setwd("/Volumes/GoogleDrive/Mi unidad/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)
library(emmeans)
#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
## Gráficas contrastes de medias diametro
#Gen
contrast <- emmeans(aov.diam, ~gen)
## NOTE: Results may be misleading due to involvement in interactions
plot(contrast, comparisons = TRUE, xlab ="Diámetro")

medias.gen <- emmeans(aov.diam, pairwise ~ gen)
## NOTE: Results may be misleading due to involvement in interactions
medias.gen
## $emmeans
##  gen   emmean    SE  df lower.CL upper.CL
##  CCN51   5.67 0.100 641     5.48     5.87
##  TCS01   5.57 0.101 641     5.37     5.77
##  TCS06   5.27 0.116 641     5.04     5.49
##  TCS13   5.42 0.101 641     5.22     5.62
##  TCS19   5.50 0.112 641     5.28     5.72
## 
## Results are averaged over the levels of: forestal, bloque 
## Confidence level used: 0.95 
## 
## $contrasts
##  contrast      estimate    SE  df t.ratio p.value
##  CCN51 - TCS01   0.1012 0.142 641   0.711  0.9540
##  CCN51 - TCS06   0.4073 0.153 641   2.660  0.0612
##  CCN51 - TCS13   0.2510 0.142 641   1.765  0.3953
##  CCN51 - TCS19   0.1771 0.150 641   1.179  0.7635
##  TCS01 - TCS06   0.3061 0.154 641   1.984  0.2751
##  TCS01 - TCS13   0.1498 0.143 641   1.047  0.8333
##  TCS01 - TCS19   0.0759 0.151 641   0.502  0.9871
##  TCS06 - TCS13  -0.1563 0.154 641  -1.015  0.8485
##  TCS06 - TCS19  -0.2303 0.161 641  -1.426  0.6108
##  TCS13 - TCS19  -0.0739 0.151 641  -0.489  0.9883
## 
## Results are averaged over the levels of: forestal, bloque 
## P value adjustment: tukey method for comparing a family of 5 estimates
cld_gen <-multcomp::cld(contrast, alpha = 0.05, Letters = LETTERS, reversed=T)
cld_gen
##  gen   emmean    SE  df lower.CL upper.CL .group
##  CCN51   5.67 0.100 641     5.48     5.87  A    
##  TCS01   5.57 0.101 641     5.37     5.77  A    
##  TCS19   5.50 0.112 641     5.28     5.72  A    
##  TCS13   5.42 0.101 641     5.22     5.62  A    
##  TCS06   5.27 0.116 641     5.04     5.49  A    
## 
## Results are averaged over the levels of: forestal, bloque 
## Confidence level used: 0.95 
## P value adjustment: tukey method for comparing a family of 5 estimates 
## significance level used: alpha = 0.05 
## NOTE: Compact letter displays can be misleading
##       because they show NON-findings rather than findings.
##       Consider using 'pairs()', 'pwpp()', or 'pwpm()' instead.
#Forestal
contrast <- emmeans(aov.diam, ~forestal)
## NOTE: Results may be misleading due to involvement in interactions
plot(contrast, comparisons = TRUE, xlab ="Diámetro")

medias.forestal <- emmeans(aov.diam, pairwise ~ forestal)
## NOTE: Results may be misleading due to involvement in interactions
medias.forestal
## $emmeans
##  forestal   emmean     SE  df lower.CL upper.CL
##  Abarco       5.37 0.0820 641     5.20     5.53
##  Roble        5.72 0.0832 641     5.55     5.88
##  Terminalia   5.38 0.0825 641     5.22     5.54
## 
## Results are averaged over the levels of: gen, bloque 
## Confidence level used: 0.95 
## 
## $contrasts
##  contrast            estimate    SE  df t.ratio p.value
##  Abarco - Roble       -0.3519 0.117 641  -3.005  0.0078
##  Abarco - Terminalia  -0.0119 0.116 641  -0.103  0.9942
##  Roble - Terminalia    0.3400 0.117 641   2.902  0.0107
## 
## Results are averaged over the levels of: gen, bloque 
## P value adjustment: tukey method for comparing a family of 3 estimates
cld_forestal <-multcomp::cld(contrast, alpha = 0.05, Letters = LETTERS, reversed=T)
