Análisis de Diseño Factorial
Thomas Jimenez Uribe
Abril 09 de 2025
Problema a analizar
Se desea probar el efecto de factores fisico-químicos (hormonales y luminosidad) sobre la micropopagación in vitro de aguacate.
Analisis de resultados
Se llevó a cabo un análisis estadístico de tipo ANOVA factorial con el objetivo de evaluar el efecto de dos factores fisicoquímicos —el tipo de medio de cultivo (Factor A) y el tipo de bacteria (Factor B)— sobre la Concentración Mínima Inhibitoria (CMI)
Fuente de los datos: Suministrados por Vivian Castañeda.
Lectura de datos
library(readxl)
MRANOVA <- read_excel("C:/Users/thoma/Dropbox/My PC (LAPTOP-VP55P98S)/Downloads/Rstudio/CMI_AF.xlsx", col_types = c("text", "text", "numeric","numeric"))
View(MRANOVA)
attach(MRANOVA)
names(MRANOVA)## [1] "Medio" "Bacteria" "Replica" "CMI"str(MRANOVA)## tibble [35 × 4] (S3: tbl_df/tbl/data.frame)
## $ Medio : chr [1:35] "Sabouraud" "Sabouraud" "Sabouraud" "Sabouraud" ...
## $ Bacteria: chr [1:35] "Streptococcus pyogenes" "Streptococcus pyogenes" "Streptococcus pyogenes" "Enterobacter cloacae" ...
## $ Replica : num [1:35] 1 2 3 1 2 3 2 3 1 2 ...
## $ CMI : num [1:35] 0.75 0.58 0.58 0.62 0.41 0.43 0.61 0.46 1.28 1.08 ...Cambio de variables
FactorA <- factor(Medio)
FactorB <- factor(Bacteria)
Respuesta_CMI <- MRANOVA$CMIDiagramas Boxplot
library(ggplot2)## Warning: package 'ggplot2' was built under R version 4.3.3library(gridExtra)## Warning: package 'gridExtra' was built under R version 4.3.3p1 <- ggplot(data = MRANOVA, aes(x = Medio, y = CMI)) +
geom_boxplot() + theme_bw()
p2 <- ggplot(data = MRANOVA, aes(x = Bacteria, y = CMI)) +
geom_boxplot() + theme_bw()
p3 <- ggplot(data = MRANOVA, aes(x = Medio, y = CMI, colour = Bacteria)) +
geom_boxplot() + theme_bw()
grid.arrange(p1, p2, ncol = 2)
p3
Analisis
El medio de cultivo tiene un efecto altamente significativo sobre la CMI (p < 0.001), lo que indica que los diferentes medios utilizados generan diferencias claras en la respuesta del sistema.
El tipo de bacteria no presentó un efecto significativo (p = 0.156), lo que sugiere que la variación en este factor no influye de manera importante en la respuesta medida.
No se observó interacción significativa entre medio y bacteria (p = 0.477), lo cual implica que el efecto del medio es consistente independientemente del tipo de bacteria utilizado.
