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, ProgramLocationID, OriginalLongitude, OriginalLatitude, ParameterUnits) %>%
  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", linewidth=0.4, alpha = 0.3, bw = 0.001) +
  geom_density(fill = "steelblue", linewidth=0.1, alpha = 0.1, bw = 0.01) +
  geom_density(fill = "steelblue", linewidth=0.1, alpha = 0.1, bw = 0.1) +
  geom_vline(xintercept = 0, linetype = "dashed", color = "gray")+
  scale_y_continuous(trans = "sqrt") +
  labs(title = "Density of Site Slopes",
       x = "Slope (rate of change)",
       y = "Density") +
  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	ProgramLocationID	OriginalLongitude	OriginalLatitude	ParameterUnits	slope	n_values	mean	min	max	coefficient.of.variation	significant_slope	pvalue
Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys	1	-80.31363	25.41024	PCU	-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	10	-80.92481	24.93983	PCU	-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	11	-80.91957	24.90527	PCU	-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	12	-80.94092	24.89959	PCU	-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	13	-81.06128	24.89657	PCU	-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	14	-81.02604	24.85157	PCU	-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	15	-80.98455	24.77961	PCU	-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	16	-81.02738	24.76750	PCU	-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	17	-80.96101	24.77255	PCU	-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	18	-80.91780	24.77380	PCU	-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	19	-81.00241	24.80966	PCU	-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	2	-80.32572	25.41282	PCU	-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	20	-80.98710	24.80362	PCU	-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	21	-80.88658	24.87484	PCU	-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	22	-81.25722	24.75557	PCU	-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	23	-81.26681	24.75194	PCU	-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	24	-81.28412	24.78335	PCU	-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	25	-81.41273	24.83377	PCU	-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	26	-81.37915	24.85346	PCU	-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	27	-81.40956	24.86979	PCU	-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	28	-81.49701	24.90185	PCU	-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	29	-81.43426	25.02244	PCU	-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	3	-80.34841	25.40010	PCU	-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	30	-81.54415	25.19548	PCU	-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	31	-81.43758	25.39761	PCU	-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	32	-81.41248	25.47344	PCU	-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	33	-81.38007	25.50204	PCU	-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	34	-81.39526	25.50814	PCU	-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	35	-81.01582	25.14907	PCU	-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	36	-80.94329	25.12738	PCU	-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	37	-80.95047	25.12713	PCU	-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	38	-80.89945	25.15951	PCU	-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	39	-81.07608	25.40518	PCU	-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	4	-80.52974	25.12019	PCU	-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	40	-81.09621	25.41633	PCU	-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	5	-80.53855	25.10463	PCU	-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	6	-80.53613	25.06735	PCU	-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	7	-80.77413	24.96683	PCU	-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	8	-80.79947	24.95060	PCU	-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	9	-80.81166	24.93791	PCU	-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	B1	-80.18311	25.73919	PCU	-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	B10	-80.36151	25.29705	PCU	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	B11	-80.37595	25.23872	PCU	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	B12	-80.42246	25.25572	PCU	-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	B13	-80.42324	25.17490	PCU	-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	B14	-80.21336	25.46780	PCU	-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	B15	-80.19836	25.58023	PCU	-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	B16	-80.18718	25.66213	PCU	-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	B17	-80.29133	25.61505	PCU	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	B2	-80.24794	25.69038	PCU	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	B3	-80.26368	25.65428	PCU	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	B4	-80.26372	25.59146	PCU	-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	B5	-80.31391	25.53003	PCU	-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	B6	-80.25184	25.49237	PCU	-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	B7	-80.32531	25.46321	PCU	-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	B8	-80.24347	25.40512	PCU	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	B9	-80.32137	25.33333	PCU	-0.0521666667	52	13.906173	0.239	48.378	0.6363270	NA	0.937884809