cld_forestal
##  forestal   emmean     SE  df lower.CL upper.CL .group
##  Roble        5.72 0.0832 641     5.55     5.88  A    
##  Terminalia   5.38 0.0825 641     5.22     5.54   B   
##  Abarco       5.37 0.0820 641     5.20     5.53   B   
## 
## Results are averaged over the levels of: gen, bloque 
## Confidence level used: 0.95 
## P value adjustment: tukey method for comparing a family of 3 estimates 
## significance level used: alpha = 0.05 
## NOTE: Compact letter displays can be misleading
##       because they show NON-findings rather than findings.
##       Consider using 'pairs()', 'pwpp()', or 'pwpm()' instead.
#Forestal*Gen
contrast <- emmeans(aov.diam, ~gen*forestal)
## NOTE: Results may be misleading due to involvement in interactions
plot(contrast, comparisons = TRUE, xlab ="Diámetro")

medias.forestal.gen <- emmeans(aov.diam, pairwise ~ gen*forestal)
## NOTE: Results may be misleading due to involvement in interactions
medias.forestal.gen
## $emmeans
##  gen   forestal   emmean    SE  df lower.CL upper.CL
##  CCN51 Abarco       5.66 0.171 641     5.32     5.99
##  TCS01 Abarco       4.96 0.175 641     4.62     5.31
##  TCS06 Abarco       5.03 0.204 641     4.63     5.43
##  TCS13 Abarco       5.69 0.173 641     5.35     6.03
##  TCS19 Abarco       5.49 0.189 641     5.12     5.86
##  CCN51 Roble        5.90 0.166 641     5.57     6.23
##  TCS01 Roble        5.70 0.185 641     5.34     6.07
##  TCS06 Roble        5.77 0.201 641     5.37     6.16
##  TCS13 Roble        5.46 0.176 641     5.12     5.81
##  TCS19 Roble        5.75 0.196 641     5.37     6.14
##  CCN51 Terminalia   5.46 0.182 641     5.11     5.82
##  TCS01 Terminalia   6.05 0.166 641     5.72     6.38
##  TCS06 Terminalia   5.01 0.198 641     4.62     5.39
##  TCS13 Terminalia   5.12 0.176 641     4.77     5.46
##  TCS19 Terminalia   5.25 0.198 641     4.86     5.64
## 
## Results are averaged over the levels of: bloque 
## Confidence level used: 0.95 
## 
## $contrasts
##  contrast                             estimate    SE  df t.ratio p.value
##  CCN51 Abarco - TCS01 Abarco          0.693269 0.244 641   2.837  0.2299
##  CCN51 Abarco - TCS06 Abarco          0.629313 0.266 641   2.364  0.5428
##  CCN51 Abarco - TCS13 Abarco         -0.029020 0.243 641  -0.119  1.0000
##  CCN51 Abarco - TCS19 Abarco          0.168473 0.255 641   0.661  1.0000
##  CCN51 Abarco - CCN51 Roble          -0.242375 0.238 641  -1.017  0.9996
##  CCN51 Abarco - TCS01 Roble          -0.045174 0.252 641  -0.179  1.0000
##  CCN51 Abarco - TCS06 Roble          -0.108424 0.264 641  -0.411  1.0000
##  CCN51 Abarco - TCS13 Roble           0.194395 0.246 641   0.792  1.0000
##  CCN51 Abarco - TCS19 Roble          -0.095986 0.261 641  -0.368  1.0000
##  CCN51 Abarco - CCN51 Terminalia      0.193748 0.250 641   0.776  1.0000
##  CCN51 Abarco - TCS01 Terminalia     -0.393088 0.238 641  -1.649  0.9469
##  CCN51 Abarco - TCS06 Terminalia      0.652490 0.262 641   2.491  0.4487
##  CCN51 Abarco - TCS13 Terminalia      0.539041 0.246 641   2.194  0.6691
##  CCN51 Abarco - TCS19 Terminalia      0.410130 0.262 641   1.567  0.9650
##  TCS01 Abarco - TCS06 Abarco         -0.063956 0.269 641  -0.238  1.0000
##  TCS01 Abarco - TCS13 Abarco         -0.722289 0.246 641  -2.940  0.1810
##  TCS01 Abarco - TCS19 Abarco         -0.524796 0.258 641  -2.036  0.7762
##  TCS01 Abarco - CCN51 Roble          -0.935644 0.241 641  -3.883  