setwd("~/Google Drive/Agrosavia/colaboraciones/Laura")
datos2<-read.table("paez.csv", header=T, sep=',')
datos2$gen<-as.factor(datos2$gen)
datos2$forestal<-as.factor(datos2$forestal)
datos2$bloque<-as.factor(datos2$bloque)
attach(datos2)
library(ggplot2)
#Gráfica diámetro
ggplot(datos2, aes(semana, diam, group = gen, colour = gen)) +
facet_grid(~forestal) +
geom_smooth(method="lm", se=F) +
theme_classic() +
xlab ("Semana") +
ylab ("Diámetro") +
labs(colour = "Genotipo") +
theme_linedraw() +
theme(
plot.title = element_text(hjust = 0.5, size = 16),
strip.text = element_text(size = 16),
axis.title.y = element_text(size = 16),
axis.title.x = element_text(size = 16),
axis.text.x = element_text(size = 14),
axis.text.y = element_text(size = 14)
)
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 275 rows containing non-finite values (stat_smooth).
# Gráfica altura
ggplot(datos2, aes(semana, alt, group = gen, colour = gen)) +
facet_grid(~forestal) +
geom_smooth(method="lm", se=F) +
theme_classic() +
xlab ("Semana") +
ylab ("Altura") +
labs(colour = "Genotipo") +
theme_linedraw() +
theme(
plot.title = element_text(hjust = 0.5, size = 16),
strip.text = element_text(size = 16),
axis.title.y = element_text(size = 16),
axis.title.x = element_text(size = 16),
axis.text.x = element_text(size = 14),
axis.text.y = element_text(size = 14)
)
## `geom_smooth()` using formula 'y ~ x'
## Warning: Removed 275 rows containing non-finite values (stat_smooth).
# Anova general
aov.diam<-aov(diam~semana*forestal*gen+bloque)
aov.alt<-aov(alt~semana*forestal*gen+bloque)
#Análisis para diámetro
library(nlme)
fit.compsym.diam <- gls(diam ~ semana*forestal*gen+bloque, data=datos2, corr=corCompSymm(, form= ~ 1 | gen),na.action=na.exclude)
fit.ar1.diam <- gls(diam ~ semana*forestal*gen+bloque, data=datos2, corr=corAR1(, form= ~ 1 | gen), na.action=na.exclude)
fit.ar1het.diam <- gls(diam ~ semana*forestal*gen+bloque, data=datos2, corr=corAR1(, form= ~ 1 | gen), weights=varIdent(form = ~ 1 | semana), na.action=na.exclude)
anova(fit.compsym.diam, fit.ar1.diam, fit.ar1het.diam) #compares the models
## Model df AIC BIC logLik Test L.Ratio p-value
## fit.compsym.diam 1 34 2325.655 2483.765 -1128.828
## fit.ar1.diam 2 34 2313.326 2471.436 -1122.663
## fit.ar1het.diam 3 37 2312.321 2484.381 -1119.160 2 vs 3 7.005676 0.0717
anova(fit.ar1.diam)
## Denom. DF: 773
## numDF F-value p-value
## (Intercept) 1 9933.582 <.0001
## semana 1 219.131 <.0001
## forestal 2 14.401 <.0001
## gen 4 1.644 0.1612
## bloque 2 33.825 <.0001
## semana:forestal 2 5.243 0.0055
## semana:gen 4 0.284 0.8886
## forestal:gen 8 2.082 0.0352
## semana:forestal:gen 8 1.055 0.3929
anova(fit.ar1het.diam)
## Denom. DF: 773
## numDF F-value p-value
## (Intercept) 1 10072.937 <.0001
## semana 1 258.211 <.0001
## forestal 2 12.715 <.0001
## gen 4 1.532 0.1911
## bloque 2 35.498 <.0001
## semana:forestal 2 5.858 0.0030
## semana:gen 4 0.302 0.8768
## forestal:gen 8 1.939 0.0515
## semana:forestal:gen 8 1.092 0.3662
# Análisis para altura
fit.compsym.alt <- gls(alt ~ semana*forestal*gen+bloque, data=datos2, corr=corCompSymm(, form= ~ 1 | gen),na.action=na.exclude)
fit.ar1.alt <- gls(alt ~ semana*forestal*gen+bloque, data=datos2, corr=corAR1(, form= ~ 1 | gen), na.action=na.exclude)
