Merge pull request #19 from jmzobitz/fix/invalid-html5

Fix/invalid html5

.Rbuildignore

@@ -5,3 +5,4 @@
 ^LICENSE\.md$
 ^swc-corrections$
 ^data-raw$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check-HTML5.yaml

@@ -0,0 +1,42 @@
+# 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, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check-HTML5
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      _R_CHECK_RD_VALIDATE_RD2HTML_: TRUE
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install pdflatex
+        run: sudo apt-get install texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra
+
+      - name: Install tidy
+        run: sudo apt install tidy
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'devel'
+          http-user-agent: 'release'
+          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:
+          args: '"--as-cran"'
+          build_args: 'character()'
+          error-on: '"note"'

R/acquire_neon_data.R

@@ -19,21 +19,24 @@
 #' @export
 
 
-# changelog and author contributions / copyrights
-#   John Zobitz (2021-07-22)
-#     original creation
-#     update to fix auto download (2021-07-25)
-#     2022-06-10: update to correct flags on swc
-#     2024-04-08: update to get namespaces correct
-#     2024-04-10: update to get the swc depths corrected
-#     2024-04-23: update to allow provisional data
-#     2024-05-23: update to prepare for CRAN submission
+
 
 acquire_neon_data <- function(site_name,
                               download_date,
                               time_frequency = "30_minute",
                               provisional = FALSE) {
 
+
+  # changelog and author contributions / copyrights
+  #   John Zobitz (2021-07-22)
+  #     original creation
+  #     update to fix auto download (2021-07-25)
+  #     2022-06-10: update to correct flags on swc
+  #     2024-04-08: update to get namespaces correct
+  #     2024-04-10: update to get the swc depths corrected
+  #     2024-04-23: update to allow provisional data
+  #     2024-05-23: update to prepare for CRAN submission
+
   .data = NULL  # Appease R CMD Check
 
   # Define the columns that we are plucking from each dataset:

R/check_qf_flags.R

@@ -11,14 +11,16 @@
 #'
 #' @return A data frame of startDateTime, horizontalPosition, and the associated QF flag.
 
-#'
-#' # changelog and author contributions / copyrights
-#   John Zobitz (2024-05-08)
-#     original creation
+
 
 
 check_qf_flags <- function(measurement_name,data) {
 
+  #'
+  #' # changelog and author contributions / copyrights
+  #   John Zobitz (2024-05-08)
+  #     original creation
+
   .data = NULL  # Appease R CMD Check
   ## Function takes data and the measurement, checks to see if there are more than 2 measurements for swc, temperature, and co2 at a given spatial location and time.
   ## For atmospheric pressure, just checks to see if we have a measurement

R/co2_to_umol.R

@@ -20,15 +20,19 @@
 
 #' @export
 
-# changelog and author contributions / copyrights
-#   John Zobitz (2021-07-21)
-#     original creation
-#   2023-07-18: Included experimental uncertainty in the mix.
-#     2024-04-08: update to get namespaces correct
-#   2024-04-15: update to fix error in calculation of partial derivative of pressure (from Yang song)
+
 
 
 co2_to_umol <- function(temperature, pressure, co2, temperature_err, pressure_err, co2_err, zOffset) {
+
+  # changelog and author contributions / copyrights
+  #   John Zobitz (2021-07-21)
+  #     original creation
+  #   2023-07-18: Included experimental uncertainty in the mix.
+  #     2024-04-08: update to get namespaces correct
+  #   2024-04-15: update to fix error in calculation of partial derivative of pressure (from Yang song)
+
+
   # Since pressure is a single value, make it equal to all the other lengths
   pressure <- rep(pressure, length(temperature))
   pressure_err <- rep(pressure_err, length(temperature_err))

R/compute_monthly_mean.R

@@ -52,19 +52,20 @@
 
 #' @export
 
-# changelog and author contributions / copyrights
-#   Zoey Werbin (@zoey-rw): original author https://github.com/zoey-rw/microbialForecasts/blob/caa7b1a8aa8a131a5ff9340f1562cd3a3cb6667b/data_construction/covariate_prep/soil_moisture/clean_NEON_sensor_moisture_data.r
-#   John Zobitz (2024-01-17)
-#     modified to also compute the depth (zOffset) from the max of all zOffsets that month
-#   John Zobitz (2024-01-10)
-#     original creation
-#     2024-04-08: update to get namespaces correct
-
 #' @references
 #' Zoey Werbin (@zoey-rw): original author https://github.com/zoey-rw/microbialForecasts/blob/caa7b1a8aa8a131a5ff9340f1562cd3a3cb6667b/data_construction/covariate_prep/soil_moisture/clean_NEON_sensor_moisture_data.r
 
 compute_monthly_mean <- function(NEON_data, position_columns = c("horizontalPosition", "verticalPosition")) {
 