0.0097
##  TCS01 Abarco - TCS01 Roble          -0.738443 0.254 641  -2.910  0.1945
##  TCS01 Abarco - TCS06 Roble          -0.801693 0.266 641  -3.009  0.1528
##  TCS01 Abarco - TCS13 Roble          -0.498874 0.248 641  -2.012  0.7908
##  TCS01 Abarco - TCS19 Roble          -0.789255 0.262 641  -3.008  0.1530
##  TCS01 Abarco - CCN51 Terminalia     -0.499521 0.252 641  -1.980  0.8096
##  TCS01 Abarco - TCS01 Terminalia     -1.086357 0.241 641  -4.509  0.0007
##  TCS01 Abarco - TCS06 Terminalia     -0.040779 0.264 641  -0.154  1.0000
##  TCS01 Abarco - TCS13 Terminalia     -0.154228 0.248 641  -0.622  1.0000
##  TCS01 Abarco - TCS19 Terminalia     -0.283139 0.264 641  -1.073  0.9992
##  TCS06 Abarco - TCS13 Abarco         -0.658333 0.267 641  -2.462  0.4696
##  TCS06 Abarco - TCS19 Abarco         -0.460840 0.277 641  -1.661  0.9438
##  TCS06 Abarco - CCN51 Roble          -0.871688 0.263 641  -3.310  0.0668
##  TCS06 Abarco - TCS01 Roble          -0.674488 0.276 641  -2.440  0.4860
##  TCS06 Abarco - TCS06 Roble          -0.737737 0.287 641  -2.572  0.3909
##  TCS06 Abarco - TCS13 Roble          -0.434918 0.270 641  -1.610  0.9563
##  TCS06 Abarco - TCS19 Roble          -0.725299 0.285 641  -2.548  0.4075
##  TCS06 Abarco - CCN51 Terminalia     -0.435565 0.273 641  -1.593  0.9600
##  TCS06 Abarco - TCS01 Terminalia     -1.022401 0.263 641  -3.882  0.0097
##  TCS06 Abarco - TCS06 Terminalia      0.023177 0.285 641   0.081  1.0000
##  TCS06 Abarco - TCS13 Terminalia     -0.090272 0.270 641  -0.334  1.0000
##  TCS06 Abarco - TCS19 Terminalia     -0.219183 0.285 641  -0.770  1.0000
##  TCS13 Abarco - TCS19 Abarco          0.197493 0.256 641   0.771  1.0000
##  TCS13 Abarco - CCN51 Roble          -0.213355 0.240 641  -0.890  0.9999
##  TCS13 Abarco - TCS01 Roble          -0.016154 0.253 641  -0.064  1.0000
##  TCS13 Abarco - TCS06 Roble          -0.079404 0.265 641  -0.299  1.0000
##  TCS13 Abarco - TCS13 Roble           0.223415 0.247 641   0.905  0.9999
##  TCS13 Abarco - TCS19 Roble          -0.066966 0.262 641  -0.256  1.0000
##  TCS13 Abarco - CCN51 Terminalia      0.222768 0.251 641   0.888  0.9999
##  TCS13 Abarco - TCS01 Terminalia     -0.364068 0.240 641  -1.519  0.9732
##  TCS13 Abarco - TCS06 Terminalia      0.681510 0.263 641   2.590  0.3786
##  TCS13 Abarco - TCS13 Terminalia      0.568061 0.247 641   2.300  0.5908
##  TCS13 Abarco - TCS19 Terminalia      0.439150 0.263 641   1.671  0.9412
##  TCS19 Abarco - CCN51 Roble          -0.410849 0.252 641  -1.631  0.9514
##  TCS19 Abarco - TCS01 Roble          -0.213648 0.265 641  -0.806  1.0000
##  TCS19 Abarco - TCS06 Roble          -0.276897 0.276 641  -1.004  0.9996
##  TCS19 Abarco - TCS13 Roble           0.025922 0.259 641   0.100  1.0000
##  TCS19 Abarco - TCS19 Roble          -0.264459 0.274 641  -0.967  0.9997
##  TCS19 Abarco - CCN51 Terminalia      0.025275 0.262 641   0.096  1.0000
##  TCS19 Abarco - TCS01 Terminalia     -0.561561 0.252 641  -2.229  0.6433
##  TCS19 Abarco - TCS06 Terminalia      0.484017 0.275 641   1.762  0.9121
##  TCS19 Abarco - TCS13 Terminalia      0.370567 0.259 641   1.431  0.9843
##  TCS19 Abarco - TCS19 Terminalia      0.241656 0.274 641   0.882  0.9999
##  CCN51 Roble - TCS01 Roble            0.197201 0.248 641   0.794  1.0000
##  CCN51 Roble - TCS06 Roble            0.133951 0.261 641   0.513  1.0000
##  CCN51 Roble - TCS13 Roble            0.436771 0.242 641   1.804  