setwd("~/Google Drive/Agrosavia/colaboraciones/Laura")
datos3<-read.table("sanluis.csv", header=T, sep=',')
datos3$gen<-as.factor(datos3$gen)
datos3$forestal<-as.factor(datos3$forestal)
datos3$bloque<-as.factor(datos3$bloque)
attach(datos3)
library(ggplot2)
#Gráfica diámetro
ggplot(datos3, 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 137 rows containing non-finite values (stat_smooth).
# Gráfica altura
ggplot(datos3, 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 137 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=datos3, corr=corCompSymm(, form= ~ 1 | gen),na.action=na.exclude)
fit.ar1.diam <- gls(diam ~ semana*forestal*gen+bloque, data=datos3, corr=corAR1(, form= ~ 1 | gen), na.action=na.exclude)
fit.ar1het.diam <- gls(diam ~ semana*forestal*gen+bloque, data=datos3, 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 2341.345 2493.088 -1136.673
## fit.ar1.diam 2 34 2292.572 2444.315 -1112.286
## fit.ar1het.diam 3 36 2296.544 2457.213 -1112.272 2 vs 3 0.02815748 0.986
anova(fit.ar1.diam)
## Denom. DF: 641
## numDF F-value p-value
## (Intercept) 1 7420.471 <.0001
## semana 1 40.360 <.0001
## forestal 2 3.978 0.0192
## gen 4 1.139 0.3372
## bloque 2 2.319 0.0991
## semana:forestal 2 0.733 0.4810
## semana:gen 4 0.149 0.9634
## forestal:gen 8 3.223 0.0013
## semana:forestal:gen 8 0.120 0.9984
anova(fit.ar1het.diam)
## Denom. DF: 641
## numDF F-value p-value
## (Intercept) 1 7415.488 <.0001
## semana 1 40.093 <.0001
## forestal 2 3.992 0.0189
## gen 4 1.139 0.3371
## bloque 2 2.311 0.1000
## semana:forestal 2 0.728 0.4833
## semana:gen 4 0.148 0.9637
## forestal:gen 8 3.225 0.0013
## semana:forestal:gen 8 0.120 0.9985
# Análisis para altura
fit.compsym.alt <- gls(alt ~ semana*forestal*gen+bloque, data=datos3, corr=corCompSymm(, form= ~ 1 | gen),na.action=na.exclude)
fit.ar1.alt <- gls(alt ~ semana*forestal*gen+bloque, data=datos3, corr=corAR1(, form= ~ 1 | gen), na.action=na.exclude)
fit.ar1het.alt <- gls(alt ~ semana*forestal*gen+bloque, data=datos3, 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 6999.878 7151.621 -3465.939
## fit.ar1.alt 2 34 6962.748 7114.491 -3447.374
## fit.ar1het.alt 3 36 6965.877 7126.546 -3446.939 2 vs 3 0.87086 0.647
anova(fit.ar1het.alt)
## Denom. DF: 641
## numDF F-value p-value
## (Intercept) 1 5993.385 <.0001
## semana 1 110.536 <.0001
## forestal 2 7.219 0.0008
## gen 4 6.155 0.0001
## bloque 2 1.822 0.1626
## semana:forestal 2 0.769 0.4637
## semana:gen 4 0.308 0.8725
## forestal:gen 8 7.771 <.0001
## semana:forestal:gen 8 0.190 0.9923
#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 b Abarco
## Roble b Roble
## Terminalia a 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 abc Abarco:CCN51
## Abarco:TCS01 a Abarco:TCS01
## Abarco:TCS06 ab Abarco:TCS06
## Abarco:TCS13 abc Abarco:TCS13
## Abarco:TCS19 abc Abarco:TCS19
## Roble:CCN51 bc Roble:CCN51
## Roble:TCS01 abc Roble:TCS01
## Roble:TCS06 abc Roble:TCS06
## Roble:TCS13 abc Roble:TCS13
## Roble:TCS19 abc Roble:TCS19
## Terminalia:CCN51 abc Terminalia:CCN51
## Terminalia:TCS01 c Terminalia:TCS01
## Terminalia:TCS06 a Terminalia:TCS06
## Terminalia:TCS13 ab Terminalia:TCS13
## Terminalia:TCS19 abc 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 b CCN51
## TCS01 a TCS01
## TCS06 a TCS06
## TCS13 a TCS13
## TCS19 a 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 b Abarco
## Roble b 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 de Abarco:CCN51
## Abarco:TCS01 b Abarco:TCS01
## Abarco:TCS06 ab Abarco:TCS06
## Abarco:TCS13 acde Abarco:TCS13
## Abarco:TCS19 ab Abarco:TCS19
## Roble:CCN51 e Roble:CCN51
## Roble:TCS01 cde Roble:TCS01
## Roble:TCS06 abc Roble:TCS06
## Roble:TCS13 acd Roble:TCS13
## Roble:TCS19 acd Roble:TCS19
## Terminalia:CCN51 acd Terminalia:CCN51
## Terminalia:TCS01 cde Terminalia:TCS01
## Terminalia:TCS06 acd Terminalia:TCS06
## Terminalia:TCS13 ab Terminalia:TCS13
## Terminalia:TCS19 abc Terminalia:TCS19
detach(datos3)