+  # changelog and author contributions / copyrights
+  #   Zoey Werbin (@zoey-rw): original author https://github.com/zoey-rw/microbialForecasts/blob/caa7b1a8aa8a131a5ff9340f1562cd3a3cb6667b/data_construction/covariate_prep/soil_moisture/clean_NEON_sensor_moisture_data.r
+  #   John Zobitz (2024-01-17)
+  #     modified to also compute the depth (zOffset) from the max of all zOffsets that month
+  #   John Zobitz (2024-01-10)
+  #     original creation
+  #     2024-04-08: update to get namespaces correct
+
+
   .data = NULL  # Appease R CMD Check
 
   out_mean <- NEON_data |>

R/compute_neon_flux.R

@@ -18,27 +18,19 @@
 #' @param input_site_megapit Required. Input list of environmental soil data.  Usually given from acquire_neon_data
 #'
 #' @examples
-#'
+#' \donttest{
 #'  # First acquire the NEON data at a given NEON site
 #' out_env_data <- acquire_neon_data("SJER","2020-05")
 #'
 #' # Then process and compute the fluxes:
-#'  out_flux <- compute_neon_flux(out_env_data$site_data,out_env_data$site_megapit)
-#'
+#'  out_flux <- compute_neon_flux(input_site_env = sjer_env_data_2022_06,
+#'  input_site_megapit = sjer_megapit_data_2022_06)
+#' }
 #' @return Data frame of fluxes and gradient from the timeperiod
 
 
 #' @export
 #'
-# changelog and author contributions / copyrights
-#   John Zobitz (2021-07-22)
-#     original creation
-#     2023-07-16: Update to take advantage of nested structures to improve / decrease computational time, allowing for multiple measurements to compute the flux.
-#     2023-10-23: Update to exit computing a flux if there are no half-hourly measurements.
-#     2024-04-08: update to get namespaces correct
-
-
-
 
 
 
@@ -47,6 +39,17 @@ compute_neon_flux <- function(input_site_env,
   .data = NULL  # Appease R CMD Check
 
 
+  # changelog and author contributions / copyrights
+  #   John Zobitz (2021-07-22)
+  #     original creation
+  #     2023-07-16: Update to take advantage of nested structures to improve / decrease computational time, allowing for multiple measurements to compute the flux.
+  #     2023-10-23: Update to exit computing a flux if there are no half-hourly measurements.
+  #     2024-04-08: update to get namespaces correct
+
+
+
+
+
   ################
   # 1) Load up the data (this may take a while)  Will be two data frames:
   # site_megapit: a nested file containing specific information about the site (for bulk density calculations, etc)

R/compute_surface_flux.R

@@ -11,19 +11,23 @@
 
 #' @return A value of the surface CO2 flux (umol m-2 s-1)
 
-# changelog and author contributions / copyrights
-#   John Zobitz (2021-07-21)
-#     original creation
-#   John Zobitz (2022-06-21)
-#     revision to account for correct directionality when computing fluxes
-#   John Zobitz (2023-07-14)
-#     revision to include value of gradient at surface and computation of quadrature errors
-#   John Zobitz (2024-01-20)
-#     revision to simplify code - fluxes are calculated via different approaches with the measurements
-
 
 compute_surface_flux <- function(input_data) {
-  .data = NULL  # Appease R CMD Check
+
+  # changelog and author contributions / copyrights
+  #   John Zobitz (2021-07-21)
+  #     original creation
+  #   John Zobitz (2022-06-21)
+  #     revision to account for correct directionality when computing fluxes
+  #   John Zobitz (2023-07-14)
+  #     revision to include value of gradient at surface and computation of quadrature errors
+  #   John Zobitz (2024-01-20)
+  #     revision to simplify code - fluxes are calculated via different approaches with the measurements
+
+
+
+
+   .data = NULL  # Appease R CMD Check
 
   # Compute the flux between the two different layers
 

R/correct_env_data.R

@@ -14,21 +14,25 @@
 #' @param input_data Required. Nested data frame from acquire_neon_data.
 #'
 #' @examples
+#' \donttest{
 #' # Note: you may need to first aqcuire the NEON data using acquire_neon_data
 #' # Now correct existing environmental data:
 #' corrected_data <- correct_env_data(sjer_env_data_2022_06)
+#' }
 
