## ggplot2 RColorBrewer grid gridExtra plyr
## TRUE TRUE TRUE TRUE TRUE
## lme4 lsmeans knitr tidyr dplyr
## TRUE TRUE TRUE TRUE TRUE
## MASS
## TRUE
Processing the data for graphical exploration and analysis.
#Reading the file
seed <- read.csv("../data/clean/seed_rot.csv")
#Summarizing data using different parameters by plyr library
seed_sum <- ddply(seed, c("Species", "Temp"), summarise,
N = length(DIx100),
mean_DI = mean(DIx100),
sd_DI = sd(DIx100),
se_DI = sd_DI/sqrt(N)
)
#Setting limits for error bars
limits <- aes(ymax = mean_DI + se_DI, ymin=mean_DI - se_DI, col=Temp)
Plotting the data by temperature using standard error and summarizing data by species.
#Creating plot for DI mean values
ggplot(seed_sum, aes(x=reorder(Species, mean_DI,median), y=mean_DI)) +
geom_point(aes(colour=Temp), stat = "summary", fun.y="mean", size=2) +
theme_gray() +
theme(axis.text.x=element_text(angle=90, hjust = 1, vjust = 0.5, face="italic")) +
scale_color_manual(values=c("#80b1d3","#fb8072")) +
geom_errorbar(limits, width=0.2) +
labs(x="Species", y="Disease Severity Index")
Subsetting the 20C seed rot assay data for statistical analysis, and testing different models to find the best fit:
#Dataset for 20C for seed rot
Seed_20C <- subset(seed, seed$Temp=="20C")
#General model AOV
fit1_20C <- aov(DIx100 ~ Species, data=Seed_20C)
summary(fit1_20C, adjust="bon")
## Df Sum Sq Mean Sq F value Pr(>F)
## Species 84 1232010 14667 64.89 <2e-16 ***
## Residuals 1841 416133 226
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#Plotting diagnostic plots for fit1 model
par(mfrow=c(2,2)) # optional layout
plot(fit1_20C)# diagnostic plots
#Plotting residuals
par(mfrow=c(1,1)) # optional layout
hist(fit1_20C$residuals)
#Test with random effect fit2 using aov
fit1.2_20C <- aov(DIx100 ~ Species + Species:Isolate + Error(Set), data=Seed_20C)
summary(fit1.2_20C, adjust="bon")
##
## Error: Set
## Df Sum Sq Mean Sq F value Pr(>F)
## Species 6 278397 46399 42.26 3.52e-08 ***
## Residuals 14 15370 1098
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Error: Within
## Df Sum Sq Mean Sq F value Pr(>F)
## Species 84 954066 11358 207.13 <2e-16 ***
## Species:Isolate 123 307200 2498 45.55 <2e-16 ***
## Residuals 1698 93111 55
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##Model 2 with fixed effect (species) and random effect (set)
fit2_20C <- lmer(DIx100 ~ Species + (1|Set), data=Seed_20C, REML = FALSE)
summary(fit2_20C)
## Linear mixed model fit by maximum likelihood ['lmerMod']
## Formula: DIx100 ~ Species + (1 | Set)
## Data: Seed_20C
##
## AIC BIC logLik deviance df.resid
## 15967.2 16451.2 -7896.6 15793.2 1839
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.9299 -0.3294 -0.0364 0.2355 4.5421
##
## Random effects:
## Groups Name Variance Std.Dev.
## Set (Intercept) 5.666 2.38
## Residual 210.313 14.50
## Number of obs: 1926, groups: Set, 21
##
## Fixed effects:
## Estimate Std. Error t value
## (Intercept) 13.1630 5.0136 2.625
## SpeciesAphanomyces cochlioides 1.6928 7.0874 0.239
## SpeciesControl -4.4328 5.3108 -0.835
## SpeciesPhytophthora aff. rosacearum 3.2668 5.8867 0.555
## SpeciesPhytophthora drechsleri 77.1237 7.0874 10.882
## SpeciesPhytophthora inundata 3.1837 5.8867 0.541
## SpeciesPhytophthora megasperma 19.9015 7.0874 2.808
## SpeciesPhytophthora rosacearum 20.8594 5.8867 3.544
## SpeciesPhytophthora sansomeana 81.1111 5.9205 13.700
## SpeciesPhytophthora sojae 13.9815 5.5819 2.505
## SpeciesPhytophthora sp. 20.7348 7.0874 2.926
## SpeciesPhytopythium aff. vexans 23.3737 6.2087 3.765
## SpeciesPhytopythium chamaehyphon 24.1928 5.8867 4.110
## SpeciesPhytopythium helicoides 78.7903 6.2087 12.690
## SpeciesPhytopythium litorale 12.4751 5.8867 2.119
## SpeciesPhytopythium megacarpum 23.7903 7.0874 3.357
## SpeciesPhytopythium mercuriale 14.6047 5.8867 2.481
## SpeciesPythiogeton sp. 27.4015 7.0874 3.866
## SpeciesPythium acanthicum 2.7321 5.8867 0.464
## SpeciesPythium acanthophoron 14.3459 7.0874 2.024
## SpeciesPythium acrogynum 1.9800 5.8867 0.336
## SpeciesPythium adhaerens 14.6237 7.0874 2.063
## SpeciesPythium aff. diclinum 19.8504 5.8867 3.372
## SpeciesPythium aff. dictyosporum 71.9848 6.2087 11.594
## SpeciesPythium aff. dissotocum 13.7037 5.5819 2.455
## SpeciesPythium aff. hypogynum 14.9015 7.0874 2.103
## SpeciesPythium aff. iwayamai 23.2348 7.0874 3.278
## SpeciesPythium aff. perplexum 26.2714 5.8867 4.463
## SpeciesPythium aff. torulosum 25.3704 5.5819 4.545
## SpeciesPythium amasculinum 1.4850 5.8867 0.252
## SpeciesPythium angustatum 14.9015 7.0874 2.103
## SpeciesPythium aphanidermatum 86.6702 5.8867 14.723
## SpeciesPythium aristosporum 4.8825 5.8867 0.829
## SpeciesPythium arrhenomanes 6.9195 5.8867 1.175
## SpeciesPythium attrantheridium 12.5926 5.5819 2.256
## SpeciesPythium camurandrum 13.2348 7.0874 1.867
## SpeciesPythium carolinianum 5.1187 5.8867 0.870
## SpeciesPythium catenulatum 17.5866 5.8867 2.988
## SpeciesPythium chondricola 15.4570 7.0874 2.181
## SpeciesPythium coloratum 36.2998 5.8867 6.166
## SpeciesPythium conidiophorum 11.2073 5.8867 1.904
## SpeciesPythium contiguanum 3.2763 5.8867 0.557
## SpeciesPythium cryptoirregulare 82.4015 7.0874 11.626
## SpeciesPythium glomeratum 4.9430 5.8867 0.840
## SpeciesPythium heterothallicum 10.6481 5.5819 1.908
## SpeciesPythium hydnosporum 18.6515 6.2087 3.004
## SpeciesPythium hypogynum 3.2158 5.8867 0.546
## SpeciesPythium inflatum 5.4172 5.8867 0.920
## SpeciesPythium intermedium 40.1887 5.8867 6.827
## SpeciesPythium irregulare 66.8519 5.5819 11.977
## SpeciesPythium kashmirense 3.0306 5.8867 0.515
## SpeciesPythium kunmingense 76.1515 6.2087 12.265
## SpeciesPythium litorale 27.6792 7.0874 3.905
## SpeciesPythium longandrum 3.3689 5.8867 0.572
## SpeciesPythium longisporangium 1.9705 5.8867 0.335
## SpeciesPythium lutarium 35.6481 5.5819 6.386
## SpeciesPythium middletonii 16.0862 5.8867 2.733
## SpeciesPythium minus 3.2668 5.8867 0.555
## SpeciesPythium monospermum 0.4986 6.2087 0.080
## SpeciesPythium nagaii 1.4565 5.8867 0.247
## SpeciesPythium nodosum 4.0284 5.8867 0.684
## SpeciesPythium nunn 3.9850 5.8867 0.677
## SpeciesPythium oligandrum 2.1652 5.8867 0.368
## SpeciesPythium oopapillum 11.6667 5.5819 2.090
## SpeciesPythium orthogonon 4.8184 5.8867 0.819
## SpeciesPythium pachycaule 0.9295 5.8867 0.158
## SpeciesPythium paroecandrum 36.2506 5.8867 6.158
## SpeciesPythium periilum 7.7113 5.8867 1.310
## SpeciesPythium periplocum 29.8409 5.8867 5.069
## SpeciesPythium perplexum 2.2691 5.8867 0.385
## SpeciesPythium pleroticum 3.4295 5.8867 0.583
## SpeciesPythium pyrilobum 13.5126 7.0874 1.907
## SpeciesPythium rhizosaccharum 4.2949 5.8867 0.730
## SpeciesPythium rostratifingens 3.3802 5.8867 0.574
## SpeciesPythium sp. balticum 3.4295 5.8867 0.583
## SpeciesPythium spinosum 31.7135 5.8867 5.387
## SpeciesPythium sterilum 32.1237 7.0874 4.532
## SpeciesPythium sylvaticum 60.8333 5.5819 10.898
## SpeciesPythium tardicrescens 32.3825 5.8867 5.501
## SpeciesPythium terrestris 64.7483 7.0874 9.136
## SpeciesPythium torulosum 4.5726 5.8867 0.777
## SpeciesPythium ultimum 86.2506 5.8867 14.652
## SpeciesPythium ultimum var. sporangiiferum 84.4444 5.5819 15.128
## SpeciesPythium ultimum var. ultimum 86.0185 5.5819 15.410
## SpeciesPythium vanterpoolii 1.0446 5.8867 0.177
##
## Correlation matrix not shown by default, as p = 85 > 20.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it
#Model 2 fitting (fitted vs residuals)
plot(fit2_20C)
#lsmeans for model 2
lsmeans_fit2_20C <- lsmeans(fit2_20C,"Species")
## Loading required namespace: pbkrtest
#Print summary for data including mean, SE, df, CIs, t-ratio and p.value
#summary(lsmeans_fit2_20C, infer=c(TRUE,TRUE), adjust="bon")
plot(lsmeans_fit2_20C)
#Estimate confidence intervals for model 2
#confint(contrast(lsmeans_fit2, "trt.vs.ctrl", ref=3))
#Model 3 with fixed effect (species) and random effect (set) and nested effect (species:isolate)
fit3_20C <- lmer(DIx100 ~ Species + (1|Set) + (1|Species:Isolate), data=Seed_20C, REML = FALSE)
summary(fit3_20C)
## Linear mixed model fit by maximum likelihood ['lmerMod']
## Formula: DIx100 ~ Species + (1 | Set) + (1 | Species:Isolate)
## Data: Seed_20C
##
## AIC BIC logLik deviance df.resid
## 14087.0 14576.6 -6955.5 13911.0 1838
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.5596 -0.4524 -0.0285 0.4412 5.2998