0.8963
##  CCN51 Roble - TCS19 Roble            0.146390 0.257 641   0.569  1.0000
##  CCN51 Roble - CCN51 Terminalia       0.436123 0.246 641   1.769  0.9095
##  CCN51 Roble - TCS01 Terminalia      -0.150713 0.235 641  -0.642  1.0000
##  CCN51 Roble - TCS06 Terminalia       0.894865 0.259 641   3.459  0.0422
##  CCN51 Roble - TCS13 Terminalia       0.781416 0.242 641   3.225  0.0854
##  CCN51 Roble - TCS19 Terminalia       0.652505 0.259 641   2.524  0.4246
##  TCS01 Roble - TCS06 Roble           -0.063250 0.273 641  -0.232  1.0000
##  TCS01 Roble - TCS13 Roble            0.239570 0.255 641   0.939  0.9998
##  TCS01 Roble - TCS19 Roble           -0.050811 0.269 641  -0.189  1.0000
##  TCS01 Roble - CCN51 Terminalia       0.238923 0.259 641   0.921  0.9999
##  TCS01 Roble - TCS01 Terminalia      -0.347913 0.248 641  -1.401  0.9871
##  TCS01 Roble - TCS06 Terminalia       0.697664 0.271 641   2.572  0.3905
##  TCS01 Roble - TCS13 Terminalia       0.584215 0.255 641   2.289  0.5992
##  TCS01 Roble - TCS19 Terminalia       0.455304 0.271 641   1.682  0.9381
##  TCS06 Roble - TCS13 Roble            0.302819 0.268 641   1.131  0.9985
##  TCS06 Roble - TCS19 Roble            0.012438 0.281 641   0.044  1.0000
##  TCS06 Roble - CCN51 Terminalia       0.302172 0.271 641   1.114  0.9987
##  TCS06 Roble - TCS01 Terminalia      -0.284664 0.261 641  -1.090  0.9990
##  TCS06 Roble - TCS06 Terminalia       0.760914 0.283 641   2.687  0.3153
##  TCS06 Roble - TCS13 Terminalia       0.647465 0.268 641   2.418  0.5020
##  TCS06 Roble - TCS19 Terminalia       0.518554 0.282 641   1.837  0.8823
##  TCS13 Roble - TCS19 Roble           -0.290381 0.264 641  -1.101  0.9989
##  TCS13 Roble - CCN51 Terminalia      -0.000647 0.254 641  -0.003  1.0000
##  TCS13 Roble - TCS01 Terminalia      -0.587483 0.242 641  -2.426  0.4963
##  TCS13 Roble - TCS06 Terminalia       0.458095 0.265 641   1.727  0.9243
##  TCS13 Roble - TCS13 Terminalia       0.344645 0.249 641   1.383  0.9886
##  TCS13 Roble - TCS19 Terminalia       0.215734 0.265 641   0.814  1.0000
##  TCS19 Roble - CCN51 Terminalia       0.289734 0.268 641   1.082  0.9991
##  TCS19 Roble - TCS01 Terminalia      -0.297102 0.257 641  -1.155  0.9982
##  TCS19 Roble - TCS06 Terminalia       0.748476 0.279 641   2.680  0.3197
##  TCS19 Roble - TCS13 Terminalia       0.635027 0.264 641   2.407  0.5103
##  TCS19 Roble - TCS19 Terminalia       0.506116 0.279 641   1.815  0.8916
##  CCN51 Terminalia - TCS01 Terminalia -0.586836 0.246 641  -2.381  0.5301
##  CCN51 Terminalia - TCS06 Terminalia  0.458742 0.270 641   1.702  0.9322
##  CCN51 Terminalia - TCS13 Terminalia  0.345293 0.254 641   1.362  0.9902
##  CCN51 Terminalia - TCS19 Terminalia  0.216382 0.269 641   0.804  1.0000
##  TCS01 Terminalia - TCS06 Terminalia  1.045578 0.259 641   4.041  0.0053
##  TCS01 Terminalia - TCS13 Terminalia  0.932129 0.242 641   3.847  0.0110
##  TCS01 Terminalia - TCS19 Terminalia  0.803218 0.259 641   3.107  0.1184
##  TCS06 Terminalia - TCS13 Terminalia -0.113449 0.265 641  -0.427  1.0000
##  TCS06 Terminalia - TCS19 Terminalia -0.242360 0.280 641  -0.864  0.9999
##  TCS13 Terminalia - TCS19 Terminalia -0.128911 0.265 641  -0.486  1.0000
## 
## Results are averaged over the levels of: bloque 
## P value adjustment: tukey method for comparing a family of 15 estimates
cld_forestal_gen <-multcomp::cld(contrast, alpha = 0.05, Letters = LETTERS, reversed=T)
