2 0.173669769 0.159174169 0.112820173 2.038596e-01 0.04945372
CST3 -0.611013138 0.142170602 -0.100829831 -6.336048e-01 0.03551382
CST4 0.127395256 0.120551195 -0.132730618 1.185197e-01 -0.16453997
Ethnic_Group1 0.008711058 0.005126656 0.042258265 5.277503e-03 0.03661752
Ethnic_Group2 -0.003975017 -0.009827856 -0.028998686 -7.665723e-05 -0.01940813
Ethnic_Group3 -0.010654279 0.002535040 -0.007927713 -1.157594e-02 -0.01235017
[,262] [,263] [,264] [,265]
(Intercept) 0.749967665 0.825620488 0.759196820 0.6816635814
pH 0.016317160 -0.009747007 0.015900943 0.0125885763
Nugent_Cat1 0.017751018 -0.046751871 0.016166926 0.0100361061
Nugent_Cat2 0.002115149 0.012415130 0.002142162 -0.0007644755
CST1 -0.628127765 0.082937483 -0.629921863 0.1677699515
CST2 0.174696421 0.151018411 0.165779127 -0.1341032729
CST3 0.160765233 -0.277307136 0.158726718 -0.3448517841
CST4 0.133537003 -0.035160479 0.127713011 0.1813312192
Ethnic_Group1 -0.004094339 0.022553671 -0.005350473 0.0185244179
Ethnic_Group2 0.007801240 -0.017714139 0.007983136 -0.0196112126
Ethnic_Group3 0.002637666 -0.004352122 0.001778044 -0.0069400293
[,266] [,267] [,268] [,269] [,270]
(Intercept) 0.6718977497 0.7503348680 0.749851993 0.91636432 0.900074841
pH 0.0243745650 0.0081559730 0.016524815 -0.01572166 -0.008169219
Nugent_Cat1 0.0203126864 0.0309324777 0.017102070 -0.12757037 -0.102774627
Nugent_Cat2 0.0151929542 -0.0021001196 0.002150129 0.04665892 0.031539534
CST1 0.1584311445 0.1458029440 -0.630104755 0.04740947 0.042417000
CST2 0.2027056640 0.1961721441 0.169784094 0.06401121 0.056778816
CST3 -0.6307645362 -0.5611726501 0.159348252 0.04634677 0.043241090
CST4 0.1212195936 0.0942784070 0.132372351 -0.21398514 -0.192726261
Ethnic_Group1 0.0071747834 0.0004746088 -0.004038408 0.04117845 0.032894868
Ethnic_Group2 -0.0009517004 0.0027106414 0.007446449 -0.01579699 -0.015236357
Ethnic_Group3 -0.0115336801 -0.0057368992 0.002121240 -0.01358207 -0.010227308
[,271] [,272] [,273] [,274] [,275]
(Intercept) 0.928654384 0.7594638681 1.035195938 0.667675500 0.674098092
pH -0.017463086 0.0158646563 -0.029692162 0.024351992 0.024633257
Nugent_Cat1 -0.123538896 0.0161433546 -0.016085325 0.020831008 0.019865103
Nugent_Cat2 0.047580475 0.0025713425 -0.007472105 0.015344876 0.016646737
CST1 0.048186569 -0.6349986508 0.052941787 0.158515853 0.161977858
CST2 0.062741277 0.1676587917 0.031551584 0.210342517 0.203141165
CST3 0.040233638 0.1603352370 0.057439922 -0.627543686 -0.633403410
CST4 -0.206110282 0.1286170275 -0.185802628 0.125449345 0.120053800
Ethnic_Group1 0.038887597 -0.0067062677 -0.014694859 0.008140509 0.005491580
Ethnic_Group2 -0.020106758 0.0081395087 0.016005274 -0.001188424 -0.000384007
Ethnic_Group3 -0.004183141 0.0008699564 0.006237415 -0.011029450 -0.011520592
[,276] [,277] [,278] [,279] [,280]
(Intercept) 0.7595123585 0.7551149083 0.741446229 0.95693319 0.94773056
pH 0.0130508534 0.0162812723 0.006856146 -0.01910385 -0.01471217
Nugent_Cat1 0.0057410413 0.0164718923 0.031306173 -0.11787048 0.06412996
Nugent_Cat2 -0.0002604848 0.0022229719 -0.003987013 0.04821679 -0.03605849
CST1 0.1770634576 -0.6326425923 0.144373776 0.04084497 -0.21647354
CST2 -0.6585964693 0.1642231353 0.208479540 0.04813006 0.09518240
CST3 0.1780019730 0.1598606239 -0.523224552 0.04999280 0.09746055
CST4 0.1670770279 0.1300758737 0.110418510 -0.18356148 -0.08370445
Ethnic_Group1 0.0039631524 -0.0054349904 0.005676372 0.03706617 -0.02691785
Ethnic_Group2 -0.0112001631 0.0076595400 -0.001668421 -0.01934836 0.02588592
Ethnic_Group3 -0.0050889271 0.0008811328 -0.003948580 -0.01334142 0.01056344
[,281] [,282] [,283] [,284]
(Intercept) 0.7412591908 0.6584425367 0.660855658 0.9219226657
pH 0.0095245150 0.0254135016 0.023110003 0.0096698580
Nugent_Cat1 0.0291979106 0.0245891281 0.027055172 0.0243180894
Nugent_Cat2 -0.0034226715 0.0107773192 0.006597996 -0.0033194923
CST1 -0.4265587075 0.1109724358 0.058405168 -0.0876419932
CST2 0.2089878106 0.2178930196 0.226466189 0.0329006130
CST3 0.1278513662 -0.6100543280 -0.573774465 0.0287338737
CST4 0.1439358484 0.1227883043 0.126595929 -0.0199087346
Ethnic_Group1 0.0004507941 0.0061580013 0.006021637 -0.0008733042
Ethnic_Group2 -0.0042875551 -0.0005251067 -0.001319456 0.0072600377
Ethnic_Group3 0.0093799813 -0.0094232982 -0.007519531 0.0054807529
[,285] [,286] [,287] [,288]
(Intercept) 8.077388e-01 0.906926901 0.749315061 0.767391768
pH 9.505566e-03 -0.022217138 0.013438909 0.005688991
Nugent_Cat1 6.384607e-03 -0.003174843 0.020514631 0.032742439
Nugent_Cat2 -7.375033e-03 -0.009781914 -0.001409264 -0.011480442
CST1 1.352846e-01 0.147326456 -0.594352724 0.086254690
CST2 -5.033195e-01 -0.477411503 0.131685407 0.074800297
CST3 1.360840e-01 0.156649829 0.167346869 0.167062747
CST4 1.330261e-01 0.053267672 0.137704946 0.160614844
Ethnic_Group1 4.065601e-03 -0.002607045 -0.004113842 0.001428120
Ethnic_Group2 -6.673164e-03 -0.004836499 0.007003143 -0.010203108
Ethnic_Group3 -9.676937e-06 0.002631869 0.004726246 0.006022554
[,289] [,290] [,291] [,292]
(Intercept) 0.6759994255 0.8662297983 0.730993583 0.818914332
pH 0.0245030948 -0.0007265615 0.017572569 -0.005735869
Nugent_Cat1 0.0196791698 -0.1124586783 0.012923511 -0.117889526
Nugent_Cat2 0.0166208159 0.0443993602 0.003853003 0.038355009
CST1 0.1612181424 0.0409921645 -0.618491853 0.058717903
CST2 0.2036447628 0.0539101519 0.183826262 0.111827109
CST3 -0.6336784500 0.0008271317 0.125718732 -0.086499638
CST4 0.1193746782 -0.1338102224 0.129511728 -0.148663193
Ethnic_Group1 0.0054464149 0.0338552011 -0.002732521 0.041240601
Ethnic_Group2 -0.0004142207 -0.0430873285 0.004825625 -0.027840568
Ethnic_Group3 -0.0114455792 0.0172666873 0.004052804 -0.004860785
[,293] [,294] [,295] [,296]
(Intercept) 0.668275251 0.763375652 0.694211617 8.313541e-01
pH 0.024214274 0.014365850 0.014216423 5.721850e-04
Nugent_Cat1 0.021600679 0.016196058 0.023784759 1.758219e-02
Nugent_Cat2 0.014055075 0.001598940 0.005793553 -3.609700e-03
CST1 0.161882681 -0.628774853 0.158366207 1.541948e-01
CST2 0.184938891 0.167314479 0.226986196 1.638710e-01
CST3 -0.620277113 0.158945743 -0.550712929 1.416111e-01
CST4 0.124961936 0.126422169 0.149508776 1.490624e-01
Ethnic_Group1 0.006953103 -0.005405405 0.013442789 4.062494e-03
Ethnic_Group2 -0.001601206 0.008010122 -0.009006024 -1.039470e-02
Ethnic_Group3 -0.011295578 0.001926404 -0.007732157 6.930958e-05
[,297] [,298] [,299] [,300]
(Intercept) 0.7018571005 0.699687115 0.8497288238 6.758910e-01
pH 0.0169832159 0.017055265 -0.0052169247 2.466803e-02
Nugent_Cat1 0.0123934179 0.026372361 0.0183149744 1.996953e-02
Nugent_Cat2 0.0020502015 0.007049795 -0.0061211645 1.707856e-02
CST1 -0.5279355002 0.155253343 0.1542450214 1.616967e-01
CST2 0.1998648295 0.207270212 0.1622383345 2.034703e-01
CST3 0.0186679653 -0.595661285 0.1433955027 -6.336969e-01
CST4 0.1350289534 0.113546642 0.1418709458 1.187773e-01
Ethnic_Group1 0.0030946039 0.004002701 0.0034677317 4.888414e-03
Ethnic_Group2 -0.0007999683 0.001441878 -0.0088653944 9.918964e-06
Ethnic_Group3 0.0053880628 -0.008592694 0.0005091973 -1.149437e-02
[,301] [,302] [,303] [,304] [,305]
(Intercept) 1.03684633 0.6721262224 6.750068e-01 0.748640897 0.956371428
pH -0.02013133 0.0149247000 2.473939e-02 0.016134961 -0.009748294
Nugent_Cat1 0.01477518 0.0266222412 1.995579e-02 0.016235506 0.082186401
Nugent_Cat2 -0.01796749 -0.0009316596 1.701656e-02 0.002033846 -0.029481553
CST1 0.03149872 0.0640361345 1.617990e-01 -0.627144907 0.109675674