##
## Random effects:
## Groups Name Variance Std.Dev.
## Species:Isolate (Intercept) 159.590 12.633
## Set (Intercept) 9.782 3.128
## Residual 54.807 7.403
## Number of obs: 1926, groups: Species:Isolate, 208; Set, 21
##
## Fixed effects:
## Estimate Std. Error t value
## (Intercept) 11.522 12.960 0.889
## SpeciesAphanomyces cochlioides 3.823 18.320 0.209
## SpeciesControl -2.791 18.110 -0.154
## SpeciesPhytophthora aff. rosacearum 5.397 15.005 0.360
## SpeciesPhytophthora drechsleri 78.798 18.320 4.301
## SpeciesPhytophthora inundata 5.010 15.005 0.334
## SpeciesPhytophthora megasperma 21.575 18.320 1.178
## SpeciesPhytophthora rosacearum 22.990 15.005 1.532
## SpeciesPhytophthora sansomeana 81.111 15.765 5.145
## SpeciesPhytophthora sojae 13.981 14.863 0.941
## SpeciesPhytophthora sp. 22.409 18.320 1.223
## SpeciesPhytopythium aff. vexans 25.048 15.899 1.575
## SpeciesPhytopythium chamaehyphon 26.323 15.005 1.754
## SpeciesPhytopythium helicoides 80.464 15.899 5.061
## SpeciesPhytopythium litorale 14.758 15.005 0.984
## SpeciesPhytopythium megacarpum 25.464 18.320 1.390
## SpeciesPhytopythium mercuriale 16.887 15.005 1.125
## SpeciesPythiogeton sp. 29.075 18.320 1.587
## SpeciesPythium acanthicum 4.939 15.005 0.329
## SpeciesPythium acanthophoron 16.020 18.320 0.874
## SpeciesPythium acrogynum 3.806 15.005 0.254
## SpeciesPythium adhaerens 16.298 18.320 0.890
## SpeciesPythium aff. diclinum 21.677 15.005 1.445
## SpeciesPythium aff. dictyosporum 73.659 15.899 4.633
## SpeciesPythium aff. dissotocum 13.704 14.863 0.922
## SpeciesPythium aff. hypogynum 16.575 18.320 0.905
## SpeciesPythium aff. iwayamai 24.909 18.320 1.360
## SpeciesPythium aff. perplexum 28.554 15.005 1.903
## SpeciesPythium aff. torulosum 25.370 14.863 1.707
## SpeciesPythium amasculinum 2.855 15.005 0.190
## SpeciesPythium angustatum 16.575 18.320 0.905
## SpeciesPythium aphanidermatum 88.040 15.005 5.867
## SpeciesPythium aristosporum 7.165 15.005 0.478
## SpeciesPythium arrhenomanes 9.202 15.005 0.613
## SpeciesPythium attrantheridium 12.593 14.863 0.847
## SpeciesPythium camurandrum 14.909 18.320 0.814
## SpeciesPythium carolinianum 7.249 15.005 0.483
## SpeciesPythium catenulatum 19.261 15.005 1.284
## SpeciesPythium chondricola 17.131 18.320 0.935
## SpeciesPythium coloratum 37.669 15.005 2.510
## SpeciesPythium conidiophorum 12.577 15.005 0.838
## SpeciesPythium contiguanum 5.103 15.005 0.340
## SpeciesPythium cryptoirregulare 84.075 18.320 4.589
## SpeciesPythium glomeratum 6.769 15.005 0.451
## SpeciesPythium heterothallicum 10.648 14.863 0.716
## SpeciesPythium hydnosporum 20.325 15.899 1.278
## SpeciesPythium hypogynum 5.499 15.005 0.366
## SpeciesPythium inflatum 7.624 15.005 0.508
## SpeciesPythium intermedium 41.558 15.005 2.770
## SpeciesPythium irregulare 66.852 14.863 4.498
## SpeciesPythium kashmirense 5.313 15.005 0.354
## SpeciesPythium kunmingense 77.825 15.899 4.895
## SpeciesPythium litorale 29.353 18.320 1.602
## SpeciesPythium longandrum 5.195 15.005 0.346
## SpeciesPythium longisporangium 4.101 15.005 0.273
## SpeciesPythium lutarium 35.648 14.863 2.398
## SpeciesPythium middletonii 18.369 15.005 1.224
## SpeciesPythium minus 5.397 15.005 0.360
## SpeciesPythium monospermum 2.325 15.899 0.146
## SpeciesPythium nagaii 3.739 15.005 0.249
## SpeciesPythium nodosum 6.235 15.005 0.416
## SpeciesPythium nunn 5.355 15.005 0.357
## SpeciesPythium oligandrum 3.991 15.005 0.266
## SpeciesPythium oopapillum 11.667 14.863 0.785
## SpeciesPythium orthogonon 6.188 15.005 0.412
## SpeciesPythium pachycaule 2.299 15.005 0.153
## SpeciesPythium paroecandrum 38.457 15.005 2.563
## SpeciesPythium periilum 9.842 15.005 0.656
## SpeciesPythium periplocum 31.971 15.005 2.131
## SpeciesPythium perplexum 4.476 15.005 0.298
## SpeciesPythium pleroticum 4.799 15.005 0.320
## SpeciesPythium pyrilobum 15.187 18.320 0.829
## SpeciesPythium rhizosaccharum 6.121 15.005 0.408
## SpeciesPythium rostratifingens 5.587 15.005 0.372
## SpeciesPythium sp. balticum 4.799 15.005 0.320
## SpeciesPythium spinosum 33.920 15.005 2.261
## SpeciesPythium sterilum 33.798 18.320 1.845
## SpeciesPythium sylvaticum 60.833 14.863 4.093
## SpeciesPythium tardicrescens 34.665 15.005 2.310
## SpeciesPythium terrestris 66.879 18.320 3.651
## SpeciesPythium torulosum 6.399 15.005 0.426
## SpeciesPythium ultimum 88.457 15.005 5.895
## SpeciesPythium ultimum var. sporangiiferum 84.444 14.863 5.682
## SpeciesPythium ultimum var. ultimum 86.019 14.863 5.787
## SpeciesPythium vanterpoolii 3.175 15.005 0.212
##
## Correlation matrix not shown by default, as p = 85 > 20.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it
#Model 3 fitting (fitted vs residuals)
plot(fit3_20C)
#lsmeans for model 3
lsmeans_fit3_20C <- lsmeans(fit3_20C, "Species")
#Print summary for data including mean, SE, df, CIs, t-ratio and p.value
#summary(lsmeans_fit3_20C, infer=c(TRUE,TRUE), adjust="bon")
plot(lsmeans_fit3_20C)
#Comparing models 2 and 3
anova(fit2_20C, fit3_20C)
## Data: Seed_20C
## Models:
## fit2_20C: DIx100 ~ Species + (1 | Set)
## fit3_20C: DIx100 ~ Species + (1 | Set) + (1 | Species:Isolate)
## Df AIC BIC logLik deviance Chisq Chi Df Pr(>Chisq)
## fit2_20C 87 15967 16451 -7896.6 15793
## fit3_20C 88 14087 14577 -6955.5 13911 1882.2 1 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Based on the model 3, which is the best model, the data was compared against the control to determine those species that are different. The p-values were adjusted with bonferroni due to large number of levels.