fit.ar1het.alt <- gls(alt ~ semana*forestal*gen+bloque, data=datos2, corr=corAR1(, form= ~ 1 | gen), weights=varIdent(form = ~ 1 | semana), na.action=na.exclude)
anova(fit.compsym.alt, fit.ar1.alt, fit.ar1het.alt) #compares the models
## Model df AIC BIC logLik Test L.Ratio p-value
## fit.compsym.alt 1 34 7958.484 8116.593 -3945.242
## fit.ar1.alt 2 34 7941.956 8100.066 -3936.978
## fit.ar1het.alt 3 37 7878.555 8050.615 -3902.277 2 vs 3 69.40135 <.0001
anova(fit.ar1het.alt)
## Denom. DF: 773
## numDF F-value p-value
## (Intercept) 1 7690.972 <.0001
## semana 1 542.437 <.0001
## forestal 2 30.987 <.0001
## gen 4 6.351 <.0001
## bloque 2 23.493 <.0001
## semana:forestal 2 11.574 <.0001
## semana:gen 4 4.154 0.0025
## forestal:gen 8 2.108 0.0329
## semana:forestal:gen 8 1.871 0.0615
#Tukey diámetro
library(multcompView)
interac.tuk.diam<-TukeyHSD(aov.diam, "forestal:gen", ordered = TRUE)
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## forestal
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## gen
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## forestal, gen
fores.tuk.diam<-TukeyHSD(aov.diam, "forestal", ordered = TRUE)
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## forestal
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## gen
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## forestal, gen
gen.tuk.diam<-TukeyHSD(aov.diam, "gen", ordered = TRUE)
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## forestal
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## gen
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## forestal, gen
#Tukey altura
interac.tuk.alt<-TukeyHSD(aov.alt, "forestal:gen", ordered = TRUE)
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## forestal
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## gen
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## forestal, gen
fores.tuk.alt<-TukeyHSD(aov.alt, "forestal", ordered = TRUE)
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## forestal
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## gen
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## forestal, gen
gen.tuk.alt<-TukeyHSD(aov.alt, "gen", ordered = TRUE)
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## forestal
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## gen
## Warning in replications(paste("~", xx), data = mf): non-factors ignored: semana,
## forestal, gen
#Etiquetas Tukey diámetro
#Genotipos
generate_label_df_gen_diam <- function(gen.tuk.diam, variable){
Tukey.levels <- gen.tuk.diam[[variable]][,4]
Tukey.labels <- data.frame(multcompLetters(Tukey.levels)['Letters'])
Tukey.labels$treatment=rownames(Tukey.labels)
Tukey.labels=Tukey.labels[order(Tukey.labels$treatment) , ]
return(Tukey.labels)
}
labels.gen.diam <- generate_label_df_gen_diam(gen.tuk.diam, "gen")
labels.gen.diam
## Letters treatment
## CCN51 a CCN51
## TCS01 a TCS01
## TCS06 a TCS06
## TCS13 a TCS13
## TCS19 a TCS19
# Forestal
generate_label_df_forestal_diam <- function(fores.tuk.diam, variable){
Tukey.levels <- fores.tuk.diam[[variable]][,2]
Tukey.labels <- data.frame(multcompLetters(Tukey.levels)['Letters'])
Tukey.labels$treatment=rownames(Tukey.labels)
Tukey.labels=Tukey.labels[order(Tukey.labels$treatment) , ]