cld_forestal_gen
##  gen   forestal   emmean    SE  df lower.CL upper.CL .group
##  TCS01 Terminalia   6.05 0.166 641     5.72     6.38  A    
##  CCN51 Roble        5.90 0.166 641     5.57     6.23  AB   
##  TCS06 Roble        5.77 0.201 641     5.37     6.16  ABC  
##  TCS19 Roble        5.75 0.196 641     5.37     6.14  ABC  
##  TCS01 Roble        5.70 0.185 641     5.34     6.07  ABC  
##  TCS13 Abarco       5.69 0.173 641     5.35     6.03  ABC  
##  CCN51 Abarco       5.66 0.171 641     5.32     5.99  ABC  
##  TCS19 Abarco       5.49 0.189 641     5.12     5.86  ABC  
##  CCN51 Terminalia   5.46 0.182 641     5.11     5.82  ABC  
##  TCS13 Roble        5.46 0.176 641     5.12     5.81  ABC  
##  TCS19 Terminalia   5.25 0.198 641     4.86     5.64  ABC  
##  TCS13 Terminalia   5.12 0.176 641     4.77     5.46   BC  
##  TCS06 Abarco       5.03 0.204 641     4.63     5.43   BC  
##  TCS06 Terminalia   5.01 0.198 641     4.62     5.39    C  
##  TCS01 Abarco       4.96 0.175 641     4.62     5.31    C  
## 
## Results are averaged over the levels of: bloque 
## Confidence level used: 0.95 
## P value adjustment: tukey method for comparing a family of 15 estimates 
## significance level used: alpha = 0.05 
## NOTE: Compact letter displays can be misleading
##       because they show NON-findings rather than findings.
##       Consider using 'pairs()', 'pwpp()', or 'pwpm()' instead.
## Gráficas contrastes de medias altura
#Gen
contrast <- emmeans(aov.alt, ~gen)
## NOTE: Results may be misleading due to involvement in interactions
plot(contrast, comparisons = TRUE, xlab ="Altura")

medias.gen <- emmeans(aov.alt, pairwise ~ gen)
## NOTE: Results may be misleading due to involvement in interactions
medias.gen
## $emmeans
##  gen   emmean   SE  df lower.CL upper.CL
##  CCN51    201 3.79 641      193      208
##  TCS01    184 3.83 641      177      192
##  TCS06    171 4.40 641      162      180
##  TCS13    178 3.83 641      171      186
##  TCS19    170 4.25 641      162      178
## 
## Results are averaged over the levels of: forestal, bloque 
## Confidence level used: 0.95 
## 
## $contrasts
##  contrast      estimate   SE  df t.ratio p.value
##  CCN51 - TCS01   16.478 5.39 641   3.057  0.0197
##  CCN51 - TCS06   29.717 5.80 641   5.126  <.0001
##  CCN51 - TCS13   22.340 5.38 641   4.149  0.0004
##  CCN51 - TCS19   30.706 5.69 641   5.400  <.0001
##  TCS01 - TCS06   13.239 5.84 641   2.266  0.1573
##  TCS01 - TCS13    5.862 5.42 641   1.082  0.8157
##  TCS01 - TCS19   14.228 5.72 641   2.488  0.0945
##  TCS06 - TCS13   -7.377 5.83 641  -1.265  0.7127
##  TCS06 - TCS19    0.989 6.11 641   0.162  0.9998
##  TCS13 - TCS19    8.365 5.72 641   1.463  0.5872
## 
## Results are averaged over the levels of: forestal, bloque 
## P value adjustment: tukey method for comparing a family of 5 estimates
cld_gen <-multcomp::cld(contrast, alpha = 0.05, Letters = LETTERS, reversed=T)
cld_gen
##  gen   emmean   SE  df lower.CL upper.CL .group
##  CCN51    201 3.79 641      193      208  A    
##  TCS01    184 3.83 641      177      192   B   
##  TCS13    178 3.83 641      171      186   B   
##  TCS06    171 4.40 641      162      180   B   
##  TCS19    170 4.25 641      162      178   B   
## 
## Results are averaged over the levels of: forestal, bloque 
## Confidence level used: 0.95 
## P value adjustment: tukey method for comparing a family of 5 estimates 
## significance level used: alpha = 0.05 
## NOTE: Compact letter displays can be misleading
##       because they show NON-findings rather than findings.
##       Consider using 'pairs()', 'pwpp()', or 'pwpm()' instead.
#Forestal
contrast <- emmeans(aov.alt, ~forestal)
## NOTE: Results may be misleading due to involvement in interactions
plot(contrast, comparisons = TRUE, xlab ="Altura")

medias.forestal <- emmeans(aov.alt, pairwise ~ forestal)
## NOTE: Results may be misleading due to involvement in interactions
medias.forestal
## $emmeans
##  forestal   emmean   SE  df lower.CL upper.CL
##  Abarco        172 3.10 641      166      178
##  Roble         190 3.15 641      184      196
##  Terminalia    181 3.12 641      175      187
## 
## Results are averaged over the levels of: gen, bloque 
## Confidence level used: 0.95 
## 
## $contrasts
##  contrast            estimate   SE  df t.ratio p.value
##  Abarco - Roble        -18.24 4.43 641  -4.114  0.0001
##  Abarco - Terminalia    -9.08 4.40 641  -2.061  0.0989
##  Roble - Terminalia      9.16 4.44 641   2.065  0.0979
## 
## Results are averaged over the levels of: gen, bloque 
## P value adjustment: tukey method for comparing a family of 3 estimates
cld_forestal <-multcomp::cld(contrast, alpha = 0.05, Letters = LETTERS, reversed=T)