Cálculo de la tabla ANOVA
Modelo <- lm(CMI ~ (FactorA + FactorB)^2)
ANOVA <- aov(Modelo)
summary(ANOVA)## Df Sum Sq Mean Sq F value Pr(>F)
## FactorA 3 1.4788 0.4929 24.908 2.08e-07 ***
## FactorB 2 0.0799 0.0400 2.019 0.156
## FactorA:FactorB 6 0.1132 0.0189 0.954 0.477
## Residuals 23 0.4552 0.0198
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Modelo <- lm(CMI ~ (FactorA + FactorB + FactorA:FactorB))
ANOVA <- aov(Modelo)
summary(ANOVA)## Df Sum Sq Mean Sq F value Pr(>F)
## FactorA 3 1.4788 0.4929 24.908 2.08e-07 ***
## FactorB 2 0.0799 0.0400 2.019 0.156
## FactorA:FactorB 6 0.1132 0.0189 0.954 0.477
## Residuals 23 0.4552 0.0198
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1summary(Modelo)##
## Call:
## lm(formula = CMI ~ (FactorA + FactorB + FactorA:FactorB))
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.18333 -0.07833 -0.03667 0.09500 0.24667
##
## Coefficients:
## Estimate Std. Error t value
## (Intercept) 0.99333 0.08122 12.230
## FactorAMalta -0.28333 0.11486 -2.467
## FactorAPDB -0.02000 0.11486 -0.174
## FactorASabouraud -0.50667 0.11486 -4.411
## FactorBPseudomonas aeruginosa 0.20000 0.11486 1.741
## FactorBStreptococcus pyogenes 0.17333 0.11486 1.509
## FactorAMalta:FactorBPseudomonas aeruginosa -0.05000 0.16244 -0.308
## FactorAPDB:FactorBPseudomonas aeruginosa -0.32000 0.16244 -1.970
## FactorASabouraud:FactorBPseudomonas aeruginosa -0.15167 0.17230 -0.880
## FactorAMalta:FactorBStreptococcus pyogenes -0.10667 0.16244 -0.657
## FactorAPDB:FactorBStreptococcus pyogenes -0.10667 0.16244 -0.657
## FactorASabouraud:FactorBStreptococcus pyogenes -0.02333 0.16244 -0.144
## Pr(>|t|)
## (Intercept) 1.51e-11 ***
## FactorAMalta 0.021514 *
## FactorAPDB 0.863295
## FactorASabouraud 0.000202 ***
## FactorBPseudomonas aeruginosa 0.095012 .
## FactorBStreptococcus pyogenes 0.144906
## FactorAMalta:FactorBPseudomonas aeruginosa 0.761003
## FactorAPDB:FactorBPseudomonas aeruginosa 0.061003 .
## FactorASabouraud:FactorBPseudomonas aeruginosa 0.387819
## FactorAMalta:FactorBStreptococcus pyogenes 0.517926
## FactorAPDB:FactorBStreptococcus pyogenes 0.517926
## FactorASabouraud:FactorBStreptococcus pyogenes 0.887035
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.1407 on 23 degrees of freedom
## Multiple R-squared: 0.786, Adjusted R-squared: 0.6837
## F-statistic: 7.68 on 11 and 23 DF, p-value: 2.177e-05Interacciones y efectos principales
library(phia)## Warning: package 'phia' was built under R version 4.3.3## Loading required package: car## Loading required package: carDataGrafica <- interactionMeans(Modelo)
plot(Grafica)
Diagnóstico del modelo
##Analisis
En términos del tamaño del efecto, se determino que el medio de cultivo explica el 69.5% de la variabilidad total observada en la CMI, siendo el factor con mayor efecto. Por el contrario, la bacteria y la interacción medio-bacteria explicaron solamente el 3.8% y 5.3% de la variabilidad.
El modelo ajustado cumplió con los supuestos fundamentales de ANOVA: los residuos presentaron una distribución normal (p = 0.0502) y se observó homogeneidad de varianzas entre los grupos (p = 0.270).