#Contrast for model 3
CvsA_fit3_20C <- contrast(lsmeans_fit3_20C, "trt.vs.ctrl", ref=3)
Results_fit3_20C <- summary(CvsA_fit3_20C, adjust="bon")
kable(Results_fit3_20C, digits = 3, format = "markdown")
contrast | estimate | SE | df | t.ratio | p.value |
---|---|---|---|---|---|
Aphanomyces cladogamus - Control | 2.791 | 23.490 | 364.281 | 0.119 | 1.000 |
Aphanomyces cochlioides - Control | 6.615 | 23.490 | 364.243 | 0.282 | 1.000 |
Phytophthora aff. rosacearum - Control | 8.189 | 19.152 | 363.376 | 0.428 | 1.000 |
Phytophthora drechsleri - Control | 81.589 | 23.490 | 364.243 | 3.473 | 0.048 |
Phytophthora inundata - Control | 7.801 | 19.152 | 363.376 | 0.407 | 1.000 |
Phytophthora megasperma - Control | 24.367 | 23.490 | 364.243 | 1.037 | 1.000 |
Phytophthora rosacearum - Control | 25.781 | 19.152 | 363.376 | 1.346 | 1.000 |
Phytophthora sansomeana - Control | 83.903 | 20.324 | 363.717 | 4.128 | 0.004 |
Phytophthora sojae - Control | 16.773 | 19.152 | 363.433 | 0.876 | 1.000 |
Phytophthora sp. - Control | 25.200 | 23.490 | 364.243 | 1.073 | 1.000 |
Phytopythium aff. vexans - Control | 27.839 | 20.324 | 363.667 | 1.370 | 1.000 |
Phytopythium chamaehyphon - Control | 29.115 | 19.152 | 363.376 | 1.520 | 1.000 |
Phytopythium helicoides - Control | 83.256 | 20.324 | 363.667 | 4.097 | 0.004 |
Phytopythium litorale - Control | 17.549 | 19.152 | 363.384 | 0.916 | 1.000 |
Phytopythium megacarpum - Control | 28.256 | 23.490 | 364.243 | 1.203 | 1.000 |
Phytopythium mercuriale - Control | 19.679 | 19.152 | 363.384 | 1.028 | 1.000 |
Pythiogeton sp. - Control | 31.867 | 23.490 | 364.243 | 1.357 | 1.000 |
Pythium acanthicum - Control | 7.730 | 19.152 | 363.333 | 0.404 | 1.000 |
Pythium acanthophoron - Control | 18.811 | 23.490 | 364.243 | 0.801 | 1.000 |
Pythium acrogynum - Control | 6.598 | 19.152 | 363.376 | 0.344 | 1.000 |
Pythium adhaerens - Control | 19.089 | 23.490 | 364.243 | 0.813 | 1.000 |
Pythium aff. diclinum - Control | 24.468 | 19.152 | 363.376 | 1.278 | 1.000 |
Pythium aff. dictyosporum - Control | 76.450 | 20.324 | 363.667 | 3.762 | 0.017 |
Pythium aff. dissotocum - Control | 16.495 | 19.152 | 363.433 | 0.861 | 1.000 |
Pythium aff. hypogynum - Control | 19.367 | 23.490 | 364.243 | 0.824 | 1.000 |
Pythium aff. iwayamai - Control | 27.700 | 23.490 | 364.243 | 1.179 | 1.000 |
Pythium aff. perplexum - Control | 31.346 | 19.152 | 363.384 | 1.637 | 1.000 |
Pythium aff. torulosum - Control | 28.162 | 19.152 | 363.433 | 1.470 | 1.000 |
Pythium amasculinum - Control | 5.646 | 19.152 | 363.384 | 0.295 | 1.000 |
Pythium angustatum - Control | 19.367 | 23.490 | 364.243 | 0.824 | 1.000 |
Pythium aphanidermatum - Control | 90.831 | 19.152 | 363.384 | 4.743 | 0.000 |
Pythium aristosporum - Control | 9.957 | 19.152 | 363.384 | 0.520 | 1.000 |
Pythium arrhenomanes - Control | 11.994 | 19.152 | 363.384 | 0.626 | 1.000 |
Pythium attrantheridium - Control | 15.384 | 19.152 | 363.433 | 0.803 | 1.000 |
Pythium camurandrum - Control | 17.700 | 23.490 | 364.243 | 0.754 | 1.000 |
Pythium carolinianum - Control | 10.041 | 19.152 | 363.376 | 0.524 | 1.000 |
Pythium catenulatum - Control | 22.052 | 19.152 | 363.376 | 1.151 | 1.000 |
Pythium chondricola - Control | 19.922 | 23.490 | 364.243 | 0.848 | 1.000 |
Pythium coloratum - Control | 40.461 | 19.152 | 363.384 | 2.113 | 1.000 |
Pythium conidiophorum - Control | 15.368 | 19.152 | 363.384 | 0.802 | 1.000 |
Pythium contiguanum - Control | 7.894 | 19.152 | 363.376 | 0.412 | 1.000 |
Pythium cryptoirregulare - Control | 86.867 | 23.490 | 364.243 | 3.698 | 0.021 |
Pythium glomeratum - Control | 9.561 | 19.152 | 363.376 | 0.499 | 1.000 |
Pythium heterothallicum - Control | 13.440 | 19.152 | 363.433 | 0.702 | 1.000 |
Pythium hydnosporum - Control | 23.117 | 20.324 | 363.667 | 1.137 | 1.000 |
Pythium hypogynum - Control | 8.290 | 19.152 | 363.384 | 0.433 | 1.000 |
Pythium inflatum - Control | 10.415 | 19.152 | 363.333 | 0.544 | 1.000 |
Pythium intermedium - Control | 44.350 | 19.152 | 363.384 | 2.316 | 1.000 |
Pythium irregulare - Control | 69.643 | 19.152 | 363.433 | 3.636 | 0.027 |
Pythium kashmirense - Control | 8.105 | 19.152 | 363.384 | 0.423 | 1.000 |
Pythium kunmingense - Control | 80.617 | 20.324 | 363.667 | 3.967 | 0.007 |
Pythium litorale - Control | 32.145 | 23.490 | 364.243 | 1.368 | 1.000 |
Pythium longandrum - Control | 7.987 | 19.152 | 363.376 | 0.417 | 1.000 |
Pythium longisporangium - Control | 6.893 | 19.152 | 363.376 | 0.360 | 1.000 |
Pythium lutarium - Control | 38.440 | 19.152 | 363.433 | 2.007 | 1.000 |
Pythium middletonii - Control | 21.160 | 19.152 | 363.384 | 1.105 | 1.000 |
Pythium minus - Control | 8.189 | 19.152 | 363.376 | 0.428 | 1.000 |
Pythium monospermum - Control | 5.116 | 20.324 | 363.667 | 0.252 | 1.000 |
Pythium nagaii - Control | 6.531 | 19.152 | 363.384 | 0.341 | 1.000 |
Pythium nodosum - Control | 9.026 | 19.152 | 363.333 | 0.471 | 1.000 |
Pythium nunn - Control | 8.146 | 19.152 | 363.384 | 0.425 | 1.000 |
Pythium oligandrum - Control | 6.783 | 19.152 | 363.376 | 0.354 | 1.000 |
Pythium oopapillum - Control | 14.458 | 19.152 | 363.433 | 0.755 | 1.000 |
Pythium orthogonon - Control | 8.979 | 19.152 | 363.384 | 0.469 | 1.000 |
Pythium pachycaule - Control | 5.091 | 19.152 | 363.384 | 0.266 | 1.000 |
Pythium paroecandrum - Control | 41.249 | 19.152 | 363.333 | 2.154 | 1.000 |
Pythium periilum - Control | 12.633 | 19.152 | 363.376 | 0.660 | 1.000 |
Pythium periplocum - Control | 34.763 | 19.152 | 363.376 | 1.815 | 1.000 |
Pythium perplexum - Control | 7.267 | 19.152 | 363.333 | 0.379 | 1.000 |
Pythium pleroticum - Control | 7.591 | 19.152 | 363.384 | 0.396 | 1.000 |
Pythium pyrilobum - Control | 17.978 | 23.490 | 364.243 | 0.765 | 1.000 |
Pythium rhizosaccharum - Control | 8.912 | 19.152 | 363.376 | 0.465 | 1.000 |
Pythium rostratifingens - Control | 8.378 | 19.152 | 363.333 | 0.437 | 1.000 |
Pythium sp. balticum - Control | 7.591 | 19.152 | 363.384 | 0.396 | 1.000 |
Pythium spinosum - Control | 36.712 | 19.152 | 363.333 | 1.917 | 1.000 |
Pythium sterilum - Control | 36.589 | 23.490 | 364.243 | 1.558 | 1.000 |
Pythium sylvaticum - Control | 63.625 | 19.152 | 363.433 | 3.322 | 0.083 |
Pythium tardicrescens - Control | 37.457 | 19.152 | 363.384 | 1.956 | 1.000 |
Pythium terrestris - Control | 69.670 | 23.490 | 364.243 | 2.966 | 0.270 |
Pythium torulosum - Control | 9.190 | 19.152 | 363.376 | 0.480 | 1.000 |
Pythium ultimum - Control | 91.249 | 19.152 | 363.333 | 4.764 | 0.000 |
Pythium ultimum var. sporangiiferum - Control | 87.236 | 19.152 | 363.433 | 4.555 | 0.001 |
Pythium ultimum var. ultimum - Control | 88.810 | 19.152 | 363.433 | 4.637 | 0.000 |
Pythium vanterpoolii - Control | 5.967 | 19.152 | 363.376 | 0.312 | 1.000 |
Subsetting the 13C seed rot assay data for statistical analysis, and testing different models to find the best fit:
#Dataset for 20C for seed rot
Seed_13C <- subset(seed, seed$Temp=="13C")
#General model AOV
fit1_13C <- aov(DIx100 ~ Species, data=Seed_13C)
summary(fit1_13C, adjust="bon")
## Df Sum Sq Mean Sq F value Pr(>F)
## Species 84 1553136 18490 64.14 <2e-16 ***
## Residuals 1841 530695 288
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#Plotting diagnostic plots for fit1 model
par(mfrow=c(2,2)) # optional layout
plot(fit1_13C)# diagnostic plots
#Plotting residuals
par(mfrow=c(1,1)) # optional layout
hist(fit1_13C$residuals)
##Model 2 with fixed effect (species) and random effect (set)
fit2_13C <- lmer(DIx100 ~ Species + (1|Set), data=Seed_13C, REML = FALSE)
summary(fit2_13C)
## Linear mixed model fit by maximum likelihood ['lmerMod']
## Formula: DIx100 ~ Species + (1 | Set)
## Data: Seed_13C
##
## AIC BIC logLik deviance df.resid
## 16456.2 16940.2 -8141.1 16282.2 1839
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.0748 -0.3724 -0.0465 0.2785 3.8864
