Package 'peptools'

Title: Analysis Tools for Importing, Wrangling, and Summarizing Suffolk County Water Quality Data
Description: Analysis tools for importing, wrangling, and summarizing Suffolk County water quality data. Functions are used to create reporting materials.
Authors: Marcus Beck [aut, cre] , Gerold Morrison [aut], Holly Greening [aut]
Maintainer: Marcus Beck <[email protected]>
License: CC0
Version: 1.1.0
Built: 2024-10-09 05:20:27 UTC
Source: https://github.com/tbep-tech/peptools

Help Index

Get attainment categories

Description

Get attainment categories for each year and bay segment using chlorophyll and secchi depth

Usage

anlz_attainpep(meddat, magdurout = FALSE, trgs = NULL)

Arguments

meddat

result returned from anlz_medpep
magdurout

logical indicating if the separate magnitude and duration estimates are returned
trgs

optional data.frame for annual bay segment water quality targets, defaults to peptargets

Value

A data.frame for each year and bay segment showing the attainment category

Examples

meddat <- anlz_medpep(rawdat)
anlz_attainpep(meddat)

Analyze daily DO values relative to threshold

Description

Analyze daily DO values relative to threshold

Usage

anlz_dodlypep(dodat, thr = 3, impute = TRUE)

Arguments

dodat

result returned from read_pepdo
thr

numeric indicating appropriate dissolved oxygen thresholds, usually 3 mg/L for acute, 4.8 mg/L for chronic
impute

logical indicating of missing dissolved oxygen values are imputed with the year, month, site average

Details

The dodat data object can be used as input without downloading USGS data

If impute = TRUE, missing dissolved oxygen values in the complete daily time series are imputed to the average for the year, month, site combination. This is often necessary to create summary values that make sense. For example, if a month has incomplete data, the maximum below_cumsum value will not show 30 or 31 days even if every day in the observed record is below the threshold.

Value

data.frame

Examples

data(dodat)
dat <- anlz_dodlypep(dodat)
dat

Analyze monthly DO values relative to threshold

Description

Analyze monthly DO values relative to threshold

Usage

anlz_domopep(dodat, thr = 3, impute = TRUE)

Arguments

dodat

result returned from read_pepdo
thr

numeric indicating appropriate dissolved oxygen thresholds, usually 3 mg/L for acute, 4.8 mg/L for chronic
impute

logical indicating of missing dissolved oxygen values are imputed with the year, month, site average

Details

The dodat data object can be used as input without downloading USGS data

The date are summarized as three different values, where do_mgl is the average of all daily DO averages across the month, below_ave is the proportion of days in a month when concentrations in a given day fell below the threshold (1 would mean all days had an instance of DO below the threshold, 0 would mean none), and below_maxrun is the maximum number of sequential days in a month when concentrations in a given day fell below the threshold (30 or 31, depending on month, would indicate all days in a month had an instance of DO below the threshold).

If impute = TRUE, missing dissolved oxygen values in the complete daily time series are imputed to the average for the year, month, site combination. This is often necessary to create summary values that make sense. For example, if a month has incomplete data, the below_ave summary may indicate a value of one if all daily averages in the available data are below the threshold, whereas the below_maxrun summary may indicate a maximum run of days not equal to the number of days in the month.

Value

data.frame

Examples

data(dodat)
dat <- anlz_domopep(dodat)
dat

Count beach exceedances for enterococcus

Description

Count beach exceedances for enterococcus

Usage

anlz_entpep(entdat, thr = 104)

Arguments

entdat

result returned from read_pepent
thr

numeric value defining threshold for exceedance

Details

The exceedance threshold is set by default as 104 cfu/100 ml criterion. This is simply based on counts in a year when any value at any station was above the threshold for each 24 hour period in the record.

The samples column shows how many days of the year were sampled at each beach and the exceedances column shows how many samples were above the threshold.