CST2 0.00601397 0.2461541747 2.038471e-01 0.159478955 0.093968446
CST3 0.02900886 -0.3427955863 -6.340450e-01 0.156753572 0.085762574
CST4 -0.08102934 0.1545943874 1.192520e-01 0.130966358 -0.041918403
Ethnic_Group1 -0.02293535 0.0171482461 5.093016e-03 -0.004869108 -0.020507642
Ethnic_Group2 0.01685897 -0.0187149180 -5.734519e-05 0.006885324 0.011105996
Ethnic_Group3 0.01021472 -0.0020579716 -1.152737e-02 0.002415970 0.008283978
[,306] [,307] [,308] [,309]
(Intercept) 0.667760871 0.7892625734 0.8501616408 0.7825279828
pH 0.023941585 -0.0056629398 -0.0004279818 0.0057571469
Nugent_Cat1 0.020916478 0.0027321965 -0.1185204303 0.0120046389
Nugent_Cat2 0.014887065 0.0002993943 0.0471434741 -0.0074913962
CST1 0.159967913 0.1336438336 0.0457846883 0.1794680576
CST2 0.211724562 0.1967083470 0.0584525339 -0.6372343838
CST3 -0.623837345 -0.5405389079 -0.0043488572 0.1790272807
CST4 0.127595889 0.0821274181 -0.1422364271 0.1478560915
Ethnic_Group1 0.009037421 0.0133526120 0.0381035414 -0.0009838826
Ethnic_Group2 -0.001900275 -0.0085237348 -0.0414527553 -0.0051511069
Ethnic_Group3 -0.010948343 -0.0074689672 0.0117569450 -0.0044261168
[,310] [,311] [,312] [,313] [,314]
(Intercept) 0.915205083 1.013526109 0.7735702867 0.909276813 0.863683695
pH -0.009175789 -0.018770819 0.0108763256 -0.015316639 -0.003213623
Nugent_Cat1 -0.112656101 -0.019139654 0.0169479718 -0.109349443 -0.130584482
Nugent_Cat2 0.041471783 -0.003784841 -0.0006119433 0.036826022 0.045426987
CST1 0.043102517 0.023958436 -0.6195461246 0.044707094 0.039435196
CST2 0.040297608 0.027970361 0.1668295176 0.079649822 0.054233277
CST3 0.045111988 0.018094799 0.1587800603 0.008197863 0.015215342
CST4 -0.168817115 -0.102059916 0.1206024022 -0.189931977 -0.149980196
Ethnic_Group1 0.029803541 0.006961215 -0.0062522631 0.040021123 0.035373924
Ethnic_Group2 -0.036031323 -0.009767755 0.0088685518 -0.018372102 -0.029576124
Ethnic_Group3 0.016118847 0.008014278 0.0039639722 -0.013138999 0.003789018
[,315] [,316] [,317] [,318] [,319]
(Intercept) 0.72287957 0.784006873 0.6827221763 0.662953767 0.6751603820
pH 0.01075190 -0.001451480 0.0215784462 0.024817201 0.0243230180
Nugent_Cat1 -0.08165702 -0.115427716 0.0193606918 0.022349093 0.0193692356
Nugent_Cat2 0.02070869 0.035922967 0.0145817671 0.013632425 0.0166457238
CST1 0.07581833 0.063374654 0.1611449655 0.149150716 0.1615413377
CST2 0.16238890 0.130368551 0.2034387219 0.213233471 0.2034672990
CST3 -0.29332695 -0.156288006 -0.6285835640 -0.622967382 -0.6327377069
CST4 -0.01512890 -0.103008936 0.1176245528 0.125831487 0.1187247190
Ethnic_Group1 0.03767699 0.039976102 0.0064776597 0.008988972 0.0056590784
Ethnic_Group2 -0.02827191 -0.030831013 -0.0007457094 -0.001729304 -0.0004484996
Ethnic_Group3 -0.01179137 -0.005300289 -0.0112212729 -0.010820907 -0.0115166002
[,320] [,321] [,322] [,323] [,324]
(Intercept) 0.667648746 0.81802822 1.008177268 0.6665263122 0.682901568
pH 0.023567121 -0.00390497 -0.029885337 0.0239464258 0.015371473
Nugent_Cat1 0.020935565 -0.10678829 -0.020122265 0.0240754715 0.026503487
Nugent_Cat2 0.014156841 0.03769207 -0.008096713 0.0101412481 -0.001376090
CST1 0.160235573 0.05603258 0.066390671 0.1108799795 -0.130249803
CST2 0.214102388 0.11507354 -0.035343295 0.2152301658 0.243265987
CST3 -0.618764069 -0.12057680 0.076353084 -0.6047618895 -0.424094021
CST4 0.130262399 -0.10962351 -0.155183128 0.1217807453 0.140742230
Ethnic_Group1 0.009542905 0.04405833 -0.006264696 0.0060224818 0.009485511
Ethnic_Group2 -0.002351037 -0.02926228 0.006624169 -0.0008045035 -0.005879525
Ethnic_Group3 -0.010538717 -0.01324635 0.007213069 -0.0091067151 -0.003597916
[,325] [,326] [,327] [,328] [,329]
(Intercept) 0.840003593 0.697041028 0.896032370 0.71233769 1.043568293
pH -0.002370223 0.013442577 -0.004624512 0.01011799 -0.028694773
Nugent_Cat1 0.023754114 -0.006052604 -0.108342591 -0.01552497 -0.030160791
Nugent_Cat2 -0.010728225 0.006698758 0.038270973 0.01266649 -0.004564050
CST1 -0.556220597 -0.439811317 0.033795161 0.14114117 0.025265379
CST2 0.153744153 0.218219502 0.040546498 0.20588198 0.011051802
CST3 0.144848629 -0.050451595 0.015198491 -0.56929512 0.029998532
CST4 0.089016577 0.116405391 -0.120501442 0.08808755 -0.096233553
Ethnic_Group1 -0.011111742 0.012206455 0.030258767 0.02045672 0.011852044
Ethnic_Group2 0.013669420 -0.011059365 -0.040225090 -0.01203085 -0.012944966
Ethnic_Group3 0.005996515 0.005933807 0.017578182 -0.01064886 0.004687597
[,330] [,331] [,332] [,333] [,334]
(Intercept) 0.954449421 0.977776794 0.756199769 0.738840691 0.6777820578
pH -0.017921532 -0.020076185 0.010834063 0.016152221 0.0236116751
Nugent_Cat1 -0.105932607 -0.103920679 -0.000135080 0.016456617 0.0195117401
Nugent_Cat2 0.041037690 0.048134748 -0.002473121 0.002460087 0.0161247534
CST1 0.044521194 0.038564119 0.176771914 -0.617786220 0.1610672840
CST2 0.042953568 0.039471810 -0.650050576 0.181651729 0.2015884059
CST3 0.050724271 0.044300924 0.177147504 0.142902782 -0.6299539464
CST4 -0.184068619 -0.161800250 0.159636556 0.132100162 0.1196784693
Ethnic_Group1 0.030029001 0.032658078 0.005692894 -0.003051490 0.0059274177
Ethnic_Group2 -0.023930869 -0.016590128 -0.011276678 0.006416030 -0.0003281969
Ethnic_Group3 0.005255679 -0.009858402 -0.004862736 0.003962547 -0.0113559724
[,335] [,336] [,337] [,338] [,339]
(Intercept) 0.682234631 0.757659629 1.085807432 0.659826229 0.692711131
pH 0.015844365 0.015618887 -0.031163070 0.022793798 0.018488184
Nugent_Cat1 0.013354026 0.015594873 0.040590521 0.027415885 0.017676758
Nugent_Cat2 0.001329408 0.001963812 -0.032244592 0.006345587 0.011379713
CST1 -0.401829304 -0.632558595 -0.004750239 0.062744066 0.157608564
CST2 0.234649477 0.168537832 0.025222268 0.230302358 0.201562274
CST3 -0.146569767 0.157622962 0.032298502 -0.571906608 -0.620924164
CST4 0.149913059 0.128802881 -0.086299968 0.129147668 0.116959118
Ethnic_Group1 0.007191994 -0.005657239 -0.025531435 0.007025700 0.006880794
Ethnic_Group2 -0.007875868 0.008423358 0.023585886 -0.001467980 -0.001002099
Ethnic_Group3 0.002181500 0.001369180 0.005222092 -0.007200775 -0.010098504
[,340] [,341] [,342] [,343]
(Intercept) 0.7579574614 0.8356728869 0.6644288444 0.7717236482
pH 0.0162440755 -0.0001831896 0.0256680658 0.0001826443
Nugent_Cat1 0.0157933499 0.0176991308 0.0226585041 0.0080432448
Nugent_Cat2 0.0027016073 -0.0031790166 0.0144216533 0.0022716846
CST1 -0.6348191493 0.1539450776 0.1445770959 0.1350523209
CST2 0.1682663284 0.1625818775 0.2095000237 0.1965779189
CST3 0.1599046080 0.1427210753 -0.6271965643 -0.5569253781
CST4 0.1292605223 0.1481616582 0.1200638843 0.0951943103
Ethnic_Group1 -0.0063038362 0.0035478982 0.0061984771 0.0100338774
Ethnic_Group2 0.0078148299 -0.0102750366 -0.0003439015 -0.0045550688
Ethnic_Group3 0.0008735191 0.0002526452 -0.0111098968 -0.0082103469
[,344] [,345] [,346] [,347]
(Intercept) 8.989276e-01 0.885088045 0.7575473502 0.976924917
pH 6.175847e-03 -0.006425726 0.0162246512 -0.022312790
Nugent_Cat1 -2.355765e-02 0.034534169 0.0158290049 -0.104600811
Nugent_Cat2 -8.203501e-03 -0.016211270 0.0025365657 0.043286535
CST1 -1.055282e-02 0.143777168 -0.6342718103 0.043946045
CST2 9.946695e-03 -0.448274481 0.1684528881 0.046674621
CST3 2.898221e-02 0.141684177 0.1585610964 0.049332334
CST4 -5.662923e-02 0.073049350 0.1294033664 -0.186790607
Ethnic_Group1 -3.666503e-05 -0.014750951 -0.0064449522 0.034720341
Ethnic_Group2 7.331269e-03 0.007065634 0.0079603447 -0.015764214
