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Time-series and summary utilities

Source: vignettes/time-series-utilities.qmd

Introduction

preMetabolizer includes utilities for regularizing logger data, converting between UTC and solar time, assigning seasons, flagging outliers, and summarizing variability or flow distributions.

Fill missing timesteps

even_timesteps() builds a complete timestamp sequence from the observed time step and inserts rows where observations are missing.

logger <- tibble::tibble(
  DateTime_UTC = as.POSIXct(
    c(
      "2024-06-01 00:00:00",
      "2024-06-01 01:00:00",
      "2024-06-01 03:00:00"
    ),
    tz = "UTC"
  ),
  temp_water = c(18.1, 18.0, 17.8)
)

even_timesteps(logger)
#> # A tibble: 4 × 2
#>   DateTime_UTC        temp_water
#>   <dttm>                   <dbl>
#> 1 2024-06-01 00:00:00       18.1
#> 2 2024-06-01 01:00:00       18  
#> 3 2024-06-01 02:00:00       NA  
#> 4 2024-06-01 03:00:00       17.8

For multi-site data, provide the site column so each site is completed independently.

multi_site <- tibble::tibble(
  Site = c("A", "A", "A", "B", "B"),
  DateTime_UTC = as.POSIXct(
    c(
      "2024-06-01 00:00:00",
      "2024-06-01 01:00:00",
      "2024-06-01 03:00:00",
      "2024-06-01 00:00:00",
      "2024-06-01 00:30:00"
    ),
    tz = "UTC"
  )
)

even_timesteps(multi_site, site_col = "Site")
#> # A tibble: 6 × 2
#>   DateTime_UTC        Site 
#>   <dttm>              <chr>
#> 1 2024-06-01 00:00:00 A    
#> 2 2024-06-01 01:00:00 A    
#> 3 2024-06-01 02:00:00 A    
#> 4 2024-06-01 03:00:00 A    
#> 5 2024-06-01 00:00:00 B    
#> 6 2024-06-01 00:30:00 B

Convert UTC and solar time

convert_UTC_to_solartime() and convert_solartime_to_UTC() move between UTC and local solar time at a site longitude. Mean solar time is the time basis expected by stream metabolism models.

utc <- as.POSIXct("2024-06-21 18:00:00", tz = "UTC")

solar <- convert_UTC_to_solartime(
  utc,
  longitude = -96.6,
  time.type = "mean solar"
)

solar
#> [1] "2024-06-21 11:34:39 UTC"

convert_solartime_to_UTC(
  solar,
  longitude = -96.6,
  time.type = "mean solar"
)
#> [1] "2024-06-21 18:00:00 UTC"

Assign seasons

get_season() classifies dates into fixed northern-hemisphere astronomical seasons.

dates <- as.Date(c(
  "2024-01-15",
  "2024-04-15",
  "2024-07-15",
  "2024-10-15"
))

tibble::tibble(
  date = dates,
  season = get_season(dates)
)
#> # A tibble: 4 × 2
#>   date       season
#>   <date>     <chr> 
#> 1 2024-01-15 Winter
#> 2 2024-04-15 Spring
#> 3 2024-07-15 Summer
#> 4 2024-10-15 Fall

Flag potential outliers

flag_z() applies a moving-window robust Z-score. The default return is a character flag vector. Set return_z = TRUE when you also want the Z-scores.

temperature <- c(18.1, 18.2, 18.0, 18.3, 29.9, 18.4, 18.2)

flag_z(temperature, width = 5)
#> [1] NA  NA  NA  NA  "Z" NA  NA

flag_z(temperature, width = 5, return_z = TRUE)
#> $z
#> [1]  0.0000000  0.6289591 -1.2804234  0.0000000 78.6786536  0.8538437 -1.0015789
#> 
#> $flag
#> [1] NA  NA  NA  NA  "Z" NA  NA

Summary statistics

calc_cv() calculates the coefficient of variation. Use robust = TRUE to summarize relative variability with the median and MAD instead of mean and standard deviation.

discharge <- c(0.12, 0.18, 0.15, 1.4, 0.09)

calc_cv(discharge)
#> [1] 146.0615
calc_cv(discharge, robust = TRUE)
#> [1] 20

calc_mode(c("riffle", "run", "riffle", "pool", "run"), multi = "all")
#> [1] "riffle" "run"

Histogram bin widths

calc_bin_width() implements several common histogram rules. This is helpful when plotting distributions that should use a consistent, data-driven bin width.

set.seed(1)
values <- stats::rexp(200)

calc_bin_width(values, method = "fd")
#> [1] 0.3417391
calc_bin_width(values, method = "doane")
#> [1] 0.4033973
ggplot(tibble::tibble(values = values), aes(values)) +
  geom_histogram(
    binwidth = calc_bin_width(values, method = "fd"),
    color = "white",
    fill = "#2c7fb8"
  ) +
  labs(x = "Value", y = "Count") +
  theme_bw()

Flow exceedance probabilities

calc_exceedance_prob() ranks flows with the Weibull plotting-position formula. Higher flows receive lower exceedance probabilities. The C++ implementation, rcpp_calc_exceedance_prob(), returns the same shape and is useful for large vectors.

flows <- tibble::tibble(
  flow_cms = c(10, 5, 0, 15, 8, NA, 0, 20)
) |>
  mutate(
    exceedance = calc_exceedance_prob(flow_cms),
    exceedance_no_zero = rcpp_calc_exceedance_prob(flow_cms, rm.zero = TRUE)
  )

flows
#> # A tibble: 8 × 3
#>   flow_cms exceedance exceedance_no_zero
#>      <dbl>      <dbl>              <dbl>
#> 1       10      0.375              0.5  
#> 2        5      0.625              0.833
#> 3        0      0.812             NA    
#> 4       15      0.25               0.333
#> 5        8      0.5                0.667
#> 6       NA     NA                 NA    
#> 7        0      0.812             NA    
#> 8       20      0.125              0.167
flows |>
  filter(!is.na(exceedance_no_zero)) |>
  ggplot(aes(exceedance_no_zero, flow_cms)) +
  geom_point(color = "#2c7fb8", size = 2) +
  scale_x_continuous(labels = \(x) paste0(round(100 * x), "%")) +
  labs(
    x = "Exceedance probability",
    y = "Flow"
  ) +
  theme_bw()