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When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

####Eggs PER PLANT ####

Sub.Eggs <- subset(mydata,
                   select=c(Nger, 
                            Isolate, 
                            EggsP) ) 
##Create a subset of the desire variable

Eggs per plant: MIAd

####Isolate: MIAd####

Sub.Eggs.MIAd <- subset(Sub.Eggs, Isolate == "MIAd", select=c(Nger, EggsP)) 
Sub.Eggs.MIAd$Nger = factor (Sub.Eggs.MIAd$Nger, labels=c("EC", "TB", "TE", "TS", "TT")) 

###Descriptive statistics calculation###
Sub.Eggs.MIAd.EC <- subset(Sub.Eggs.MIAd, Nger == "EC", select=c(Nger,EggsP))
Me.EP.MIAd.EC <- mean(Sub.Eggs.MIAd.EC$EggsP, na.mr=FALSE)
Me.EP.MIAd.EC <- round(Me.EP.MIAd.EC, digits=2)
Se.EP.MIAd.EC <- se(Sub.Eggs.MIAd.EC$EggsP)
Se.EP.MIAd.EC <- round(Se.EP.MIAd.EC, digits=2)

Sub.Eggs.MIAd.SB <- subset(Sub.Eggs.MIAd, Nger == "TB", select=c(Nger,EggsP))
Me.EP.MIAd.TB <- mean(Sub.Eggs.MIAd.SB$EggsP, na.mr=FALSE)
Me.EP.MIAd.TB <- round(Me.EP.MIAd.TB, digits=2)
Se.EP.MIAd.TB <- se(Sub.Eggs.MIAd.SB$EggsP)
Se.EP.MIAd.TB <- round(Se.EP.MIAd.TB, digits=2)

Sub.Eggs.MIAd.SB <- subset(Sub.Eggs.MIAd, Nger == "TE", select=c(Nger,EggsP))
Me.EP.MIAd.TE <- mean(Sub.Eggs.MIAd.SB$EggsP, na.mr=FALSE)
Me.EP.MIAd.TE <- round(Me.EP.MIAd.TE, digits=2)
Se.EP.MIAd.TE <- se(Sub.Eggs.MIAd.SB$EggsP)
Se.EP.MIAd.TE <- round(Se.EP.MIAd.TE, digits=2)

Sub.Eggs.MIAd.SB <- subset(Sub.Eggs.MIAd, Nger == "TS", select=c(Nger,EggsP))
Me.EP.MIAd.TS <- mean(Sub.Eggs.MIAd.SB$EggsP, na.mr=FALSE)
Me.EP.MIAd.TS <- round(Me.EP.MIAd.TS, digits=2)
Se.EP.MIAd.TS <- se(Sub.Eggs.MIAd.SB$EggsP)
Se.EP.MIAd.TS <- round(Se.EP.MIAd.TS, digits=2)

Sub.Eggs.MIAd.SB <- subset(Sub.Eggs.MIAd, Nger == "TT", select=c(Nger,EggsP))
Me.EP.MIAd.TT <- mean(Sub.Eggs.MIAd.SB$EggsP, na.mr=FALSE)
Me.EP.MIAd.TT <- round(Me.EP.MIAd.TT, digits=2)
Se.EP.MIAd.TT <- se(Sub.Eggs.MIAd.SB$EggsP)
Se.EP.MIAd.TT <- round(Se.EP.MIAd.TT, digits=2)

####Kruskall-Wallis test calculation####
KTMIAd = kruskal.test(Sub.Eggs.MIAd$EggsP ~ Sub.Eggs.MIAd$Nger)

####Dunn test calculation####
DTMIAd = dunnTest(Sub.Eggs.MIAd$EggsP ~ Sub.Eggs.MIAd$Nger, method="bonferroni")

DTMIAd.Comparison <- DTMIAd$res$Comparison
DTMIAd.Padj <- round (DTMIAd$res$P.adj, digits=5)
KrusData = data.frame(DTMIAd.Comparison, DTMIAd.Padj)
RND = nrow(DTMIAd$res)
  
  

  krustable=kable(KrusData[1:RND,])

Descriptive statistics

Non parametic test

Dunn (1964) Kruskal-Wallis multiple comparison p-values adjusted with the Bonferroni method:

if (KTMIAd$p.value>0.05) {
dif="There is no significative differences (P<0.05) between treatments (P<0.05)"
krustable="0"
} else {
dif="There is significative differences between treatments (P<0.05)."
krustable=kable(KrusData[1:RND,])
}

There is significative differences between treatments (P<0.05).

Including Plots

You can also embed plots, for example:

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.

DTMIAd$dtres

##  [1] "  Kruskal-Wallis rank sum test"                                                 
##  [2] ""                                                                               
##  [3] "data: x and g"                                                                  
##  [4] "Kruskal-Wallis chi-squared = 29.3877, df = 4, p-value = 0"                      
##  [5] ""                                                                               
##  [6] ""                                                                               
##  [7] "                             Comparison of x by g                              "
##  [8] "                                 (Bonferroni)                                  "
##  [9] "Col Mean-|"                                                                     
## [10] "Row Mean |         EC         TB         TE         TS"                         
## [11] "---------+--------------------------------------------"                         
## [12] "      TB |   5.264338"                                                          
## [13] "         |    0.0000*"                                                          
## [14] "         |"                                                                     
## [15] "      TE |   3.020269  -2.244068"                                               
## [16] "         |    0.0253*     0.2483"                                               
## [17] "         |"                                                                     
## [18] "      TS |   3.496750  -1.767587   0.476480"                                    
## [19] "         |    0.0047*     0.7713     1.0000"                                    
## [20] "         |"                                                                     
## [21] "      TT |   3.588972  -1.675365   0.568702   0.092221"                         
## [22] "         |    0.0033*     0.9386     1.0000     1.0000"                         
## [23] ""                                                                               
## [24] "alpha = 0"                                                                      
## [25] "Reject Ho if p <= alpha"