Normalidad de los residuos
shapiro.test(rstandard(Modelo))##
## Shapiro-Wilk normality test
##
## data: rstandard(Modelo)
## W = 0.93782, p-value = 0.04804Homocedasticidad
library(car)
ncvTest(Modelo)## Non-constant Variance Score Test
## Variance formula: ~ fitted.values
## Chisquare = 1.97945, Df = 1, p = 0.15945Gráficos de diagnóstico
par(mfrow = c(1,2))
plot(Modelo, which = 1:4)
par(mfrow = c(1,1))Tamaño del efecto (η²)
library(lsr)## Warning: package 'lsr' was built under R version 4.3.3etaSquared(ANOVA)## eta.sq eta.sq.part
## FactorA 0.68973610 0.7632162
## FactorB 0.03756980 0.1493492
## FactorA:FactorB 0.05323227 0.1992082Analisis
Se realizaron pruebas post-hoc mediante el test de Tukey. Estas evidenciaron diferencias significativas entre los distintos medios de cultivo, reforzando la conclusión de que el tipo de medio es determinante en la respuesta experimental. En contraste, no se detectaron diferencias significativas entre los niveles del factor bacteria
Pruebas a posteriori (Tukey)
library(agricolae)
TukeyHSD(ANOVA)## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Modelo)
##
## $FactorA
## diff lwr upr p adj
## Malta-Czapeck -0.3355556 -0.51907410 -0.15203701 0.0002211
## PDB-Czapeck -0.1622222 -0.34574077 0.02129632 0.0962246
## Sabouraud-Czapeck -0.5627778 -0.75194437 -0.37361119 0.0000002
## PDB-Malta 0.1733333 -0.01018521 0.35685188 0.0688078
## Sabouraud-Malta -0.2272222 -0.41638881 -0.03805563 0.0145762
## Sabouraud-PDB -0.4005556 -0.58972214 -0.21138897 0.0000319
##
## $FactorB
## diff lwr upr
## Pseudomonas aeruginosa-Enterobacter cloacae 0.07210859 -0.07495287 0.2191700
## Streptococcus pyogenes-Enterobacter cloacae 0.11416667 -0.02966227 0.2579956
## Streptococcus pyogenes-Pseudomonas aeruginosa 0.04205808 -0.10500337 0.1891195
## p adj
## Pseudomonas aeruginosa-Enterobacter cloacae 0.4492391
## Streptococcus pyogenes-Enterobacter cloacae 0.1378224
## Streptococcus pyogenes-Pseudomonas aeruginosa 0.7564832
##
## $`FactorA:FactorB`
## diff
## Malta:Enterobacter cloacae-Czapeck:Enterobacter cloacae -0.283333333
## PDB:Enterobacter cloacae-Czapeck:Enterobacter cloacae -0.020000000
## Sabouraud:Enterobacter cloacae-Czapeck:Enterobacter cloacae -0.506666667
## Czapeck:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae 0.200000000
## Malta:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae -0.133333333
## PDB:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae -0.140000000
## Sabouraud:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae -0.458333333
## Czapeck:Streptococcus pyogenes-Czapeck:Enterobacter cloacae 0.173333333
## Malta:Streptococcus pyogenes-Czapeck:Enterobacter cloacae -0.216666667
## PDB:Streptococcus pyogenes-Czapeck:Enterobacter cloacae 0.046666667
## Sabouraud:Streptococcus pyogenes-Czapeck:Enterobacter cloacae -0.356666667
## PDB:Enterobacter cloacae-Malta:Enterobacter cloacae 0.263333333
## Sabouraud:Enterobacter cloacae-Malta:Enterobacter cloacae -0.223333333
## Czapeck:Pseudomonas aeruginosa-Malta:Enterobacter cloacae 0.483333333
## Malta:Pseudomonas aeruginosa-Malta:Enterobacter cloacae 0.150000000
## PDB:Pseudomonas aeruginosa-Malta:Enterobacter cloacae 0.143333333
## Sabouraud:Pseudomonas aeruginosa-Malta:Enterobacter cloacae -0.175000000
## Czapeck:Streptococcus pyogenes-Malta:Enterobacter cloacae 0.456666667
## Malta:Streptococcus pyogenes-Malta:Enterobacter cloacae 0.066666667
## PDB:Streptococcus pyogenes-Malta:Enterobacter cloacae 0.330000000
## Sabouraud:Streptococcus pyogenes-Malta:Enterobacter cloacae -0.073333333
## Sabouraud:Enterobacter cloacae-PDB:Enterobacter cloacae -0.486666667
## Czapeck:Pseudomonas aeruginosa-PDB:Enterobacter cloacae 0.220000000
## Malta:Pseudomonas aeruginosa-PDB:Enterobacter cloacae -0.113333333
## PDB:Pseudomonas aeruginosa-PDB:Enterobacter cloacae -0.120000000
## Sabouraud:Pseudomonas aeruginosa-PDB:Enterobacter cloacae -0.438333333