Ethnic_Group3 -7.264377e-03 0.005515333 0.0008692615 -0.003201635
[,348] [,349] [,350] [,351] [,352]
(Intercept) 0.800666466 0.6795916411 1.071894172 0.711685114 0.900101720
pH -0.000774373 0.0226190606 -0.023207308 0.010692756 -0.020224861
Nugent_Cat1 0.034702349 0.0187085041 0.069390975 0.015612966 0.004152717
Nugent_Cat2 -0.011914716 0.0155007114 -0.038714547 -0.001154114 -0.013233112
CST1 0.149974551 0.1605705225 0.046828255 0.136293314 -0.392823943
CST2 0.182969084 0.2027809866 0.024747842 0.222627139 0.089970482
CST3 0.024998652 -0.6306024244 0.037051750 -0.474713645 0.138292513
CST4 0.096872871 0.1182088403 -0.132459577 0.141587924 0.016437935
Ethnic_Group1 -0.003826117 0.0057778346 -0.030557648 0.014454346 -0.007933088
Ethnic_Group2 -0.005783187 -0.0003946408 0.025866908 -0.013795562 0.005858458
Ethnic_Group3 0.008492220 -0.0112059589 0.007554916 -0.005332660 0.007879286
[,353] [,354] [,355] [,356]
(Intercept) 0.6802742569 0.839510767 0.6573029580 0.752152338
pH 0.0235085960 -0.002911537 0.0241131045 0.015294591
Nugent_Cat1 0.0207583881 0.022964445 0.0261394972 0.016563124
Nugent_Cat2 0.0157789914 -0.005707726 0.0083122774 0.001455163
CST1 0.1608849332 0.159169407 0.0800752658 -0.622610375
CST2 0.2026508145 0.149757053 0.2247545459 0.172910814
CST3 -0.6307118844 0.147206427 -0.5868569806 0.156094658
CST4 0.1180751896 0.144912664 0.1259070246 0.130514403
Ethnic_Group1 0.0051731759 0.001628320 0.0061999990 -0.003768384
Ethnic_Group2 -0.0001027238 -0.008985300 -0.0006516861 0.007600704
Ethnic_Group3 -0.0115937984 0.001072568 -0.0079451287 0.003178177
[,357] [,358] [,359] [,360] [,361]
(Intercept) 0.6733089227 0.668971028 0.671736402 1.041553348 0.739062234
pH 0.0247303619 0.017012957 0.021243599 -0.014063075 0.017155132
Nugent_Cat1 0.0206572022 0.019685314 0.021841761 0.043337473 0.013175972
Nugent_Cat2 0.0163824168 -0.001193454 0.011503485 -0.027846991 0.003697458
CST1 0.1592753194 -0.250601422 0.160602576 0.023901775 -0.624378351
CST2 0.2045284483 0.246113724 0.216467146 0.020686552 0.178471996
CST3 -0.6314546510 -0.307106578 -0.597863022 0.012651556 0.135061824
CST4 0.1189151034 0.151811111 0.135833406 -0.064585047 0.128571020
Ethnic_Group1 0.0055622831 0.012041873 0.010095463 -0.021742024 -0.003939613
Ethnic_Group2 -0.0000495213 -0.009246112 -0.003272383 0.015204150 0.005671267
Ethnic_Group3 -0.0116827608 -0.001885909 -0.009340039 0.008727286 0.003277265
[,362] [,363] [,364] [,365]
(Intercept) 0.705002600 6.764835e-01 0.722450903 6.762104e-01
pH 0.012862443 2.461802e-02 0.010177858 2.463181e-02
Nugent_Cat1 -0.048678968 2.001340e-02 0.009971350 2.000146e-02
Nugent_Cat2 0.020131225 1.711359e-02 0.009699029 1.712908e-02
CST1 0.114038759 1.615741e-01 0.153188198 1.616642e-01
CST2 0.194432372 2.031329e-01 0.203010239 2.033295e-01
CST3 -0.498232282 -6.327347e-01 -0.601016037 -6.333012e-01
CST4 0.080368626 1.185345e-01 0.100847492 1.186655e-01
Ethnic_Group1 0.025379557 4.892556e-03 0.008500505 4.855512e-03
Ethnic_Group2 -0.019812921 -3.849988e-06 -0.002259467 -1.387885e-05
Ethnic_Group3 -0.006297524 -1.156596e-02 -0.010262073 -1.150258e-02
[,366] [,367] [,368] [,369] [,370]
(Intercept) 0.6692466425 0.752350426 1.082236611 1.068461643 1.025243638
pH 0.0245604825 0.016587662 -0.036791772 -0.031442390 -0.012837733
Nugent_Cat1 0.0182500388 0.016468938 -0.013841522 -0.009797035 0.052738488
Nugent_Cat2 0.0158025181 0.002385250 -0.007502408 -0.010971117 -0.031504916
CST1 0.1604818811 -0.634031379 0.035391996 0.025908310 0.039916005
CST2 0.2058185997 0.170325768 0.022677589 0.033078408 0.012838543
CST3 -0.6310236453 0.159789360 0.044175932 0.035539837 0.032845159
CST4 0.1218560986 0.131679914 -0.136839451 -0.136727049 -0.108333784
Ethnic_Group1 0.0069420071 -0.005101444 -0.014885503 -0.004326641 -0.032486631
Ethnic_Group2 -0.0008409038 0.007713504 0.015320918 0.005839096 0.026828399
Ethnic_Group3 -0.0113343678 0.001198232 0.003694333 0.004384214 0.007554734
[,371] [,372] [,373] [,374]
(Intercept) 6.767592e-01 0.6855851345 6.760716e-01 6.758910e-01
pH 2.437264e-02 0.0158612929 2.388262e-02 2.466803e-02
Nugent_Cat1 2.013842e-02 0.0295431910 2.048267e-02 1.996953e-02
Nugent_Cat2 1.681457e-02 0.0007513024 1.570189e-02 1.707856e-02
CST1 1.616801e-01 -0.0374058639 1.612590e-01 1.616967e-01
CST2 2.034999e-01 0.2346264900 2.032946e-01 2.034703e-01
CST3 -6.328960e-01 -0.5009091013 -6.311140e-01 -6.336969e-01
CST4 1.185775e-01 0.1341780809 1.191456e-01 1.187773e-01
Ethnic_Group1 4.998679e-03 0.0085392800 5.583769e-03 4.888414e-03
Ethnic_Group2 -6.550087e-05 -0.0042948049 -5.544439e-05 9.918964e-06
Ethnic_Group3 -1.159270e-02 -0.0052577666 -1.178235e-02 -1.149437e-02
[,375] [,376] [,377] [,378]
(Intercept) 7.816963e-01 0.688915099 0.7803330526 0.782806690
pH 3.558342e-03 0.016461511 0.0110162482 0.001392328
Nugent_Cat1 -3.446322e-05 0.011383582 0.0180282424 0.024329302
Nugent_Cat2 -4.302041e-03 0.003137288 0.0004256156 -0.008442865
CST1 1.791630e-01 -0.458211580 -0.6137774034 0.191738770
CST2 -6.405720e-01 0.226393142 0.1626281682 -0.065767404
CST3 1.787931e-01 -0.085447391 0.1573685828 0.182428969
CST4 1.457769e-01 0.143936858 0.1188684725 0.184927105
Ethnic_Group1 4.197748e-03 0.004773159 -0.0073113506 0.005449946
Ethnic_Group2 -1.044941e-02 -0.006027540 0.0102685841 -0.015171603
Ethnic_Group3 -3.479576e-03 0.004068734 0.0031974277 0.003639058
[,379] [,380] [,381] [,382] [,383]
(Intercept) 0.759617309 1.024691304 1.092356234 0.924750021 1.060786119
pH 0.012141308 -0.027067554 -0.039838821 -0.022391191 -0.029325481
Nugent_Cat1 0.005641931 -0.027370756 0.005888004 -0.005072951 -0.029355457
Nugent_Cat2 -0.000629714 0.001107097 -0.017877381 -0.003123140 0.005551485
CST1 0.177973744 0.048026376 0.047226077 -0.348906447 0.027971402
CST2 -0.658348639 0.030130862 0.024006920 0.124467074 0.026404294
CST3 0.178276641 0.052016525 0.053423396 0.123221401 0.030966736
CST4 0.165447621 -0.178603451 -0.169633093 -0.040517817 -0.112696317
Ethnic_Group1 0.004094082 -0.004790792 -0.022572243 -0.007181675 -0.002303825
Ethnic_Group2 -0.011223527 0.011351357 0.019655865 0.005688586 -0.005836920
Ethnic_Group3 -0.005032771 0.001678838 0.006837286 0.007832751 0.010403361
[,384] [,385] [,386] [,387] [,388]
(Intercept) 1.12372410 6.762104e-01 0.7550876889 0.904314793 1.018831375
pH -0.04006790 2.463181e-02 0.0163543743 -0.016102324 -0.030371352
Nugent_Cat1 0.05371706 2.000146e-02 0.0153558128 -0.005535308 0.014836793
Nugent_Cat2 -0.03497662 1.712908e-02 0.0028176931 -0.002387253 -0.014083201
CST1 0.04943342 1.616642e-01 -0.6348996019 -0.316690098 -0.116657630
CST2 0.02654098 2.033295e-01 0.1693849595 0.120194871 0.063536600
CST3 0.04635732 -6.333012e-01 0.1570972507 0.107773422 0.072209339
CST4 -0.16359627 1.186655e-01 0.1291530250 -0.020269454 -0.110339241
Ethnic_Group1 -0.02968784 4.855512e-03 -0.0061372803 -0.003194465 -0.016936746
Ethnic_Group2 0.01992655 -1.387885e-05 0.0077046538 0.006434728 0.016642429
Ethnic_Group3 0.01120564 -1.150258e-02 0.0009859263 0.004798666 0.006223684
[,389] [,390] [,391] [,392]
(Intercept) 0.690912544 0.7564865834 0.713319235 0.946230329
pH 0.016799814 0.0019478278 0.008307395 -0.002077403
Nugent_Cat1 0.018589795 -0.0082915503 0.024212033 0.087325665
Nugent_Cat2 0.007297603 -0.0003815538 0.001862909 -0.031400425
CST1 0.159510316 0.1242737339 0.156637014 -0.168832533
CST2 0.159000625 0.2000958686 0.233554445 0.083287630
CST3 -0.586894188 -0.5275457778 -0.499594158 0.077323605
CST4 0.128143778 0.0797813733 0.153354566 -0.080011378
