tikatuwq: basic workflow

library(tikatuwq)

# Try to make wq_demo available even when the package
# cannot be temporarily reinstalled during pkgdown build.
ok <- FALSE
try({
  utils::data("wq_demo", package = "tikatuwq", envir = environment())
  ok <- exists("wq_demo", inherits = FALSE)
}, silent = TRUE)

if (!ok) {
  # Fallback: read example CSV shipped with the package
  csv <- system.file("extdata", "exemplo_chamagunga.csv", package = "tikatuwq")
  if (nzchar(csv)) {
    wq_demo <- read_wq(csv)
    ok <- TRUE
  }
}

if (!ok) {
  # Last resort: small synthetic dataset (schema-compatible)
  set.seed(1)
  wq_demo <- data.frame(
    data = as.Date("2025-01-01") + 0:9,
    rio = "Demo",
    ponto = paste0("P", seq_len(10)),
    turbidez = runif(10, 1, 50),
    od = runif(10, 5, 9),
    pH = runif(10, 6.5, 8.5),
    temperatura = runif(10, 20, 28),
    condutividade = runif(10, 50, 300),
    stringsAsFactors = FALSE
  )
}

# Coerce common numeric columns defensively (some example files may carry strings)
num_candidates <- c(
  "turbidez","od","pH","temperatura","condutividade",
  "dbo","dbo5","nitrato","fosforo","amonia",
  "coliformes","coliformes_totais","coliformes_termotolerantes"
)
for (nm in intersect(num_candidates, names(wq_demo))) {
  suppressWarnings({ wq_demo[[nm]] <- as.numeric(wq_demo[[nm]]) })
}

head(wq_demo)
#>   ponto       data   ph   od turbidez  dbo coliformes p_total nt_total
#> 1    P1 2024-06-07 7.08 5.33     63.8 5.38        331   0.080     1.30
#> 2    P1 2024-06-27 6.79 8.29     35.7 1.46         98   0.348     3.69
#> 3    P1 2024-01-14 8.43 4.23     60.6 1.22       3712   0.313     4.25
#> 4    P1 2024-07-13 8.30 6.21     50.7 4.09        200   0.447     2.54
#> 5    P1 2024-06-18 7.88 7.99     57.1 2.39         66   0.340     2.00
#> 6    P2 2024-02-19 8.09 4.61      1.0 4.11       3930   0.371     1.31
#>   temperatura tds
#> 1        23.0 249
#> 2        21.2 329
#> 3        25.6 480
#> 4        20.2 731
#> 5        28.4 201
#> 6        27.0 724

ok_iqa <- TRUE
df <- tryCatch({
  wq_demo |>
    validate_wq() |>
    iqa(na_rm = TRUE)
}, error = function(e) {
  ok_iqa <<- FALSE
  message("iqa() failed in vignette build: ", conditionMessage(e))
  wq_demo |>
    validate_wq()
})

conf <- tryCatch({
  conama_check(df, classe = "2")
}, error = function(e) {
  message("conama_check() failed in vignette build: ", conditionMessage(e))
  NULL
})