##
## Random effects:
## Groups Name Variance Std.Dev.
## Set (Intercept) 2.534 1.592
## Residual 272.955 16.521
## Number of obs: 1926, groups: Set, 21
##
## Fixed effects:
## Estimate Std. Error t value
## (Intercept) 8.62079 5.58152 1.545
## SpeciesAphanomyces cochlioides 2.19964 7.89305 0.279
## SpeciesControl -6.04142 5.94688 -1.016
## SpeciesPhytophthora aff. rosacearum 6.36631 6.48702 0.981
## SpeciesPhytophthora drechsleri 4.46703 7.89305 0.566
## SpeciesPhytophthora inundata 6.09606 6.48702 0.940
## SpeciesPhytophthora megasperma 3.91147 7.89305 0.496
## SpeciesPhytophthora rosacearum 42.66260 6.48702 6.577
## SpeciesPhytophthora sansomeana 50.27778 6.74481 7.454
## SpeciesPhytophthora sojae -6.38889 6.35907 -1.005
## SpeciesPhytophthora sp. 3.35591 7.89305 0.425
## SpeciesPhytopythium aff. vexans 3.49480 6.86558 0.509
## SpeciesPhytopythium chamaehyphon 24.23668 6.48702 3.736
## SpeciesPhytopythium helicoides 13.91147 6.86558 2.026
## SpeciesPhytopythium litorale 24.71470 6.48702 3.810
## SpeciesPhytopythium megacarpum 6.96703 7.89305 0.883
## SpeciesPhytopythium mercuriale 22.12210 6.48702 3.410
## SpeciesPythiogeton sp. 37.80036 7.89305 4.789
## SpeciesPythium acanthicum 12.22222 6.48702 1.884
## SpeciesPythium acanthophoron 1.41147 7.89305 0.179
## SpeciesPythium acrogynum 14.42939 6.48702 2.224
## SpeciesPythium adhaerens 1.13369 7.89305 0.144
## SpeciesPythium aff. diclinum 70.07754 6.48702 10.803
## SpeciesPythium aff. dictyosporum 84.74480 6.86558 12.343
## SpeciesPythium aff. dissotocum 41.85185 6.35907 6.581
## SpeciesPythium aff. hypogynum 10.30036 7.89305 1.305
## SpeciesPythium aff. iwayamai 6.96703 7.89305 0.883
## SpeciesPythium aff. perplexum 35.08507 6.48702 5.409
## SpeciesPythium aff. torulosum 42.12963 6.35907 6.625
## SpeciesPythium amasculinum 10.23262 6.48702 1.577
## SpeciesPythium angustatum 3.91147 7.89305 0.496
## SpeciesPythium aphanidermatum 44.58447 6.48702 6.873
## SpeciesPythium aristosporum 19.15914 6.48702 2.953
## SpeciesPythium arrhenomanes 18.78877 6.48702 2.896
## SpeciesPythium attrantheridium 16.66667 6.35907 2.621
## SpeciesPythium camurandrum -2.47742 7.89305 -0.314
## SpeciesPythium carolinianum 10.25520 6.48702 1.581
## SpeciesPythium catenulatum 2.80036 6.48702 0.432
## SpeciesPythium chondricola 0.02258 7.89305 0.003
## SpeciesPythium coloratum 63.01039 6.48702 9.713
## SpeciesPythium conidiophorum 49.21410 6.48702 7.587
## SpeciesPythium contiguanum 8.22569 6.48702 1.268
## SpeciesPythium cryptoirregulare 91.13369 7.89305 11.546
## SpeciesPythium glomeratum 12.11458 6.48702 1.868
## SpeciesPythium heterothallicum 21.66667 6.35907 3.407
## SpeciesPythium hydnosporum 7.24480 6.86558 1.055
## SpeciesPythium hypogynum 7.58507 6.48702 1.169
## SpeciesPythium inflatum 22.03704 6.48702 3.397
## SpeciesPythium intermedium 74.39928 6.48702 11.469
## SpeciesPythium irregulare 90.27778 6.35907 14.197
## SpeciesPythium kashmirense 10.17766 6.48702 1.569
## SpeciesPythium kunmingense 91.41147 6.86558 13.314
## SpeciesPythium litorale 10.57814 7.89305 1.340
## SpeciesPythium longandrum 8.96643 6.48702 1.382
## SpeciesPythium longisporangium 9.60705 6.48702 1.481
## SpeciesPythium lutarium 54.07407 6.35907 8.503
## SpeciesPythium middletonii 31.65914 6.48702 4.880
## SpeciesPythium minus 8.12557 6.48702 1.253
## SpeciesPythium monospermum 1.51272 6.86558 0.220
## SpeciesPythium nagaii 11.01099 6.48702 1.697
## SpeciesPythium nodosum 9.25926 6.48702 1.427
## SpeciesPythium nunn 8.28817 6.48702 1.278
## SpeciesPythium oligandrum 11.83680 6.48702 1.825
## SpeciesPythium oopapillum 42.77778 6.35907 6.727
## SpeciesPythium orthogonon 7.08447 6.48702 1.092
## SpeciesPythium pachycaule 4.21410 6.48702 0.650
## SpeciesPythium paroecandrum 85.37037 6.48702 13.160
## SpeciesPythium periilum 4.69964 6.48702 0.724
## SpeciesPythium periplocum 35.99594 6.48702 5.549
## SpeciesPythium perplexum 20.09259 6.48702 3.097
## SpeciesPythium pleroticum 13.01039 6.48702 2.006
## SpeciesPythium pyrilobum 26.41147 7.89305 3.346
## SpeciesPythium rhizosaccharum 6.37383 6.48702 0.983
## SpeciesPythium rostratifingens 9.07407 6.48702 1.399
## SpeciesPythium sp. balticum 33.01039 6.48702 5.089
## SpeciesPythium spinosum 71.94444 6.48702 11.091
## SpeciesPythium sterilum 21.41147 7.89305 2.713
## SpeciesPythium sylvaticum 90.83333 6.35907 14.284
## SpeciesPythium tardicrescens 33.51099 6.48702 5.166
## SpeciesPythium terrestris 90.53297 7.89305 11.470
## SpeciesPythium torulosum 20.91087 6.48702 3.223
## SpeciesPythium ultimum 90.55556 6.48702 13.960
## SpeciesPythium ultimum var. sporangiiferum 87.87037 6.35907 13.818
## SpeciesPythium ultimum var. ultimum 91.20370 6.35907 14.342
## SpeciesPythium vanterpoolii 20.07001 6.48702 3.094
##
## Correlation matrix not shown by default, as p = 85 > 20.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it
#Model 2 fitting (fitted vs residuals)
plot(fit2_13C)
#lsmeans for model 2
lsmeans_fit2_13C <- lsmeans(fit2_13C,"Species")
#Print summary for data including mean, SE, df, CIs, t-ratio and p.value
#summary(lsmeans_fit2_13C, infer=c(TRUE,TRUE), adjust="bon")
plot(lsmeans_fit2_13C)
#Estimate confidence intervals for model 2
#confint(contrast(lsmeans_fit2, "trt.vs.ctrl", ref=3))
#Model 3 with fixed effect (species) and random effect (set) and nested effect (species:isolate)
fit3_13C <- lmer(DIx100 ~ Species + (1|Set) + (1|Species:Isolate), data=Seed_13C, REML = FALSE)
summary(fit3_13C)
## Linear mixed model fit by maximum likelihood ['lmerMod']
## Formula: DIx100 ~ Species + (1 | Set) + (1 | Species:Isolate)
## Data: Seed_13C
##
## AIC BIC logLik deviance df.resid
## 14821.9 15311.5 -7323.0 14645.9 1838
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.9567 -0.4647 -0.0336 0.3953 5.8344