Ethnic_Group1 0.007993433 0.0173861929 0.015346121 -0.029276915
Ethnic_Group2 -0.003589372 -0.0111633055 -0.013382769 0.025260736
Ethnic_Group3 -0.009289506 -0.0104816353 -0.006052377 0.008854761
[,393] [,394]
(Intercept) 6.754085e-01 0.6945959059
pH 2.468552e-02 0.0190029962
Nugent_Cat1 2.010658e-02 0.0190244866
Nugent_Cat2 1.709697e-02 0.0104575997
CST1 1.608872e-01 0.1559172936
CST2 2.037514e-01 0.2012704541
CST3 -6.331973e-01 -0.6164295891
CST4 1.186110e-01 0.1152337040
Ethnic_Group1 4.877688e-03 0.0059017357
Ethnic_Group2 5.854052e-05 -0.0008032827
Ethnic_Group3 -1.150903e-02 -0.0098114307
$f.perms
[,1] [,2] [,3] [,4]
[1,] 1.20427899 1.2134344 1.4326479 0.9644000
[2,] 0.84871275 0.8880063 0.6356123 0.8963290
[3,] 1.79086775 0.7734532 0.9520784 0.5415733
[4,] 1.44834415 0.4005677 1.4222856 0.8604371
[5,] 2.11360779 0.3981884 0.6181303 0.9999963
[6,] 0.38444286 1.0237069 0.9494159 0.7512770
[7,] 1.00432008 0.9847499 0.7925581 1.1679207
[8,] 0.41045461 1.3362914 1.0571694 0.4693382
[9,] 1.01901209 0.4636332 0.5933456 0.5260927
[10,] 0.68264943 0.7575540 0.8586599 0.5807758
[11,] 0.89962777 0.4850300 1.5769414 0.9615639
[12,] 0.73653020 2.0411462 1.1736718 1.6502936
[13,] 0.52097421 1.4469473 0.7738227 1.7032800
[14,] 3.16729638 0.7406081 1.2243034 0.7794719
[15,] 0.40804477 0.8524704 1.1982098 0.7839110
[16,] 1.03366110 1.8670012 0.6851805 1.0728708
[17,] 0.55202846 1.3165521 1.2795603 1.4326372
[18,] 0.80178071 0.4542254 0.9116055 0.7128197
[19,] 1.43500073 0.9739555 0.7820472 0.7098340
[20,] 0.58318859 1.1665767 1.1703468 0.4896592
[21,] 1.56100125 0.8376839 1.1123918 1.1559085
[22,] 0.53266699 0.7044704 0.9927757 1.4517968
[23,] 0.58994567 1.2805481 0.8720901 0.5221207
[24,] 0.59902534 1.2649073 1.0786009 0.8257892
[25,] 0.87598554 0.9887295 1.3525279 0.7217681
[26,] 0.62618673 0.2924550 0.7252697 1.1723852
[27,] 1.57492659 0.4532117 0.8870265 0.9195593
[28,] 2.15854855 0.9398185 1.0212640 1.2551900
[29,] 1.65497198 1.0592500 0.7236640 1.7804789
[30,] 0.69177470 1.0382596 1.2984040 1.0430193
[31,] 0.30914609 0.9672501 0.6997218 0.4277706
[32,] 0.29916721 1.3965507 0.6983657 1.4111246
[33,] 1.44560706 0.9889414 1.0327924 1.4221807
[34,] 1.05748673 0.6792943 1.4288009 1.6307059
[35,] 0.82134880 0.5083626 1.0454921 0.7531222
[36,] 0.85442327 0.5322803 0.9098092 1.1870127
[37,] 0.47895790 0.9750381 0.5894475 1.0204222
[38,] 1.72871629 2.3964507 0.8577444 1.0892685
[39,] 0.45748197 0.9503237 1.2525159 1.1291185
[40,] 0.34547750 0.4731382 0.7124270 0.6235968
[41,] 0.77707399 1.2042961 0.6277822 0.9104902
[42,] 0.69485250 0.5295078 0.6315264 0.5923739
[43,] 1.04449144 0.8499853 1.1849615 1.3124298
[44,] 2.11467033 2.1241252 0.8247556 1.5287671
[45,] 0.61539994 0.6432258 0.9444987 1.0051620
[46,] 1.90629610 0.4760339 1.1189535 1.5118833
[47,] 0.81912975 1.0957443 1.1680129 0.8078717
[48,] 2.22074667 0.5426680 0.7890904 1.3251659
[49,] 0.67271571 0.5869788 0.8944409 0.4685427
[50,] 0.34508804 1.1863543 0.6224974 0.6871958
[51,] 0.95476675 0.5104707 0.7587311 0.8609763
[52,] 0.59324008 0.9343311 1.6582027 0.9894278
[53,] 1.01586457 0.8323419 1.4808136 1.0175734
[54,] 1.17419168 0.6328790 0.9623090 1.1640289
[55,] 1.63988211 1.1998068 1.3272143 0.7511812
[56,] 1.67206015 1.0757152 1.1523211 0.8780614
[57,] 1.59809759 0.8356992 1.0593340 1.3567076
[58,] 0.86832015 1.2429931 1.9693947 1.6170086
[59,] 1.36352757 0.5181731 0.7732426 0.9629392
[60,] 0.88004896 0.7838895 1.1809526 0.7327697
[61,] 3.08207562 2.6066578 1.1062917 2.0373723
[62,] 0.85682929 1.1179552 0.6086195 1.5190414
[63,] 1.29326572 1.5092082 1.1921527 0.6129073
[64,] 1.76574863 1.0251098 1.5064773 1.0859782
[65,] 0.60581809 0.9993517 0.6919208 1.5467567
[66,] 2.42768186 1.8394980 0.9965983 1.0217268
[67,] 0.92450163 0.9913893 0.7789385 1.5557734
[68,] 0.12591525 1.0302144 0.7081478 0.6421661
[69,] 1.08664891 1.7970062 0.6806922 0.6455023
[70,] 2.35736227 0.8908142 0.6062874 0.6495847
[71,] 1.85758730 0.9298303 1.1011863 0.7208802
[72,] 0.43780014 2.8333507 1.3081705 0.6907687
[73,] 1.97160398 0.6385357 0.9529238 0.4983249
[74,] 1.74175404 0.4235543 1.3046419 1.5133330
[75,] 0.38388253 0.7266773 0.9998080 1.0309436
[76,] 0.59421016 0.9623744 1.0474784 1.4278434
[77,] 0.97611581 0.8563002 0.7423502 1.3480608
[78,] 0.46335183 1.1122558 0.6705258 1.0159636
[79,] 0.90282170 0.6219874 0.6936329 1.2732003
[80,] 1.15383926 1.2553008 0.6430487 1.0996652
[81,] 0.64777612 0.7281709 0.8885510 0.8979809
[82,] 0.57042742 0.6939909 0.8999444 1.0688030
[83,] 0.48895591 1.0032122 0.9538524 0.8798401
[84,] 0.46104930 0.7071834 1.2039998 1.3012044
[85,] 0.52826729 1.2865464 0.6593869 0.5711642
[86,] 0.74836693 0.5298806 0.8233969 0.7609387
[87,] 0.45247872 1.5486290 0.8025941 0.9927913
[88,] 0.47245394 0.5301940 1.0061405 2.1677659
[89,] 0.45925052 1.0833671 1.9353673 0.8400871
[90,] 0.58707261 1.1109292 0.6999005 1.1057216
[91,] 0.34670465 0.5326857 1.9680577 1.0708450
[92,] 2.00897209 1.4609417 0.8442912 0.6399668
[93,] 2.02145406 2.1538223 0.8338103 0.2854972
[94,] 1.73099875 0.9152682 1.1031776 1.0548091
[95,] 2.67552850 0.8661861 0.6498670 0.7618481
[96,] 0.35256155 0.7424345 0.9583638 0.8754529
[97,] 1.52041715 0.7284882 1.1506473 0.9707964
[98,] 0.80334523 0.5809405 1.0635081 1.1216092
[99,] 1.64760778 0.9511399 0.7029597 1.3399411
[100,] 1.01871715 0.7175970 1.0275652 0.7922589
[101,] 0.70484533 0.6183695 1.1157508 1.2125844
[102,] 1.30241200 0.5338333 1.0714206 0.7802191
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[104,] 0.43763796 0.8279907 1.0672926 1.3449086
[105,] 0.83424779 0.5764489 0.5339323 0.8271745
[106,] 3.25532472 0.5887682 1.5780299 0.9206579
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[108,] 1.90718904 0.7180270 0.6270158 0.8353247
[109,] 1.47721573 1.5272295 1.5521348 1.8803437
[110,] 0.20233670 0.6883511 0.4939398 0.7836324
[111,] 1.03715481 0.5730649 1.0812642 1.2636152
[112,] 0.62282274 0.2968513 0.8514919 1.4898279
[113,] 1.01827055 0.6234779 0.8455284 0.5634344
[114,] 0.95145779 0.9402134 1.5187794 1.4291539
[115,] 2.27470233 0.6877924 0.6585193 0.7000126
[116,] 0.87402229 1.3166632 0.9857737 1.7381787
[117,] 0.96298611 1.2892170 0.4986028 0.8463640
[118,] 1.55980504 0.4316683 1.6951907 0.7472635
[119,] 0.52557021 0.7026060 0.6387564 0.7647778
[120,] 0.68568175 0.8629222 0.8965001 1.8862474
[121,] 0.79043960 0.6921994 0.8681213 1.2911532
[122,] 1.25404116 0.8430733 1.7058158 1.5681375
[123,] 1.07201091 0.3647141 1.3810549 1.0896024
[124,] 1.40420566 0.6005490 1.0012708 1.2325790
[125,] 0.60887229 1.2400699 0.7065252 1.3854289
[126,] 0.99546158 0.6315728 1.1373814 1.4827104
[127,] 1.32133658 0.7456826 1.0063487 0.7642573
[128,] 0.77155081 0.6940339 0.6386763 0.8398026
[129,] 0.49926949 1.2972491 1.0971169 1.2136323
[130,] 0.49192412 0.7275764 1.8764269 0.7227470
[131,] 1.22107955 0.8545816 0.6447874 0.6267137
[132,] 2.21630435 1.4484861 1.0441211 1.0205208
[133,] 1.09926713 1.4254277 1.0773688 1.2454911
[134,] 0.54802065 0.7285157 1.8263025 0.5469070
[135,] 0.30815830 1.2179297 0.6622844 0.9046531
[136,] 0.60836403 0.8233383 1.0426196 1.3694395
[137,] 0.73368710 1.1414370 0.7278124 1.1136609
[138,] 0.10334637 0.8312554 0.7261341 0.6120707
[139,] 1.01387465 0.4586733 0.9962520 0.6769996
[140,] 0.70609099 1.0677665 1.0842864 1.1925345
[141,] 0.95867676 1.1241146 1.0502513 0.3310071
[142,] 0.56734038 0.5727521 1.5764063 0.6687292
[143,] 0.46454852 0.7669272 0.9075416 1.4958937
[144,] 0.39529009 1.3880184 0.6480666 0.6263163