cld_forestal
##  forestal   emmean   SE  df lower.CL upper.CL .group
##  Roble         190 3.15 641      184      196  A    
##  Terminalia    181 3.12 641      175      187  AB   
##  Abarco        172 3.10 641      166      178   B   
## 
## Results are averaged over the levels of: gen, bloque 
## Confidence level used: 0.95 
## P value adjustment: tukey method for comparing a family of 3 estimates 
## significance level used: alpha = 0.05 
## NOTE: Compact letter displays can be misleading
##       because they show NON-findings rather than findings.
##       Consider using 'pairs()', 'pwpp()', or 'pwpm()' instead.
#Forestal*Gen
contrast <- emmeans(aov.alt, ~gen*forestal)
## NOTE: Results may be misleading due to involvement in interactions
plot(contrast, comparisons = TRUE, xlab ="Altura")
## Warning: Comparison discrepancy in group "1", TCS06 Roble - TCS01 Terminalia:
##     Target overlap = 2e-04, overlap on graph = -7e-04

medias.forestal.gen <- emmeans(aov.alt, pairwise ~ gen*forestal)
## NOTE: Results may be misleading due to involvement in interactions
medias.forestal.gen
## $emmeans
##  gen   forestal   emmean   SE  df lower.CL upper.CL
##  CCN51 Abarco        205 6.47 641      192      218
##  TCS01 Abarco        142 6.61 641      129      155
##  TCS06 Abarco        160 7.74 641      145      175
##  TCS13 Abarco        191 6.54 641      178      204
##  TCS19 Abarco        160 7.17 641      146      174
##  CCN51 Roble         217 6.29 641      204      229
##  TCS01 Roble         205 6.99 641      192      219
##  TCS06 Roble         171 7.62 641      156      186
##  TCS13 Roble         178 6.67 641      165      192
##  TCS19 Roble         178 7.43 641      163      192
##  CCN51 Terminalia    180 6.89 641      167      194
##  TCS01 Terminalia    205 6.29 641      193      217
##  TCS06 Terminalia    181 7.51 641      166      196
##  TCS13 Terminalia    165 6.68 641      152      178
##  TCS19 Terminalia    172 7.50 641      157      187
## 
## Results are averaged over the levels of: bloque 
## Confidence level used: 0.95 
## 
## $contrasts
##  contrast                            estimate    SE  df t.ratio p.value
##  CCN51 Abarco - TCS01 Abarco           62.804  9.25 641   6.789  <.0001
##  CCN51 Abarco - TCS06 Abarco           44.647 10.08 641   4.430  0.0011
##  CCN51 Abarco - TCS13 Abarco           13.769  9.20 641   1.497  0.9765
##  CCN51 Abarco - TCS19 Abarco           44.763  9.65 641   4.641  0.0004
##  CCN51 Abarco - CCN51 Roble           -11.681  9.02 641  -1.294  0.9940
##  CCN51 Abarco - TCS01 Roble            -0.480  9.53 641  -0.050  1.0000
##  CCN51 Abarco - TCS06 Roble            33.483 10.00 641   3.350  0.0592
##  CCN51 Abarco - TCS13 Roble            26.357  9.30 641   2.835  0.2310
##  CCN51 Abarco - TCS19 Roble            27.120  9.86 641   2.750  0.2776
##  CCN51 Abarco - CCN51 Terminalia       24.413  9.45 641   2.583  0.3835
##  CCN51 Abarco - TCS01 Terminalia       -0.158  9.02 641  -0.018  1.0000
##  CCN51 Abarco - TCS06 Terminalia       23.754  9.92 641   2.395  0.5193
##  CCN51 Abarco - TCS13 Terminalia       39.627  9.30 641   4.261  0.0022
##  CCN51 Abarco - TCS19 Terminalia       32.967  9.91 641   3.328  0.0632
##  TCS01 Abarco - TCS06 Abarco          -18.157 10.19 641  -1.782  0.9047
##  TCS01 Abarco - TCS13 Abarco          -49.035  9.30 641  -5.272  <.0001
##  TCS01 Abarco - TCS19 Abarco          -18.041  9.76 641  -1.849  0.8770
##  TCS01 Abarco - CCN51 Roble           -74.485  9.12 641  -8.167  <.0001
##  TCS01 Abarco - TCS01 Roble           -63.284  9.61 641  -6.587  <.0001
##  TCS01 Abarco - TCS06 Roble           -29.322 10.09 641  -2.907  0.1958
##  TCS01 Abarco - TCS13 Roble           -36.447  9.39 641  -3.883  0.0097
##  TCS01 Abarco - TCS19 Roble           -35.685  9.93 641  -3.593  0.0272
##  TCS01 Abarco - CCN51 Terminalia      -38.392  9.55 641  -4.020  