Value

A data.frame with counts of exceedances per year for each beach

Examples

anlz_entpep(entdat)

Estimate annual medians

Description

Estimate annual medians by segment for chlorophyll, secchi, and total nitrogen data

Usage

anlz_medpep(dat)

Arguments

dat

data.frame formatted from read_pepwq

Value

Median estimates for chlorophyll, secchi, and total nitrogen

Examples

# view median estimates
anlz_medpep(rawdat)

Bathing beaches

Description

Bathing beaches

Usage

beaches

Format

A data.frame object

Examples

## Not run: 

library(sf)
library(dplyr)

beaches <- read.csv('inst/extdata/beaches.csv') %>% 
  st_as_sf(
     coords = c('Longitude', 'Latitude'), 
     crs = '+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs'
  )

save(beaches, file = 'data/beaches.RData')


## End(Not run)

Dissolved oxygen data for USGS stations

Description

Dissolved oxygen data for USGS stations

Usage

dodat

Format

A data.frame object

Examples

## Not run: 

# 01304562 is Peconic River, 01304200 is Orient Harbor, 01304650 is Shelter Island
dodat <- read_pepdo(site = c('01304562', '01304200', '01304650'), 
  nms = c('Peconic River', 'Orient Harbor', 'Shelter Island'))

save(dodat, file = 'data/dodat.RData', compress = 'xz')


## End(Not run)

Raw beach pathogen data from Suffolk County

Description

Raw beach pathogen data from Suffolk County

Usage

entdat

Format

A data.frame object

Examples

## Not run: 
library(dplyr)
entdat1 <- read_pepent() %>% 
  filter(lubridate::year(Date) < 2022)

entdat2 <- read_pepent(path = '~/Desktop/Enterodata_2023.xlsx') %>%
  filter(lubridate::year(Date) >= 2022)

entdat <- bind_rows(entdat1, entdat2)

save(entdat, file = 'data/entdat.RData', compress = 'xz')

# or the file can be manually downloaded from here (format is not the same as path input from SCM)
# https://gis.suffolkcountyny.gov/portal/home/item.html?id=e3b344ff82b74762b625cacaa3e9621a
entdat <- read.csv('~/Desktop/Beach_Water_Quality_Data.csv', header = T) |> 
  dplyr::filter(Type %in% c('Enterococcus', 'Enterococci')) %>% 
  dplyr::select(
    Name,
    FieldNum, 
    Date = ColDate, 
    value = Result, 
    status = Character
  ) %>% 
  dplyr::mutate(
    status = gsub('[[:digit:]]+|\\.', '', value), 
    status = ifelse(status == '', '=', status), 
    value = as.numeric(gsub('>|<', '', value)),
    Date = suppressWarnings({dplyr::case_when(
      grepl('\\/', Date) ~ lubridate::mdy(Date), 
      grepl("^[[:digit:]]+$", Date) ~ as.Date(as.numeric(Date), origin = "1899-12-30"),
      T ~ NA
    )}), 
    Name = dplyr::case_when(
      Name == 'Crescent Beach - Shelter Island' ~ 'Crescent Beach - Suffolk', 
      T ~ Name
    )
  ) %>% 
  dplyr::filter(Name %in% beaches$Name) |> 
  dplyr::arrange(Name, FieldNum, Date)

save(entdat, file = 'data/entdat.RData')

## End(Not run)

Polygon shapefile of segment boundaries

Description

Polygon shapefile of segment boundaries

Usage

pepseg

Format

A sf object

Examples

## Not run: 
library(sf)
library(dplyr)

pepseg <- st_read('~/Desktop/TBEP/Peconic/PEPSegments/PEP_Seg_Reeves.shp') %>%
  st_transform(crs = '+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs') %>% 
  select(bay_segment = NewSegment) %>% 
  st_buffer(dist = 0) %>% 
  st_crop(xmin = -72.76, xmax = -71.8, ymin = 40.83, ymax = 41.2)
 
save(pepseg, file = 'data/pepseg.RData', compress = 'xz')

## End(Not run)

Bay stations by segment

Description

Bay stations by segment

Usage

pepstations

Format

A data.frame object

Examples

## Not run: 
library(tidyr)
library(sf)
library(dplyr)
library(readxl)
library(mapedit)
library(mapview)

prj <- 4326

locs <- read_xlsx('inst/extdata/stationmeta.xlsx') %>%
  select(BayStation = `Station Number`, StationName, Longitude = LON, Latitude = LAT) %>%
  mutate(
    BayStation = as.character(BayStation)
  ) %>% 
  sf::st_as_sf(coords = c("Longitude", "Latitude"), crs = prj)