[145,] 0.33284864 1.0254189 0.8766322 0.4834175
[146,] 1.89968464 0.3907257 0.7903804 0.4566985
[147,] 0.30057402 0.5505302 1.9597611 0.7354144
[148,] 0.81518974 0.6266741 0.6114729 1.0422252
[149,] 1.15918881 0.9674447 0.6061201 0.7934912
[150,] 1.62753373 1.0567658 1.0415438 1.3494806
[151,] 0.23999085 0.7960668 1.6145616 1.7557258
[152,] 0.72945001 0.7497714 1.2257026 0.5217352
[153,] 1.59098282 0.6647079 1.0486228 1.1004743
[154,] 0.52188148 0.6742716 1.5693369 0.9125908
[155,] 1.10102631 2.8357761 0.5371623 0.8957316
[156,] 0.53891560 1.3465975 0.8522515 1.0925647
[157,] 1.23764407 1.2310213 1.0131447 0.6682606
[158,] 0.59840829 1.2374920 0.9949786 2.1098825
[159,] 0.31838226 1.2518169 1.4767412 0.9044426
[160,] 0.67699967 1.3343948 0.9521236 2.2280462
[161,] 1.70860399 0.8344018 1.1241572 0.8835370
[162,] 0.79343099 0.9560607 0.6901449 1.7691342
[163,] 0.51382571 0.9296057 0.9917987 1.0008596
[164,] 0.70206348 1.7145545 0.8585342 1.1820006
[165,] 0.45235105 1.2621743 0.6220510 1.5783763
[166,] 1.04792371 0.5487411 1.1919131 0.8309013
[167,] 1.28725583 0.9376466 0.6451509 0.6020934
[168,] 0.28896022 0.6933875 0.3912121 1.4447660
[169,] 1.00057425 0.5897869 0.8178845 1.3937566
[170,] 0.21552845 0.8358548 1.5938439 1.0957517
[171,] 0.52428423 1.3000969 0.7046116 0.9692593
[172,] 0.47319123 0.4454416 0.6097772 1.2927598
[173,] 1.29531997 1.9336288 0.9577290 0.9246472
[174,] 0.94680239 1.2151797 1.5611842 0.5645652
[175,] 0.74976984 1.9891314 0.9446129 1.2921458
[176,] 2.16005752 0.3585717 1.3080711 1.3046665
[177,] 0.55556188 1.7646728 0.8508559 0.5477300
[178,] 1.00728880 0.8457973 1.7665249 1.2742864
[179,] 1.23774627 0.2932292 0.7536530 0.6958257
[180,] 0.45227766 0.6737824 0.4948304 1.4858466
[181,] 0.40485701 0.4085965 1.1840470 1.1593636
[182,] 0.19269760 0.9049672 0.5537477 0.9578243
[183,] 1.78849360 1.4194074 0.8891978 0.4016011
[184,] 1.07578549 0.5470820 1.1510466 0.8614615
[185,] 1.70411930 0.9651527 1.6336244 1.0120116
[186,] 0.84597782 0.6524080 0.6788783 1.2792435
[187,] 0.25019223 0.8511317 0.8111606 1.0059468
[188,] 0.78990137 0.8669370 1.1767456 1.1621835
[189,] 0.59012755 2.1821850 0.8545803 0.8152241
[190,] 0.47701082 0.3400427 0.8710202 0.7268409
[191,] 0.49172852 1.3155074 0.9479267 1.4290430
[192,] 0.53417938 1.3943912 0.8205504 0.5693673
[193,] 1.17567235 0.4774092 1.6739085 0.5970509
[194,] 1.18466132 0.4580478 0.9051880 0.9101912
[195,] 0.64261471 0.9786607 1.0275802 0.9826478
[196,] 0.45281879 0.7042164 0.6105620 1.0889947
[197,] 0.36410765 0.5391194 1.1353573 0.7771250
[198,] 0.48738582 0.9048174 0.9662717 0.7758176
[199,] 0.40348859 1.2034843 0.8831925 0.7318223
[200,] 0.90811431 0.7513879 0.8769622 0.3830775
[201,] 2.28477582 0.9365133 1.1820749 0.8713685
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[203,] 0.30840702 1.5538784 0.8765801 0.7383785
[204,] 0.30670256 0.6301033 0.6308216 1.1429256
[205,] 1.17089055 0.4659107 0.9826495 1.1213543
[206,] 0.57346256 0.8415308 1.4143186 0.6021241
[207,] 0.54318287 1.3487788 1.0359561 0.7078655
[208,] 0.33493392 0.4654025 1.1208901 0.7597421
[209,] 0.37707454 1.4057531 0.9397123 1.0787219
[210,] 1.48788829 1.3021873 0.6724801 0.7830509
[211,] 0.09679091 1.4813408 1.6344622 1.7280524
[212,] 2.48122827 1.3688416 1.7633044 0.5608878
[213,] 0.49600645 0.4551763 0.7905786 1.4589901
[214,] 0.96160164 1.1836355 0.5939001 0.5554733
[215,] 0.88810998 0.9414240 0.8312462 0.4253531
[216,] 2.65033639 0.6868563 0.8257434 0.5881403
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[218,] 1.39245777 0.8712305 1.8454329 1.2598036
[219,] 0.69223475 0.5419187 1.8164407 0.8464768
[220,] 0.40511690 0.4530821 0.8945863 0.4290107
[221,] 0.90201692 0.8870044 0.8716778 0.9942058
[222,] 0.58279854 0.3553291 1.4468103 0.9197303
[223,] 0.79940881 1.3360809 1.0043546 0.9175707
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[225,] 0.64841836 0.5990252 1.4456206 1.0049416
[226,] 0.82178288 2.0650523 1.0243358 1.2726815
[227,] 1.42248448 0.5914932 0.4536995 0.6605387
[228,] 1.69517644 1.2201050 1.7367543 0.6985490
[229,] 1.43294600 0.9547276 1.2103654 1.1396141
[230,] 0.69626926 1.7114181 1.1451280 0.9282950
[231,] 0.41679546 0.3625008 0.8669855 1.8002438
[232,] 0.58110336 0.6251473 0.5684082 0.7110047
[233,] 1.11043683 0.9383120 1.1468479 0.8164720
[234,] 0.87968713 2.3156452 1.5103173 0.8951322
[235,] 0.99249122 1.0414508 0.6662700 1.2408221
[236,] 1.44046862 1.2843403 1.6180178 1.3626354
[237,] 0.89672529 1.3762872 0.5160372 1.0907510
[238,] 0.77752507 1.2858359 0.7471092 1.0064551
[239,] 1.51034231 0.8014690 0.7006536 0.3959350
[240,] 0.71238160 1.1434178 0.6977798 0.7168761
[241,] 0.75636867 2.1643633 0.9800056 0.8805026
[242,] 0.70596955 0.9945856 0.8989125 1.0871344
[243,] 0.42849350 1.3230178 1.1730938 1.1120261
[244,] 0.49297232 1.2278883 0.9440736 0.4403842
[245,] 1.24686489 0.8151427 1.9824519 1.6245523
[246,] 4.99797278 1.4094560 1.6981294 0.4382710
[247,] 0.90458720 0.8635914 1.8486793 1.4710852
[248,] 0.49137724 1.5178905 1.1148736 0.6827294
[249,] 1.22664512 1.1573159 0.5739148 0.6744917
[250,] 1.36671491 0.7731742 1.6781972 2.3250958
[251,] 1.16947586 1.6924116 1.0538290 0.7872510
[252,] 0.72487181 1.1204530 1.1087102 1.2099532
[253,] 0.66271111 2.0094009 1.3468159 1.4539130
[254,] 0.99889422 1.3477972 1.0293043 0.3472276
[255,] 1.59224096 1.7842137 0.7498913 2.0855246
[256,] 0.50761865 1.2886470 1.2909849 0.6834794
[257,] 0.29435940 0.7540938 0.9281992 1.1337103
[258,] 1.15487741 1.7149105 1.4713798 1.1316935
[259,] 0.83715674 0.4567749 0.8434023 0.9277860
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[261,] 0.68163935 0.8505901 1.4011813 0.7606194
[262,] 0.64883084 1.0892572 1.1965866 0.8124323
[263,] 0.27440499 1.2219983 1.4470107 1.5987601
[264,] 1.09374503 1.1613016 0.8183232 0.4453448
[265,] 0.48024552 0.6764278 0.9674876 1.7552206
[266,] 1.12482455 2.3426229 0.9797802 0.9412951
[267,] 0.67686120 1.1318038 1.1405225 1.0023056
[268,] 0.29913083 1.7614551 0.7079774 0.9140165
[269,] 2.22148406 0.7962644 1.0488535 0.8111564
[270,] 0.88888957 0.5359859 0.8591218 1.4774254
[271,] 0.36623831 0.5726129 1.0040698 0.9729528
[272,] 0.77042397 0.9783090 0.6772492 1.3215857
[273,] 0.52710697 1.3868756 0.8591138 0.6811408
[274,] 0.51786093 1.7748730 1.3213077 1.0233980
[275,] 0.38966010 0.8093242 1.0136089 0.8635194
[276,] 0.82454803 1.4715850 1.6420491 0.9145936
[277,] 0.94399431 0.5770648 0.9191118 1.2221129
[278,] 1.91895508 0.8291960 0.8813670 1.2481127
[279,] 1.49931836 1.2561066 0.9381775 1.0936943
[280,] 3.26958038 0.7524785 1.1216789 0.8566270
[281,] 0.40652021 1.1535495 1.1010352 1.6905300
[282,] 0.66838715 1.6727702 1.4507166 1.0109870
[283,] 1.34536837 0.9360824 1.0500773 0.6477942
[284,] 0.50612110 0.6557603 0.7520626 0.6784890
[285,] 0.37175515 1.3289126 0.7220735 1.5434759
[286,] 0.49290522 2.0184241 1.9403757 1.5926348
[287,] 2.19467496 1.0628817 1.0347470 0.9667313
[288,] 1.39455162 1.2033806 1.2776933 0.8920813
[289,] 1.80011445 1.1128625 1.6245947 0.7342963
[290,] 0.34242498 1.9585502 0.9139139 0.4132815
[291,] 0.80476246 1.4009529 1.1431932 0.5251555
[292,] 1.46333651 0.4060571 1.1190247 0.3138321
[293,] 0.29314967 0.9248635 1.2062481 1.2883209
[294,] 0.70897995 1.0167327 1.0704044 0.3943146
[295,] 1.32695144 0.4857282 0.7732505 1.7657053
[296,] 0.35125060 0.5180686 0.7661933 1.2692785
[297,] 1.78788812 1.0353419 0.7850847 1.3253924
[298,] 1.18415164 0.5597143 0.8990615 0.6115595
