Merge pull request #20 from sean-rohan-NOAA/main

Correct tau_par() call, make internal CTD functions noRd, add CTD example to example script
afsc-gap-products · Apr 4, 2024 · 44f3b2f · 44f3b2f
2 parents f7d4eaa + 68acb43
commit 44f3b2f
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diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,45 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -25,6 +25,7 @@ URL: https://github.com/afsc-gap-products/GAPsurvey
 Description: Provides at-sea data management tools for RACE GAP surveys. 
 Encoding: UTF-8
 LazyData: true
+LazyDataCompression: xz
 Imports: 
     stats, 
     utils

diff --git a/GAPsurvey.Rproj b/GAPsurvey.Rproj
@@ -18,3 +18,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace
diff --git a/NAMESPACE b/NAMESPACE
@@ -3,20 +3,10 @@
 export(calc_net_spread)
 export(convert_bvdr_marp)
 export(convert_ctd_btd)
-export(convert_do_to_o2sat)
 export(convert_log_gps)
 export(convert_ted_btd)
-export(extract_calibration_xmlcon)
 export(fix_path)
-export(get_calibration_parameter)
 export(get_catch_haul_history)
 export(get_sunrise_sunset)
-export(hex_to_cnv)
-export(integer_to_conductivity)
-export(integer_to_ph)
-export(integer_to_pressure)
-export(integer_to_temperature)
 export(numbers0)
-export(oxygen_saturation)
-export(tau_par)
 export(text_list)
diff --git a/R/hex_to_cnv.R b/R/hex_to_cnv.R
@@ -218,7 +218,7 @@ calc_depth_from_pressure <- function(latitude, pressure, nsmall = 3) {
 #' @param sample_interval Sampling interval for scans; 0.25 for a typical SBE19plus V2 deployment.
 #' @param output_channels Optional. Named vector of output channels and their names. Do not use unless outputs are are not the defaults.
 #' @param output_sig_digits Optional. Significant digits after the decimal place for output channels. Only change if a subset of channels. Do not use unless outputs are are not the defaults.
-#' @export
+#' @noRd
 #' @author Sean Rohan
 
 hex_to_cnv <- function(hex_path,
@@ -481,7 +481,7 @@ hex_to_cnv <- function(hex_path,
 #' @param par3 Temperature calibration parameter par3
 #' @param par4 Temperature calibration parameter par4
 #' @param par5 Temperature calibration parameter par5
-#' @export
+#' @noRd
 #' @author Sean Rohan
 
 integer_to_temperature <- function(temperature_integer,
@@ -536,7 +536,7 @@ integer_to_temperature <- function(temperature_integer,
 #' @param par0 tvoltage_integer conversion constant
 #' @param sig_figs number of significant digits to use for temperature (default = 3)
 #' @param convert_to_dbar Should pressure be returned in or decibars (TRUE) or pounds per square inch without offset (FALSE)
-#' @export
+#' @noRd
 #' @author Sean Rohan
 
 integer_to_pressure <- function(pressure_integer,
@@ -598,7 +598,7 @@ integer_to_pressure <- function(pressure_integer,
 #' @param par0 Constant to convert integer to voltage
 #' @param par1 Constant to convert integer to voltage
 #' @param sig_figs number of significant digits to use for conductivity (default = 6)
-#' @export
+#' @noRd
 #' @author Sean Rohan
 
 integer_to_conductivity <- function(conductivity_integer, temperature, pressure, condg, condh, condi, condj, cpcor, ctcor, par0 = 256, par1 = 1000, sig_figs = 6) {
@@ -623,7 +623,7 @@ integer_to_conductivity <- function(conductivity_integer, temperature, pressure,
 #' @param temperature temperature in degrees C
 #' @param sig_figs number of significant digits to use for conductivity (default = 3)
 #' @param par0 ph_integer conversion constant
-#' @export
+#' @noRd
 #' @author Sean Rohan
 
 integer_to_ph <- function(ph_integer, ph_offset, ph_slope, temperature, sig_figs = 3, par0 = 13107) {
@@ -649,7 +649,7 @@ integer_to_ph <- function(ph_integer, ph_offset, ph_slope, temperature, sig_figs
 #'
 #' @param temperature Temperature (degrees Celsius).
 #' @param salinity Salinity (PSU, PSS-78).
-#' @export
+#' @noRd
 #' @references Garcia, H.E., Gordon, L.I., 1992. Oxygen solubility in seawater: Better fitting equations. Limnol. Oceanogr. 37, 1307–1312. https://doi.org/10.4319/lo.1992.37.6.1307
 #' @author Sean Rohan
 
