Florida’s Coral Reef Water Quality Data Compilation (FCRWQDC)

This website is a collection of research notebooks including data ingestion, quality control, and initial analysis of water quality data ingested from multiple providers in Florida. Section of source code for reproducing these analyses can be expanded, and the full source code (including code for making this website) has been published on GitHub.

For information on specific analytes and data providers, see the analyte reports and provider reports.

Files of unified data produced by these research notebooks can be downloaded here

This work is a product of the University of South Florida Institute for Marine Remote Sensing (IMaRS), funded by the Florida Department of Environmental Protection.

get data across all programs 
library("here")
df_all <- read.csv(here("data/exports/allDataRaw.csv"))
select subset & create unified csv 
# select subset of reported analytes
source(here("R/dropNonStandardAnalytes.R"))
df <- dropNonStandardAnalytes(df_all)

# drop rows with depth > 1m, keep any with depth==NA or depth==NULL
df <- filter(
  df,
  is.na(Activity.Depth) | Activity.Depth <= 1)

source(here("R/mutateWINTo2025.R"))
# reduce to only cols we need & save to csv
write.csv(mutateWINTo2025(df), here("data", "exports", "dashboardData.csv"))

Included Samples by Analyte & Program:

Plot providers row count grouped by analyte 
library(ggplot2)

ggplot(df, aes(x = program, fill = DEP.Analyte.Name)) +
  geom_bar() +
  scale_y_log10() +
  labs(
    title = "Count of Observations by Program and Parameter",
    x = "Program Name",
    y = "Count (Log Scale)",
    fill = "Parameter"
  ) +
  theme_minimal() +
  theme(
    legend.position = "bottom",
    axis.text.x = element_text(angle = 45, hjust = 1)
  )

Included Analytes:

print analyte sample count 
library(dplyr)
library(knitr)

df %>%
  count(DEP.Analyte.Name, sort = TRUE) %>%
  rename(Count = n) %>%
  kable()
DEP.Analyte.Name Count
Water Temperature 191360
Salinity 188313
Dissolved Oxygen 185109
pH 150832
Turbidity 84437
NO2+3, Filtered 66093
Total Phosphorus 55277
Nitrite (NO2) 48842
Phosphate, Filtered (PO4) 48475
Ammonium, Filtered (NH4) 36157
Total Kjeldahl Nitrogen 35122
Chlorophyll a, Corrected for Pheophytin 35108
Nitrate (NO3) 35019
Total Nitrogen 33805
Chlorophyll a, Uncorrected for Pheophytin 29851
Nitrogen, organic 25554
Ammonia, Un-ionized (NH3) 20555
Total Suspended Solids 4300
Specific Conductivity 2856
Dissolved Oxygen Saturation 528

Excluded Analytes:

The following analytes are reported by some programs but not included in the output csv files or other analyses. These may be analytes that are not included in the SEACAR vocabulary or they may not have been properly mapped to the SEACAR vocabulary.

print excluded analytes & associated programs 
library(dplyr)

# 1. Get the list of analyte names that are in df_all but not in df
diff_analytes <- setdiff(unique(df_all$DEP.Analyte.Name), unique(df$DEP.Analyte.Name))

# 2. Filter df_all for those analytes and create a summary
analyte_programs_summary <- df_all %>%
  filter(DEP.Analyte.Name %in% diff_analytes) %>%
  group_by(DEP.Analyte.Name) %>%
  summarise(Associated.Programs = paste(unique(program), collapse = ", "))

# 3. Print the resulting summary table
DT::datatable(analyte_programs_summary)

Overall statistics:

skimr on all data 
library(skimr)
skim(df)
Data summary
Name df
Number of rows 1277593
Number of columns 133
_______________________
Column type frequency:
character 63
complex 1
logical 16
numeric 53
________________________
Group variables None