[299,] 2.74486089 0.6071082 0.9764881 0.6763068
[300,] 1.34437374 0.7587100 0.9408404 0.8136725
[301,] 0.24517377 0.6261496 0.7077383 0.5921868
[302,] 0.54231475 0.4684025 1.0660013 1.2546943
[303,] 0.74136079 1.1542221 1.3779599 0.9282516
[304,] 1.80229697 0.6949124 1.2015583 1.4454241
[305,] 0.64478783 0.3920201 0.8638759 0.9281519
[306,] 0.60760905 1.3905481 0.9472978 1.4165757
[307,] 0.99313716 0.9438848 0.8304254 0.9170724
[308,] 2.15909595 0.7706959 0.8584274 1.3636240
[309,] 0.47032670 0.7346278 1.4325369 0.5461103
[310,] 0.88443530 0.8591249 0.9876224 1.0451859
[311,] 0.47238584 1.4641878 1.1613917 1.2031514
[312,] 0.97352534 0.4738810 1.2754791 0.6058437
[313,] 1.95053224 1.1552891 0.9199316 0.9037052
[314,] 0.37954045 0.9699980 0.6177735 1.9113704
[315,] 2.41024799 1.3262360 1.7733774 0.9750081
[316,] 0.32311097 0.9377820 1.2107685 1.7487571
[317,] 0.63021732 2.3751345 1.0272342 0.7574055
[318,] 0.63068446 1.2239834 2.2902746 1.5420257
[319,] 0.82722844 0.7417248 0.9922042 0.6185851
[320,] 1.44402452 0.9101632 0.8341046 0.9814673
[321,] 0.35382507 0.6665608 0.8193382 0.8426609
[322,] 0.83418546 0.8739152 1.0406784 0.7126463
[323,] 0.17542965 0.5982385 0.9808799 0.4731701
[324,] 0.40154541 1.1882789 0.8755948 0.9287876
[325,] 0.52186194 1.0040554 1.1245210 0.5912004
[326,] 0.78245506 1.0004799 0.7350758 1.0097906
[327,] 0.61199499 0.5332400 0.9414436 0.7106313
[328,] 1.10835655 1.4149276 1.3392433 2.0129989
[329,] 0.26385765 1.1011948 0.8794323 0.4383332
[330,] 0.30304939 1.3656629 0.5559041 0.8626560
[331,] 0.71180260 1.1841573 1.0956755 0.6756307
[332,] 3.92179901 1.0796769 0.7968331 0.9319855
[333,] 0.65571696 0.5302603 1.2538200 1.0904090
[334,] 0.59980908 1.4248753 1.1292291 0.5194444
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[911,] 0.38580841 1.3340122 0.7494506 0.6271053
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[936,] 4.04211884 2.2961767 1.9074660 1.3176527
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[943,] 0.78592701 0.8283221 0.7727308 0.9958523
[944,] 0.52054277 0.9190829 1.0280459 0.3667610
[945,] 0.34797841 1.1700154 0.9056039 0.9287844
[946,] 0.39104431 0.6626465 0.7529142 0.7953488
[947,] 1.67660980 0.6976339 0.9822758 0.7136133
[948,] 0.55734501 1.1536409 0.7567402 1.2268833
[949,] 0.62627463 1.0367160 0.4595332 1.4838909
[950,] 0.75429486 1.4673451 0.5899362 0.7941407
[951,] 0.22697619 0.8783254 1.7701607 0.9787812
[952,] 2.38572267 1.1792463 0.9777802 1.7439584
[953,] 3.08305404 0.6612831 1.8109304 1.2618709
[954,] 0.40779845 1.4581097 1.4098117 1.1231591
[955,] 1.62102440 0.5511877 1.0307052 0.7298591
[956,] 0.20716864 1.2951846 0.9686562 0.3784809
[957,] 1.24750459 1.9946469 1.0088203 0.5725633
[958,] 0.44086412 0.4811919 0.6026809 0.9936704
[959,] 1.47182518 0.3517998 1.1313483 0.7888779
[960,] 0.98627609 0.9472375 0.8430548 0.5587328
[961,] 1.38525279 0.8307085 0.6870768 0.8423203
[962,] 0.95431148 0.3791221 0.7399611 0.7443176
[963,] 0.29465692 0.5585184 0.5049281 0.7322262
[964,] 2.09457551 0.6643137 0.9461584 0.6669666
[965,] 3.03030765 1.3744433 0.9480833 0.7792530
[966,] 0.51404698 0.7203748 0.8300815 0.7081022
[967,] 2.08719535 1.0283623 1.2706243 1.8040024
[968,] 0.74529286 0.9510982 0.6703305 0.6042951
[969,] 1.52203804 0.4893772 0.7996106 0.8414228
[970,] 3.45799592 0.7006649 0.6370116 0.7478947
[971,] 0.39879400 0.8600447 1.5289721 2.0932109
[972,] 0.32730266 0.6952427 1.4250287 0.6919964
[973,] 1.98521906 0.8703650 0.5648765 0.5699654
[974,] 0.41759169 0.4844511 1.0531666 0.6780237
[975,] 1.42881686 1.0013924 0.9697131 0.9844546
[976,] 1.85896983 0.3602859 0.8541486 1.0735612
[977,] 1.43877762 0.4889482 0.6529477 1.2837084
[978,] 0.58954144 0.8494992 0.8777203 0.7286928
[979,] 0.89015976 1.4472256 1.0349672 0.5575808
[980,] 0.28729168 1.7355504 1.8822587 1.1927156
[981,] 0.33396870 0.5415009 1.4386682 0.6491626
[982,] 1.10124317 0.6582157 1.0416338 1.1829785
[983,] 0.49481247 1.3101219 1.1904331 0.3894601
[984,] 2.10444223 0.5577737 0.8753427 1.1845111
[985,] 0.29947022 2.1494503 0.5979694 0.9572720
[986,] 1.10767202 1.0899799 0.9624538 1.0312411
[987,] 0.42025138 1.0488087 1.7468414 0.6913516
[988,] 0.95671967 1.2543389 0.5266237 0.5334741
[989,] 0.46288273 0.4665863 1.0127688 1.1068107
[990,] 0.81625585 1.8402958 1.6513952 1.2828998
[991,] 0.39179940 1.1322242 1.1717567 0.9717304
[992,] 0.38235083 0.7307726 0.9247266 0.6499995
[993,] 1.26892284 1.0411084 1.0823095 0.6503081
[994,] 0.58167762 1.6251472 1.0527819 0.8397382
[995,] 0.86075495 0.7935033 0.6807928 1.0154396
[996,] 0.65840638 0.6741810 1.0175390 0.5698432
[997,] 0.56084775 1.1681780 0.8439951 0.5313445
[998,] 0.73460769 0.6492594 0.5327208 0.6360370
[999,] 1.20374273 2.3332795 0.6342783 1.5196228
$model.matrix
(Intercept) pH Nugent_Cat1 Nugent_Cat2 CST1 CST2 CST3 CST4 Ethnic_Group1
S001 1 4.0 -1 -1 1 0 0 0 1
S002 1 4.0 -1 -1 0 1 0 0 -1
S003 1 4.0 -1 -1 0 0 1 0 0
S004 1 4.7 -1 -1 1 0 0 0 1
S005 1 5.0 0 1 0 0 0 1 0
S006 1 4.0 -1 -1 1 0 0 0 -1
S007 1 4.7 -1 -1 0 1 0 0 -1
S008 1 5.8 1 0 0 0 0 1 -1
S009 1 4.4 -1 -1 0 0 1 0 -1
S010 1 4.4 -1 -1 1 0 0 0 0
S011 1 4.0 -1 -1 0 0 1 0 -1
S012 1 5.0 1 0 0 0 0 1 -1
S013 1 4.7 -1 -1 0 0 1 0 -1
S014 1 4.4 -1 -1 0 1 0 0 0
S015 1 4.4 -1 -1 1 0 0 0 -1
S016 1 5.8 -1 -1 0 0 1 0 -1
S017 1 7.0 0 1 0 0 1 0 1
S018 1 4.0 -1 -1 1 0 0 0 0
S019 1 4.0 -1 -1 0 0 1 0 0
S020 1 4.0 -1 -1 0 0 1 0 0
S021 1 4.7 -1 -1 0 1 0 0 0
S022 1 5.0 -1 -1 -1 -1 -1 -1 -1
S023 1 7.0 1 0 0 0 0 1 0
S024 1 4.0 -1 -1 0 0 1 0 0
S025 1 5.0 1 0 0 0 0 1 0
S026 1 4.4 -1 -1 1 0 0 0 0
S027 1 4.0 -1 -1 1 0 0 0 0
S028 1 5.5 0 1 0 0 0 1 0
S029 1 4.0 -1 -1 1 0 0 0 -1
S030 1 5.8 1 0 0 0 0 1 0
S031 1 5.0 1 0 0 0 0 1 0
S032 1 4.0 -1 -1 1 0 0 0 -1
S033 1 4.4 -1 -1 0 0 1 0 -1
S034 1 4.0 -1 -1 1 0 0 0 0
S035 1 5.0 -1 -1 0 0 0 1 0
S036 1 4.4 -1 -1 1 0 0 0 0
S037 1 4.0 -1 -1 1 0 0 0 0
S038 1 5.5 1 0 0 0 0 1 0
S039 1 5.3 1 0 0 0 0 1 0
S040 1 4.7 -1 -1 0 0 1 0 0
S041 1 4.4 -1 -1 0 0 1 0 0
S042 1 5.5 1 0 0 0 0 1 0
S043 1 4.0 -1 -1 -1 -1 -1 -1 0
S044 1 4.4 -1 -1 0 0 0 1 0
S045 1 5.5 1 0 0 0 0 1 0
S046 1 4.0 -1 -1 0 0 1 0 0
S047 1 5.3 1 0 0 0 1 0 -1
S048 1 5.0 1 0 0 0 0 1 0
S049 1 4.7 1 0 0 0 0 1 0
S050 1 4.0 -1 -1 0 0 1 0 0
S051 1 5.5 1 0 0 0 0 1 0
S052 1 5.3 0 1 0 1 0 0 0
S053 1 5.0 1 0 0 0 0 1 0
S054 1 4.4 -1 -1 0 0 1 0 0
S055 1 4.0 -1 -1 1 0 0 0 0
S056 1 5.0 -1 -1 1 0 0 0 0
S057 1 5.5 -1 -1 0 0 0 1 0
S058 1 4.0 -1 -1 1 0 0 0 0
S059 1 4.0 -1 -1 0 0 1 0 0
S060 1 4.0 -1 -1 0 0 1 0 0
S061 1 4.0 0 1 0 1 0 0 0
S062 1 5.8 1 0 0 0 0 1 0
S063 1 5.4 1 0 0 1 0 0 0
S064 1 5.4 1 0 0 0 0 1 0
S065 1 4.0 -1 -1 1 0 0 0 0
S066 1 4.0 -1 -1 0 0 1 0 -1
S067 1 4.0 -1 -1 1 0 0 0 1
S068 1 4.0 0 1 0 0 1 0 -1
S069 1 4.0 -1 -1 1 0 0 0 -1
S070 1 5.0 1 0 0 0 0 1 0
S071 1 5.0 -1 -1 0 0 1 0 0
S072 1 5.5 1 0 0 0 1 0 0
S073 1 5.3 1 0 0 0 0 1 1
S074 1 4.4 -1 -1 1 0 0 0 -1
S075 1 4.0 -1 -1 0 0 1 0 1
S076 1 4.7 0 1 0 1 0 0 -1
S077 1 4.0 -1 -1 0 0 1 0 1
S078 1 4.0 -1 -1 1 0 0 0 -1
S079 1 4.0 -1 -1 1 0 0 0 0
S080 1 4.0 -1 -1 1 0 0 0 -1
S081 1 4.0 -1 -1 -1 -1 -1 -1 1
S082 1 4.0 -1 -1 1 0 0 0 -1
S083 1 5.0 -1 -1 -1 -1 -1 -1 -1
S084 1 4.0 -1 -1 1 0 0 0 0
S085 1 5.5 1 0 0 0 0 1 0
S086 1 4.7 -1 -1 -1 -1 -1 -1 -1
S087 1 4.4 -1 -1 1 0 0 0 -1
S088 1 5.3 -1 -1 0 0 1 0 -1
S089 1 5.5 -1 -1 1 0 0 0 -1
S090 1 4.0 -1 -1 0 0 0 1 -1
S091 1 4.0 -1 -1 0 0 1 0 0
S092 1 4.0 -1 -1 1 0 0 0 -1
S093 1 5.0 0 1 1 0 0 0 -1
S094 1 4.0 -1 -1 1 0 0 0 0
S095 1 4.0 -1 -1 1 0 0 0 0
S096 1 5.0 0 1 0 1 0 0 -1
S097 1 4.4 -1 -1 1 0 0 0 0
