calc_det_rate: Calculate detection rate of pathogens
In MartinHoldrege/turnr: Normalization of Test Utilization Rate

Description Usage Arguments Value Examples

Calculate the percentage of total tests that are of a specific pathogen using the output from the calc_path_TURN function. It is calculated as Y for the pathogen divided by total Y. Since the Ys are calculate with the same denominator this is equivelant to tests for that pathogen/total tests. A three week moving average is applied to the numerator and denominator prior to calculation.

calc_det_rate(
  df,
  group_vars = vars(TargetName),
  return_week = TRUE,
  window = 3
)

`df`	dataframe with at least columns of "InstrumentVersion", "epi_n_days", "Y", "path_Y", "epidate", and any other columns included in group_vars.
`group_vars`	names of columns to group by, wrapped in vars(). Must included TargetName and can also include other columns to group by (e.g. a column defining regions).
`return_week`	logical whether output should include epiweek and epiyear columns
`window`	width of the window over which to apply rolling window sum to calculate detection rate.

data frame that includes a column 'det_rate', which is the detection rate (in percent), and TUR_mws which is the moving window sum of TUR

###############################################
############## Generating data ################
national_list <- calc_TURN(TUR_dat, return_means = TRUE)
means <- national_list$means
# national TURN
TURN_national <- national_list$df

# regional (state) TURN
site_info <- get_site_info(rp_raw)
TURN_region <- calc_TURN(TUR_dat,
                         group_vars = vars(InstrumentVersion, Region),
                         site_info = site_info,
                         means = means)

# calculate TURN for each pathogen -- national
path_turn_national <- calc_path_TURN(df = path_dat,
               TURN_df = TURN_national,
               means = means)

# calculate TURN for each pathogen -- regional
path_turn_region <- calc_path_TURN(df = path_dat,
               TURN_df = TURN_region,
               means = means,
               group_vars = vars(InstrumentVersion, Region),
               site_info = site_info)

###############################################
############## detection rate ################

# calculate detection rate--national
calc_det_rate(path_turn_national)
# calculate detection rate--regional
calc_det_rate(path_turn_region, group_vars = vars(TargetName, Region))