##
## Random effects:
## Groups Name Variance Std.Dev.
## Species:Isolate (Intercept) 194.765 13.956
## Set (Intercept) 5.878 2.424
## Residual 82.648 9.091
## Number of obs: 1926, groups: Species:Isolate, 208; Set, 21
##
## Fixed effects:
## Estimate Std. Error t value
## (Intercept) 8.6739 14.3392 0.605
## SpeciesAphanomyces cochlioides 2.0757 20.2763 0.102
## SpeciesControl -6.0945 20.0352 -0.304
## SpeciesPhytophthora aff. rosacearum 6.2424 16.5880 0.376
## SpeciesPhytophthora drechsleri 4.5910 20.2763 0.226
## SpeciesPhytophthora inundata 6.0134 16.5880 0.363
## SpeciesPhytophthora megasperma 4.0354 20.2763 0.199
## SpeciesPhytophthora rosacearum 42.5387 16.5880 2.564
## SpeciesPhytophthora sansomeana 50.2778 17.4906 2.875
## SpeciesPhytophthora sojae -6.3889 16.4903 -0.387
## SpeciesPhytophthora sp. 3.4799 20.2763 0.172
## SpeciesPhytopythium aff. vexans 3.6187 17.5827 0.206
## SpeciesPhytopythium chamaehyphon 24.1127 16.5880 1.454
## SpeciesPhytopythium helicoides 14.0354 17.5827 0.798
## SpeciesPhytopythium litorale 24.6734 16.5880 1.487
## SpeciesPhytopythium megacarpum 7.0910 20.2763 0.350
## SpeciesPhytopythium mercuriale 22.0808 16.5880 1.331
## SpeciesPythiogeton sp. 37.9243 20.2763 1.870
## SpeciesPythium acanthicum 12.2222 16.5880 0.737
## SpeciesPythium acanthophoron 1.5354 20.2763 0.076
## SpeciesPythium acrogynum 14.3468 16.5880 0.865
## SpeciesPythium adhaerens 1.2576 20.2763 0.062
## SpeciesPythium aff. diclinum 69.9949 16.5880 4.220
## SpeciesPythium aff. dictyosporum 84.8687 17.5827 4.827
## SpeciesPythium aff. dissotocum 41.8519 16.4903 2.538
## SpeciesPythium aff. hypogynum 10.4243 20.2763 0.514
## SpeciesPythium aff. iwayamai 7.0910 20.2763 0.350
## SpeciesPythium aff. perplexum 35.0438 16.5880 2.113
## SpeciesPythium aff. torulosum 42.1296 16.4903 2.555
## SpeciesPythium amasculinum 9.9847 16.5880 0.602
## SpeciesPythium angustatum 4.0354 20.2763 0.199
## SpeciesPythium aphanidermatum 44.3366 16.5880 2.673
## SpeciesPythium aristosporum 19.1178 16.5880 1.153
## SpeciesPythium arrhenomanes 18.7475 16.5880 1.130
## SpeciesPythium attrantheridium 16.6667 16.4903 1.011
## SpeciesPythium camurandrum -2.3535 20.2763 -0.116
## SpeciesPythium carolinianum 10.1313 16.5880 0.611
## SpeciesPythium catenulatum 2.9243 16.5880 0.176
## SpeciesPythium chondricola 0.1465 20.2763 0.007
## SpeciesPythium coloratum 62.7625 16.5880 3.784
## SpeciesPythium conidiophorum 48.9662 16.5880 2.952
## SpeciesPythium contiguanum 8.1431 16.5880 0.491
## SpeciesPythium cryptoirregulare 91.2576 20.2763 4.501
## SpeciesPythium glomeratum 12.0319 16.5880 0.725
## SpeciesPythium heterothallicum 21.6667 16.4903 1.314
## SpeciesPythium hydnosporum 7.3687 17.5827 0.419
## SpeciesPythium hypogynum 7.5438 16.5880 0.455
## SpeciesPythium inflatum 22.0370 16.5880 1.328
## SpeciesPythium intermedium 74.1514 16.5880 4.470
## SpeciesPythium irregulare 90.2778 16.4903 5.475
## SpeciesPythium kashmirense 10.1363 16.5880 0.611
## SpeciesPythium kunmingense 91.5354 17.5827 5.206
## SpeciesPythium litorale 10.7021 20.2763 0.528
## SpeciesPythium longandrum 8.8838 16.5880 0.536
## SpeciesPythium longisporangium 9.4831 16.5880 0.572
## SpeciesPythium lutarium 54.0741 16.4903 3.279
## SpeciesPythium middletonii 31.6178 16.5880 1.906
## SpeciesPythium minus 8.0016 16.5880 0.482
## SpeciesPythium monospermum 1.4301 17.5827 0.081
## SpeciesPythium nagaii 10.9697 16.5880 0.661
## SpeciesPythium nodosum 9.2593 16.5880 0.558
## SpeciesPythium nunn 8.0403 16.5880 0.485
## SpeciesPythium oligandrum 11.7542 16.5880 0.709
## SpeciesPythium oopapillum 42.7778 16.4903 2.594
## SpeciesPythium orthogonon 6.8366 16.5880 0.412
## SpeciesPythium pachycaule 3.9662 16.5880 0.239
## SpeciesPythium paroecandrum 85.3704 16.5880 5.147
## SpeciesPythium periilum 4.5757 16.5880 0.276
## SpeciesPythium periplocum 35.8720 16.5880 2.163
## SpeciesPythium perplexum 20.0926 16.5880 1.211
## SpeciesPythium pleroticum 12.7625 16.5880 0.769
## SpeciesPythium pyrilobum 26.5354 20.2763 1.309
## SpeciesPythium rhizosaccharum 6.2912 16.5880 0.379
## SpeciesPythium rostratifingens 9.0741 16.5880 0.547
## SpeciesPythium sp. balticum 32.7625 16.5880 1.975
## SpeciesPythium spinosum 71.9444 16.5880 4.337
## SpeciesPythium sterilum 21.5354 20.2763 1.062
## SpeciesPythium sylvaticum 90.8333 16.4903 5.508
## SpeciesPythium tardicrescens 33.4697 16.5880 2.018
## SpeciesPythium terrestris 90.4090 20.2763 4.459
## SpeciesPythium torulosum 20.8282 16.5880 1.256
## SpeciesPythium ultimum 90.5556 16.5880 5.459
## SpeciesPythium ultimum var. sporangiiferum 87.8704 16.4903 5.329
## SpeciesPythium ultimum var. ultimum 91.2037 16.4903 5.531
## SpeciesPythium vanterpoolii 19.9461 16.5880 1.202
##
## Correlation matrix not shown by default, as p = 85 > 20.
## Use print(x, correlation=TRUE) or
## vcov(x) if you need it
#Model 3 fitting (fitted vs residuals)
plot(fit3_13C)
#lsmeans for model 3
lsmeans_fit3_13C <- lsmeans(fit3_13C, "Species")
#Print summary for data including mean, SE, df, CIs, t-ratio and p.value
#summary(lsmeans_fit3_13C, infer=c(TRUE,TRUE), adjust="bon")
plot(lsmeans_fit3_13C)
#Comparing models 2 and 3
anova(fit2_13C, fit3_13C)
## Data: Seed_13C
## Models:
## fit2_13C: DIx100 ~ Species + (1 | Set)
## fit3_13C: DIx100 ~ Species + (1 | Set) + (1 | Species:Isolate)
## Df AIC BIC logLik deviance Chisq Chi Df Pr(>Chisq)
## fit2_13C 87 16456 16940 -8141.1 16282
## fit3_13C 88 14822 15312 -7323.0 14646 1636.3 1 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Based on the model 3, which is the best model, the data was compared against the control to determine those species that are different. The p-values were adjusted with bonferroni due to large number of levels.