S098 1 5.0 -1 -1 -1 -1 -1 -1 -1
S099 1 4.7 -1 -1 1 0 0 0 -1
S100 1 4.0 -1 -1 1 0 0 0 0
S101 1 4.4 -1 -1 0 0 1 0 -1
S102 1 5.0 1 0 0 0 0 1 0
S103 1 4.0 -1 -1 1 0 0 0 0
S104 1 5.0 0 1 0 0 0 1 0
S105 1 5.5 1 0 0 0 0 1 0
S106 1 4.4 -1 -1 1 0 0 0 0
S107 1 4.0 -1 -1 1 0 0 0 -1
S108 1 4.0 -1 -1 1 0 0 0 0
S109 1 5.8 1 0 0 0 0 1 0
S110 1 5.5 1 0 0 0 1 0 0
S111 1 4.0 -1 -1 1 0 0 0 0
S112 1 4.0 -1 -1 1 0 0 0 -1
S113 1 4.4 -1 -1 -1 -1 -1 -1 -1
S114 1 5.8 1 0 0 0 0 1 -1
S115 1 4.0 -1 -1 1 0 0 0 0
S116 1 4.0 -1 -1 1 0 0 0 0
S117 1 4.0 -1 -1 1 0 0 0 -1
S118 1 5.0 -1 -1 0 1 0 0 0
S119 1 4.0 -1 -1 0 0 1 0 0
S120 1 4.0 -1 -1 1 0 0 0 -1
S121 1 4.7 -1 -1 -1 -1 -1 -1 0
S122 1 4.0 -1 -1 1 0 0 0 0
S123 1 4.7 1 0 0 0 1 0 0
S124 1 4.0 -1 -1 1 0 0 0 -1
S125 1 4.0 -1 -1 1 0 0 0 -1
S126 1 4.0 -1 -1 1 0 0 0 0
S127 1 4.4 -1 -1 -1 -1 -1 -1 -1
S128 1 4.4 -1 -1 1 0 0 0 1
S129 1 4.0 1 0 0 0 0 1 1
S130 1 5.0 1 0 0 0 0 1 0
S131 1 5.0 -1 -1 0 0 1 0 -1
S132 1 4.0 -1 -1 0 0 1 0 -1
S133 1 5.0 -1 -1 0 0 1 0 0
S134 1 5.5 1 0 0 0 0 1 0
S135 1 5.0 -1 -1 0 0 1 0 0
S136 1 5.0 -1 -1 0 0 1 0 0
S137 1 4.5 0 1 0 0 0 1 0
S138 1 5.8 1 0 0 0 0 1 0
S139 1 4.4 -1 -1 1 0 0 0 0
S140 1 5.5 1 0 0 0 0 1 0
S141 1 5.3 1 0 0 0 0 1 0
S142 1 5.0 -1 -1 0 0 1 0 0
S143 1 5.5 1 0 0 0 0 1 0
S144 1 5.5 1 0 0 0 0 1 0
S145 1 5.0 -1 -1 0 0 0 1 0
S146 1 5.0 0 1 0 1 0 0 0
S147 1 7.0 1 0 0 0 0 1 0
S148 1 4.4 -1 -1 0 0 1 0 0
S149 1 5.5 0 1 0 0 1 0 0
S150 1 5.0 0 1 0 0 1 0 0
S151 1 4.7 1 0 0 0 0 1 0
S152 1 5.0 0 1 0 0 0 1 0
S153 1 4.4 -1 -1 0 0 1 0 0
S154 1 4.4 0 1 0 0 1 0 0
S155 1 4.7 1 0 0 0 1 0 0
S156 1 4.7 -1 -1 0 0 1 0 0
S157 1 5.3 -1 -1 0 0 1 0 0
S158 1 5.3 1 0 0 0 1 0 0
S159 1 5.0 1 0 0 0 0 1 0
S160 1 5.0 -1 -1 0 0 0 1 0
S161 1 5.5 0 1 0 0 1 0 0
S162 1 5.0 -1 -1 0 0 1 0 0
S163 1 5.0 -1 -1 -1 -1 -1 -1 0
S164 1 4.7 -1 -1 0 0 1 0 0
S165 1 4.4 -1 -1 0 0 1 0 0
S166 1 4.4 -1 -1 0 0 1 0 0
S167 1 4.4 -1 -1 0 0 1 0 0
S168 1 4.4 -1 -1 1 0 0 0 0
S169 1 5.0 0 1 0 1 0 0 0
S170 1 4.7 -1 -1 0 0 1 0 0
S171 1 4.4 -1 -1 0 0 1 0 0
S172 1 5.3 1 0 0 0 0 1 0
S173 1 4.7 -1 -1 -1 -1 -1 -1 0
S174 1 5.8 1 0 0 0 0 1 0
S175 1 5.3 1 0 0 0 0 1 0
S176 1 4.4 0 1 0 0 0 1 0
S177 1 5.0 1 0 0 0 0 1 0
S178 1 5.5 0 1 0 0 0 1 0
S179 1 7.0 1 0 0 0 0 1 0
S180 1 4.4 -1 -1 0 0 1 0 0
S181 1 4.0 -1 -1 1 0 0 0 0
S182 1 4.0 -1 -1 1 0 0 0 0
S183 1 4.4 0 1 0 0 1 0 0
S184 1 4.0 0 1 0 1 0 0 0
S185 1 5.0 1 0 0 0 0 1 0
S186 1 5.3 1 0 0 0 0 1 0
S187 1 4.0 1 0 0 0 1 0 0
S188 1 5.5 1 0 0 0 0 1 0
S189 1 4.0 -1 -1 0 0 1 0 1
S190 1 4.0 -1 -1 1 0 0 0 0
S191 1 4.4 -1 -1 1 0 0 0 -1
S192 1 5.5 1 0 0 0 0 1 0
S193 1 4.0 -1 -1 1 0 0 0 0
S194 1 4.7 -1 -1 1 0 0 0 1
S195 1 5.0 0 1 -1 -1 -1 -1 0
S196 1 4.0 -1 -1 1 0 0 0 -1
S197 1 4.0 -1 -1 1 0 0 0 -1
S198 1 4.0 -1 -1 1 0 0 0 -1
S199 1 5.0 1 0 0 0 0 1 0
S200 1 4.0 -1 -1 0 0 1 0 0
S201 1 4.7 -1 -1 1 0 0 0 1
S202 1 5.5 1 0 0 0 0 1 0
S203 1 4.0 -1 -1 0 0 1 0 -1
S204 1 4.0 -1 -1 0 0 1 0 0
S205 1 4.0 0 1 0 0 1 0 -1
S206 1 7.0 0 1 0 1 0 0 -1
S207 1 4.0 -1 -1 1 0 0 0 0
S208 1 5.0 1 0 0 0 1 0 -1
S209 1 5.3 1 0 0 0 0 1 0
S210 1 4.0 -1 -1 1 0 0 0 -1
S211 1 5.0 -1 -1 0 1 0 0 -1
S212 1 4.0 -1 -1 1 0 0 0 0
S213 1 5.0 -1 -1 0 0 1 0 1
S214 1 4.0 -1 -1 0 0 1 0 0
S215 1 5.0 1 0 0 0 1 0 -1
S216 1 4.4 -1 -1 1 0 0 0 -1
S217 1 5.0 1 0 0 0 1 0 0
S218 1 4.0 -1 -1 0 0 1 0 -1
S219 1 4.0 -1 -1 0 0 1 0 -1
S220 1 4.0 0 1 0 0 1 0 -1
S221 1 5.5 -1 -1 0 0 1 0 0
S222 1 4.0 -1 -1 1 0 0 0 -1
S223 1 4.0 -1 -1 0 0 1 0 1
S224 1 7.0 1 0 0 0 0 1 -1
S225 1 4.0 -1 -1 1 0 0 0 -1
S226 1 4.0 -1 -1 1 0 0 0 -1
S227 1 4.0 -1 -1 0 0 1 0 0
S228 1 5.0 0 1 0 0 1 0 0
S229 1 5.5 1 0 0 0 0 1 0
S230 1 4.0 -1 -1 0 1 0 0 0
S231 1 4.0 -1 -1 1 0 0 0 0
S232 1 4.0 -1 -1 1 0 0 0 1
S233 1 4.0 -1 -1 1 0 0 0 -1
S234 1 4.7 -1 -1 0 0 1 0 0
S235 1 4.4 -1 -1 0 0 1 0 0
S236 1 4.4 -1 -1 1 0 0 0 1
S237 1 4.0 -1 -1 0 0 1 0 0
S238 1 4.0 -1 -1 0 0 1 0 0
S239 1 5.5 1 0 0 0 0 1 0
S240 1 4.0 -1 -1 1 0 0 0 -1
S241 1 4.0 -1 -1 0 0 1 0 0
S242 1 4.7 -1 -1 0 0 1 0 0
S243 1 5.8 1 0 0 0 0 1 0
S244 1 5.3 1 0 0 0 0 1 0
S245 1 4.4 -1 -1 1 0 0 0 -1
S246 1 4.4 -1 -1 -1 -1 -1 -1 -1
S247 1 5.0 -1 -1 1 0 0 0 -1
S248 1 4.7 0 1 0 0 1 0 0
S249 1 4.0 -1 -1 0 0 1 0 -1
S250 1 5.5 1 0 0 0 0 1 1
S251 1 4.7 -1 -1 0 1 0 0 0
S252 1 4.7 -1 -1 0 0 1 0 0
S253 1 5.0 1 0 0 0 0 1 0
S254 1 4.0 -1 -1 0 0 1 0 0
S255 1 5.3 1 0 0 0 0 1 0
S256 1 4.0 -1 -1 1 0 0 0 -1
S257 1 5.0 -1 -1 0 0 1 0 0
S258 1 4.0 -1 -1 -1 -1 -1 -1 -1
S259 1 5.8 1 0 0 0 0 1 0
S260 1 4.0 -1 -1 0 0 1 0 1
S261 1 5.3 1 0 0 0 0 1 0
S262 1 4.0 -1 -1 1 0 0 0 -1
S263 1 5.8 1 0 0 0 0 1 0
S264 1 4.0 -1 -1 1 0 0 0 -1
S265 1 4.0 -1 -1 0 0 1 0 0
S266 1 4.4 -1 -1 0 0 1 0 0
S267 1 4.7 -1 -1 0 0 1 0 -1
S268 1 4.4 -1 -1 1 0 0 0 0
S269 1 5.8 1 0 0 0 0 1 -1
S270 1 5.0 1 0 0 0 0 1 0
S271 1 5.5 1 0 0 0 0 1 -1
S272 1 4.4 -1 -1 1 0 0 0 1
S273 1 5.0 1 0 0 0 0 1 1
S274 1 4.4 -1 -1 0 0 1 0 -1
S275 1 4.0 -1 -1 0 0 1 0 1
S276 1 5.0 -1 -1 0 1 0 0 -1
S277 1 4.0 -1 -1 1 0 0 0 -1
S278 1 4.4 0 1 0 0 1 0 -1
S279 1 5.5 1 0 0 0 0 1 0
S280 1 4.7 0 1 0 0 0 1 -1
S281 1 4.0 -1 -1 1 0 0 0 0
S282 1 4.0 -1 -1 0 0 1 0 1
S283 1 4.0 -1 -1 0 0 1 0 1
S284 1 4.0 -1 -1 0 0 0 1 -1
S285 1 4.7 0 1 0 1 0 0 -1
S286 1 5.5 0 1 0 1 0 0 1
S287 1 4.0 -1 -1 1 0 0 0 1
S288 1 4.4 0 1 -1 -1 -1 -1 1
S289 1 5.0 -1 -1 0 0 1 0 1
S290 1 5.0 1 0 0 0 0 1 0
S291 1 4.0 -1 -1 1 0 0 0 -1
S292 1 5.5 1 0 0 0 0 1 0
S293 1 4.0 -1 -1 0 0 1 0 -1
S294 1 4.4 -1 -1 1 0 0 0 -1
S295 1 4.7 -1 -1 0 0 1 0 1
S296 1 4.0 0 1 -1 -1 -1 -1 1
S297 1 4.0 -1 -1 1 0 0 0 -1
S298 1 4.0 -1 -1 0 0 1 0 1
S299 1 5.0 -1 -1 -1 -1 -1 -1 -1
S300 1 4.0 -1 -1 0 0 1 0 1
S301 1 5.5 1 0 0 0 0 1 1
S302 1 4.0 -1 -1 0 0 1 0 1
S303 1 5.3 -1 -1 0 0 1 0 1
S304 1 4.0 -1 -1 1 0 0 0 1
S305 1 5.8 -1 -1 0 0 0 1 1
S306 1 4.0 -1 -1 0 0 1 0 0
S307 1 5.3 0 1 0 0 1 0 0
S308 1 5.5 1 0 0 0 0 1 0
S309 1 5.5 0 1 0 1 0 0 0
S310 1 4.7 1 0 0 0 0 1 0
S311 1 5.3 0 1 0 0 0 1 0
S312 1 4.0 -1 -1 1 0 0 0 0
S313 1 5.5 1 0 0 0 0 1 0
S314 1 5.0 1 0 0 0 0 1 0
S315 1 4.7 0 1 0 0 0 1 0
S316 1 4.7 1 0 0 0 0 1 0
S317 1 4.0 -1 -1 0 0 1 0 0
S318 1 4.0 0 1 0 0 1 0 0
S319 1 4.0 -1 -1 0 0 1 0 0
S320 1 4.0 -1 -1 0 0 1 0 0
S321 1 4.4 1 0 0 0 0 1 0
S322 1 5.0 1 0 0 0 0 1 0
S323 1 4.0 -1 -1 0 0 1 0 0
S324 1 4.7 -1 -1 0 0 1 0 1
S325 1 4.0 -1 -1 1 0 0 0 -1
S326 1 5.5 -1 -1 1 0 0 0 -1
S327 1 5.5 1 0 0 0 0 1 0
S328 1 5.0 1 0 0 0 1 0 0
S329 1 5.0 1 0 0 0 0 1 0
S330 1 5.8 1 0 0 0 0 1 0
S331 1 5.0 1 0 0 0 0 1 0
S332 1 5.0 0 1 0 1 0 0 1
S333 1 4.4 -1 -1 1 0 0 0 1
S334 1 4.0 -1 -1 0 0 1 0 1
S335 1 4.0 -1 -1 1 0 0 0 1
S336 1 4.0 -1 -1 1 0 0 0 1
S337 1 5.8 0 1 0 0 0 1 1
S338 1 4.0 -1 -1 0 0 1 0 1
S339 1 4.4 -1 -1 0 0 1 0 1
S340 1 4.0 -1 -1 1 0 0 0 1
S341 1 4.4 -1 -1 -1 -1 -1 -1 1
S342 1 4.0 -1 -1 0 0 1 0 1
S343 1 5.5 -1 -1 0 0 1 0 1
S344 1 4.7 1 0 0 0 0 1 1
S345 1 5.8 -1 -1 0 1 0 0 1
S346 1 4.4 -1 -1 1 0 0 0 1
S347 1 5.5 1 0 0 0 0 1 -1
S348 1 5.0 0 1 -1 -1 -1 -1 1
S349 1 5.5 -1 -1 0 0 1 0 1
S350 1 5.0 0 1 0 0 0 1 1
S351 1 4.4 0 1 0 0 1 0 1
S352 1 5.0 0 1 1 0 0 0 1
S353 1 4.7 -1 -1 0 0 1 0 1
S354 1 4.7 -1 -1 -1 -1 -1 -1 1
S355 1 4.0 -1 -1 0 0 1 0 1
S356 1 4.0 -1 -1 1 0 0 0 -1
S357 1 4.0 -1 -1 0 0 1 0 -1
S358 1 4.0 -1 -1 1 0 0 0 -1
S359 1 4.0 -1 -1 0 0 1 0 -1
S360 1 5.8 0 1 0 0 0 1 1
S361 1 4.0 -1 -1 1 0 0 0 1
S362 1 5.0 1 0 0 0 1 0 1
S363 1 4.0 -1 -1 0 0 1 0 1
S364 1 4.0 -1 -1 0 0 1 0 1
S365 1 5.0 -1 -1 0 0 1 0 1
S366 1 4.0 1 0 0 0 1 0 1
S367 1 4.4 -1 -1 1 0 0 0 1
S368 1 5.8 1 0 0 0 0 1 1
S369 1 5.8 0 1 0 0 0 1 1
S370 1 4.4 1 0 0 0 0 1 1
S371 1 4.0 -1 -1 0 0 1 0 1
S372 1 4.7 -1 -1 0 0 1 0 1
S373 1 4.4 -1 -1 0 0 1 0 1
S374 1 4.0 -1 -1 0 0 1 0 1
S375 1 4.4 0 1 0 1 0 0 1
S376 1 4.4 -1 -1 1 0 0 0 1
