Colored Dissolved Organic Matter Rate of Change Analysis

A rate of change is calculated for each station using a seasonal Mann Kendall slope calculation.

get data for params$batch_value

source(here::here(glue::glue("{params$batch_name}/getData.R")))

df <- getData(params$batch_value)

[1] "getting data for Colored Dissolved Organic Matter"

create station statistics dataframe

library(here)
library(lubridate)  # for mdy_hms()
library(pander)  # for display
library(dplyr)  # for %>%
library(tidyr)  # for unnest_wider
source(here("R/seasonalMannKendall.R"))

# add statistics for each station
sample_stats_df <- df %>%
  group_by(ProgramName, LocationID) %>%
  summarize(
    mk_results = list(seasonalMannKendall(SampleDate, ResultValue)),
    n_values = n(),
    mean = mean(ResultValue, na.rm = TRUE),
    min = as.numeric(min(ResultValue, na.rm = TRUE)),
    max = as.numeric(max(ResultValue, na.rm = TRUE)),
    coefficient.of.variation = sd(ResultValue, na.rm = TRUE) / mean(ResultValue, na.rm = TRUE),
    .groups = 'drop'
  )

# unnest the seasonal Mann Kendall results
sample_stats_df <- sample_stats_df %>%
  tidyr::unnest_wider(mk_results)

sample_stats_df <- sample_stats_df %>%
  mutate(
    # create column significant_slope
    significant_slope = ifelse(z <= 0.05, slope, NA_real_),
    pvalue = z
  ) %>%
  # drop unwanted columns added by seasonalMannKendall
  select(
    -z,
    -tau,
    -chi_square
  )

# print(head(sample_stats_df))
# # display sample_stats_df with pander
# pander(sample_stats_df)

save stats to csv

dataDir <- here("data", "exports", params$batch_name)

# create dir if does not exist
if (!dir.exists(dataDir)) {
  dir.create(dataDir)
}

# save file
sample_stats_df %>%
  write.csv(paste0(dataDir, "/", params$batch_value, ".csv"))

plot distribution of slopes

library(ggplot2)

ggplot(sample_stats_df, aes(x = slope)) +
  geom_density(fill = "steelblue", alpha = 0.7) +
  labs(title = "Density Plot of Site Slopes",
       x = "Slope (rate of change)",
       y = "Density (log scale)") +
  theme_minimal()

display with gt

library(gt)
library(scales)
library(tidyselect)  # for all_of()
library(RColorBrewer) # for brewer.pal()

# ── color_column() ─────────────────────────────────────────────────────────────
# gt_tbl   : a gt object that you’ve already created (e.g. `sample_stats_df %>% gt()`)
# df       : the original data.frame (must contain the column you want to color)
# column   : a string, e.g. "slope" or "n_values"
# palette  : a character vector of colours to feed to col_numeric()
#
color_column <- function(gt_tbl, df, column, 
                         palette = c("red", "orange", "yellow", "green", "blue", "violet"),
                         domain = NULL) {
  # 1) Pull out that column’s numeric values
  vals <- df[[column]]
  if (!is.numeric(vals)) {
    stop(sprintf("`%s` is not numeric; data_color() requires a numeric column.", column))
  }
  
  # 2) Compute its min and max (ignoring NA)
  min_val <- min(vals, na.rm = TRUE)
  max_val <- max(vals, na.rm = TRUE)
  if (is.null(domain)) {
    domain <- c(min_val, max_val)
  }
  
  # 3) Call data_color() on the gt table for that single column
  gt_tbl %>%
    data_color(
      columns = all_of(column),
      colors  = col_numeric(
        palette = palette,
        domain  = domain
      )
    )
}
library(dplyr)
library(gt)

# 1) First build your gt table as usual:
gt_tbl <- sample_stats_df %>% 
  gt()

# slope blue (-) to red (+) (0 centered)
tryCatch({
  min_slope <- min(sample_stats_df$slope,  na.rm = TRUE)
  max_slope <- max(sample_stats_df$slope,  na.rm = TRUE)
  max_abs_slope <- max(abs(min_slope), abs(max_slope))
  gt_tbl <- color_column(
    gt_tbl, 
    df     = sample_stats_df, 
    column = "slope",
    palette = rev(brewer.pal(11, "RdBu")),
    domain  = c(-max_abs_slope, max_abs_slope)
  )
}, error = function(e) {
  print("Error in slope color column")
  print(e)
})