# # use this for spatial selection
# p <- mapview(pepseg) + mapview(locs)
# e1 <- editMap(p)
# locs[e1$finished, ] %>% pull(BayStation) %>% dput

pepstations <- list(
  `1a` = c("60280", "60275", "60270", "60265", "60266", "60260", "60250", 
              "60240", "60230", "60210", "60220"),
  `1b` = c("60170", "60101", "60130", "60290", "60148"), 
  `2` = c("60102", "60103", "60113", "60104", "60300", "60105", "60106", 
              "60107", "60310", "60320", "60114", "60109", "60340", "60121", 
              "60124", "60119", "60127", "60126", "60111", "60131", "60118"),
  `3` = c("60122", "60115", "60116", "60330", "60132", "60137", "60133", 
              "60134", "60135")
) %>%
  tibble::enframe('bay_segment', 'BayStation') %>%
  unnest(BayStation) %>%
  left_join(locs, ., by = 'BayStation')
crds <- st_coordinates(pepstations)
pepstations <- pepstations %>%
  st_set_geometry(NULL) %>%
  mutate(
    Longitude = crds[, 1],
    Latitude = crds[, 2], 
    bay_segment = factor(bay_segment, levels = c('1a', '1b', '2', '3'))
  )

save(pepstations, file = 'data/pepstations.RData', compress = 'xz')

## End(Not run)

Bay segment targets

Description

Bay segment targets

Usage

peptargets

Format

A data.frame object

Examples

## Not run: 
peptargets <- tibble::tibble(
  bay_segment = factor(c('1a', '1b', '2', '3'), 
    levels = c('1a', '1b', '2', '3')), 
  name = factor(c('1a', '1b', '2', '3'), 
    levels = c('1a', '1b', '2', '3')), 
  sd_thresh = c(6.5, 6.5, 6.5, 6.5),
  chla_thresh = c(5.5, 5.5, 5.5, 5.5), 
  tn_thresh = c(0.4, 0.4, 0.4, 0.4)
)
save(peptargets, file = 'data/peptargets.RData', compress= 'xz')

## End(Not run)

Raw data from Suffolk County

Description

Raw data from Suffolk County

Usage

rawdat

Format

A data.frame object

Examples

## Not run: 
path <- system.file("extdata", "currentdata.xlsx", package="peptools")
rawdat <- read_pepwq(path)
save(rawdat, file = 'data/rawdat.RData', compress = 'xz')

## End(Not run)

Import dissolved oxygen data

Description

Import dissolved oxygen data

Usage

read_pepdo(
  site = c("01304562", "01304200", "01304650"),
  nms = c("Peconic River", "Orient Harbor", "Shelter Island"),
  startDate = "2013-01-01",
  endDate = "2023-12-31"
)

Arguments

site

chr string of site numbers for USGS stations
nms

chr string vector of names to reassign to site numbers
startDate

chr string of start date in YYYY-MM-DD
endDate

chr string of end date in YYYY-MM-DD

Details

Raw data are downloaded using the USGS dataRetrieval R package, this function is a simple wrapper to the readNWISuv function.

Note that downloading the station data with the default arguments may take a few minutes. Sites are 01304562 for Peconic River, 01304200 for Orient Harbor, 01304650 for Shelter Island.

Value

data.frame

Examples

## Not run: 
dodat <- read_pepdo(site = c('01304562', '01304200', '01304650'), 
  nms = c('Peconic River', 'Orient Harbor', 'Shelter Island'), 
  StartDate = '2020-06-01', endDate = '2021-06-30')
dodat

## End(Not run)

Import raw enterococcus data

Description

Import raw enterococcus data

Usage

read_pepent(path = NULL)

Arguments

path

chr string of path for excel file (optional)

Details

Data are from the ArcGIS REST Services here https://gis.suffolkcountyny.gov/hosted/rest/services/Hosted/Beach_Water_Quality_Data/FeatureServer/.

The API is queried by beach names in the beaches data object. The queries are done individually for each beach to not exceed the 2000 record limit.

