update 2023 benthic and sediment data

tbep-tech · Dec 12, 2024 · 1ba5699 · 1ba5699
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tbeptools
 Title: Data and Indicators for the Tampa Bay Estuary Program
-Version: 3.0.0.9006
-Date: 2024-12-03
+Version: 3.0.0.9007
+Date: 2024-12-12
 Authors@R: c(
     person(given = "Marcus",
       family = "Beck",

diff --git a/R/anlz_sedimentaddtot.R b/R/anlz_sedimentaddtot.R
@@ -14,7 +14,7 @@
 #'
 #' @examples
 #' anlz_sedimentaddtot(sedimentdata)
-anlz_sedimentaddtot <- function(sedimentdata, yrrng = c(1993, 2022), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP', param = NULL, pelave = TRUE){
+anlz_sedimentaddtot <- function(sedimentdata, yrrng = c(1993, 2023), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP', param = NULL, pelave = TRUE){
 
   # make yrrng two if only one year provided
   if(length(yrrng) == 1)

diff --git a/R/anlz_sedimentave.R b/R/anlz_sedimentave.R
@@ -19,7 +19,7 @@
 #'
 #' @examples
 #' anlz_sedimentave(sedimentdata, param = 'Arsenic')
-anlz_sedimentave <- function(sedimentdata, param, yrrng = c(1993, 2022), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP'){
+anlz_sedimentave <- function(sedimentdata, param, yrrng = c(1993, 2023), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP'){
 
   # add totals
   sedimentdata <- anlz_sedimentaddtot(sedimentdata, yrrng = yrrng, bay_segment = bay_segment,

diff --git a/R/anlz_sedimentpel.R b/R/anlz_sedimentpel.R
@@ -21,7 +21,7 @@
 #'
 #' @examples
 #' anlz_sedimentpel(sedimentdata)
-anlz_sedimentpel <- function(sedimentdata, yrrng = c(1993, 2022), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP'){
+anlz_sedimentpel <- function(sedimentdata, yrrng = c(1993, 2023), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP'){
 
   # combine all, take average, get grade
   out <- anlz_sedimentaddtot(sedimentdata, yrrng = yrrng, bay_segment = bay_segment, funding_proj = funding_proj, pelave = TRUE) %>%

diff --git a/R/anlz_sedimentpelave.R b/R/anlz_sedimentpelave.R
@@ -15,7 +15,7 @@
 #'
 #' @examples
 #' anlz_sedimentpelave(sedimentdata)
-anlz_sedimentpelave <- function(sedimentdata, yrrng = c(1993, 2022), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP'){
+anlz_sedimentpelave <- function(sedimentdata, yrrng = c(1993, 2023), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP'){
 
   levs <- c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB')
 

diff --git a/R/anlz_tbbimed.R b/R/anlz_tbbimed.R
@@ -20,7 +20,7 @@
 #' @examples
 #' tbbiscr <- anlz_tbbiscr(benthicdata)
 #' anlz_tbbimed(tbbiscr)
-anlz_tbbimed <- function(tbbiscr, bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB',  'All', 'All (wt)'), rev = FALSE, yrrng = c(1993, 2022)) {
+anlz_tbbimed <- function(tbbiscr, bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB',  'All', 'All (wt)'), rev = FALSE, yrrng = c(1993, 2023)) {
 
   # sanity checks
   stopifnot(length(yrrng) == 2)

diff --git a/R/benthicdata.R b/R/benthicdata.R
@@ -1,6 +1,6 @@
-#' Benthic data for the Tampa Bay Benthic Index current as of 03132024
+#' Benthic data for the Tampa Bay Benthic Index current as of 20241212
 #'
-#' Benthic data for the Tampa Bay Benthic Index current as of 03132024
+#' Benthic data for the Tampa Bay Benthic Index current as of 20241212
 #'
 #' @format A nested \code{\link[tibble]{tibble}} with 3 rows and 2 variables:
 #' \describe{

