Run formulae in loops and handle error

How to set up formulae from strings, and log the errors without breaking the loop

Create logs with logr

library(logr)

# Create temp file location
# create log 
tmp <- file.path("/cloud/project/test.log")
# Open log
# once open, can write stuff in it
lf <- log_open(tmp)
lf
# Send message to log
log_print("High Mileage Cars Subset")

# Close log
# once closed, need to open again to write in the same log
log_close()

An example combined with the loop:

for (i in 1:10) {
  tryCatch({
    print(i)
    if (i==7) stop("Urgh, the iphone is in the blender !")
  }, 
  error=function(e){
    # print to the log
    log_print(paste0('error at point ', i, '\n'))
    log_print(paste0("ERROR :",conditionMessage(e), "\n"))
  })
}

Create formula list

paste0(c('a','b','c'), ' ~ fp(age)')

# load the data
d_nosup <- read_csv("data/nutrient_nosup_spade.csv")
var_nosup <- colnames(d_nosup)[6:44]
fml_nosup_list <- paste0(var_nosup, ' ~ fp(age)')
fml <- as.formula('Fullk ~ fp(age)')

Put together

# create log 
log_nosup_male <- file.path("/cloud/project/log_nosup_male.log")

# Open log
log_open(log_nosup_male)


for (i in 1:length(fml_nosup_list)) {
  varname <- var_nosup[i]
  
  tryCatch({
    
    fml <- fml_nosup_list[i]
    fml <- as.formula(fml)
    
    f.spade(
      frml.ia = fml, # model for intake amounts,
      frml.if = "no.if", 
      prb = c(25, 50, 75, 95, 97.5)/100,
      data = d_nosup,
      min.age = 18,
      max.age = 80,
      sex.label = "male", 
      seed = 29062020,
      spade.output.path = "output_nutrient_nosup"
    )
    
  }, 
  
  error=function(e){
    # print to the log
    log_print(paste0('Error at variable ', i, ': ', 
                     # mark which variable it is
                     varname, ' : ',
                     #also print the error message
                     conditionMessage(e),'\n'))
    # log_print(paste0("ERROR :",conditionMessage(e), "\n"))
  })
}

# close log
log_close()