Data can also be imported from an Excel if the path argument is used for the location to the file.

Value

data.frame

Examples

## Not run: 
entdat <- read_pepent()

## End(Not run)
head(entdat)

Import raw water quality data

Description

Import raw water quality data

Usage

read_pepwq(path)

Arguments

path

chr string of path for excel file

Details

Raw data from here https://gis.suffolkcountyny.gov/portal/home/item.html?id=5d4b53ec44204219a8da685f1859e096

All data prior to 1990 are removed - some exist but the data are scarce.

Value

data.frame

Examples

path <- system.file("extdata", "currentdata.xlsx", package="peptools")
dat <- read_pepwq(path)
dat

Plot annual water quality value and thresholds for all segments

Description

Plot annual water quality values and thresholds for all bay segments

Usage

show_allthrpep(
  dat,
  param = c("chla", "sd", "tn"),
  trgs = NULL,
  yrrng = NULL,
  family = NA,
  labelexp = TRUE,
  txtlab = TRUE
)

Arguments

dat

data frame of data returned by read_pepwq
param

chr string indicating which water quality value and appropriate threshold to plot, one of "chla" for chlorophyll, "sd" for secchi depth, or "tn" for total nitrogen
trgs

optional data.frame for annual bay segment water quality thresholds, defaults to peptargets
yrrng

numeric vector indicating min, max years to include
family

optional chr string indicating font family for text labels
labelexp

logical indicating if y axis and target labels are plotted as expressions, default TRUE
txtlab

logical indicating if a text label for the target value is shown in the plot

Details

This function is conceptually similar to show_thrpep, but results are shown as annual medians across all bay segments for the selected parameter.

Value

A ggplot object

Examples

show_allthrpep(rawdat, param = 'chl')

Plot monthly chlorophyll, secchi, or tn values values for a segment

Description

Plot monthly chlorophyl, secchi, or tn values values for a bay segment

Usage

show_boxpep(
  dat,
  param = c("chla", "sd", "tn"),
  yrsel = NULL,
  yrrng = NULL,
  ptsz = 0.5,
  bay_segment = c("1a", "1b", "2", "3"),
  trgs = NULL,
  family = NA,
  labelexp = TRUE,
  txtlab = TRUE
)

Arguments

dat

data frame of data returned by read_pepwq
param

chr string indicating which water quality value and appropriate threshold to plot, one of "chla" for chlorophyll, "sd" for secchi depth, or "tn" for total nitrogen
yrsel

numeric for year to emphasize, shown as separate red points on the plot
yrrng

numeric vector indicating min, max years to include
ptsz

numeric indicating point size of observations not in yrsel
bay_segment

chr string for the bay segment, one of "1a", "1b", "2", or "3"
trgs

optional data.frame for annual bay segment water quality targets, defaults to peptargets
family

optional chr string indicating font family for text labels
labelexp

logical indicating if y axis and target labels are plotted as expressions, default TRUE
txtlab

logical indicating if a text label for the target value is shown in the plot

Details

Points not included in yrsel are plotted over the box plots using position_jitter. Use ptsz = -1 to suppress.

Value

A ggplot object

Examples

show_boxpep(rawdat, bay_segment = '1a')

Create a colorized table for reporting dissolved oxygen data by site

Description

Create a colorized table for reporting dissolved oxygen data by site

Usage

show_domatrix(
  dodat,
  site,
  show = c("below_ave", "below_maxrun"),
  txtsz = 3,
  thr = 4.8,
  impute = TRUE,
  yrrng = NULL,
  family = NA
)

Arguments

dodat

data frame of dissolved oxygen data returned by read_pepdo
site

character string of the site to plot taken from the nms argument in read_pepdo, usually one of "Peconic River", "Orient Harbor", or "Shelter Island"
show

chr string indicating which summary value to plot from anlz_domopep, one of 'below_ave' or 'below_maxrun'
txtsz

numeric for size of text in the plot, applies only if asreact = FALSE
thr

numeric indicating appropriate dissolved oxygen thresholds, usually 3 mg/L for acute, 4.8 mg/L for chronic
impute

logical indicating of missing dissolved oxygen values are imputed with the year, month, site average
yrrng

numeric vector indicating min, max years to include
family

optional chr string indicating font family for text labels

Value

A static ggplot object is returned.