## Czapeck:Streptococcus pyogenes-PDB:Enterobacter cloacae 0.193333333
## Malta:Streptococcus pyogenes-PDB:Enterobacter cloacae -0.196666667
## PDB:Streptococcus pyogenes-PDB:Enterobacter cloacae 0.066666667
## Sabouraud:Streptococcus pyogenes-PDB:Enterobacter cloacae -0.336666667
## Czapeck:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae 0.706666667
## Malta:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae 0.373333333
## PDB:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae 0.366666667
## Sabouraud:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae 0.048333333
## Czapeck:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae 0.680000000
## Malta:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae 0.290000000
## PDB:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae 0.553333333
## Sabouraud:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae 0.150000000
## Malta:Pseudomonas aeruginosa-Czapeck:Pseudomonas aeruginosa -0.333333333
## PDB:Pseudomonas aeruginosa-Czapeck:Pseudomonas aeruginosa -0.340000000
## Sabouraud:Pseudomonas aeruginosa-Czapeck:Pseudomonas aeruginosa -0.658333333
## Czapeck:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa -0.026666667
## Malta:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa -0.416666667
## PDB:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa -0.153333333
## Sabouraud:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa -0.556666667
## PDB:Pseudomonas aeruginosa-Malta:Pseudomonas aeruginosa -0.006666667
## Sabouraud:Pseudomonas aeruginosa-Malta:Pseudomonas aeruginosa -0.325000000
## Czapeck:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa 0.306666667
## Malta:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa -0.083333333
## PDB:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa 0.180000000
## Sabouraud:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa -0.223333333
## Sabouraud:Pseudomonas aeruginosa-PDB:Pseudomonas aeruginosa -0.318333333
## Czapeck:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa 0.313333333
## Malta:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa -0.076666667
## PDB:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa 0.186666667
## Sabouraud:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa -0.216666667
## Czapeck:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa 0.631666667
## Malta:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa 0.241666667
## PDB:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa 0.505000000
## Sabouraud:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa 0.101666667
## Malta:Streptococcus pyogenes-Czapeck:Streptococcus pyogenes -0.390000000
## PDB:Streptococcus pyogenes-Czapeck:Streptococcus pyogenes -0.126666667
## Sabouraud:Streptococcus pyogenes-Czapeck:Streptococcus pyogenes -0.530000000
## PDB:Streptococcus pyogenes-Malta:Streptococcus pyogenes 0.263333333
## Sabouraud:Streptococcus pyogenes-Malta:Streptococcus pyogenes -0.140000000
## Sabouraud:Streptococcus pyogenes-PDB:Streptococcus pyogenes -0.403333333
## lwr
## Malta:Enterobacter cloacae-Czapeck:Enterobacter cloacae -0.69924239
## PDB:Enterobacter cloacae-Czapeck:Enterobacter cloacae -0.43590906
## Sabouraud:Enterobacter cloacae-Czapeck:Enterobacter cloacae -0.92257572
## Czapeck:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae -0.21590906
## Malta:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae -0.54924239
## PDB:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae -0.55590906
## Sabouraud:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae -0.92333379
## Czapeck:Streptococcus pyogenes-Czapeck:Enterobacter cloacae -0.24257572
## Malta:Streptococcus pyogenes-Czapeck:Enterobacter cloacae -0.63257572
## PDB:Streptococcus pyogenes-Czapeck:Enterobacter cloacae -0.36924239
## Sabouraud:Streptococcus pyogenes-Czapeck:Enterobacter cloacae -0.77257572
## PDB:Enterobacter