# slope blue (-) to red (+) (0 centered)
tryCatch({
  min_slope <- min(sample_stats_df$significant_slope,  na.rm = TRUE)
  max_slope <- max(sample_stats_df$significant_slope,  na.rm = TRUE)
  max_abs_slope <- max(abs(min_slope), abs(max_slope))
  gt_tbl <- color_column(
    gt_tbl, 
    df     = sample_stats_df, 
    column = "significant_slope",
    palette = rev(brewer.pal(11, "RdBu")),
    domain  = c(-max_abs_slope, max_abs_slope)
  )
}, error = function(e) {
  print("Error in significant_slope color column")
  print(e)
})

tryCatch({
  # mean values blue to red (0 centered)
  min_mean <- min(sample_stats_df$mean,  na.rm = TRUE)
  max_mean <- max(sample_stats_df$mean,  na.rm = TRUE)
  max_abs_mean <- max(abs(min_mean), abs(max_mean))
  gt_tbl <- color_column(
    gt_tbl, 
    df     = sample_stats_df, 
    column = "mean",
    palette = rev(brewer.pal(11, "RdBu")),
    domain  = c(-max_abs_mean, max_abs_mean)
  )
}, error = function(e) {
  print("Error in mean color column")
  print(e)
})

tryCatch({
  # n values white to green
  gt_tbl <- color_column(
    gt_tbl, 
    df      = sample_stats_df, 
    column  = "n_values", 
    palette = scales::brewer_pal(palette = "Greens")(9)
  )
}, error = function(e) {
  print("Error in n_values color column")
  print(e)
})

tryCatch({
  # min
  gt_tbl <- color_column(
    gt_tbl, 
    df      = sample_stats_df, 
    column  = "min", 
    palette = scales::brewer_pal(palette = "Blues")(9)
  )
}, error = function(e) {
  print("Error in min color column")
  print(e)
})

tryCatch({
  # max
  gt_tbl <- color_column(
    gt_tbl, 
    df      = sample_stats_df, 
    column  = "max", 
    palette = scales::brewer_pal(palette = "Blues")(9)
  )
}, error = function(e) {
  print("Error in max color column")
  print(e)
})

tryCatch({
  # coefficient.of.variation
  gt_tbl <- color_column(
    gt_tbl, 
    df      = sample_stats_df, 
    column  = "coefficient.of.variation", 
    palette = scales::brewer_pal(palette = "Blues")(9)
  )
}, error = function(e) {
  print("Error in coefficient.of.variation color column")
  print(e)
})