#Contrast for model 3
CvsA_fit3_13C <- contrast(lsmeans_fit3_13C, "trt.vs.ctrl", ref=3)
Results_fit3_13C <- summary(CvsA_fit3_13C, adjust="bon", level=.90)
kable(Results_fit3_13C, format = "markdown")
contrast | estimate | SE | df | t.ratio | p.value |
---|---|---|---|---|---|
Aphanomyces cladogamus - Control | 6.0945436 | 26.05928 | 354.8147 | 0.2338723 | 1.0000000 |
Aphanomyces cochlioides - Control | 8.1702382 | 26.05928 | 354.7950 | 0.3135251 | 1.0000000 |
Phytophthora aff. rosacearum - Control | 12.3369048 | 21.22774 | 353.7264 | 0.5811689 | 1.0000000 |
Phytophthora drechsleri - Control | 10.6855157 | 26.05928 | 354.7950 | 0.4100464 | 1.0000000 |
Phytophthora inundata - Control | 12.1079696 | 21.22774 | 353.7264 | 0.5703842 | 1.0000000 |
Phytophthora megasperma - Control | 10.1299601 | 26.05928 | 354.7950 | 0.3887275 | 1.0000000 |
Phytophthora rosacearum - Control | 48.6332011 | 21.22774 | 353.7264 | 2.2910207 | 1.0000000 |
Phytophthora sansomeana - Control | 56.3723214 | 22.53296 | 354.1110 | 2.5017715 | 1.0000000 |
Phytophthora sojae - Control | -0.2943453 | 21.22774 | 353.7557 | -0.0138661 | 1.0000000 |
Phytophthora sp. - Control | 9.5744045 | 26.05928 | 354.7950 | 0.3674086 | 1.0000000 |
Phytopythium aff. vexans - Control | 9.7132934 | 22.53296 | 354.0849 | 0.4310704 | 1.0000000 |
Phytopythium chamaehyphon - Control | 30.2072752 | 21.22774 | 353.7264 | 1.4230092 | 1.0000000 |
Phytopythium helicoides - Control | 20.1299601 | 22.53296 | 354.0849 | 0.8933561 | 1.0000000 |
Phytopythium litorale - Control | 30.7679233 | 21.22774 | 353.7307 | 1.4494203 | 1.0000000 |
Phytopythium megacarpum - Control | 13.1855157 | 26.05928 | 354.7950 | 0.5059815 | 1.0000000 |
Phytopythium mercuriale - Control | 28.1753307 | 21.22774 | 353.7307 | 1.3272880 | 1.0000000 |
Pythiogeton sp. - Control | 44.0188490 | 26.05928 | 354.7950 | 1.6891812 | 1.0000000 |
Pythium acanthicum - Control | 18.3167658 | 21.22774 | 353.7048 | 0.8628692 | 1.0000000 |
Pythium acanthophoron - Control | 7.6299601 | 26.05928 | 354.7950 | 0.2927924 | 1.0000000 |
Pythium acrogynum - Control | 20.4413029 | 21.22774 | 353.7264 | 0.9629522 | 1.0000000 |
Pythium adhaerens - Control | 7.3521823 | 26.05928 | 354.7950 | 0.2821330 | 1.0000000 |
Pythium aff. diclinum - Control | 76.0894511 | 21.22774 | 353.7264 | 3.5844342 | 0.0323584 |
Pythium aff. dictyosporum - Control | 90.9632934 | 22.53296 | 354.0849 | 4.0368991 | 0.0055791 |
Pythium aff. dissotocum - Control | 47.9463954 | 21.22774 | 353.7557 | 2.2586665 | 1.0000000 |
Pythium aff. hypogynum - Control | 16.5188490 | 26.05928 | 354.7950 | 0.6338950 | 1.0000000 |
Pythium aff. iwayamai - Control | 13.1855157 | 26.05928 | 354.7950 | 0.5059815 | 1.0000000 |
Pythium aff. perplexum - Control | 41.1382936 | 21.22774 | 353.7307 | 1.9379494 | 1.0000000 |
Pythium aff. torulosum - Control | 48.2241732 | 21.22774 | 353.7557 | 2.2717521 | 1.0000000 |
Pythium amasculinum - Control | 16.0792661 | 21.22774 | 353.7307 | 0.7574647 | 1.0000000 |
Pythium angustatum - Control | 10.1299601 | 26.05928 | 354.7950 | 0.3887275 | 1.0000000 |
Pythium aphanidermatum - Control | 50.4311180 | 21.22774 | 353.7307 | 2.3757173 | 1.0000000 |
Pythium aristosporum - Control | 25.2123677 | 21.22774 | 353.7307 | 1.1877083 | 1.0000000 |
Pythium arrhenomanes - Control | 24.8419973 | 21.22774 | 353.7307 | 1.1702608 | 1.0000000 |
Pythium attrantheridium - Control | 22.7612103 | 21.22774 | 353.7557 | 1.0722388 | 1.0000000 |
Pythium camurandrum - Control | 3.7410712 | 26.05928 | 354.7950 | 0.1435600 | 1.0000000 |
Pythium carolinianum - Control | 16.2257937 | 21.22774 | 353.7264 | 0.7643673 | 1.0000000 |
Pythium catenulatum - Control | 9.0188490 | 21.22774 | 353.7264 | 0.4248614 | 1.0000000 |
Pythium chondricola - Control | 6.2410712 | 26.05928 | 354.7950 | 0.2394951 | 1.0000000 |
Pythium coloratum - Control | 68.8570439 | 21.22774 | 353.7307 | 3.2437287 | 0.1085400 |
Pythium conidiophorum - Control | 55.0607476 | 21.22774 | 353.7307 | 2.5938106 | 0.8304476 |
Pythium contiguanum - Control | 14.2375992 | 21.22774 | 353.7264 | 0.6707071 | 1.0000000 |
Pythium cryptoirregulare - Control | 97.3521823 | 26.05928 | 354.7950 | 3.7357968 | 0.0183095 |
Pythium glomeratum - Control | 18.1264881 | 21.22774 | 353.7264 | 0.8539055 | 1.0000000 |
Pythium heterothallicum - Control | 27.7612103 | 21.22774 | 353.7557 | 1.3077796 | 1.0000000 |
Pythium hydnosporum - Control | 13.4632934 | 22.53296 | 354.0849 | 0.5974933 | 1.0000000 |
Pythium hypogynum - Control | 13.6382936 | 21.22774 | 353.7307 | 0.6424749 | 1.0000000 |
Pythium inflatum - Control | 28.1315806 | 21.22774 | 353.7048 | 1.3252270 | 1.0000000 |
Pythium intermedium - Control | 80.2459328 | 21.22774 | 353.7307 | 3.7802384 | 0.0154431 |
Pythium irregulare - Control | 96.3723214 | 21.22774 | 353.7557 | 4.5399229 | 0.0006489 |
Pythium kashmirense - Control | 16.2308862 | 21.22774 | 353.7307 | 0.7646072 | 1.0000000 |
Pythium kunmingense - Control | 97.6299601 | 22.53296 | 354.0849 | 4.3327619 | 0.0016134 |
Pythium litorale - Control | 16.7966268 | 26.05928 | 354.7950 | 0.6445545 | 1.0000000 |
Pythium longandrum - Control | 14.9783400 | 21.22774 | 353.7264 | 0.7056021 | 1.0000000 |
Pythium longisporangium - Control | 15.5776456 | 21.22774 | 353.7264 | 0.7338342 | 1.0000000 |
Pythium lutarium - Control | 60.1686177 | 21.22774 | 353.7557 | 2.8344330 | 0.4077599 |
Pythium middletonii - Control | 37.7123677 | 21.22774 | 353.7307 | 1.7765603 | 1.0000000 |
Pythium minus - Control | 14.0961641 | 21.22774 | 353.7264 | 0.6640444 | 1.0000000 |
Pythium monospermum - Control | 7.5246363 | 22.53296 | 354.0849 | 0.3339391 | 1.0000000 |
Pythium nagaii - Control | 17.0642196 | 21.22774 | 353.7307 | 0.8038640 | 1.0000000 |
Pythium nodosum - Control | 15.3538028 | 21.22774 | 353.7048 | 0.7232894 | 1.0000000 |
Pythium nunn - Control | 14.1348217 | 21.22774 | 353.7307 | 0.6658655 | 1.0000000 |
Pythium oligandrum - Control | 17.8487104 | 21.22774 | 353.7264 | 0.8408199 | 1.0000000 |
Pythium oopapillum - Control | 48.8723214 | 21.22774 | 353.7557 | 2.3022852 | 1.0000000 |
Pythium orthogonon - Control | 12.9311180 | 21.22774 | 353.7307 | 0.6091612 | 1.0000000 |
Pythium pachycaule - Control | 10.0607476 | 21.22774 | 353.7307 | 0.4739433 | 1.0000000 |
Pythium paroecandrum - Control | 91.4649140 | 21.22774 | 353.7048 | 4.3087439 | 0.0017896 |
Pythium periilum - Control | 10.6702382 | 21.22774 | 353.7264 | 0.5026553 | 1.0000000 |
Pythium periplocum - Control | 41.9665345 | 21.22774 | 353.7264 | 1.9769663 | 1.0000000 |
Pythium perplexum - Control | 26.1871362 | 21.22774 | 353.7048 | 1.2336278 | 1.0000000 |
Pythium pleroticum - Control | 18.8570439 | 21.22774 | 353.7307 | 0.8883207 | 1.0000000 |
Pythium pyrilobum - Control | 32.6299601 | 26.05928 | 354.7950 | 1.2521435 | 1.0000000 |
Pythium rhizosaccharum - Control | 12.3857474 | 21.22774 | 353.7264 | 0.5834698 | 1.0000000 |
Pythium rostratifingens - Control | 15.1686177 | 21.22774 | 353.7048 | 0.7145657 | 1.0000000 |
