Deprecated functions from dplyr: funs

[dfalster]

dplyr no longer uses mutate_at(vars(...), funs(...)) syntax, which is used in the custom_R_code from Dwyer_2017. Results in a warning, which will shortly elevate to failure as

options(warn=2)
remake::make("Dwyer_2017")
[ BUILD ] Dwyer_2017                     |  Dwyer_2017 <- dataset_process("data/Dwyer_2017/data.csv", Dwyer_2017_con...
Error: (converted from warning) `funs()` was deprecated in dplyr 0.8.0.
Please use a list of either functions or lambdas: 

  # Simple named list: 
  list(mean = mean, median = median)

  # Auto named with `tibble::lst()`: 
  tibble::lst(mean, median)

  # Using lambdas
  list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated

Looking ay the custom_R_code for Dwyer_2017 we have

data <- read_csv("data/Dwyer_2017/data.csv")

data %>% 
     group_by(species, remnant) %>% 
     mutate(
         count_plants = sum(count), 
         seed_mass = round(seed_mass,6), 
         max_height = round(max_height,6), 
         specific_leaf_area = round(specific_leaf_area,6)
     ) %>% 
     mutate_at(vars(count_plants,max_height, specific_leaf_area),
               funs(replace(.,duplicated(.),NA))) %>% 
     ungroup() %>% 
     group_by(species) %>% 
     mutate_at(vars(seed_mass),funs(replace(.,duplicated(.),NA))) %>% 
     ungroup()

Note the custom function has now been formalised as a function replace_duplicates_with_NA

So the line

     mutate_at(vars(count_plants,max_height, specific_leaf_area),
               funs(replace(.,duplicated(.),NA))) %>% 

can be modified as

mutate(
    across(c(count_plants, max_height, specific_leaf_area), replace_duplicates_with_NA))