# 4) Render/display:
gt_tbl

ProgramName	LocationID	slope	n_values	mean	min	max	coefficient.of.variation	significant_slope	pvalue
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307545	-0.3058166667	68	16.883662	0.000	43.363	0.4910093	NA	0.280530900
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307546	-0.9614000000	67	23.599627	0.323	55.961	0.4488004	-0.9614000	0.045999021
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307547	-1.1330000000	67	19.527657	0.101	42.548	0.4454291	-1.1330000	0.002274799
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307548	-0.9401818182	67	25.409866	0.267	51.199	0.4500360	NA	0.127035799
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307549	-0.7427375000	66	22.412591	0.434	57.760	0.5445383	NA	0.082347876
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307550	-0.4218482143	66	15.035864	1.212	60.259	0.6622946	NA	0.063306726
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307551	-0.2381883117	66	12.464545	0.267	36.862	0.6119738	NA	0.375651673
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307559	-0.1538989899	66	14.680636	0.045	149.025	1.2618396	NA	0.436124058
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307560	-0.2532500000	65	9.431369	0.076	34.383	0.7307403	NA	0.540544333
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307561	-0.3320000000	65	7.681785	0.073	15.429	0.4764746	NA	0.057337131
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307562	-0.2408958333	66	11.636242	0.000	52.608	0.6049585	NA	0.208395798
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307563	-0.7256875000	68	18.776735	0.128	55.686	0.5370080	-0.7256875	0.044007047
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307564	-0.2519222222	64	10.997938	0.267	29.484	0.4568682	NA	0.490636141
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307566	-0.2310000000	65	12.151538	0.000	43.126	0.5391759	NA	0.202353370
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307574	-0.6580000000	65	13.138862	0.184	42.923	0.5216171	-0.6580000	0.029147611
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307577	-0.2914444444	65	14.217446	0.000	43.262	0.5117157	NA	0.225536978
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307578	-0.1528888889	64	16.501781	0.073	43.704	0.4797157	NA	0.460463934
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307579	-0.7523125000	65	23.470231	0.323	53.872	0.4804131	NA	0.366582209
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307581	-0.4200000000	64	21.032375	0.045	51.101	0.4970035	NA	0.389184629
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307582	-0.4334000000	64	21.652562	0.378	47.845	0.5002435	NA	0.712096743
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307583	-0.1818750000	64	24.221187	0.490	49.595	0.4730671	NA	0.538508971
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307586	-1.0150476190	65	25.806138	0.490	56.690	0.4803962	NA	0.062044063
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307589	-0.2330500000	68	18.868353	0.073	77.187	0.5870526	NA	0.185668732
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307590	-0.8151714286	65	22.835923	0.490	62.425	0.4909733	NA	0.104118030
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307593	-1.0980000000	65	26.889308	0.378	70.250	0.4875921	NA	0.080881374
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307595	-1.0663571429	64	23.096781	0.120	64.223	0.5304060	NA	0.094038478
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307597	-1.5236458333	64	24.792109	0.573	60.870	0.4804925	-1.5236458	0.003558980
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307599	-0.6720000000	62	15.907903	3.491	39.583	0.5455627	NA	0.088508829
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307601	-0.5073333333	64	19.186172	0.323	45.269	0.4825404	NA	0.121037339
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307603	-0.5772777778	65	22.489169	0.212	51.004	0.4801898	NA	0.433916059
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307604	-0.3142500000	64	18.039313	0.434	45.026	0.5685455	NA	0.664200162
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307605	-0.5881388889	64	14.289719	0.184	39.243	0.5464146	NA	0.153753073
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307607	-0.3720888889	64	12.593172	0.184	32.225	0.5149897	NA	0.420112680
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307608	-0.4438000000	68	24.258941	0.017	47.699	0.4071041	NA	0.074448116
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307609	-0.2264166667	64	10.970422	0.184	26.704	0.4264935	NA	0.153753073
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307620	-0.8430000000	67	28.054851	0.128	72.915	0.4572195	NA	0.158977366
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307642	-0.5316666667	65	29.461338	0.212	56.788	0.4155379	NA	0.468755176
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307657	-0.3364444444	67	38.138761	0.406	81.975	0.4564233	NA	0.557282270
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307661	-1.1720000000	67	32.629119	0.684	64.175	0.4142380	-1.1720000	0.045999021
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307663	-1.3021666667	67	31.908060	0.740	67.966	0.4182612	-1.3021667	0.004846871
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307679	-0.3510500000	53	16.620226	0.573	86.278	0.7638057	NA	0.579198994
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307680	0.1244571429	53	19.404264	0.201	53.028	0.5159918	NA	0.938380746
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307681	0.0108750000	52	18.891981	0.323	35.280	0.4114267	NA	0.875265790
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307682	-0.8930000000	52	35.486750	0.628	71.486	0.4016902	NA	0.271849206
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307683	-0.4700000000	52	21.151808	0.101	41.492	0.3694753	NA	0.271849206
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307684	-0.0140000000	52	8.405423	0.184	138.152	2.2215494	NA	1.000000000
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307685	-0.0351666667	52	6.570385	0.212	19.554	0.6878644	NA	0.812139784
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307686	-0.0218833333	52	10.750731	0.101	84.750	1.2528395	NA	0.935211985
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307687	1.0341000000	35	23.147229	0.545	77.089	0.6395636	NA	0.896706705
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307688	0.1460000000	53	24.874642	0.351	85.155	0.5646763	NA	0.872914671
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307689	0.0002777778	52	33.560173	0.684	126.281	0.7544195	NA	1.000000000
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307690	-0.1540333333	51	9.486725	0.101	26.024	0.5618077	NA	0.934634799
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307691	-1.0118571429	53	36.193623	0.795	108.629	0.6269206	NA	0.749032993
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307692	-0.1056250000	52	7.218231	0.017	20.542	0.6380195	NA	0.807333428
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307693	-0.2076000000	53	20.840472	0.351	61.004	0.6680065	NA	0.522283516
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307694	0.0368714286	52	6.544481	0.017	23.867	0.6745346	NA	0.807333428
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1307695	-0.0521666667	52	13.906173	0.239	48.378	0.6363270	NA	0.937884809