Some error bars do not appear on "sciplot" graph

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Some error bars do not appear on "sciplot" graph

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There is a problem when I am making a averages chart in R using the "sciplot" package. For starters, this is the code for a part of my dataset:

dados <- structure(list(Dias = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 
6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 
7L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 
8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 
9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 10L, 10L, 
10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 
10L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 
11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L), .Label = c("0", 
"3", "6", "9", "12", "15", "18", "21", "24", "27", "30"), class = "factor"), 
    Tratamento = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L), .Label = c("Alagado", "Controle"), class = "factor"), 
    Var = c(0.483954721, 0.402513452, 0.512025757, 0.344985618, 
    0.418409264, 0.418409264, 0.511319767, 0.543889494, 0.246440891, 
    0.302144414, 0.34349692, 0.479154807, 0.34349692, 0.34349692, 
    0.415664423, 0.223458159, 0.250861003, 0.434646743, 0.34349692, 
    0.257196387, 0.540148383, 0.517620793, 0.447490544, 0.287040092, 
    0.174128921, 0.489415586, 0.568275611, 0.39165419, 0.529013636, 
    0.374811179, 0.369840511, 0.559673798, 0.506560116, 0.252093219, 
    0.473819853, 0.563274295, 0.532371759, 0.258446375, 0.482760493, 
    0.385915684, 0.40587382, 0.394261898, 0.570618986, 0.418202774, 
    0.342299789, 0.481900239, 0.39861235, 0.378118216, 0.310233914, 
    0.358616211, 0.364058679, 0.395026017, 0.305758233, 0.497028634, 
    0.498580504, 0.245504252, 0.265180056, 0.348491714, 0.216797337, 
    0.348491714, 0.352196, 0.31906076, 0.329692909, 0.434979622, 
    0.412968366, 0.336259781, 0.394290597, 0.391050623, 0.280468087, 
    0.270996386, 0.289080223, 0.351599493, 0.289080223, 0.237839736, 
    0.289080223, 0.423445676, 0.195595218, 0.360309076, 0.289080223, 
    0.165692143, 0.466055527, 0.498216599, 0.612262951, 0.457407711, 
    0.402567153, 0.432520596, 0.446234159, 0.433097588, 0.479705616, 
    0.334278466, 0.220010369, 0.375294032, 0.574471328, 0.377909951, 
    0.34732317, 0.347616995, 0.270351352, 0.477391563, 0.371043001, 
    0.373490196, 0.256574725, 0.298053469, 0.322380312, 0.287292048, 
    0.212319809, 0.24631103, 0.176862546, 0.141438726, 0.242654083, 
    0.242654083, 0.142837656, 0.175949172, 0.175949172, 0.158684528, 
    0.122141631, 0.175949172, 0.164364339, 0.11907127, 0.175949172, 
    0.175949172, 0.283410497, 0.278052602, 0.263745, 0.262582543, 
    0.244684158, 0.263745, 0.263745, 0.263745, 0.263745, 0.263745, 
    0.211983691, 0.036175954, 0.124079823, 0.124079823, 0.124079823, 
    0.124079823, 0.124079823, 0.124079823, 0.124079823, 0.124079823, 
    0.541883571, 0.425976278, 0.472908724, 0.462862966, 0.491197094, 
    0.440611376, 0.553310475, 0.535958712, 0.479224575, 0.388311983, 
    0.337605, 0.337290226, 0.337605, 0.360191501, 0.159098255, 
    0.212415407, 0.445623893, 0.485658868, 0.343586622, 0.416791451, 
    0.466813153, 0.530845846, 0.563399265, 0.446772564, 0.341090484, 
    0.440579265, 0.440579265, 0.440579265, 0.358498545, 0.376635, 
    0.0362885, 0.038825342, 0.069852283, 0.057607035, 0.061824905, 
    0.0454871, 0.061824905, 0.074349388, 0.039976409, 0.064498082, 
    0.204017899, 0.212166919, 0.232099119, 0.20038374, 0.212166919, 
    0.212166919, 0.212166919, 0.212166919, 0.212166919, 0.212166919, 
    0.034938801, 0.034938801, 0.034938801, 0.034938801, 0.034938801, 
    0.034938801, 0.034938801, 0.034938801, 0.034938801, 0.034938801, 
    0.384175286, 0.384175286, 0.384175286, 0.384175286, 0.384175286, 
    0.384175286, 0.384175286, 0.384175286, 0.384175286, 0.384175286, 
    0.049557242, 0.049557242, 0.049557242, 0.049557242, 0.049557242, 
    0.049557242, 0.049557242, 0.049557242, 0.049557242, 0.049557242
    )), row.names = c(NA, -220L), class = "data.frame")