0.0057
##  TCS01 Abarco - TCS01 Terminalia      -62.962  9.12 641  -6.903  <.0001
##  TCS01 Abarco - TCS06 Terminalia      -39.050 10.00 641  -3.904  0.0090
##  TCS01 Abarco - TCS13 Terminalia      -23.178  9.39 641  -2.468  0.4652
##  TCS01 Abarco - TCS19 Terminalia      -29.838  9.99 641  -2.986  0.1619
##  TCS06 Abarco - TCS13 Abarco          -30.878 10.12 641  -3.050  0.1374
##  TCS06 Abarco - TCS19 Abarco            0.116 10.50 641   0.011  1.0000
##  TCS06 Abarco - CCN51 Roble           -56.328  9.97 641  -5.649  <.0001
##  TCS06 Abarco - TCS01 Roble           -45.127 10.47 641  -4.312  0.0017
##  TCS06 Abarco - TCS06 Roble           -11.165 10.86 641  -1.028  0.9995
##  TCS06 Abarco - TCS13 Roble           -18.290 10.23 641  -1.788  0.9023
##  TCS06 Abarco - TCS19 Roble           -17.528 10.78 641  -1.627  0.9524
##  TCS06 Abarco - CCN51 Terminalia      -20.235 10.35 641  -1.954  0.8240
##  TCS06 Abarco - TCS01 Terminalia      -44.805  9.97 641  -4.494  0.0008
##  TCS06 Abarco - TCS06 Terminalia      -20.893 10.79 641  -1.937  0.8337
##  TCS06 Abarco - TCS13 Terminalia       -5.021 10.23 641  -0.491  1.0000
##  TCS06 Abarco - TCS19 Terminalia      -11.681 10.78 641  -1.084  0.9991
##  TCS13 Abarco - TCS19 Abarco           30.994  9.69 641   3.197  0.0925
##  TCS13 Abarco - CCN51 Roble           -25.450  9.07 641  -2.805  0.2469
##  TCS13 Abarco - TCS01 Roble           -14.249  9.58 641  -1.487  0.9778
##  TCS13 Abarco - TCS06 Roble            19.713 10.04 641   1.963  0.8194
##  TCS13 Abarco - TCS13 Roble            12.588  9.35 641   1.347  0.9912
##  TCS13 Abarco - TCS19 Roble            13.350  9.91 641   1.347  0.9911
##  TCS13 Abarco - CCN51 Terminalia       10.643  9.50 641   1.120  0.9987
##  TCS13 Abarco - TCS01 Terminalia      -13.928  9.07 641  -1.535  0.9707
##  TCS13 Abarco - TCS06 Terminalia        9.985  9.96 641   1.002  0.9996
##  TCS13 Abarco - TCS13 Terminalia       25.857  9.35 641   2.766  0.2684
##  TCS13 Abarco - TCS19 Terminalia       19.197  9.95 641   1.929  0.8378
##  TCS19 Abarco - CCN51 Roble           -56.444  9.54 641  -5.919  <.0001
##  TCS19 Abarco - TCS01 Roble           -45.243 10.04 641  -4.508  0.0007
##  TCS19 Abarco - TCS06 Roble           -11.281 10.44 641  -1.080  0.9991
##  TCS19 Abarco - TCS13 Roble           -18.406  9.80 641  -1.877  0.8638
##  TCS19 Abarco - TCS19 Roble           -17.643 10.36 641  -1.703  0.9317
##  TCS19 Abarco - CCN51 Terminalia      -20.350  9.93 641  -2.050  0.7672
##  TCS19 Abarco - TCS01 Terminalia      -44.921  9.54 641  -4.711  0.0003
##  TCS19 Abarco - TCS06 Terminalia      -21.009 10.40 641  -2.020  0.7856
##  TCS19 Abarco - TCS13 Terminalia       -5.136  9.80 641  -0.524  1.0000
##  TCS19 Abarco - TCS19 Terminalia      -11.796 10.37 641  -1.138  0.9984
##  CCN51 Roble - TCS01 Roble             11.201  9.40 641   1.191  0.9974
##  CCN51 Roble - TCS06 Roble             45.163  9.88 641   4.570  0.0006
##  CCN51 Roble - TCS13 Roble             38.038  9.17 641   4.149  0.0034
##  CCN51 Roble - TCS19 Roble             38.800  9.74 641   3.985  0.0066
##  CCN51 Roble - CCN51 Terminalia        36.093  9.33 641   3.868  0.0102
##  CCN51 Roble - TCS01 Terminalia        11.523  8.89 641   1.296  0.9939
##  CCN51 Roble - TCS06 Terminalia        35.435  9.79 641   3.618  0.0250
##  CCN51 Roble - TCS13 Terminalia        51.307  9.17 641   5.594  <.0001
##  CCN51 Roble - TCS19 Terminalia        44.647  9.79 641   4.562  0.0006
##  TCS01 Roble - TCS06 Roble             33.963 10.33 641   3.287  0.0713
##  TCS01 Roble - TCS13 Roble             26.837  9.66 641   2.779  0.2611
##  TCS01 Roble - TCS19 Roble             27.600 10.16 641   2.715  0.2979
##  TCS01 Roble - CCN51 Terminalia        24.893  9.82 641   2.535  0.4167
##  TCS01 Roble - TCS01 Terminalia         0.322  9.40 641   0.034  1.0000
##  TCS01 Roble - TCS06 Terminalia        24.234 10.27 641   