S377 1 4.4 -1 -1 1 0 0 0 1
S378 1 4.4 -1 -1 -1 -1 -1 -1 1
S379 1 4.4 -1 -1 0 1 0 0 1
S380 1 4.7 1 0 0 0 0 1 1
S381 1 5.5 1 0 0 0 0 1 1
S382 1 4.7 -1 -1 1 0 0 0 1
S383 1 5.8 1 0 0 0 0 1 1
S384 1 5.8 -1 -1 0 0 0 1 1
S385 1 4.0 -1 -1 0 0 1 0 1
S386 1 4.0 -1 -1 1 0 0 0 1
S387 1 4.0 -1 -1 1 0 0 0 1
S388 1 5.0 -1 -1 0 0 0 1 1
S389 1 4.4 -1 -1 0 0 1 0 1
S390 1 7.0 0 1 0 0 1 0 1
S391 1 4.4 -1 -1 0 0 1 0 1
S392 1 4.4 -1 -1 0 0 0 1 1
S393 1 4.4 -1 -1 0 0 1 0 1
S394 1 4.4 -1 -1 0 0 1 0 1
Ethnic_Group2 Ethnic_Group3
S001 0 0
S002 -1 -1
S003 1 0
S004 0 0
S005 1 0
S006 -1 -1
S007 -1 -1
S008 -1 -1
S009 -1 -1
S010 1 0
S011 -1 -1
S012 -1 -1
S013 -1 -1
S014 1 0
S015 -1 -1
S016 -1 -1
S017 0 0
S018 1 0
S019 1 0
S020 0 1
S021 1 0
S022 -1 -1
S023 1 0
S024 1 0
S025 1 0
S026 1 0
S027 1 0
S028 1 0
S029 -1 -1
S030 1 0
S031 1 0
S032 -1 -1
S033 -1 -1
S034 0 1
S035 0 1
S036 0 1
S037 0 1
S038 0 1
S039 0 1
S040 0 1
S041 0 1
S042 0 1
S043 0 1
S044 0 1
S045 0 1
S046 0 1
S047 -1 -1
S048 0 1
S049 0 1
S050 0 1
S051 0 1
S052 0 1
S053 0 1
S054 0 1
S055 0 1
S056 0 1
S057 0 1
S058 0 1
S059 0 1
S060 0 1
S061 0 1
S062 0 1
S063 0 1
S064 0 1
S065 0 1
S066 -1 -1
S067 0 0
S068 -1 -1
S069 -1 -1
S070 1 0
S071 1 0
S072 1 0
S073 0 0
S074 -1 -1
S075 0 0
S076 -1 -1
S077 0 0
S078 -1 -1
S079 1 0
S080 -1 -1
S081 0 0
S082 -1 -1
S083 -1 -1
S084 1 0
S085 1 0
S086 -1 -1
S087 -1 -1
S088 -1 -1
S089 -1 -1
S090 -1 -1
S091 1 0
S092 -1 -1
S093 -1 -1
S094 1 0
S095 1 0
S096 -1 -1
S097 1 0
S098 -1 -1
S099 -1 -1
S100 1 0
S101 -1 -1
S102 1 0
S103 1 0
S104 1 0
S105 1 0
S106 1 0
S107 -1 -1
S108 1 0
S109 1 0
S110 1 0
S111 1 0
S112 -1 -1
S113 -1 -1
S114 -1 -1
S115 1 0
S116 1 0
S117 -1 -1
S118 1 0
S119 1 0
S120 -1 -1
S121 0 1
S122 1 0
S123 1 0
S124 -1 -1
S125 -1 -1
S126 0 1
S127 -1 -1
S128 0 0
S129 0 0
S130 1 0
S131 -1 -1
S132 -1 -1
S133 0 1
S134 0 1
S135 0 1
S136 0 1
S137 0 1
S138 0 1
S139 0 1
S140 0 1
S141 0 1
S142 0 1
S143 0 1
S144 0 1
S145 0 1
S146 0 1
S147 0 1
S148 0 1
S149 0 1
S150 0 1
S151 0 1
S152 0 1
S153 0 1
S154 0 1
S155 0 1
S156 0 1
S157 0 1
S158 0 1
S159 0 1
S160 0 1
S161 0 1
S162 0 1
S163 0 1
S164 0 1
S165 0 1
S166 0 1
S167 0 1
S168 0 1
S169 0 1
S170 0 1
S171 0 1
S172 0 1
S173 0 1
S174 0 1
S175 0 1
S176 0 1
S177 0 1
S178 0 1
S179 0 1
S180 0 1
S181 0 1
S182 0 1
S183 0 1
S184 0 1
S185 0 1
S186 0 1
S187 0 1
S188 0 1
S189 0 0
S190 0 1
S191 -1 -1
S192 1 0
S193 0 1
S194 0 0
S195 1 0
S196 -1 -1
S197 -1 -1
S198 -1 -1
S199 1 0
S200 1 0
S201 0 0
S202 1 0
S203 -1 -1
S204 1 0
S205 -1 -1
S206 -1 -1
S207 1 0
S208 -1 -1
S209 1 0
S210 -1 -1
S211 -1 -1
S212 1 0
S213 0 0
S214 1 0
S215 -1 -1
S216 -1 -1
S217 1 0
S218 -1 -1
S219 -1 -1
S220 -1 -1
S221 1 0
S222 -1 -1
S223 0 0
S224 -1 -1
S225 -1 -1
S226 -1 -1
S227 1 0
S228 1 0
S229 1 0
S230 1 0
S231 1 0
S232 0 0
S233 -1 -1
S234 1 0
S235 1 0
S236 0 0
S237 1 0
S238 1 0
S239 1 0
S240 -1 -1
S241 1 0
S242 1 0
S243 1 0
S244 1 0
S245 -1 -1
S246 -1 -1
S247 -1 -1
S248 1 0
S249 -1 -1
S250 0 0
S251 1 0
S252 1 0
S253 1 0
S254 1 0
S255 1 0
S256 -1 -1
S257 1 0
S258 -1 -1
S259 1 0
S260 0 0
S261 1 0
S262 -1 -1
S263 1 0
S264 -1 -1
S265 0 1
S266 0 1
S267 -1 -1
S268 1 0
S269 -1 -1
S270 1 0
S271 -1 -1
S272 0 0
S273 0 0
S274 -1 -1
S275 0 0
S276 -1 -1
S277 -1 -1
S278 -1 -1
S279 1 0
S280 -1 -1
S281 1 0
S282 0 0
S283 0 0
S284 -1 -1
S285 -1 -1
S286 0 0
S287 0 0
S288 0 0
S289 0 0
S290 1 0
S291 -1 -1
S292 1 0
S293 -1 -1
S294 -1 -1
S295 0 0
S296 0 0
S297 -1 -1
S298 0 0
S299 -1 -1
S300 0 0
S301 0 0
S302 0 0
S303 0 0
S304 0 0
S305 0 0
S306 0 1
S307 1 0
S308 1 0
S309 0 1
S310 1 0
S311 1 0
S312 1 0
S313 1 0
S314 1 0
S315 1 0
S316 1 0
S317 1 0
S318 1 0
S319 1 0
S320 1 0
S321 1 0
S322 1 0
S323 1 0
S324 0 0
S325 -1 -1
S326 -1 -1
S327 1 0
S328 1 0
S329 1 0
S330 1 0
S331 0 1
S332 0 0
S333 0 0
S334 0 0
S335 0 0
S336 0 0
S337 0 0
S338 0 0
S339 0 0
S340 0 0
S341 0 0
S342 0 0
S343 0 0
S344 0 0
S345 0 0
S346 0 0
S347 -1 -1
S348 0 0
S349 0 0
S350 0 0
S351 0 0
S352 0 0
S353 0 0
S354 0 0
S355 0 0
S356 -1 -1
S357 -1 -1
S358 -1 -1
S359 -1 -1
S360 0 0
S361 0 0
S362 0 0
S363 0 0
S364 0 0
S365 0 0
S366 0 0
S367 0 0
S368 0 0
S369 0 0
S370 0 0
S371 0 0
S372 0 0
S373 0 0
S374 0 0
S375 0 0
S376 0 0
S377 0 0
S378 0 0
S379 0 0
S380 0 0
S381 0 0
S382 0 0
S383 0 0
S384 0 0
S385 0 0
S386 0 0
S387 0 0
S388 0 0
S389 0 0
S390 0 0
S391 0 0
S392 0 0
S393 0 0
S394 0 0
$terms
dist.bc ~ pH + Nugent_Cat + CST + Ethnic_Group
attr(,"variables")
list(dist.bc, pH, Nugent_Cat, CST, Ethnic_Group)
attr(,"factors")
pH Nugent_Cat CST Ethnic_Group
dist.bc 0 0 0 0
pH 1 0 0 0
Nugent_Cat 0 1 0 0
CST 0 0 1 0
Ethnic_Group 0 0 0 1
attr(,"term.labels")
[1] "pH" "Nugent_Cat" "CST" "Ethnic_Group"
attr(,"order")
[1] 1 1 1 1
attr(,"intercept")
[1] 1
attr(,"response")
[1] 1
attr(,".Environment")
<environment: R_GlobalEnv>
attr(,"class")
[1] "adonis"The results show that all covariates tested are significant but that some explain more variability than others. For example, CST is the highest structuring factor with 52.6% of variability explained (after controlling for pH and Nugent category) against 0.6% for Ethnic group (after controlling for all other covariates)
Heatmap
We have shown that the samples cluster well by CST when considering the Bray-Curtis distances. We will now investigate the content of those CST by looking at the raw count table. To make counts comparables across samples and avoid being misled by differences in sample sizes, we work with the rarefied version of our dataset. We also group the samples by CST using the faceting mechanism.
plot_heatmap(ravel_rare, low = "yellow", high = "red", na.value = "white") +
facet_grid(~CST, scales = "free_x", space = "free_x")
The whole figure hints as some results we already know:
- CST IV is very diverse (and other CST less so)
- samples are very similar within each CST (and hence cluster together)
- CST I-III and V appear to be dominated by a single OTU (and thus have low effective diversity)
- The dominant OTU of CST I-III and V is also frequently present in other samples (and thus the Jaccard distance may have a hard time distinguishing between samples from different CSTs)
To make the figure easier to read, we can zoom in on the 50 (for example) most abundant taxa
top_50_taxa <- taxa_sums(ravel_rare) %>% sort(decreasing = TRUE) %>% names() %>% head(n = 50)
p <- plot_heatmap(prune_taxa(top_50_taxa, ravel_rare),
low = "yellow", high = "red", na.value = "white") +
facet_grid(~CST, scales = "free_x", space = "free_x")plot(p)
This small help us identify the dominant OTU in each CST:
- CST I: Lactobacillus crispatus
- CST II: Lactobacillus gasseri
- CST III: Lactobacillus iners
- CST V: Lactobacillus jensenii
A few conclusions
The different elements we’ve seen allow us to draw a few conclusions:
- Vaginosis (as diagnosed by high Nugent scores) correspond to a quite diverse microbiota;
- CST are archetypes of communities, 4 of which correspond to healthy communities. They can be defined by clustering the samples according to the Bray-Curtis distance;
- The four healthy CST have low diversity and are dominated by a different lactic acid bacteria, which explains their low pH (and as explained in the paper, the very acid pH ensures that non commensal taxa do not invade and that the ecosystem remains healthy);
- Jaccard distance is not very useful to characterize the CST as samples typically share many OTUs, although in very different abundances;
- After controlling for CST, pH and Nugent category, ethnic group explains almost no difference between samples.