Variable type: character

skim_variable n_missing complete_rate min max empty n_unique whitespace
keyfield 1219353 0.05 24 43 0 5823 0
Activity.ID 996631 0.22 5 36 0 66138 0
time 1219353 0.05 5 5 0 1422 0
Activity.Start.Date.Time 20 1.00 10 10 0 4123 0
Monitoring.Location.ID 20 1.00 1 25 0 2011 0
station_type 1219373 0.05 1 1 0 2 0
depth_class 1219373 0.05 6 7 0 2 0
depth_order 1219373 0.05 4 4 0 2 0
notes 1277543 0.00 17 75 0 5 0
DEP.Analyte.Name 0 1.00 2 41 0 20 0
Habitat 1023193 0.20 12 21 0 3 0
IndicatorName 1253642 0.02 9 13 0 3 0
ManagedAreaName 1253642 0.02 29 38 0 2 0
Activity.Type 1046234 0.18 5 15 0 4 0
RelativeDepth 1181166 0.08 0 7 528 3 0
DetectionUnit 1275427 0.00 4 4 0 1 0
Value.Qualifier 848035 0.34 0 4 156863 90 0
Result.Comments 1047094 0.18 0 874 207346 689 0
SEACAR_QAQCFlagCode 1253642 0.02 2 13 0 26 0
SEACAR_QAQC_Description 1253642 0.02 31 195 0 26 0
ExportVersion 1253642 0.02 23 23 0 3 0
Region 1204069 0.06 2 19 0 22 0
DEP.Result.Unit 62260 0.95 0 10 14858 21 0
program 0 1.00 3 19 0 16 0
ProgramName 1253642 0.02 25 36 0 2 0
ParameterName 1254552 0.02 2 23 0 10 0
ParameterUnits 1254552 0.02 3 9 0 6 0
ProgramLocationID 1254552 0.02 1 2 0 55 0
ActivityType 1254552 0.02 5 6 0 2 0
SampleDate 1254552 0.02 23 23 0 2134 0
ResultComments 1275427 0.00 21 21 0 1 0
SEACAR_EventID 1254552 0.02 36 36 0 2394 0
data_source 1250109 0.02 5 10 0 2 0
CLIENT.SAMPLE.ID 1273150 0.00 1 3 0 70 0
MATRIX 1273150 0.00 5 5 0 1 0
COLLECTED 1273150 0.00 10 10 0 23 0
ANALYTE 1273150 0.00 8 27 0 9 0
SAMPLE.RESULT 1273496 0.00 3 6 0 1385 0
UNITS 1273150 0.00 3 10 0 6 0
METHOD 1273150 0.00 10 29 0 5 0
ANALYZED 1273150 0.00 10 10 0 104 0
PREPARED 1273150 0.00 10 10 0 95 0
source_file 1273150 0.00 19 22 0 23 0
SAMPLE.COLLECTION.DATE 1273150 0.00 9 10 0 23 0
BASIN 850951 0.33 2 5 0 7 0
CLUSTER 865207 0.32 2 4 0 37 0
ZSI 866516 0.32 2 5 0 25 0
ZONE 1159926 0.09 3 7 0 10 0
Date 1273573 0.00 11 14 0 663 0
Organization.ID 562879 0.56 7 16 0 10 0
SEGMENT 1263337 0.01 2 5 0 8 0
DATE 1263337 0.01 10 19 0 260 0
SITE 1263337 0.01 8 28 0 52 0
Sampling.Agency.Name 566899 0.56 14 58 0 9 0
Org.Latitude..DD.MM.SS.SSSS. 1047144 0.18 0 11 222785 22 0
Org.Longitude..DD.MM.SS.SSSS. 1047144 0.18 0 12 222785 22 0
WBID 1047144 0.18 0 6 10428 115 0
Sample.Collection.Type 1047144 0.18 0 22 42 4 0
Activity.Depth.Unit 1047144 0.18 0 2 42 3 0
DEP.Result.Value.Text 1047144 0.18 0 12 230297 2 0
Sample.Fraction 1047144 0.18 0 9 129643 3 0
Lab.ID 1047144 0.18 0 6 102313 10 0
source 1047144 0.18 3 9 0 6 0

Variable type: complex

skim_variable n_missing complete_rate mean
STATION 1263337 0.01 313.52+0.46i

Variable type: logical

skim_variable n_missing complete_rate mean count
nisk_start 1277593 0 NaN :
nisk_end 1277593 0 NaN :
ValueQualifierSource 1277593 0 NaN :
ActivityDepth_m 1277593 0 NaN :
ValueQualifier 1277593 0 NaN :
SampleFraction 1277593 0 NaN :
TIME 1277593 0 NaN :
DETECTION.LIMITS 1277593 0 NaN :
NO3.DL 1277593 0 NaN :
DIN.DL 1277593 0 NaN :
TON.DL 1277593 0 NaN :
APA.DL 1277593 0 NaN :
Activity.Top.Depth 1277593 0 NaN :
Activity.Bottom.Depth 1277593 0 NaN :
Activity.Depth.Top.Bottom.Unit 1277593 0 NaN :
Audit.Censored.Decisions 1277593 0 NaN :

