Evaluate hydrochemical data per location

For a dataset as returned by get_chem, return summary statistics (data availability and/or numeric properties) of the specified hydrochemical variables, for each location.

Usage

eval_chem(
  data,
  chem_var = c("P-PO4", "N-NO3", "N-NO2", "N-NH4", "HCO3", "SO4", "Cl", "Na", "K", "Ca",
    "Mg", "Fe", "Mn", "Si", "Al", "CondF", "CondL", "pHF", "pHL"),
  type = c("avail", "num", "both"),
  uniformity_test = FALSE
)

Arguments

data

An object returned by get_chem.

chem_var

A character vector to select chemical variables for which statistics will be computed. To specify chemical variables, use the codes from the column chem_variable in data.

type

A string defining the requested type of summary statistics. See section 'Value'. Either:

• "avail": availability statistics (the default);

• "num": numeric summary statistics;

• "both": both types will be returned.

uniformity_test

Should the availability statistic pval_uniform_totalspan be added (see section 'Value')? Defaults to FALSE as this takes much more time to calculate than everything else.

Value

A tibble with variables loc_code (see get_locs), chem_variable (character; see Details) and summary statistics (at the level of loc_code x chem_variable) depending on the state of type (type = "both" combines both cases):

With type = "avail" (the default):

• nryears: number of calendar years for which the chemical variable is available (on one date at least)

• nrdates: number of dates at which the chemical variable is available

• firstdate: earliest date at which the chemical variable is available

• lastdate: latest date at which the chemical variable is available

• timespan_years: duration as years from the first calendar year (year of firstdate) to the last calendar year (year of lastdate) with data available

• timespan_totalspan_ratio: the ratio of timespan_years to the 'total span', which is the duration as years from the first to the last calendar year for the whole of data.

• nryears_totalspan_ratio: the ratio of nryears to the 'total span'

• pval_uniform_totalspan: Only returned with uniformity_test = TRUE. p-value of an exact, one-sample two-sided Kolmogorov-Smirnov test for the discrete uniform distribution of the calendar years with data of the chemical variable available within the series of consecutive calendar years defined by the 'total span' (see above). The smaller the p-value, the less uniform the years are spread within the total span. A perfectly uniform spread results in a p-value of 1.

With type = "num": summary statistics based on the chemical values, i.e. excluding the 'combined' level:

• val_min: minimum value

• val_pct10, val_pct25, val_pct50, val_pct75, val_pct90: percentiles

• val_max: maximum value

• val_range: range

• val_mean: mean

• val_geometric_mean: geometric mean. Only calculated when all values are strictly positive.

• unit

• prop_below_loq: the proportion of measurements below the limit of quantification (as derived from below_loq == TRUE), i.e. relative to the total number of measurements for which below_loq is not NA. This statistic neglects measurements with value NA for below_loq! If all measurements have value NA for below_loq, this statistic is set to NA.

Details

For the availability statistics, an extra level "combined" is added in the column chem_variable whenever the arguments data and chem_var imply more than one chemical variable to be investigated. This 'combined' level defines data availability for a water sample as the availability of data for all corresponding chemical variables.

See also

Other functions to evaluate locations: eval_xg3_avail(), eval_xg3_series()

Examples

if (FALSE) { # \dontrun{
watina <- connect_watina()
library(dplyr)
mylocs <- get_locs(watina, area_codes = "ZWA")
mydata <-
  mylocs %>%
  get_chem(watina, "1/1/2010")
mydata %>% arrange(loc_code, date, chem_variable)
mydata %>%
  pull(date) %>%
  lubridate::year(.) %>%
  (function(x) c(firstyear = min(x), lastyear = max(x)))
mydata %>%
  eval_chem(chem_var = c("P-PO4", "N-NO3", "N-NO2", "N-NH4")) %>%
  arrange(desc(loc_code))
mydata %>%
  eval_chem(
    chem_var = c("P-PO4", "N-NO3", "N-NO2", "N-NH4"),
    type = "both"
  ) %>%
  arrange(desc(loc_code)) %>%
  as.data.frame() %>%
  head(10)
mydata %>%
  eval_chem(
    chem_var = c("P-PO4", "N-NO3", "N-NO2", "N-NH4"),
    uniformity_test = TRUE
  ) %>%
  arrange(desc(loc_code)) %>%
  select(loc_code, chem_variable, pval_uniform_totalspan)
# Disconnect:
dbDisconnect(watina)
} # }