See Also

anlz_domopep, anlz_dodlypep

Examples

show_domatrix(dodat, site = 'Peconic River')

Create a colorized table for beach pathogen exceedances

Description

Create a colorized table for beach pathogen exceedances

Usage

show_entmatrix(entdat, txtsz = 2, thr = 104, yrrng = NULL, family = NA)

Arguments

entdat

data frame of enterococcus data returned by read_pepent
txtsz

numeric for size of text in the plot, applies only if asreact = FALSE
thr

numeric value defining threshold for exceedance
yrrng

numeric vector indicating min, max years to include
family

optional chr string indicating font family for text labels

Value

A static ggplot object is returned if asreact = FALSE, otherwise a reactable table is returned

See Also

anlz_entpep

Examples

show_entmatrix(entdat)

Create a colorized table for indicator reporting

Description

Create a colorized table for indicator reporting

Usage

show_matrixpep(
  dat,
  txtsz = 3,
  trgs = NULL,
  yrrng = NULL,
  bay_segment = c("1a", "1b", "2", "3"),
  asreact = FALSE,
  nrows = 10,
  abbrev = FALSE,
  family = NA
)

Arguments

dat

data frame of water quality data returned by read_pepwq
txtsz

numeric for size of text in the plot, applies only if asreact = FALSE
trgs

optional data.frame for annual bay segment water quality targets, defaults to peptargets
yrrng

numeric vector indicating min, max years to include
bay_segment

chr string for bay segments to include, one to all of "1a", "1b", "2", or "3"
asreact

logical indicating if a reactable object is returned
nrows

if asreact = TRUE, a numeric specifying number of rows in the table
abbrev

logical indicating if text labels in the plot are abbreviated as the first letter
family

optional chr string indicating font family for text labels

Value

A static ggplot object is returned if asreact = FALSE, otherwise a reactable table is returned

Examples

show_matrixpep(rawdat)

Plot chlorophyll and secchi data together with matrix outcomes

Description

Plot chlorophyll and secchi data together with matrix outcomes

Usage

show_plotlypep(
  dat,
  bay_segment = c("1a", "1b", "2", "3"),
  yrrng = NULL,
  chllim = NULL,
  seclim = NULL
)

Arguments

dat

data.frame formatted from read_pepwq
bay_segment

chr string for the bay segment, one of "1a", "1b", "2", or "3"
yrrng

numeric for year range to plot
chllim

numeric vector of length two indicating range for the chlorophyll y-axis
seclim

numeric vector of length two indicating range for the secchi y-axis

Value

An interactive plotly object

Examples

show_plotlypep(rawdat)

Create reactable table from matrix data

Description

Create reactable table from matrix data

Usage

show_reactablepep(totab, colfun, nrows = 10)

Arguments

totab

A data frame in wide format of summarized results
colfun

Function specifying how colors are treated in cell background
nrows

numeric specifying number of rows in the table

Details

This function is used internally within show_matrixpep

Value

A reactable table

Create a colorized table for water quality outcomes and exceedances by segment

Description

Create a colorized table for water quality outcomes by segment that includes the management action and chlorophyll, and secchi exceedances

Usage

show_segmatrixpep(
  dat,
  txtsz = 3,
  trgs = NULL,
  yrrng = NULL,
  bay_segment = c("1a", "1b", "2", "3"),
  abbrev = FALSE,
  family = NA
)

Arguments

dat

data.frame formatted from read_pepwq
txtsz

numeric for size of text in the plot, applies only if tab = FALSE
trgs

optional data.frame for annual bay segment water quality targets, defaults to peptargets
yrrng

numeric vector indicating min, max years to include
bay_segment

chr string for bay segments to include, one to all of "1a", "1b", "2", or "3"
abbrev

logical indicating if text labels in the plot are abbreviated as the first letter, applies only to center column
family

optional chr string indicating font family for text labels

Details

This function provides a combined output for the show_wqmatrixpep and show_matrixpep functions. Only one bay segment can be plotted for each function call.

