Use of summarySE function for graph construction in ggplot2

Question

Hello, I am looking for an aid to improve a script in R. I develop it with the help of the ggplot2 package. I have some errors and would like to get some feedback. In the study, I evaluated the effect of intra- and interspecific interaction between two species of tadpoles with two size classes "p" and "g" on the use of spatial resources through two response variables: vertical displacement (sec) and horizontal displacement (cm).

Mistakes:

• In the execution of the summarySE function: "/Warning message:In Qt(conf.interval/2 + 0.5, datac$N - 1) Nans produced"

• When executing Legend.title=element_blank(): Error: Unexpected Symbol in:"Legend.title=element_blank() Legend.title"

follows the script

#Importar dados. Pacotes para o gráfico
pmed<-read.table("https://drive.google.com/open?id=1cET5cROSb-_D-cZYud3yKBHGR-qamind",header=T, sep=',') 
require(Rmisc)
require(ggplot2)
require(EnvStats)
require(sciplot)
require(dplyr)
summarypmed <- summarySE(pmed, measurevar="PV", groupvars=c("ID","INT"),na.rm=T)
# gráfico 1
                graf1 <- ggplot(summarypmed, aes(x=INT, y= PV, fill=INT)+ facet_wrap(~INT) +  
                geom_dotplot(binwidth=0.05,binaxis="y",stackdir = "center") +                  
                geom_errorbar(aes (ymin=PV.y-se,ymax=PV.y+se),width = 0.25,size=0.25)+         
                  xlab("Tratamentos") +                  
                  ylab(" Posição Vertical (cm)") +                  
                  geom_text(aes(label = paste("N", "==",N,sep = "")), 
                                              parse = TRUE, y=-0.15) +
                  geom_point(aes(y=PV.y), size=1,show.legend = F) +
                  theme_bw () +                  
                  scale_fill_manual(values=c("grey85","grey30")) +     
                    theme(axis.ticks.x=element_blank(),                          
                    axis.title.x=element_blank(),                    
                    axis.text=element_text(size=7),                    
                    axis.text.y=element_text(size=10),                    
                    axis.text.x=element_blank(),                    
                    axis.title.y=element_text(size=11),                    
                    plot.title=element_text(size=12, hjust = 0.5),                    
                    panel.grid=element_blank(),                    
                    plot.title=element_text(vjust=2),     
                    legend.title=element_blank())

Answer 1

This problem has no solution with the provided dataset. The function help summarySE says the following (my griffin):

Gives Count, Mean, standard deviation, standard error of the Mean, and Confidence interval (default 95%).

The three measures I highlighted above are measures of dispersion or variability. All three of these measures depend on the sample variance. The sampling variance formula is given by

Note that the sum is divided by n-1. So in order to measure variability in a data set, we need at least two observations. After all, if n=1, we’ll have a split by zero.

In your original question, by grouping the data by ID (groupvars=c("ID","INT"), you are saying that you want to calculate the variability per ID of the subjects. But look at the following code, where I count the number of subjects per ID:

library(dplyr)
pmed %>%
  select(ID) %>%
  count()
 ID freq
  1    2
  2    2
  3    2
  4    2
  5    2
  6    1
  7    1
  8    2
  9    1
 10    2
 11    2
 12    2
 13    2
 15    2
 16    1
 17    1
 18    1
 19    1
 20    1
 21    1
 22    1
 23    1
 24    1
 25    1
 26    1
 27    1
 29    1
 30    1

Many Ids have only one subject. Therefore, it is impossible to calculate a measure of variability in these cases, as data is missing. That’s why you got a Warning regarding NaN (acronym for Not to NUmber) that are created.