Then I run the following codes:

dados$Dias <- as.factor(dados$Dias)
str(dados)

library(sciplot)

#Gráfico
lineplot.CI(dados$Dias, dados$Var, group = dados$Tratamento, las = 1,
xlab = "Time (days)",
ylab = "Var",
err.width = 0.1, bty = "l")

In the sequence, these warning messages appear and the graph:

Warning messages:
1: In arrows(leg.vals$xvals[CI.seln], CI.plot[, 1], leg.vals$xvals[CI.seln],  :
  zero-length arrow is of indeterminate angle and so skipped
2: In arrows(leg.vals$xvals[CI.seln], CI.plot[, 1], leg.vals$xvals[CI.seln],  :
  zero-length arrow is of indeterminate angle and so skipped
3: In arrows(leg.vals$xvals[CI.seln], CI.plot[, 1], leg.vals$xvals[CI.seln],  :
  zero-length arrow is of indeterminate angle and so skipped

I have done a lot of research on different websites into the meaning of these warnings, but I have not found a satisfactory answer to my situation. It is possible to notice that the last two points of the class "flooded" and the last of "control" do not have the error bars. Would anyone know what might be going on?

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by Marcus Nunes • **17,915** points · Answer 1 · 2019-10-11T11:06:34+00:00

The Warning gives a good idea of what is happening (my griffins):

Warning messages:

1: In Arrows(Leg.vals$xvals[CI.seln], CI.Plot[, 1], Leg.vals$xvals[CI.seln], : zero-length Arrow is of indeterminate Angle and so skipped

2: In Arrows(Leg.vals$xvals[CI.seln], CI.Plot[, 1], Leg.vals$xvals[CI.seln], : zero-length Arrow is of indeterminate Angle and so skipped

3: In Arrows(Leg.vals$xvals[CI.seln], CI.Plot[, 1], Leg.vals$xvals[CI.seln], : zero-length Arrow is of indeterminate Angle and so skipped

There are bars of zero length. Since these bars represent the variability of the data, there are probably cases where there is no variability in them. You can check this with the code below:

library(tidyverse)

dados %>%
  group_by(Dias, Tratamento) %>%
  summarise(desvPad = sd(Var)) %>%
  arrange(desvPad)
## # A tibble: 22 x 3
## # Groups:   Dias [11]
##    Dias  Tratamento desvPad
##    <fct> <fct>        <dbl>
##  1 27    Alagado    0      
##  2 30    Alagado    0      
##  3 30    Controle   0      
##  4 27    Controle   0.00818
##  5 18    Controle   0.0102 
##  6 24    Alagado    0.0138 
##  7 15    Alagado    0.0228 
##  8 18    Alagado    0.0414 
##  9 21    Controle   0.0534 
## 10 15    Controle   0.0549 
## # … with 12 more rows

Note that the combinations of days and treatments that do not have error bars in the graph are precisely those in which the variability is zero. Checking the data set for the 30th, we see that this is true.

dados %>%
  filter(Dias == 30)
##    Dias Tratamento        Var
## 1    30   Controle 0.38417529
## 2    30   Controle 0.38417529
## 3    30   Controle 0.38417529
## 4    30   Controle 0.38417529
## 5    30   Controle 0.38417529
## 6    30   Controle 0.38417529
## 7    30   Controle 0.38417529
## 8    30   Controle 0.38417529
## 9    30   Controle 0.38417529
## 10   30   Controle 0.38417529
## 11   30    Alagado 0.04955724
## 12   30    Alagado 0.04955724
## 13   30    Alagado 0.04955724
## 14   30    Alagado 0.04955724
## 15   30    Alagado 0.04955724
## 16   30    Alagado 0.04955724
## 17   30    Alagado 0.04955724
## 18   30    Alagado 0.04955724
## 19   30    Alagado 0.04955724
## 20   30    Alagado 0.04955724

Therefore, these error bars will never appear using this data set.