diff --git a/R/sedimentdata.R b/R/sedimentdata.R
@@ -1,8 +1,8 @@
-#' Sediment data for the Tampa Bay current as of 12142023
+#' Sediment data for the Tampa Bay current as of 20241212
 #'
-#' Sediment data for the Tampa Bay current as of 12142023
+#' Sediment data for the Tampa Bay current as of 20241212
 #'
-#' @format A \code{data.frame} with 216627 rows and 24 variables:
+#' @format A \code{data.frame} with 226589 rows and 24 variables:
 #' \describe{
 #'   \item{ProgramId}{int}
 #'   \item{ProgramName}{chr}

diff --git a/R/show_sedimentalratio.R b/R/show_sedimentalratio.R
@@ -28,7 +28,7 @@
 #'
 #' @examples
 #' show_sedimentalratio(sedimentdata, param = 'Arsenic')
-show_sedimentalratio <- function(sedimentdata, param, yrrng = c(1993, 2022), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP', lnsz = 1, base_size = 12, plotly = FALSE, family = NA, width = NULL, height = NULL){
+show_sedimentalratio <- function(sedimentdata, param, yrrng = c(1993, 2023), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP', lnsz = 1, base_size = 12, plotly = FALSE, family = NA, width = NULL, height = NULL){
 
   # check paramater is an available metal
   metals <- sedimentdata %>%

diff --git a/R/show_sedimentave.R b/R/show_sedimentave.R
@@ -20,7 +20,7 @@
 #'
 #' @examples
 #' show_sedimentave(sedimentdata, param = 'Arsenic')
-show_sedimentave <- function(sedimentdata, param, yrrng = c(1993, 2022), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP', lnsz = 1, base_size = 12, plotly = FALSE, family = NA, width = NULL, height = NULL){
+show_sedimentave <- function(sedimentdata, param, yrrng = c(1993, 2023), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP', lnsz = 1, base_size = 12, plotly = FALSE, family = NA, width = NULL, height = NULL){
 
   toplo <- anlz_sedimentave(sedimentdata, param = param, yrrng = yrrng, bay_segment = bay_segment, funding_proj = funding_proj)
 

diff --git a/R/show_sedimentmap.R b/R/show_sedimentmap.R
@@ -17,7 +17,7 @@
 #'
 #' @examples
 #' show_sedimentmap(sedimentdata, param = 'Arsenic')
-show_sedimentmap <- function(sedimentdata, param, yrrng = c(1993, 2022), funding_proj = 'TBEP', weight = 1.5){
+show_sedimentmap <- function(sedimentdata, param, yrrng = c(1993, 2023), funding_proj = 'TBEP', weight = 1.5){
 
   # add totals
   sedimentdata <- anlz_sedimentaddtot(sedimentdata, yrrng = yrrng, funding_proj = funding_proj, param = param, pelave = FALSE)

diff --git a/R/show_sedimentpelave.R b/R/show_sedimentpelave.R
@@ -22,7 +22,7 @@
 #'
 #' @examples
 #' show_sedimentpelave(sedimentdata)
-show_sedimentpelave <- function(sedimentdata, yrrng = c(1993, 2022), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP', alph = 1, ylim = c(0, 0.4), lnsz = 1, base_size = 12, plotly = FALSE, family = NA, width = NULL, height = NULL){
+show_sedimentpelave <- function(sedimentdata, yrrng = c(1993, 2023), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP', alph = 1, ylim = c(0, 0.4), lnsz = 1, base_size = 12, plotly = FALSE, family = NA, width = NULL, height = NULL){
 