return(Tukey.labels)
}
labels.forestal.diam <- generate_label_df_forestal_diam(fores.tuk.diam, "forestal")
labels.forestal.diam
## Letters treatment
## Abarco a Abarco
## Roble ab Roble
## Terminalia b Terminalia
# Interacción Forestal:Genotipo
generate_label_df_interac_diam <- function(interac.tuk.diam, variable){
Tukey.levels <- interac.tuk.diam[[variable]][,4]
Tukey.labels <- data.frame(multcompLetters(Tukey.levels)['Letters'])
Tukey.labels$treatment=rownames(Tukey.labels)
Tukey.labels=Tukey.labels[order(Tukey.labels$treatment) , ]
return(Tukey.labels)
}
labels.interac.diam <- generate_label_df_interac_diam(interac.tuk.diam, "forestal:gen")
labels.interac.diam
## Letters treatment
## Abarco:CCN51 ac Abarco:CCN51
## Abarco:TCS01 ac Abarco:TCS01
## Abarco:TCS06 ac Abarco:TCS06
## Abarco:TCS13 ac Abarco:TCS13
## Abarco:TCS19 ac Abarco:TCS19
## Roble:CCN51 ac Roble:CCN51
## Roble:TCS01 abc Roble:TCS01
## Roble:TCS06 ab Roble:TCS06
## Roble:TCS13 b Roble:TCS13
## Roble:TCS19 ab Roble:TCS19
## Terminalia:CCN51 ac Terminalia:CCN51
## Terminalia:TCS01 ac Terminalia:TCS01
## Terminalia:TCS06 c Terminalia:TCS06
## Terminalia:TCS13 ac Terminalia:TCS13
## Terminalia:TCS19 c Terminalia:TCS19
#Etiquetas Tukey altura
#Genotipos
generate_label_df_gen_alt <- function(gen.tuk.alt, variable){
Tukey.levels <- gen.tuk.alt[[variable]][,4]
Tukey.labels <- data.frame(multcompLetters(Tukey.levels)['Letters'])
Tukey.labels$treatment=rownames(Tukey.labels)
Tukey.labels=Tukey.labels[order(Tukey.labels$treatment) , ]
return(Tukey.labels)
}
labels.gen.alt <- generate_label_df_gen_alt(gen.tuk.alt, "gen")
labels.gen.alt
## Letters treatment
## CCN51 ac CCN51
## TCS01 c TCS01
## TCS06 ab TCS06
## TCS13 b TCS13
## TCS19 ab TCS19
# Forestal
generate_label_df_forestal_alt <- function(fores.tuk.alt, variable){
Tukey.levels <- fores.tuk.alt[[variable]][,2]
Tukey.labels <- data.frame(multcompLetters(Tukey.levels)['Letters'])
Tukey.labels$treatment=rownames(Tukey.labels)
Tukey.labels=Tukey.labels[order(Tukey.labels$treatment) , ]
return(Tukey.labels)
}
labels.forestal.alt <- generate_label_df_forestal_alt(fores.tuk.alt, "forestal")
labels.forestal.alt
## Letters treatment
## Abarco a Abarco
## Roble a Roble
## Terminalia a Terminalia
# Interacción Forestal:Genotipo
generate_label_df_interac_alt <- function(interac.tuk.alt, variable){
Tukey.levels <- interac.tuk.alt[[variable]][,4]
Tukey.labels <- data.frame(multcompLetters(Tukey.levels)['Letters'])
Tukey.labels$treatment=rownames(Tukey.labels)
Tukey.labels=Tukey.labels[order(Tukey.labels$treatment) , ]
return(Tukey.labels)
}
labels.interac.alt <- generate_label_df_interac_alt(interac.tuk.alt, "forestal:gen")
labels.interac.alt
## Letters treatment
## Abarco:CCN51 cde Abarco:CCN51
## Abarco:TCS01 de Abarco:TCS01
## Abarco:TCS06 cd Abarco:TCS06
## Abarco:TCS13 cd Abarco:TCS13
## Abarco:TCS19 acd Abarco:TCS19
## Roble:CCN51 acd Roble:CCN51
## Roble:TCS01 acd Roble:TCS01
## Roble:TCS06 ab Roble:TCS06
## Roble:TCS13 b Roble:TCS13
## Roble:TCS19 ac Roble:TCS19
## Terminalia:CCN51 de Terminalia:CCN51
## Terminalia:TCS01 e Terminalia:TCS01
## Terminalia:TCS06 de Terminalia:TCS06
## Terminalia:TCS13 de Terminalia:TCS13
## Terminalia:TCS19 acde Terminalia:TCS19
detach(datos2)