cloacae-Malta:Enterobacter cloacae -0.15257572
## Sabouraud:Enterobacter cloacae-Malta:Enterobacter cloacae -0.63924239
## Czapeck:Pseudomonas aeruginosa-Malta:Enterobacter cloacae 0.06742428
## Malta:Pseudomonas aeruginosa-Malta:Enterobacter cloacae -0.26590906
## PDB:Pseudomonas aeruginosa-Malta:Enterobacter cloacae -0.27257572
## Sabouraud:Pseudomonas aeruginosa-Malta:Enterobacter cloacae -0.64000046
## Czapeck:Streptococcus pyogenes-Malta:Enterobacter cloacae 0.04075761
## Malta:Streptococcus pyogenes-Malta:Enterobacter cloacae -0.34924239
## PDB:Streptococcus pyogenes-Malta:Enterobacter cloacae -0.08590906
## Sabouraud:Streptococcus pyogenes-Malta:Enterobacter cloacae -0.48924239
## Sabouraud:Enterobacter cloacae-PDB:Enterobacter cloacae -0.90257572
## Czapeck:Pseudomonas aeruginosa-PDB:Enterobacter cloacae -0.19590906
## Malta:Pseudomonas aeruginosa-PDB:Enterobacter cloacae -0.52924239
## PDB:Pseudomonas aeruginosa-PDB:Enterobacter cloacae -0.53590906
## Sabouraud:Pseudomonas aeruginosa-PDB:Enterobacter cloacae -0.90333379
## Czapeck:Streptococcus pyogenes-PDB:Enterobacter cloacae -0.22257572
## Malta:Streptococcus pyogenes-PDB:Enterobacter cloacae -0.61257572
## PDB:Streptococcus pyogenes-PDB:Enterobacter cloacae -0.34924239
## Sabouraud:Streptococcus pyogenes-PDB:Enterobacter cloacae -0.75257572
## Czapeck:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae 0.29075761
## Malta:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae -0.04257572
## PDB:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae -0.04924239
## Sabouraud:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae -0.41666713
## Czapeck:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae 0.26409094
## Malta:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae -0.12590906
## PDB:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae 0.13742428
## Sabouraud:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae -0.26590906
## Malta:Pseudomonas aeruginosa-Czapeck:Pseudomonas aeruginosa -0.74924239
## PDB:Pseudomonas aeruginosa-Czapeck:Pseudomonas aeruginosa -0.75590906
## Sabouraud:Pseudomonas aeruginosa-Czapeck:Pseudomonas aeruginosa -1.12333379
## Czapeck:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa -0.44257572
## Malta:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa -0.83257572
## PDB:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa -0.56924239
## Sabouraud:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa -0.97257572
## PDB:Pseudomonas aeruginosa-Malta:Pseudomonas aeruginosa -0.42257572
## Sabouraud:Pseudomonas aeruginosa-Malta:Pseudomonas aeruginosa -0.79000046
## Czapeck:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa -0.10924239
## Malta:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa -0.49924239
## PDB:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa -0.23590906
## Sabouraud:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa -0.63924239
## Sabouraud:Pseudomonas aeruginosa-PDB:Pseudomonas aeruginosa -0.78333379
## Czapeck:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa -0.10257572
## Malta:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa -0.49257572
## PDB:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa -0.22924239
## Sabouraud:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa -0.63257572
## Czapeck:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa 0.16666621
## Malta:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa -0.22333379
## PDB:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa 0.03999954
## Sabouraud:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa -0.36333379
## Malta:Streptococcus pyogenes-Czapeck:Streptococcus pyogenes -0.80590906
## PDB:Streptococcus pyogenes-Czapeck:Streptococcus pyogenes -0.54257572
## Sabouraud:Streptococcus pyogenes-Czapeck:Streptococcus pyogenes -0.94590906
## PDB:Streptococcus pyogenes-Malta:Streptococcus pyogenes -0.15257572
## Sabouraud:Streptococcus pyogenes-Malta:Streptococcus pyogenes -0.55590906
## Sabouraud:Streptococcus pyogenes-PDB:Streptococcus pyogenes -0.81924239
## upr
## Malta:Enterobacter cloacae-Czapeck:Enterobacter cloacae 0.1325757229
## PDB:Enterobacter cloacae-Czapeck:Enterobacter cloacae 0.3959090562
## Sabouraud:Enterobacter cloacae-Czapeck:Enterobacter cloacae -0.0907576104
## Czapeck:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae 0.6159090562
## Malta:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae 0.2825757229
## PDB:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae 0.2759090562
## Sabouraud:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae 0.0066671277
## Czapeck:Streptococcus pyogenes-Czapeck:Enterobacter cloacae 0.5892423896
## Malta:Streptococcus pyogenes-Czapeck:Enterobacter cloacae 0.1992423896
## PDB:Streptococcus pyogenes-Czapeck:Enterobacter cloacae 0.4625757229
## Sabouraud:Streptococcus pyogenes-Czapeck:Enterobacter cloacae 0.0592423896
## PDB:Enterobacter cloacae-Malta:Enterobacter cloacae 0.6792423896
## Sabouraud:Enterobacter cloacae-Malta:Enterobacter cloacae 0.1925757229
## Czapeck:Pseudomonas aeruginosa-Malta:Enterobacter cloacae 0.8992423896
## Malta:Pseudomonas aeruginosa-Malta:Enterobacter cloacae 0.5659090562
## PDB:Pseudomonas aeruginosa-Malta:Enterobacter cloacae 0.5592423896
## Sabouraud:Pseudomonas aeruginosa-Malta:Enterobacter cloacae 0.2900004611
## Czapeck:Streptococcus pyogenes-Malta:Enterobacter cloacae 0.8725757229
## Malta:Streptococcus pyogenes-Malta:Enterobacter cloacae 0.4825757229
## PDB:Streptococcus pyogenes-Malta:Enterobacter cloacae 0.7459090562
## Sabouraud:Streptococcus pyogenes-Malta:Enterobacter cloacae 0.3425757229
## Sabouraud:Enterobacter cloacae-PDB:Enterobacter cloacae -0.0707576104
## Czapeck:Pseudomonas aeruginosa-PDB:Enterobacter cloacae 0.6359090562
## Malta:Pseudomonas aeruginosa-PDB:Enterobacter cloacae 0.3025757229
## PDB:Pseudomonas aeruginosa-PDB:Enterobacter cloacae 0.2959090562
## Sabouraud:Pseudomonas aeruginosa-PDB:Enterobacter cloacae 0.0266671277
## Czapeck:Streptococcus pyogenes-PDB:Enterobacter cloacae 0.6092423896
## Malta:Streptococcus pyogenes-PDB:Enterobacter cloacae 0.2192423896
## PDB:Streptococcus pyogenes-PDB:Enterobacter cloacae 0.4825757229
## Sabouraud:Streptococcus pyogenes-PDB:Enterobacter cloacae 0.0792423896
## Czapeck:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae 1.1225757229
## Malta:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae 0.7892423896
## PDB:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae 0.7825757229
## Sabouraud:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae 0.5133337944
## Czapeck:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae 1.0959090562
## Malta:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae 0.7059090562
## PDB:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae 0.9692423896
## Sabouraud:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae 0.5659090562
## Malta:Pseudomonas aeruginosa-Czapeck:Pseudomonas aeruginosa 0.0825757229
## PDB:Pseudomonas aeruginosa-Czapeck:Pseudomonas aeruginosa 0.0759090562
## Sabouraud:Pseudomonas aeruginosa-Czapeck:Pseudomonas aeruginosa -0.1933328723
## Czapeck:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa 0.3892423896
## Malta:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa -0.0007576104
## PDB:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa 0.2625757229
## Sabouraud:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa -0.1407576104
## PDB:Pseudomonas aeruginosa-Malta:Pseudomonas aeruginosa 0.4092423896
## Sabouraud:Pseudomonas aeruginosa-Malta:Pseudomonas aeruginosa 0.1400004611
## Czapeck:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa 0.7225757229
## Malta:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa 0.3325757229
## PDB:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa 0.5959090562
## Sabouraud:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa 0.1925757229
## Sabouraud:Pseudomonas aeruginosa-PDB:Pseudomonas aeruginosa 0.1466671277
## Czapeck:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa 0.7292423896
## Malta:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa 0.3392423896
## PDB:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa 0.6025757229
## Sabouraud:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa 0.1992423896
## Czapeck:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa 1.0966671277
## Malta:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa 0.7066671277
## PDB:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa 0.9700004611
## Sabouraud:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa 0.5666671277
## Malta:Streptococcus pyogenes-Czapeck:Streptococcus pyogenes 0.0259090562
## PDB:Streptococcus pyogenes-Czapeck:Streptococcus pyogenes 0.2892423896
## Sabouraud:Streptococcus pyogenes-Czapeck:Streptococcus pyogenes -0.1140909438
## PDB:Streptococcus pyogenes-Malta:Streptococcus pyogenes 0.6792423896
## Sabouraud:Streptococcus pyogenes-Malta:Streptococcus pyogenes 0.2759090562
## Sabouraud:Streptococcus pyogenes-PDB:Streptococcus pyogenes 0.0125757229
## p adj
## Malta:Enterobacter cloacae-Czapeck:Enterobacter cloacae 0.4049989
## PDB:Enterobacter cloacae-Czapeck:Enterobacter cloacae 1.0000000
## Sabouraud:Enterobacter cloacae-Czapeck:Enterobacter cloacae 0.0085768
## Czapeck:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae 0.8317320
## Malta:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae 0.9872324
## PDB:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae 0.9816077
## Sabouraud:Pseudomonas aeruginosa-Czapeck:Enterobacter cloacae 0.0557984
## Czapeck:Streptococcus pyogenes-Czapeck:Enterobacter cloacae 0.9232079
## Malta:Streptococcus pyogenes-Czapeck:Enterobacter cloacae 0.7558132
## PDB:Streptococcus pyogenes-Czapeck:Enterobacter cloacae 0.9999994
## Sabouraud:Streptococcus pyogenes-Czapeck:Enterobacter cloacae 0.1410838
## PDB:Enterobacter cloacae-Malta:Enterobacter cloacae 0.5076182
## Sabouraud:Enterobacter cloacae-Malta:Enterobacter cloacae 0.7224213
## Czapeck:Pseudomonas aeruginosa-Malta:Enterobacter cloacae 0.0136689
## Malta:Pseudomonas aeruginosa-Malta:Enterobacter cloacae 0.9698908
## PDB:Pseudomonas aeruginosa-Malta:Enterobacter cloacae 0.9781722
## Sabouraud:Pseudomonas aeruginosa-Malta:Enterobacter cloacae 0.9597692
## Czapeck:Streptococcus pyogenes-Malta:Enterobacter cloacae 0.0230714
## Malta:Streptococcus pyogenes-Malta:Enterobacter cloacae 0.9999753
## PDB:Streptococcus pyogenes-Malta:Enterobacter cloacae 0.2145536
## Sabouraud:Streptococcus pyogenes-Malta:Enterobacter cloacae 0.9999364
## Sabouraud:Enterobacter cloacae-PDB:Enterobacter cloacae 0.0127936
## Czapeck:Pseudomonas aeruginosa-PDB:Enterobacter cloacae 0.7392949
## Malta:Pseudomonas aeruginosa-PDB:Enterobacter cloacae 0.9965348
## PDB:Pseudomonas aeruginosa-PDB:Enterobacter cloacae 0.9944380
## Sabouraud:Pseudomonas aeruginosa-PDB:Enterobacter cloacae 0.0770521
## Czapeck:Streptococcus pyogenes-PDB:Enterobacter cloacae 0.8583668
## Malta:Streptococcus pyogenes-PDB:Enterobacter cloacae 0.8453442
## PDB:Streptococcus pyogenes-PDB:Enterobacter cloacae 0.9999753
## Sabouraud:Streptococcus pyogenes-PDB:Enterobacter cloacae 0.1938594
## Czapeck:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae 0.0001453
## Malta:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae 0.1067660
## PDB:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae 0.1195253
## Sabouraud:Pseudomonas aeruginosa-Sabouraud:Enterobacter cloacae 0.9999997
## Czapeck:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae 0.0002493
## Malta:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae 0.3731367
## PDB:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae 0.0033279