if (!is.null(conf)) head(conf)
#>   ponto       data   ph   od turbidez  dbo coliformes p_total nt_total
#> 1    P1 2024-06-07 7.08 5.33     63.8 5.38        331   0.080     1.30
#> 2    P1 2024-06-27 6.79 8.29     35.7 1.46         98   0.348     3.69
#> 3    P1 2024-01-14 8.43 4.23     60.6 1.22       3712   0.313     4.25
#> 4    P1 2024-07-13 8.30 6.21     50.7 4.09        200   0.447     2.54
#> 5    P1 2024-06-18 7.88 7.99     57.1 2.39         66   0.340     2.00
#> 6    P2 2024-02-19 8.09 4.61      1.0 4.11       3930   0.371     1.31
#>   temperatura tds      IQA ph_ok ph_status ph__lim_min ph__lim_max ph__delta
#> 1        23.0 249 8.169772  TRUE        ok           6           9         0
#> 2        21.2 329 8.772986  TRUE        ok           6           9         0
#> 3        25.6 480 7.195704  TRUE        ok           6           9         0
#> 4        20.2 731 8.022852  TRUE        ok           6           9         0
#> 5        28.4 201 8.789324  TRUE        ok           6           9         0
#> 6        27.0 724 7.422467  TRUE        ok           6           9         0
#>   od_ok        od_status od__lim_min od__lim_max od__delta turbidez_ok
#> 1  TRUE               ok           5          NA      0.00        TRUE
#> 2  TRUE               ok           5          NA      0.00        TRUE
#> 3 FALSE abaixo_do_minimo           5          NA     -0.77        TRUE
#> 4  TRUE               ok           5          NA      0.00        TRUE
#> 5  TRUE               ok           5          NA      0.00        TRUE
#> 6 FALSE abaixo_do_minimo           5          NA     -0.39        TRUE
#>   turbidez_status turbidez__lim_min turbidez__lim_max turbidez__delta dbo_ok
#> 1              ok                NA               100               0  FALSE
#> 2              ok                NA               100               0   TRUE
#> 3              ok                NA               100               0   TRUE
#> 4              ok                NA               100               0   TRUE
#> 5              ok                NA               100               0   TRUE
#> 6              ok                NA               100               0   TRUE
#>        dbo_status dbo__lim_min dbo__lim_max dbo__delta coliformes_ok
#> 1 acima_do_maximo           NA            5       0.38          TRUE
#> 2              ok           NA            5       0.00          TRUE
#> 3              ok           NA            5       0.00         FALSE
#> 4              ok           NA            5       0.00          TRUE
#> 5              ok           NA            5       0.00          TRUE
#> 6              ok           NA            5       0.00         FALSE
#>   coliformes_status coliformes__lim_min coliformes__lim_max coliformes__delta
#> 1                ok                  NA                1000                 0
#> 2                ok                  NA                1000                 0
#> 3   acima_do_maximo                  NA                1000              2712
#> 4                ok                  NA                1000                 0
#> 5                ok                  NA                1000                 0
#> 6   acima_do_maximo                  NA                1000              2930
#>   p_total_ok  p_total_status p_total__lim_min p_total__lim_max p_total__delta
#> 1      FALSE acima_do_maximo               NA             0.05          0.030
#> 2      FALSE acima_do_maximo               NA             0.05          0.298
#> 3      FALSE acima_do_maximo               NA             0.05          0.263
#> 4      FALSE acima_do_maximo               NA             0.05          0.397
#> 5      FALSE acima_do_maximo               NA             0.05          0.290
#> 6      FALSE acima_do_maximo               NA             0.05          0.321

if (isTRUE(ok_iqa)) {
  plot_iqa(df)
}

conf_long <- tryCatch(conama_summary(df, classe = "2"), error = function(e) NULL)
if (!is.null(conf_long)) head(conf_long)
#> # A tibble: 6 × 7
#>   parametro valor lim_min lim_max status ok    delta
#>   <chr>     <dbl>   <dbl>   <dbl> <chr>  <lgl> <dbl>
#> 1 ph         7.08       6       9 ok     TRUE      0
#> 2 ph         6.79       6       9 ok     TRUE      0
#> 3 ph         8.43       6       9 ok     TRUE      0
#> 4 ph         8.3        6       9 ok     TRUE      0
#> 5 ph         7.88       6       9 ok     TRUE      0
#> 6 ph         8.09       6       9 ok     TRUE      0

# Avoid running nested rendering during vignette build on CRAN
out_file <- render_report(df)
out_file

if (eval_interactive) {
  # Minimal example dataset with coordinates
  df_map <- data.frame(
    rio = c("Buranhem","Chamagunga"),
    ponto = c("P1","P2"),
    data = as.Date(c("2025-09-20","2025-09-21")),
    latitude  = c(-16.435, -16.498),
    longitude = c(-39.062, -39.080),
    iqa = c(72, 58)
  )

  plot_map(
    df_map,
    popup_cols = c("rio","ponto","data","iqa"),
    color_by = "iqa"
  )
}

if (eval_interactive) {
  plot_map(
    df_map,
    popup_cols = c("rio","ponto","data","iqa"),
    cluster = FALSE,
    tiles = "CartoDB.Positron"
  )
}