Value

A static ggplot object is returned

See Also

show_wqmatrixpep, show_matrixpep

Examples

show_segmatrixpep(rawdat, bay_segment = '1a')

Map water quality data for a selected year

Description

Map water quality data for a selected year

Usage

show_sitemappep(
  dat,
  yrsel = NULL,
  mosel = NULL,
  param = c("chla", "sd", "tn"),
  bay_segment = c("1a", "1b", "2", "3"),
  maxrel = 0.99,
  relative = FALSE
)

Arguments

dat

data frame of data returned by read_pepwq
yrsel

numeric for years to plot, see details
mosel

numeric for months to plot, see details
param

chr string indicating which water quality value to plot, one of "chla" for chlorophyll, "sd" for secchi depth, or "tn" for total nitrogen
bay_segment

chr string for the bay segment, one or all of "1a", "1b", "2", or "3"
maxrel

numeric for the maximum quantile value for scaling if relative = T, this prevents outliers from skewing the scale
relative

logical indicating if sizes and colors are relative to the entire water quality data base, otherwise scaling is relative only for the points on the map

Details

Year estimates for the selected parameter are based on median observations across months. All twelve months are used if mosel = NULL (default). Monthly estimates for the selected parameter are based on median observations across years. All years are used if yrsel = NULL (default).

The color ramp and size scaling of points are reversed for Secchi observations.

Value

A leaflet object

Examples

# 2018, all months
show_sitemappep(rawdat, yrsel = 2018)

# 2018, July only
show_sitemappep(rawdat, yrsel = 2018, mosel = 7)

# July only, all years
show_sitemappep(rawdat, mosel = 7)

Plot annual water quality value and thresholds for a segment

Description

Plot annual water quality values and thresholds for a bay segment

Usage

show_thrpep(
  dat,
  bay_segment = c("1a", "1b", "2", "3"),
  param = c("chla", "sd", "tn"),
  ylim = NULL,
  trgs = NULL,
  yrrng = NULL,
  family = NA,
  labelexp = TRUE,
  txtlab = TRUE
)

Arguments

dat

data frame of data returned by read_pepwq
bay_segment

chr string for the bay segment, one of "1a", "1b", "2", or "3"
param

chr string indicating which water quality value and appropriate threshold to plot, one of "chla" for chlorophyll, "sd" for secchi depth, or "tn" for total nitrogen
ylim

numeric vector of length two indicating range for the y-axis
trgs

optional data.frame for annual bay segment water quality thresholds, defaults to peptargets
yrrng

numeric vector indicating min, max years to include
family

optional chr string indicating font family for text labels
labelexp

logical indicating if y axis and target labels are plotted as expressions, default TRUE
txtlab

logical indicating if a text label for the target value is shown in the plot

Value

A ggplot object

Examples

show_thrpep(rawdat, bay_segment = '1a', param = 'chl')

Create a colorized table for chlorophyll or secchi exceedances

Description

Create a colorized table for chlorophyll or secchi exceedances

Usage

show_wqmatrixpep(
  dat,
  param = c("chla", "sd"),
  txtsz = 3,
  trgs = NULL,
  yrrng = NULL,
  alpha = 1,
  bay_segment = c("1a", "1b", "2", "3"),
  asreact = FALSE,
  nrows = 10,
  family = NA
)

Arguments

dat

data.frame formatted from read_pepwq
param

chr string for which parameter to plot, one of "chla" for chlorophyll or "sd" for secchi
txtsz

numeric for size of text in the plot, applies only if tab = FALSE
trgs

optional data.frame for annual bay segment water quality targets, defaults to peptargets
yrrng

numeric vector indicating min, max years to include
alpha

numeric indicating color transparency
bay_segment

chr string for bay segments to include, one to all of "1a", "1b", "2", or "3"
asreact

logical indicating if a reactable object is returned
nrows

if asreact = TRUE, a numeric specifying number of rows in the table
family

optional chr string indicating font family for text labels

Value

A static ggplot object is returned if asreact = FALSE, otherwise a reactable table is returned

See Also

show_matrixpep, show_segmatrixpep

Examples

show_wqmatrixpep(rawdat)