Pythium sp. balticum - Control | 38.8570439 | 21.22774 | 353.7307 | 1.8304839 | 1.0000000 |
Pythium spinosum - Control | 78.0389880 | 21.22774 | 353.7048 | 3.6762733 | 0.0229640 |
Pythium sterilum - Control | 27.6299601 | 26.05928 | 354.7950 | 1.0602733 | 1.0000000 |
Pythium sylvaticum - Control | 96.9278769 | 21.22774 | 353.7557 | 4.5660941 | 0.0005770 |
Pythium tardicrescens - Control | 39.5642196 | 21.22774 | 353.7307 | 1.8637976 | 1.0000000 |
Pythium terrestris - Control | 96.5035715 | 26.05928 | 354.7950 | 3.7032322 | 0.0207277 |
Pythium torulosum - Control | 26.9227844 | 21.22774 | 353.7264 | 1.2682829 | 1.0000000 |
Pythium ultimum - Control | 96.6500991 | 21.22774 | 353.7048 | 4.5530085 | 0.0006120 |
Pythium ultimum var. sporangiiferum - Control | 93.9649140 | 21.22774 | 353.7557 | 4.4265144 | 0.0010731 |
Pythium ultimum var. ultimum - Control | 97.2982473 | 21.22774 | 353.7557 | 4.5835416 | 0.0005333 |
Pythium vanterpoolii - Control | 26.0406086 | 21.22774 | 353.7264 | 1.2267252 | 1.0000000 |
#Sorting tables for seed rot at 13C and 20C
Seed_13C <- Seed_13C[order(Seed_13C[,1], Seed_13C[,2], Seed_13C[,3]),]
Seed_20C <- Seed_20C[order(Seed_20C[,1], Seed_20C[,2], Seed_20C[,3]),]
#Join tables using isolate, species, set and replicate
Seed_temps <- left_join(Seed_13C,Seed_20C,by=c("Isolate","Species","Set","Rep"))
Seed_temps <- Seed_temps %>% dplyr::select(Set, Isolate, Rep, Species, Temp.x, Temp.y, DIx100.x, DIx100.y)
#Sanity check
#dim(Seed_temps)
#Relabel columns for analysis
Seed_temps <- rename(Seed_temps, Temp13C=Temp.x, Temp_20C=Temp.y, DI_13C=DIx100.x, DI_20C=DIx100.y)
head(Seed_temps)
## Set Isolate Rep Species Temp13C Temp_20C
## 1 Set_1-1 AR_15.S.2.7.A R1 Pythium aff. torulosum 13C 20C
## 2 Set_1-1 AR_15.S.2.7.A R2 Pythium aff. torulosum 13C 20C
## 3 Set_1-1 AR_15.S.2.7.A R3 Pythium aff. torulosum 13C 20C
## 4 Set_1-1 AR_160.S.1.9.A R1 Pythium aff. dissotocum 13C 20C
## 5 Set_1-1 AR_160.S.1.9.A R2 Pythium aff. dissotocum 13C 20C
## 6 Set_1-1 AR_160.S.1.9.A R3 Pythium aff. dissotocum 13C 20C
## DI_13C DI_20C
## 1 100.0 57.5
## 2 100.0 72.5
## 3 100.0 70.0
## 4 97.5 35.0
## 5 82.5 45.0
## 6 90.0 55.0
#lda
#r <- lda(formula=Species ~ DI_13C + DI_20C, data=Seed_temps)
#Summarizing data using different parameters by plyr library
seed_lda_isol <- ddply(Seed_temps, c("Species"), summarise,
N = length(DI_13C),
mean_DI13 = mean(DI_13C),
std_DI13 = std(DI_13C),
mean_DI20 = mean(DI_20C),
std_DI20 = std(DI_20C)
)
library(car)
#Clustering by isolate
scatterplotMatrix(seed_lda_isol[c(3,5)])
#Hierarchical clustering
library(ape)
seed_cluster <- seed_lda_isol[,-c(2,4,6)]
rownames(seed_cluster) <- make.names(seed_cluster[,1], unique = TRUE)
seed_cluster <- seed_cluster[,-1]
d_isol <- dist(seed_cluster, method="euclidean")
fit_isol <- hclust(d_isol, method="ward.D")
plot(fit_isol)
groups_isol <- cutree(fit_isol, k=3)
rect.hclust(fit_isol,k=3, border="red")
###Clustering with a different package
library(plyr)
seed_rot_isol <- cbind(seed_lda_isol,groups_isol)
cluster_seed_rot <- gather(seed_rot_isol, Temp, DI, c(mean_DI13, mean_DI20))
cluster_seed_rot$groups_isol <- as.factor(cluster_seed_rot$groups_isol)
#Change levels
cluster_seed_rot$groups_isol <- revalue(cluster_seed_rot$groups_isol, c("1" = "A", "2"="C", "3"="B"))
#Reorder levels
cluster_seed_rot$groups_isol <- ordered(cluster_seed_rot$groups_isol, levels=c("A","B","C"))
library(ggplot2)
bp <- ggplot(data=cluster_seed_rot, aes(x=groups_isol, y=DI)) +
geom_boxplot(aes(fill=Temp), position=position_dodge(width=1)) +
labs(x="Clusters", y="Disease Severity Index") +
scale_fill_discrete(labels=c("13ºC","20ºC"))
# library(mclust)
# set.seed(0)
# fit2 <- Mclust(seed_lda)
# summary(fit2)
library(cluster)
clusplot(seed_lda_isol,groups_isol, color = TRUE, shade = TRUE, labels=2, lines=0)
#kable(seed_lda_)
library(ggtree)
library(cowplot)
#mypal = c("#1a1a1a","#008837","#2b83ba")
#htree <- plot(as.phylo(fit_isol), cex=0.6, type="phylogram", tip.color = mypal[groups_isol])
P <- as.phylo(fit_isol)
P <- groupClade(P, node=c(90, 89, 87))
htree2 <- ggtree(P, aes(colour=group), size=0.5) + geom_text(aes(label=label), size=3, hjust=-0.05) +
scale_color_manual(values = c("#1a1a1a","#1a1a1a","#008837","#2b83ba"))
htree2.1 <- htree2 %>%
annotation_clade(node=90, "Cluster A", offset.text = 20, offset = 400, color="#636363") %>%
annotation_clade(node=89, "Cluster B", offset.text = 20, offset = 400, color="#525252") %>%
annotation_clade(node=87, "Cluster C", offset.text = 20, offset = 400, color="#252525")
plot_grid(htree2.1, bp, labels=c("A","B"), ncol=2)
#library(ggdendro)
#ggdendrogram(fit_isol, size=1, color="tomato")
seed_spp <- ddply(Seed_temps, c("Species"), summarise,
N = length(DI_13C)/9,
mean_DI13 = mean(DI_13C),
std_DI13 = std(DI_13C),
mean_DI20 = mean(DI_20C),
std_DI20 = std(DI_20C)
)
#Transforming dataframes to remove " - " and split the column into species and control (reference for comparison)
library(reshape2)
DI_13C <- separate(Results_fit3_13C, contrast, into = c("Species", "Control"), " - ")
DI_20C <- separate(Results_fit3_20C, contrast, into = c("Species", "Control"), " - ")
#merge tables together
Seed_pvalue <- left_join(DI_13C,DI_20C,by="Species")
#Rename important columns
Seed_pvalue<- rename(Seed_pvalue, Control=Control.x,
Estimate_13C=estimate.x,
Pval_13C=p.value.x,
Estimate_20C=estimate.y,
Pval_20C=p.value.y
)
#Merge last table
Seed_pvalue <- left_join(Seed_pvalue,seed_spp, by="Species")
## Warning in left_join_impl(x, y, by$x, by$y): joining factor and character
## vector, coercing into character vector
Seed_rot_final <- Seed_pvalue %>% dplyr::select(Species,
N,
mean_DI13,
std_DI13,
Pval_13C,
mean_DI20,
std_DI20,
Pval_20C
)
kable(Seed_rot_final, format = "markdown")
Species | N | mean_DI13 | std_DI13 | Pval_13C | mean_DI20 | std_DI20 | Pval_20C |
---|---|---|---|---|---|---|---|
Aphanomyces cladogamus | 1 | 8.611111 | 1.4500426 | 1.0000000 | 13.61111 | 1.9144512 | 1.0000000 |
Aphanomyces cochlioides | 1 | 10.833333 | 0.9316950 | 1.0000000 | 14.72222 | 1.7402728 | 1.0000000 |
Phytophthora aff. rosacearum | 3 | 15.000000 | 1.0591482 | 1.0000000 | 16.29630 | 0.8582843 | 1.0000000 |
Phytophthora drechsleri | 1 | 13.055556 | 3.1944444 | 1.0000000 | 90.27778 | 2.0174776 | 0.0483834 |
Phytophthora inundata | 3 | 14.722222 | 1.1810268 | 1.0000000 | 16.29630 | 0.6450884 | 1.0000000 |
Phytophthora megasperma | 1 | 12.500000 | 1.5023130 | 1.0000000 | 33.05556 | 4.7099514 | 1.0000000 |
Phytophthora rosacearum | 3 | 51.296296 | 6.9020549 | 1.0000000 | 33.88889 | 3.9502185 | 1.0000000 |
Phytophthora sansomeana | 2 | 58.888889 | 10.0065792 | 1.0000000 | 94.72222 | 1.3081083 | 0.0038097 |
Phytophthora sojae | 3 | 2.222222 | 0.2777778 | 1.0000000 | 27.59259 | 2.0949738 | 1.0000000 |
Phytophthora sp. | 1 | 11.944444 | 1.7066952 | 1.0000000 | 33.88889 | 3.7985540 | 1.0000000 |
Phytopythium aff. vexans | 2 | 12.083333 | 1.4469090 | 1.0000000 | 36.52778 | 2.8015729 | 1.0000000 |
Phytopythium chamaehyphon | 3 | 32.870370 | 3.9780015 | 1.0000000 | 37.22222 | 3.6012357 | 1.0000000 |
