Random script converting symbols and numbers to just numbers

cat_help_symbols_to_nums.R

# load package
library(dplyr)
library(tidyr)

# read in data
d <- readRDS('~/Desktop/subs_GUD')

glimpse(d)

# need to group by tray1,day, site, trayno, type
# the subject column has the correct grouping but the identifier is not numeric - it goes 1-9 then uses symbols (long story).
# these just need to be consecutive numbers to represent the visit number for that tray, for that day at that site etc

# lets have an easy example
x <- c(1,1,1,2,2,2,3,3,3,'a','a','a')

# want these to be 1,2,3,4 etc
nums <- 1:length(unique(x))
as.character(factor(x, labels = 1:length(unique(x))))
# works!!!

x <- d$subject
nums <- 1:length(unique(x))
as.character(factor(x, levels = unique(x), labels = 1:length(unique(x))))

# method 1
d <- group_by(d, tray1, day, site, trayno, type) %>%
  mutate(subject2 = as.character(factor(subject, levels = unique(x), labels = 1:length(unique(subject))))) %>%
  ungroup()

# method 2
d <- mutate(d, subject3 = group_indices(d, factor(subject, levels = unique(subject)), tray1, day, site, trayno, type)) %>%
  ungroup()

# essentially when characters are coerced into factors the levels of the factor are assigned a certain way, and both method 1 and method 2 assign symbols first (i.e. ! = 1, ? = 2, 1 = 3, instead of 1 = 1, 2 = 2 etc)
# so I had to change the levels to be unique(x) for method 1 and method 2