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
X 0 1.00 1.300088e+06 816360.41 1.000000e+00 4.327410e+05 1.629405e+06 1.965588e+06 2.513255e+06 ▆▂▁▇▅
year 1219373 0.05 2.020090e+03 2.97 2.014000e+03 2.018000e+03 2.021000e+03 2.023000e+03 2.024000e+03 ▅▅▅▇▇
month 1219353 0.05 6.610000e+00 3.54 0.000000e+00 3.000000e+00 7.000000e+00 1.000000e+01 1.200000e+01 ▅▅▇▅▇
day 1219373 0.05 1.445000e+01 8.62 1.000000e+00 7.000000e+00 1.400000e+01 2.200000e+01 3.100000e+01 ▇▆▆▆▃
lat_deg 1219373 0.05 2.509000e+01 0.99 2.400000e+01 2.400000e+01 2.500000e+01 2.500000e+01 2.800000e+01 ▅▇▂▂▁
lat_min 1219373 0.05 3.033000e+01 15.94 3.000000e-02 2.041000e+01 3.309000e+01 4.261000e+01 5.983000e+01 ▆▅▇▇▅
Org.Decimal.Latitude 488728 0.62 2.557000e+01 0.54 2.440000e+01 2.518000e+01 2.555000e+01 2.587000e+01 2.878000e+01 ▅▇▂▁▁
lon_deg 1219373 0.05 -8.113000e+01 0.82 -8.500000e+01 -8.200000e+01 -8.100000e+01 -8.100000e+01 -8.000000e+01 ▁▁▃▇▃
lon_min 1219373 0.05 2.643000e+01 17.03 0.000000e+00 1.214000e+01 2.253000e+01 4.296000e+01 6.000000e+01 ▇▇▅▃▅
Org.Decimal.Longitude 488728 0.62 -8.082000e+01 0.65 -8.502000e+01 -8.130000e+01 -8.072000e+01 -8.024000e+01 -8.002000e+01 ▁▁▁▅▇
Activity.Depth 945466 0.26 4.100000e-01 0.27 0.000000e+00 1.000000e-01 5.000000e-01 5.000000e-01 1.000000e+00 ▅▁▇▂▁
cast 1219373 0.05 5.900000e-01 0.50 0.000000e+00 0.000000e+00 1.000000e+00 1.000000e+00 2.000000e+00 ▆▁▇▁▁
DEP.Result.Value.Number 44119 0.97 1.113000e+01 454.36 -3.000000e-02 1.000000e-01 1.000000e+00 4.800000e+00 5.346500e+04 ▇▁▁▁▁
RowID 1254552 0.02 1.009723e+06 798651.12 4.862170e+05 5.143680e+05 5.349680e+05 1.551534e+06 3.870318e+06 ▇▂▁▁▁
ProgramID 0 1.00 2.720790e+03 2444.79 3.000000e+00 5.090000e+02 4.018000e+03 4.018000e+03 1.001300e+04 ▇▁▇▁▁
IndicatorID 1253642 0.02 6.730000e+00 0.63 6.000000e+00 6.000000e+00 7.000000e+00 7.000000e+00 8.000000e+00 ▆▁▇▁▂
ParameterID 1253642 0.02 8.600000e+00 6.56 1.000000e+00 3.000000e+00 6.000000e+00 1.600000e+01 1.900000e+01 ▇▃▁▂▅
AreaID 1253642 0.02 6.090000e+00 0.89 6.000000e+00 6.000000e+00 6.000000e+00 6.000000e+00 1.500000e+01 ▇▁▁▁▁
Year 502984 0.61 2.009100e+03 9.68 1.989480e+03 2.000950e+03 2.006640e+03 2.020000e+03 2.024000e+03 ▂▆▅▁▇
Month 502964 0.61 6.550000e+00 3.44 0.000000e+00 4.000000e+00 7.000000e+00 1.000000e+01 1.200000e+01 ▅▅▇▅▇
TotalDepth_m 1277530 0.00 6.222000e+01 105.84 1.100000e+00 2.100000e+00 2.850000e+00 8.500000e+00 2.500000e+02 ▇▁▁▁▂
MDL 1149433 0.10 7.000000e-02 0.60 0.000000e+00 0.000000e+00 3.000000e-02 8.000000e-02 5.050000e+01 ▇▁▁▁▁
PQL 1149433 0.10 2.100000e-01 2.92 0.000000e+00 1.000000e-02 6.000000e-02 2.500000e-01 2.500000e+02 ▇▁▁▁▁
Include 1253642 0.02 1.000000e+00 0.03 0.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 ▁▁▁▁▇
MADup 1253642 0.02 1.000000e+00 0.00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 ▁▁▇▁▁
ResultValue 1254552 0.02 1.286000e+01 41.22 0.000000e+00 2.900000e-01 4.890000e+00 2.447000e+01 5.389000e+03 ▇▁▁▁▁
