Argument "by" is missing, with no default

Question

Here is my reprodicible sample and code:

set.seed(42)
n <- 1000
dat <- data.frame(Confidence=1:5, 
                  Type = ("Your confidence"),
                  Correct=sample(0:1, n, replace=TRUE)
)

dat %>%
  group_by(Confidence,Type) %>%
  summarize(Accuracy = mean(Correct),
            se = (sd(Correct, na.rm = TRUE)/sqrt(n())))%>%
  ggplot(aes(x=Confidence, y= Accuracy, color = Type, group = Type)) +
  geom_line() + 
  geom_errorbar(aes(ymin = Accuracy - se, ymax = Accuracy + se), color = "Black", size = .15, width = .3) + 
  geom_point(size = 2)+ 
  scale_y_continuous(labels = scales::percent)+ 
  labs(y= "YOU ARE RIGHT ___% OF THE TIME.", x = "WHEN YOU ARE ___ % CONFIDENT IN YOUR ANSWER...")+
  theme_minimal() + 
  scale_color_brewer(palette = "Set1")

When I run this i get this error:

Error in summarize(., Accuracy = mean(Correct), se = (sd(Correct, na.rm = TRUE)/sqrt(n()))) : 
  argument "by" is missing, with no default

Has anyone seen this error before and know how to fix it? Thank you!

How to make a reproducible example: https://reprex.tidyverse.org/ — Baraliuh, Feb 24 '22 at 20:14

score 7 · Accepted Answer · answered Feb 24 '22 at 20:18

summarize is found in multiple packages and if we load many packages that have the summarize (depending on the order of loading the package) it could mask the function. e.g. the error seems to be coming from Hmisc::summarize

> dat %>%
+   group_by(Confidence,Type) %>%
+   Hmisc::summarize(Accuracy = mean(Correct),
+             se = (sd(Correct, na.rm = TRUE)/sqrt(n())))%>%
+   ggplot(aes(x=Confidence, y= Accuracy, color = Type, group = Type)) +
+   geom_line() + 
+   geom_errorbar(aes(ymin = Accuracy - se, ymax = Accuracy + se), color = "Black", size = .15, width = .3) + 
+   geom_point(size = 2)+ 
+   scale_y_continuous(labels = scales::percent)+ 
+   labs(y= "YOU ARE RIGHT ___% OF THE TIME.", x = "WHEN YOU ARE ___ % CONFIDENT IN YOUR ANSWER...")+
+   theme_minimal() + 
+   scale_color_brewer(palette = "Set1")
Error in Hmisc::summarize(., Accuracy = mean(Correct), se = (sd(Correct,  : 
  argument "by" is missing, with no default

If we change it to dplyr::summarize

dat %>%
  group_by(Confidence,Type) %>%
  dplyr::summarize(Accuracy = mean(Correct),
            se = (sd(Correct, na.rm = TRUE)/sqrt(n())))%>%
  ggplot(aes(x=Confidence, y= Accuracy, color = Type, group = Type)) +
  geom_line() + 
  geom_errorbar(aes(ymin = Accuracy - se, ymax = Accuracy + se), color = "Black", size = .15, width = .3) + 
  geom_point(size = 2)+ 
  scale_y_continuous(labels = scales::percent)+ 
  labs(y= "YOU ARE RIGHT ___% OF THE TIME.", x = "WHEN YOU ARE ___ % CONFIDENT IN YOUR ANSWER...")+
  theme_minimal() + 
  scale_color_brewer(palette = "Set1")

-output

Argument "by" is missing, with no default

1 Answers1