 
 
 #' @return List of all QF flags over time period and Data frame of environmental measurements for flux computation
 
-# changelog and author contributions / copyrights
-#   John Zobitz (2024-05-07)
-#     original creation
 
 
 correct_env_data <- function(input_data) {
 
+  # changelog and author contributions / copyrights
+  #   John Zobitz (2024-05-07)
+  #     original creation
+
+
   .data = NULL  # Appease R CMD Check
   ################
 

R/dejong_shappert_flux.R

@@ -21,14 +21,17 @@
 #'
 #' Maier, M., and H. Schack-Kirchner. 2014. “Using the Gradient Method to Determine Soil Gas Flux: A Review.” Agricultural and Forest Meteorology 192–193 (July):78–95. https://doi.org/10.1016/j.agrformet.2014.03.006.
 
-# changelog and author contributions / copyrights
-#   John Zobitz (2023-01-20)
-#     original creation
-#     2024-04-08: update to get namespaces correct
 
 
 dejong_shappert_flux <- function(zOffset, co2, co2_err, diffusive, diffusive_err) {
-  # Define the output vector:
+
+  # changelog and author contributions / copyrights
+  #   John Zobitz (2023-01-20)
+  #     original creation
+  #     2024-04-08: update to get namespaces correct
+
+
+   # Define the output vector:
   out_flux <- tibble::tibble(flux = NA, flux_err = NA, method = "dejong_shappert_1972")
 
   if (any(is.na(co2)) | any(is.na(co2_err)) | any(is.na(diffusive)) | any(is.na(diffusive_err))) {

R/depth_interpolate.R

@@ -16,21 +16,24 @@
 #' @return A nested data frame with interpolated measurements.
 
 
-# changelog and author contributions / copyrights
-#   John Zobitz (2021-07-20)
-#     original creation
-#   2022-06-06: Modification of the interpolation to accelerate computation
-#   2022-06-11: Modification to improve fitting
-#   2023-07-14: Extensive modification to improve interpolation of multiple columns of data.
-#               This now includes all the input data, but only interpolates measurements
-#     2024-04-08: update to get namespaces correct
-##############################################################################################
-
 
 depth_interpolate <- function(input_measurements,
                               measurement_name,
                               measurement_interpolate) {
 
+
+
+  # changelog and author contributions / copyrights
+  #   John Zobitz (2021-07-20)
+  #     original creation
+  #   2022-06-06: Modification of the interpolation to accelerate computation
+  #   2022-06-11: Modification to improve fitting
+  #   2023-07-14: Extensive modification to improve interpolation of multiple columns of data.
+  #               This now includes all the input data, but only interpolates measurements
+  #     2024-04-08: update to get namespaces correct
+  ##############################################################################################
+
+
   .data = NULL  # Appease R CMD Check
 
   # Get out the depths to which we will interpolate, make it into a nested data frame

R/determine_position.R

@@ -11,13 +11,16 @@
 
 
 #' @return A data frame that reports the measurement depth for and associated environmental measurement.
-# changelog and author contributions / copyrights
-#   John Zobitz (2024-01-17)
-#     original creation
-
 
 
 determine_position <- function(input_positions, input_measurement) {
+
+  # changelog and author contributions / copyrights
+  #   John Zobitz (2024-01-17)
+  #     original creation
+
+
+
   .data = NULL  # Appease R CMD Check
 
   # Define %within% so we can use here

R/diffusivity.R

@@ -23,14 +23,18 @@
 
 #' @export
 
-# changelog and author contributions / copyrights
-#   John Zobitz (2021-07-21)
-#     original creation
-#   John Zobitz (2024-01-20)
-#     modified to account if soil water > porosity - just set to 0
-
 
 diffusivity <- function(temperature, soil_water, pressure, temperature_err, soil_water_err, pressure_err, zOffset, porVol2To20) {
+
+  # changelog and author contributions / copyrights
+  #   John Zobitz (2021-07-21)
+  #     original creation
+  #   John Zobitz (2024-01-20)
+  #     modified to account if soil water > porosity - just set to 0
+
+
+
+
   # Since pressure is a single value, make it equal to all the other lengths
   pressure <- rep(pressure, length(temperature))
   pressure_err <- rep(pressure_err, length(temperature_err))