Unify parameter naming conventions

[simon-smart88]

e.g. prepare_data() uses camelCase, snake_case and dot.notation

We'll need to figure out a way to provide backwards compatibility but there must be a way to handle that

[simon-smart88]

Something like this:

my_func <- function(x.old = NULL, x_new = NULL, yold = NULL, y_new = 10) {
  if (!is.null(x.old) && missing(x_new)){
    x_new <- x.old
    message("x.old is now deprecated please use x_new instead")
  }
    if (!is.null(yold) && missing(y_new)){
    y_new <- yold
    message("yold is now deprecated please use y_new instead")
  }

  x_new * y_new
}

my_func(x.old = 5, yold = 2)

[simon-smart88]

• mesh.args > mesh_args in build_mesh()
• newdata > new_data in predict_uncertainty()

Various in the priors list of fit_model. This may need a different approach to the above example, and whilst we are at it, is the prior_ necessary?:

• priormean_intercept > prior_mean_intercept
• priorsd_intercept > prior_sd_intercept
• priormean_slope > prior_mean_slope
• priorsd_slope > prior_sd_slope
• prior_iideffect_sd_max > prior_iid_effect_sd_max
• prior_iideffect_sd_prob > prior_iid_effect_sd_prob

In as.disag_data:

• coordsForFit > coords_for_fit
• coordsForPrediction > coords_for_prediction
• startendindex > start_end_index