@@ -689,7 +689,7 @@ oxygen_saturation <- function(temperature, salinity) {
 #' @param oxygen Dissolved oxygen in ml/l
 #' @param temperature Temperature (IPTS-68, degrees Celsius).
 #' @param salinity Salinity (PSU, PSS-78).
-#' @export
+#' @noRd
 #' @references Garcia, H.E., Gordon, L.I., 1992. Oxygen solubility in seawater: Better fitting equations. Limnol. Oceanogr. 37, 1307–1312. https://doi.org/10.4319/lo.1992.37.6.1307
 #' @author Sean Rohan
 
@@ -755,7 +755,7 @@ integer_to_dissolved_oxygen <- function(do_integer,
   dVdt <- c(0, diff(do_voltage)/sample_interval)
 
   if(tau_correction) {
-    tau <- DO_tau_correction(temperature, pressure, tau20, d0, d1, d2)
+    tau <- tau_par(temperature, pressure, tau20, d0, d1, d2)
   }
 
   temperature_K <- temperature + 273.15
@@ -781,7 +781,7 @@ integer_to_dissolved_oxygen <- function(do_integer,
 #' @param d1 Tau correction calibration parameter D1.
 #' @param d2 Tau correction calibration parameter D2.
 #' @param tau20 Tau correction calibration parameter Tau20.
-#' @export
+#' @noRd
 #' @references Edwards, B., Murphy, D., Janzen, C., Larson, A.N., 2010. Calibration, response, and hysteresis in deep-sea dissolved oxygen measurements. J. Atmos. Ocean. Technol. 27, 920–931. https://doi.org/10.1175/2009JTECHO693.1
 #' @author Sean Rohan
 
@@ -810,7 +810,7 @@ integer_to_ox_voltage <- function(ox_integer) {
 #' @param start_block starting index for lines of the header to search
 #' @param end_block ending index for lines of the leader to search
 #' @param make_numeric Logical. Should the tag value be forced to a numeric?
-#' @export
+#' @noRd
 #' @author Sean Rohan
 
 get_calibration_parameter <- function(header, cal_par, start_block = NULL, end_block = NULL, make_numeric = TRUE) {
@@ -881,7 +881,7 @@ write_to_cnv <- function(data_list, output_path) {
                        " [Instrument's time stamp, header]"))
   out <- c(out, paste0("# bad_flag = -9.990e-29"))
   out <- c(out, paste0("# gapctd_date = ", format(Sys.time(), "%b %d %Y %T"),
-                       ", gapctd ", gsub(pattern = "'", replacement = "", x = packageVersion("gapctd"))))
+                       ", GAPSurvey ", gsub(pattern = "[^0-9.-]", "", packageVersion("GAPSurvey"))))
   out <- c(out, paste0("# gapctd_in = ", dl$hex_path))
   out <- c(out, paste0("# file_type = ascii"))
   out <- c(out, "*END*")
@@ -913,7 +913,7 @@ write_to_cnv <- function(data_list, output_path) {
 #' Retrives calibration parameters for temperature, conductivity, pressure, oxygen, and pH sensors from an instrument configuration (.xmlcon) file.
 #'
 #' @param xmlcon_path Path to an xmlcon file.
-#' @export
+#' @noRd
 #' @author Sean Rohan
 
 extract_calibration_xmlcon <- function(xmlcon_path) {

diff --git a/inst/r/example_script.R b/inst/r/example_script.R
@@ -49,3 +49,21 @@ get_sunrise_sunset(chosen_date = Sys.Date(),
 # get_sunrise_sunset(chosen_date = "2023-06-10",
 #                    latitude = 52.6,
 #                    longitude = -169.4364)
+
+
+## Convert CTD data to BTD as a backup for SBE39 (aka 'the BT') ----------------
+
+convert_ctd_btd(
+  filepath_hex = system.file(paste0("exdata/convert_ctd_btd/",
+                                    "SBE19plus_01908106_2023_06_18_0001.hex"),
+                             package = "GAPsurvey"),
+  filepath_xmlcon = system.file(paste0("exdata/convert_ctd_btd/",
+                                       "SBE19plusV2_8106_ph_DO_leg2.xmlcon"),
+                                package = "GAPsurvey"),
+  VESSEL = 162,
+  CRUISE = 202301,
+  HAUL = 97,
+  latitude = 59.01693, # Approximate - for depth estimation
+  MODEL_NUMBER = "",
+  VERSION_NUMBER = "",
+  SERIAL_NUMBER = 8106)
diff --git a/man/convert_do_to_o2sat.Rd b/man/convert_do_to_o2sat.Rd
diff --git a/man/extract_calibration_xmlcon.Rd b/man/extract_calibration_xmlcon.Rd
diff --git a/man/get_calibration_parameter.Rd b/man/get_calibration_parameter.Rd
diff --git a/man/hex_to_cnv.Rd b/man/hex_to_cnv.Rd
diff --git a/man/integer_to_conductivity.Rd b/man/integer_to_conductivity.Rd