2.360  0.5454
##  TCS01 Roble - TCS13 Terminalia        40.107  9.66 641   4.151  0.0034
##  TCS01 Roble - TCS19 Terminalia        33.447 10.25 641   3.263  0.0765
##  TCS06 Roble - TCS13 Roble             -7.126 10.14 641  -0.703  1.0000
##  TCS06 Roble - TCS19 Roble             -6.363 10.64 641  -0.598  1.0000
##  TCS06 Roble - CCN51 Terminalia        -9.070 10.26 641  -0.884  0.9999
##  TCS06 Roble - TCS01 Terminalia       -33.641  9.88 641  -3.404  0.0501
##  TCS06 Roble - TCS06 Terminalia        -9.728 10.72 641  -0.907  0.9999
##  TCS06 Roble - TCS13 Terminalia         6.144 10.14 641   0.606  1.0000
##  TCS06 Roble - TCS19 Terminalia        -0.516 10.69 641  -0.048  1.0000
##  TCS13 Roble - TCS19 Roble              0.763  9.98 641   0.076  1.0000
##  TCS13 Roble - CCN51 Terminalia        -1.944  9.60 641  -0.203  1.0000
##  TCS13 Roble - TCS01 Terminalia       -26.515  9.17 641  -2.892  0.2027
##  TCS13 Roble - TCS06 Terminalia        -2.603 10.04 641  -0.259  1.0000
##  TCS13 Roble - TCS13 Terminalia        13.270  9.44 641   1.406  0.9867
##  TCS13 Roble - TCS19 Terminalia         6.610 10.04 641   0.658  1.0000
##  TCS19 Roble - CCN51 Terminalia        -2.707 10.14 641  -0.267  1.0000
##  TCS19 Roble - TCS01 Terminalia       -27.278  9.74 641  -2.801  0.2486
##  TCS19 Roble - TCS06 Terminalia        -3.365 10.57 641  -0.318  1.0000
##  TCS19 Roble - TCS13 Terminalia        12.507  9.99 641   1.252  0.9957
##  TCS19 Roble - TCS19 Terminalia         5.847 10.56 641   0.554  1.0000
##  CCN51 Terminalia - TCS01 Terminalia  -24.571  9.33 641  -2.633  0.3496
##  CCN51 Terminalia - TCS06 Terminalia   -0.659 10.20 641  -0.065  1.0000
##  CCN51 Terminalia - TCS13 Terminalia   15.214  9.60 641   1.585  0.9616
##  CCN51 Terminalia - TCS19 Terminalia    8.554 10.18 641   0.840  1.0000
##  TCS01 Terminalia - TCS06 Terminalia   23.912  9.79 641   2.441  0.4849
##  TCS01 Terminalia - TCS13 Terminalia   39.785  9.17 641   4.338  0.0016
##  TCS01 Terminalia - TCS19 Terminalia   33.125  9.79 641   3.385  0.0532
##  TCS06 Terminalia - TCS13 Terminalia   15.873 10.05 641   1.580  0.9626
##  TCS06 Terminalia - TCS19 Terminalia    9.212 10.62 641   0.868  0.9999
##  TCS13 Terminalia - TCS19 Terminalia   -6.660 10.04 641  -0.663  1.0000
## 
## Results are averaged over the levels of: bloque 
## P value adjustment: tukey method for comparing a family of 15 estimates
cld_forestal_gen <-multcomp::cld(contrast, alpha = 0.05, Letters = LETTERS, reversed=T)
cld_forestal_gen
##  gen   forestal   emmean   SE  df lower.CL upper.CL .group
##  CCN51 Roble         217 6.29 641      204      229  A    
##  TCS01 Roble         205 6.99 641      192      219  AB   
##  TCS01 Terminalia    205 6.29 641      193      217  AB   
##  CCN51 Abarco        205 6.47 641      192      218  AB   
##  TCS13 Abarco        191 6.54 641      178      204  ABC  
##  TCS06 Terminalia    181 7.51 641      166      196   BC  
##  CCN51 Terminalia    180 6.89 641      167      194   BC  
##  TCS13 Roble         178 6.67 641      165      192   BC  
##  TCS19 Roble         178 7.43 641      163      192   BC  
##  TCS19 Terminalia    172 7.50 641      157      187   BCD 
##  TCS06 Roble         171 7.62 641      156      186   BCD 
##  TCS13 Terminalia    165 6.68 641      152      178    CD 
##  TCS06 Abarco        160 7.74 641      145      175    CD 
##  TCS19 Abarco        160 7.17 641      146      174    CD 
##  TCS01 Abarco        142 6.61 641      129      155     D 
## 
## Results are averaged over the levels of: bloque 
## Confidence level used: 0.95 
## P value adjustment: tukey method for comparing a family of 15 estimates 
## significance level used: alpha = 0.05 
## NOTE: Compact letter displays can be misleading
##       because they show NON-findings rather than findings.
##       Consider using 'pairs()', 'pwpp()', or 'pwpm()' instead.
detach(datos3)