Phytopythium helicoides | 2 | 22.500000 | 1.8959882 | 1.0000000 | 91.94444 | 1.6112801 | 0.0043462 |
Phytopythium litorale | 3 | 33.333333 | 3.1997819 | 1.0000000 | 25.46296 | 1.5677769 | 1.0000000 |
Phytopythium megacarpum | 1 | 15.555556 | 1.9444444 | 1.0000000 | 36.94444 | 4.1411254 | 1.0000000 |
Phytopythium mercuriale | 3 | 30.740741 | 1.6816358 | 1.0000000 | 27.59259 | 1.6260077 | 1.0000000 |
Pythiogeton sp. | 1 | 46.388889 | 6.4966753 | 1.0000000 | 40.55556 | 2.5609846 | 1.0000000 |
Pythium acanthicum | 3 | 20.833333 | 1.0840727 | 1.0000000 | 15.74074 | 0.7162990 | 1.0000000 |
Pythium acanthophoron | 1 | 10.000000 | 1.2500000 | 1.0000000 | 27.50000 | 2.8867513 | 1.0000000 |
Pythium acrogynum | 3 | 23.055556 | 3.0642843 | 1.0000000 | 15.09259 | 0.7367234 | 1.0000000 |
Pythium adhaerens | 1 | 9.722222 | 1.2804923 | 1.0000000 | 27.77778 | 4.9378858 | 1.0000000 |
Pythium aff. diclinum | 3 | 78.703704 | 2.5013186 | 0.0323584 | 32.96296 | 5.2823367 | 1.0000000 |
Pythium aff. dictyosporum | 2 | 93.333333 | 1.1433239 | 0.0055791 | 85.13889 | 4.2225286 | 0.0165204 |
Pythium aff. dissotocum | 3 | 50.462963 | 5.1179761 | 1.0000000 | 27.31481 | 2.5139423 | 1.0000000 |
Pythium aff. hypogynum | 1 | 18.888889 | 3.4638789 | 1.0000000 | 28.05556 | 1.1620278 | 1.0000000 |
Pythium aff. iwayamai | 1 | 15.555556 | 2.5609846 | 1.0000000 | 36.38889 | 4.1481068 | 1.0000000 |
Pythium aff. perplexum | 3 | 43.703704 | 7.5994948 | 1.0000000 | 39.25926 | 7.0278937 | 1.0000000 |
Pythium aff. torulosum | 3 | 50.740741 | 7.2744024 | 1.0000000 | 38.98148 | 4.4040484 | 1.0000000 |
Pythium amasculinum | 3 | 18.888889 | 1.2612269 | 1.0000000 | 14.72222 | 0.5867321 | 1.0000000 |
Pythium angustatum | 1 | 12.500000 | 0.7216878 | 1.0000000 | 28.05556 | 6.3571069 | 1.0000000 |
Pythium aphanidermatum | 3 | 53.240741 | 3.8230418 | 1.0000000 | 99.90741 | 0.0925926 | 0.0002549 |
Pythium aristosporum | 3 | 27.777778 | 2.5989442 | 1.0000000 | 17.87037 | 1.0048290 | 1.0000000 |
Pythium arrhenomanes | 3 | 27.407407 | 3.0267136 | 1.0000000 | 19.90741 | 1.4524851 | 1.0000000 |
Pythium attrantheridium | 3 | 25.277778 | 2.5713928 | 1.0000000 | 26.20370 | 1.7519341 | 1.0000000 |
Pythium camurandrum | 1 | 6.111111 | 0.6054026 | 1.0000000 | 26.38889 | 1.5651983 | 1.0000000 |
Pythium carolinianum | 3 | 18.888889 | 1.3299458 | 1.0000000 | 18.14815 | 1.3712075 | 1.0000000 |
Pythium catenulatum | 3 | 11.388889 | 0.9180577 | 1.0000000 | 30.74074 | 2.0836103 | 1.0000000 |
Pythium chondricola | 1 | 8.611111 | 1.1866672 | 1.0000000 | 28.61111 | 3.1488289 | 1.0000000 |
Pythium coloratum | 3 | 71.666667 | 6.2418037 | 0.1085400 | 49.53704 | 7.2489279 | 1.0000000 |
Pythium conidiophorum | 3 | 57.870370 | 5.2377651 | 0.8304476 | 24.44444 | 1.9490178 | 1.0000000 |
Pythium contiguanum | 3 | 16.851852 | 2.5198379 | 1.0000000 | 16.38889 | 0.6847616 | 1.0000000 |
Pythium cryptoirregulare | 1 | 99.722222 | 0.2777778 | 0.0183095 | 95.55556 | 1.0015420 | 0.0210676 |
Pythium glomeratum | 3 | 20.740741 | 1.4047058 | 1.0000000 | 18.05556 | 0.7704169 | 1.0000000 |
Pythium heterothallicum | 3 | 30.277778 | 3.5161748 | 1.0000000 | 24.25926 | 1.2361398 | 1.0000000 |
Pythium hydnosporum | 2 | 15.833333 | 1.7850139 | 1.0000000 | 31.80556 | 3.4347653 | 1.0000000 |
Pythium hypogynum | 3 | 16.203704 | 1.3567021 | 1.0000000 | 16.20370 | 0.8157370 | 1.0000000 |
Pythium inflatum | 3 | 30.648148 | 2.6873947 | 1.0000000 | 18.42593 | 0.6136527 | 1.0000000 |
Pythium intermedium | 3 | 83.055556 | 4.7803114 | 0.0154431 | 53.42593 | 6.6427833 | 1.0000000 |
Pythium irregulare | 3 | 98.888889 | 0.4492264 | 0.0006489 | 80.46296 | 3.5305873 | 0.0265826 |
Pythium kashmirense | 3 | 18.796296 | 1.6525598 | 1.0000000 | 16.01852 | 0.7923609 | 1.0000000 |
Pythium kunmingense | 2 | 100.000000 | 0.0000000 | 0.0016134 | 89.30556 | 1.4962583 | 0.0073752 |
Pythium litorale | 1 | 19.166667 | 1.9543399 | 1.0000000 | 40.83333 | 4.8947251 | 1.0000000 |
Pythium longandrum | 3 | 17.592593 | 1.0204592 | 1.0000000 | 16.48148 | 0.7579030 | 1.0000000 |
Pythium longisporangium | 3 | 18.240741 | 2.4343767 | 1.0000000 | 15.00000 | 1.1935248 | 1.0000000 |
Pythium lutarium | 3 | 62.685185 | 6.5015968 | 0.4077599 | 49.25926 | 6.4353773 | 1.0000000 |
Pythium middletonii | 3 | 40.277778 | 6.1792049 | 1.0000000 | 29.07407 | 4.3957296 | 1.0000000 |
Pythium minus | 3 | 16.759259 | 1.4360465 | 1.0000000 | 16.29630 | 1.2824865 | 1.0000000 |
Pythium monospermum | 2 | 10.138889 | 0.8918710 | 1.0000000 | 13.61111 | 0.7622159 | 1.0000000 |
Pythium nagaii | 3 | 19.629630 | 1.2208401 | 1.0000000 | 14.44444 | 0.5555556 | 1.0000000 |
Pythium nodosum | 3 | 17.870370 | 1.5138470 | 1.0000000 | 17.03704 | 0.4999472 | 1.0000000 |
Pythium nunn | 3 | 16.944444 | 1.5975706 | 1.0000000 | 17.22222 | 0.9277048 | 1.0000000 |
Pythium oligandrum | 3 | 20.462963 | 1.6235723 | 1.0000000 | 15.27778 | 0.8153327 | 1.0000000 |
Pythium oopapillum | 3 | 51.388889 | 4.6976485 | 1.0000000 | 25.27778 | 1.8067879 | 1.0000000 |
Pythium orthogonon | 3 | 15.740741 | 1.5551061 | 1.0000000 | 18.05556 | 0.9277048 | 1.0000000 |
Pythium pachycaule | 3 | 12.870370 | 0.8193670 | 1.0000000 | 14.16667 | 0.5967624 | 1.0000000 |
Pythium paroecandrum | 3 | 93.981482 | 1.6357129 | 0.0017896 | 49.25926 | 4.3686407 | 1.0000000 |
Pythium periilum | 3 | 13.333333 | 1.0162497 | 1.0000000 | 20.74074 | 2.0096580 | 1.0000000 |
Pythium periplocum | 3 | 44.629630 | 7.5434446 | 1.0000000 | 42.87037 | 7.9121149 | 1.0000000 |
Pythium perplexum | 3 | 28.703704 | 1.4082225 | 1.0000000 | 15.27778 | 0.4872545 | 1.0000000 |
Pythium pleroticum | 3 | 21.666667 | 1.8149820 | 1.0000000 | 16.66667 | 0.4992872 | 1.0000000 |
Pythium pyrilobum | 1 | 35.000000 | 2.7003086 | 1.0000000 | 26.66667 | 2.4650332 | 1.0000000 |
Pythium rhizosaccharum | 3 | 15.000000 | 0.5661385 | 1.0000000 | 17.40741 | 0.8799107 | 1.0000000 |
Pythium rostratifingens | 3 | 17.685185 | 0.7539772 | 1.0000000 | 16.38889 | 0.5867321 | 1.0000000 |
Pythium sp. balticum | 3 | 41.666667 | 3.5656241 | 1.0000000 | 16.66667 | 0.7308817 | 1.0000000 |
Pythium spinosum | 3 | 80.555556 | 4.1179488 | 0.0229640 | 44.72222 | 6.9993556 | 1.0000000 |
Pythium sterilum | 1 | 30.000000 | 6.3873790 | 1.0000000 | 45.27778 | 4.2378184 | 1.0000000 |
Pythium sylvaticum | 3 | 99.444444 | 0.2436272 | 0.0005770 | 74.44444 | 2.6363573 | 0.0826669 |
Pythium tardicrescens | 3 | 42.129630 | 7.4484263 | 1.0000000 | 45.37037 | 7.4889564 | 1.0000000 |
Pythium terrestris | 1 | 99.166667 | 0.5892557 | 0.0207277 | 77.77778 | 3.4218569 | 0.2702305 |
Pythium torulosum | 3 | 29.537037 | 2.9988039 | 1.0000000 | 17.68519 | 0.7420750 | 1.0000000 |
Pythium ultimum | 3 | 99.166667 | 0.2983812 | 0.0006120 | 99.25926 | 0.3217766 | 0.0002303 |
Pythium ultimum var. sporangiiferum | 3 | 96.481482 | 1.0444131 | 0.0010731 | 98.05556 | 0.7227152 | 0.0006017 |
Pythium ultimum var. ultimum | 3 | 99.814815 | 0.1284028 | 0.0005333 | 99.62963 | 0.2194148 | 0.0004146 |
Pythium vanterpoolii | 3 | 28.703704 | 3.2723328 | 1.0000000 | 14.07407 | 0.7565967 | 1.0000000 |