   # get avg pel ratios by station, then get averages
   toplo <- anlz_sedimentpelave(sedimentdata, yrrng = yrrng, bay_segment = bay_segment, funding_proj = funding_proj)

diff --git a/R/show_sedimentpelmap.R b/R/show_sedimentpelmap.R
@@ -14,7 +14,7 @@
 #'
 #' @examples
 #' show_sedimentpelmap(sedimentdata)
-show_sedimentpelmap <- function(sedimentdata, yrrng = c(1993, 2022), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP', weight = 1.5){
+show_sedimentpelmap <- function(sedimentdata, yrrng = c(1993, 2023), bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB'), funding_proj = 'TBEP', weight = 1.5){
 
   # map prep
   tomap <- anlz_sedimentpel(sedimentdata, yrrng = yrrng, bay_segment = bay_segment, funding_proj = funding_proj) %>%

diff --git a/R/show_tbbimatrix.R b/R/show_tbbimatrix.R
@@ -28,7 +28,7 @@
 #' tbbiscr <- anlz_tbbiscr(benthicdata)
 #' show_tbbimatrix(tbbiscr)
 show_tbbimatrix <- function(tbbiscr, bay_segment = c('HB', 'OTB', 'MTB', 'LTB', 'TCB', 'MR', 'BCB', 'All', 'All (wt)'),
-                            yrrng = c(1993, 2022), alph = 1, txtsz = 3, family = NA, rev = FALSE, position = 'top',
+                            yrrng = c(1993, 2023), alph = 1, txtsz = 3, family = NA, rev = FALSE, position = 'top',
                             plotly = FALSE, width = NULL, height = NULL){
 
   # annual average by segment

diff --git a/data/benthicdata.RData b/data/benthicdata.RData
diff --git a/data/sedimentdata.RData b/data/sedimentdata.RData
diff --git a/man/anlz_sedimentaddtot.Rd b/man/anlz_sedimentaddtot.Rd
diff --git a/man/anlz_sedimentave.Rd b/man/anlz_sedimentave.Rd
diff --git a/man/anlz_sedimentpel.Rd b/man/anlz_sedimentpel.Rd
diff --git a/man/anlz_sedimentpelave.Rd b/man/anlz_sedimentpelave.Rd
diff --git a/man/anlz_tbbimed.Rd b/man/anlz_tbbimed.Rd
diff --git a/man/benthicdata.Rd b/man/benthicdata.Rd
diff --git a/man/sedimentdata.Rd b/man/sedimentdata.Rd
diff --git a/man/show_sedimentalratio.Rd b/man/show_sedimentalratio.Rd
diff --git a/man/show_sedimentave.Rd b/man/show_sedimentave.Rd
diff --git a/man/show_sedimentmap.Rd b/man/show_sedimentmap.Rd
diff --git a/man/show_sedimentpelave.Rd b/man/show_sedimentpelave.Rd
diff --git a/man/show_sedimentpelmap.Rd b/man/show_sedimentpelmap.Rd
diff --git a/man/show_tbbimatrix.Rd b/man/show_tbbimatrix.Rd
diff --git a/tests/testthat/test-anlz_sedimentave.R b/tests/testthat/test-anlz_sedimentave.R
@@ -1,4 +1,4 @@
 test_that("Checking anlz_sedimentave class", {
-  result <- anlz_sedimentave(sedimentdata, param = 'Arsenic', yrrng = 2022)
+  result <- anlz_sedimentave(sedimentdata, param = 'Arsenic', yrrng = 2023)
   expect_is(result, 'tbl_df')
 })
diff --git a/tests/testthat/test-anlz_sedimentpel.R b/tests/testthat/test-anlz_sedimentpel.R
@@ -1,4 +1,4 @@
 test_that("Checking anlz_sedimentpel class", {
-  result <- anlz_sedimentpel(sedimentdata, yrrng = 2022)
+  result <- anlz_sedimentpel(sedimentdata, yrrng = 2023)
   expect_is(result, 'tbl_df')
 })
diff --git a/tests/testthat/test-anlz_sedimentpelave.R b/tests/testthat/test-anlz_sedimentpelave.R
@@ -1,4 +1,4 @@
 test_that("Checking anlz_sedimentpelave class", {
-  result <- anlz_sedimentpelave(sedimentdata, yrrng = 2022)
+  result <- anlz_sedimentpelave(sedimentdata, yrrng = 2023)
   expect_is(result, 'tbl_df')
 })
diff --git a/tests/testthat/test-show_sedimentalratio.R b/tests/testthat/test-show_sedimentalratio.R
@@ -11,11 +11,11 @@ test_that("Checking show_sedimentalratio sanity checks", {
 