## Sabouraud:Streptococcus pyogenes-Sabouraud:Enterobacter cloacae 0.9698908
## Malta:Pseudomonas aeruginosa-Czapeck:Pseudomonas aeruginosa 0.2040048
## PDB:Pseudomonas aeruginosa-Czapeck:Pseudomonas aeruginosa 0.1841116
## Sabouraud:Pseudomonas aeruginosa-Czapeck:Pseudomonas aeruginosa 0.0016087
## Czapeck:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa 1.0000000
## Malta:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa 0.0493044
## PDB:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa 0.9649829
## Sabouraud:Streptococcus pyogenes-Czapeck:Pseudomonas aeruginosa 0.0031088
## PDB:Pseudomonas aeruginosa-Malta:Pseudomonas aeruginosa 1.0000000
## Sabouraud:Pseudomonas aeruginosa-Malta:Pseudomonas aeruginosa 0.3699240
## Czapeck:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa 0.2999537
## Malta:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa 0.9997816
## PDB:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa 0.9041945
## Sabouraud:Streptococcus pyogenes-Malta:Pseudomonas aeruginosa 0.7224213
## Sabouraud:Pseudomonas aeruginosa-PDB:Pseudomonas aeruginosa 0.3982311
## Czapeck:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa 0.2734791
## Malta:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa 0.9999019
## PDB:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa 0.8825620
## Sabouraud:Streptococcus pyogenes-PDB:Pseudomonas aeruginosa 0.7558132
## Czapeck:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa 0.0026227
## Malta:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa 0.7583233
## PDB:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa 0.0254072
## Sabouraud:Streptococcus pyogenes-Sabouraud:Pseudomonas aeruginosa 0.9995055
## Malta:Streptococcus pyogenes-Czapeck:Streptococcus pyogenes 0.0799125
## PDB:Streptococcus pyogenes-Czapeck:Streptococcus pyogenes 0.9914205
## Sabouraud:Streptococcus pyogenes-Czapeck:Streptococcus pyogenes 0.0053525
## PDB:Streptococcus pyogenes-Malta:Streptococcus pyogenes 0.5076182
## Sabouraud:Streptococcus pyogenes-Malta:Streptococcus pyogenes 0.9816077
## Sabouraud:Streptococcus pyogenes-PDB:Streptococcus pyogenes 0.0629414plot(TukeyHSD(ANOVA))
outHSD_A <- HSD.test(ANOVA, "FactorA", console = TRUE)##
## Study: ANOVA ~ "FactorA"
##
## HSD Test for CMI
##
## Mean Square Error: 0.01979058
##
## FactorA, means
##
## CMI std r se Min Max Q25 Q50 Q75
## Czapeck 1.1177778 0.1809543 9 0.04689300 0.81 1.41 1.0600 1.11 1.2400
## Malta 0.7822222 0.1219403 9 0.04689300 0.63 1.03 0.7000 0.74 0.8500
## PDB 0.9555556 0.1479959 9 0.04689300 0.71 1.18 0.9000 0.93 1.0200
## Sabouraud 0.5550000 0.1147668 8 0.04973754 0.41 0.75 0.4525 0.58 0.6125
##
## Alpha: 0.05 ; DF Error: 23
## Critical Value of Studentized Range: 3.91356
##
## Groups according to probability of means differences and alpha level( 0.05 )
##
## Treatments with the same letter are not significantly different.
##
## CMI groups
## Czapeck 1.1177778 a
## PDB 0.9555556 ab
## Malta 0.7822222 b
## Sabouraud 0.5550000 coutHSD_B <- HSD.test(ANOVA, "FactorB", console = TRUE)##
## Study: ANOVA ~ "FactorB"
##
## HSD Test for CMI
##
## Mean Square Error: 0.01979058
##
## FactorB, means
##
## CMI std r se Min Max Q25 Q50
## Enterobacter cloacae 0.7908333 0.2561412 12 0.04061053 0.41 1.24 0.6275 0.790
## Pseudomonas aeruginosa 0.8900000 0.2651792 11 0.04241631 0.46 1.41 0.7050 0.920
## Streptococcus pyogenes 0.9050000 0.2356230 12 0.04061053 0.58 1.28 0.7300 0.915
## Q75
## Enterobacter cloacae 0.9075
## Pseudomonas aeruginosa 1.0450
## Streptococcus pyogenes 1.0950
##
## Alpha: 0.05 ; DF Error: 23
## Critical Value of Studentized Range: 3.541666
##
## Groups according to probability of means differences and alpha level( 0.05 )
##
## Treatments with the same letter are not significantly different.
##
## CMI groups
## Streptococcus pyogenes 0.9050000 a
## Pseudomonas aeruginosa 0.8900000 a
## Enterobacter cloacae 0.7908333 a