Improve code style for readability

[annakrystalli]

I feel some of the code could be cleaner:

• [x] avoid long lines

• [ ] avoid pipes within function calls, e.g.

  head(mean_ens |>
  dplyr::filter(
  output_type %in% c("quantile", "median"),
  output_type_id %in% c(0.01, 0.1, 0.25, 0.75, 0.9, 0.99, NA),
  origin_date == "2022-12-12",
  location == "US",
  horizon == 7
  ))

  Better to use:

  mean_ens |>
  dplyr::filter(
  output_type %in% c("quantile", "median"),
  output_type_id %in% c(0.01, 0.1, 0.25, 0.75, 0.9, 0.99, NA),
  origin_date == "2022-12-12",
  location == "US",
  horizon == 7
  ) |>
  head()

• [ ] Loading libraries but then using hubEnsembles:: in the code. I feel it will look better and still be quite clear to only load dplyr (which is used repeatedly throughout and a very familiar package to users) and hubEnsembles and avoid using :: when calling functions from those packages. All other packages we use :: to clarify where the functions are coming from.

As none of these changes actually affect the results, they are just for better style and visual clarity, and to avoid potential merge confilcts with the current open branches, I would be happy to take a look at this once the manuscript is nearly done (and decisions re Infectious-Disease-Modeling-Hubs/hubEnsembles-manuscript#11 & Infectious-Disease-Modeling-Hubs/hubEnsembles-manuscript#12 have been made

[elray1]

additionally, standardize indentation amounts (currently there is a mix of 2 spaces, 4 spaces, and 6 spaces)

[elray1]

also: use double quotes consistently, consistency of spacing around operators and specification of function arguments like =