OriginalLatitude 1254552 0.02 2.580000e+01 0.02 2.577000e+01 2.578000e+01 2.579000e+01 2.581000e+01 2.587000e+01 ▆▇▂▁▂
OriginalLongitude 1254552 0.02 -8.015000e+01 0.01 -8.017000e+01 -8.016000e+01 -8.015000e+01 -8.013000e+01 -8.012000e+01 ▇▆▅▅▇
LAB.SAMPLE.ID 1273150 0.00 3.588884e+10 22277401.92 3.585419e+10 3.586685e+10 3.588708e+10 3.590707e+10 3.592746e+10 ▇▆▆▆▇
REPORTING.LIMIT 1275618 0.00 1.890000e+00 2.96 0.000000e+00 3.000000e-02 5.000000e-02 5.000000e-01 7.000000e+00 ▇▁▁▁▂
DILUTION 1273150 0.00 1.000000e+00 0.00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 ▁▁▇▁▁
DEP.Result.ID 996633 0.22 8.856591e+06 5455584.81 1.180000e+02 5.815863e+06 9.447332e+06 1.355247e+07 1.787779e+07 ▆▇▇▆▇
SURV 850951 0.33 1.192000e+02 54.92 -8.000000e+00 7.600000e+01 1.230000e+02 1.650000e+02 2.110000e+02 ▂▆▇▇▇
STA 865207 0.32 1.423400e+02 163.89 1.000000e+00 2.800000e+01 6.200000e+01 1.330000e+02 4.790000e+02 ▇▂▁▁▂
YEAR 865207 0.32 2.001260e+03 4.50 1.989480e+03 1.997790e+03 2.001560e+03 2.005030e+03 2.008730e+03 ▁▅▇▇▇
NOX.DL 865207 0.32 0.000000e+00 0.00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 ▇▃▆▁▁
NO2.DL 865207 0.32 0.000000e+00 0.00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 ▆▇▁▁▁
NH4.DL 865207 0.32 0.000000e+00 0.00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e-02 ▇▁▁▁▂
TN.DL 865207 0.32 3.000000e-02 0.03 0.000000e+00 0.000000e+00 3.000000e-02 5.000000e-02 8.000000e-02 ▇▃▁▆▂
TP.DL 865207 0.32 0.000000e+00 0.00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 ▇▁▁▁▁
SRP.DL 865207 0.32 0.000000e+00 0.00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 ▇▂▁▅▅
CHLA.DL 865207 0.32 1.000000e-01 0.00 1.000000e-01 1.000000e-01 1.000000e-01 1.000000e-01 1.000000e-01 ▁▁▇▁▁
TOC.DL 865207 0.32 1.200000e-01 0.04 5.000000e-02 1.200000e-01 1.200000e-01 1.600000e-01 1.600000e-01 ▅▁▁▇▆
SiO2.DL 865207 0.32 0.000000e+00 0.00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e-02 ▇▁▁▁▁
Station 1273573 0.00 2.894200e+02 80.47 2.000000e+02 2.310000e+02 2.700000e+02 3.140000e+02 5.090000e+02 ▇▇▁▁▂
LATDEC 1263337 0.01 2.470000e+01 0.14 2.455000e+01 2.462000e+01 2.466000e+01 2.477000e+01 2.548000e+01 ▇▃▁▁▁
LONDEC 1263337 0.01 -8.147000e+01 0.39 -8.259000e+01 -8.172000e+01 -8.163000e+01 -8.134000e+01 -8.012000e+01 ▁▇▃▂▁
DEPTH 1264309 0.01 9.700000e-01 0.11 0.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 ▁▁▁▁▇
Long.Deg 1227990 0.04 -7.559000e+01 26.43 -8.100000e+01 -8.000000e+01 -8.000000e+01 -8.000000e+01 8.000000e+01 ▇▁▁▁▁
Long.Min 1227990 0.04 3.488000e+01 16.19 0.000000e+00 1.956000e+01 3.748000e+01 4.761000e+01 6.575000e+01 ▃▅▅▇▃
Lat.Deg 1227990 0.04 2.479000e+01 0.40 2.400000e+01 2.500000e+01 2.500000e+01 2.500000e+01 2.500000e+01 ▂▁▁▁▇
Lat.Min 1227990 0.04 2.159000e+01 21.51 0.000000e+00 4.030000e+00 9.020000e+00 3.970000e+01 6.000000e+01 ▇▁▂▁▃
Value.1 843173 0.34 1.250000e+01 63.97 -7.730000e+01 3.160000e+00 7.810000e+00 2.418000e+01 4.136100e+04 ▇▁▁▁▁

If you have visualization ideas for this data, please open a github issue here.