 
 test_that("Checking show_sedimentalratio class", {
-  result <- show_sedimentalratio(sedimentdata, param = 'Arsenic', yrrng = 2022)
+  result <- show_sedimentalratio(sedimentdata, param = 'Arsenic', yrrng = 2023)
   expect_is(result, 'ggplot')
 })
 
 test_that("Checking show_sedimentalratio plotly class", {
-  result <- show_sedimentalratio(sedimentdata, param = 'Arsenic', yrrng = 2022, plotly = T)
+  result <- show_sedimentalratio(sedimentdata, param = 'Arsenic', yrrng = 2023, plotly = T)
   expect_is(result, 'plotly')
 })
diff --git a/tests/testthat/test-show_sedimentave.R b/tests/testthat/test-show_sedimentave.R
@@ -1,9 +1,9 @@
 test_that("Checking show_sedimentave class", {
-  result <- show_sedimentave(sedimentdata, param = 'Arsenic', yrrng = 2022)
+  result <- show_sedimentave(sedimentdata, param = 'Arsenic', yrrng = 2023)
   expect_is(result, 'ggplot')
 })
 
 test_that("Checking show_sedimentave plotly class", {
-  result <- show_sedimentave(sedimentdata, param = 'Arsenic', yrrng = 2022, plotly = T)
+  result <- show_sedimentave(sedimentdata, param = 'Arsenic', yrrng = 2023, plotly = T)
   expect_is(result, 'plotly')
 })
diff --git a/tests/testthat/test-show_sedimentmap.R b/tests/testthat/test-show_sedimentmap.R
@@ -1,9 +1,9 @@
 test_that("Checking show_sedimentmap class", {
-  result <- show_sedimentmap(sedimentdata, param = 'Arsenic', yrrng = 2022)
+  result <- show_sedimentmap(sedimentdata, param = 'Arsenic', yrrng = 2023)
   expect_is(result, 'leaflet')
 })
 
 test_that("Checking show_sedimentmap class, no TEL/PEL", {
-  result <- expect_warning(show_sedimentmap(sedimentdata, param = 'Selenium', yrrng = 2022))
+  result <- expect_warning(show_sedimentmap(sedimentdata, param = 'Selenium', yrrng = 2023))
   expect_is(result, 'leaflet')
 })
diff --git a/tests/testthat/test-show_sedimentpelave.R b/tests/testthat/test-show_sedimentpelave.R
@@ -1,9 +1,9 @@
 test_that("Checking show_sedimentpelave class", {
-  result <- show_sedimentpelave(sedimentdata, yrrng = 2022)
+  result <- show_sedimentpelave(sedimentdata, yrrng = 2023)
   expect_is(result, 'ggplot')
 })
 
 test_that("Checking show_sedimentpelave plotly class", {
-  result <- show_sedimentpelave(sedimentdata, yrrng = 2022, plotly = T)
+  result <- show_sedimentpelave(sedimentdata, yrrng = 2023, plotly = T)
   expect_is(result, 'plotly')
 })
diff --git a/tests/testthat/test-show_sedimentpelmap.R b/tests/testthat/test-show_sedimentpelmap.R
@@ -1,4 +1,4 @@
 test_that("Checking show_sedimentpelmap class", {
-  result <- show_sedimentpelmap(sedimentdata, yrrng = 2022)
+  result <- show_sedimentpelmap(sedimentdata, yrrng = 2023)
   expect_is(result, 'leaflet')
 })