Release v0.4.0

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

@@ -25,7 +25,7 @@ jobs:
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: '4.0.0'}
+          - {os: ubuntu-latest,   r: '4.1.0'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: BioCroField
-Version: 0.3.0
+Version: 0.4.0
 Title: Tools for BioCro Field Data
 Description: A collection of tools for processing field data related to BioCro
     crop growth simulations.
@@ -12,9 +12,10 @@ Authors@R: c(
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-Depends: R (>= 4.0.0)
+Depends: R (>= 4.1.0)
 Imports:
-    rmarkdown
+    rmarkdown,
+    BioCro
 Suggests:
     knitr,
     testthat (>= 3.0.0),

NEWS.md

@@ -8,15 +8,24 @@ major.minor.patch structure of semantic versioning. When applicable, entries
 should include direct links to the relevant pull requests.
 
 Then, when a new release is made, "# Unreleased" should be replaced by a heading
-with the new version number, such as "# CHANGES IN BioCroField VERSION 2.0.0."
+with the new version number, such as "# BioCroField version 2.0.0."
 This section will combine all of the release notes from all of the pull requests
 merged in since the previous release.
 
 Subsequent commits will then include a new "Unreleased" section in preparation
 for the next release.
 -->
 
-# BioCroField VERSION 0.3.0
+# BioCroField version 0.4.0
+
+- It is now possible to specify extra columns to be returned in the output from
+  `biomass_table`.
+- Values of `time` are now calculated using `BioCro::add_time_to_weather_data`
+  to ensure they are always consistent with BioCro's time definition.
+- Values of partitioned leaf mass can be set to `NA` when creating a
+  `harvest_point`, which is treated as if the leaf mass had not been provided.
+
+# BioCroField version 0.3.0
 
 - LMA is now included in the output from `biomass_table`.
 - New crop-specific guides to harvesting and weighing are now available, along
@@ -26,7 +35,7 @@ for the next release.
 - A new vignette has been added (`images_from_the_field`) that illustrates
   parts of the harvesting and weighing process using pictures from the field.
 
-# BioCroField VERSION 0.2.0
+# BioCroField version 0.2.0
 
 - Two new methods for estimating LAI were added to `process`:
   `LAI_from_planting_density` and `LAI_from_measured_population`. The original
@@ -45,7 +54,7 @@ for the next release.
   - https://github.com/biocro/BioCroField/pull/4
   - https://github.com/biocro/BioCroField/pull/5
 
-# BioCroField VERSION 0.1.1
+# BioCroField version 0.1.1
 
 - A bug related to partial name matching for partitioning components was
   detected and fixed. In short, if a value of `leaf` mass was not supplied but
@@ -57,7 +66,7 @@ for the next release.
 - PRs related to creating this version:
   - https://github.com/biocro/BioCroField/pull/2
 
-# BioCroField VERSION 0.1.0
+# BioCroField version 0.1.0
 
 - This is the first version of BioCroField. At this point, the package is in a
   state of rapid development, and not all changes will be described here.

R/add_seed_biomass.R

@@ -157,8 +157,10 @@ add_seed_biomass <- function(
     initial_biomass[['year']] <- year
     initial_biomass[['doy']] <- doy
     initial_biomass[['hour']] <- hour
-    initial_biomass[['time']] <-
-        initial_biomass[['doy']] + initial_biomass[['hour']] / 24.0
+
+    time_list <- list(doy = doy, hour = hour)
+    time_list <- BioCro::add_time_to_weather_data(time_list)
+    initial_biomass[['time']] <- time_list[['time']]
 
     # Reset certain columns to zero; there is no leaf area when the plant is a
     # seed, so also make sure to set all LAI estimates to zero

R/biomass_table.R

@@ -1,4 +1,17 @@
-biomass_table <- function(..., zero_when_missing = character()) {
+biomass_table <- function(
+    ...,
+    zero_when_missing = character(),
+    other_columns = c(
+        'leaf_area_per_plant',
+        'LAI_from_planting_density',
+        'LAI_from_measured_population',
+        'agb_per_area',
+        'agb_per_plant_row',
+        'agb_per_plant_partitioning',
+        'measured_population'
+    )
+)
+{
     x <- list(...)
 
     types <- lapply(x, class)
@@ -9,12 +22,26 @@ biomass_table <- function(..., zero_when_missing = character()) {
     UseMethod('biomass_table', x[[1]])
 }
 
-biomass_table.harvest_point <- function(..., zero_when_missing = character()) {
+biomass_table.harvest_point <- function(
+    ...,
+    zero_when_missing = character(),
+    other_columns = c(
+        'leaf_area_per_plant',
+        'LAI_from_planting_density',
+        'LAI_from_measured_population',
+        'agb_per_area',
+        'agb_per_plant_row',
+        'agb_per_plant_partitioning',
+        'measured_population'
+    )
+)
+{
     x <- list(...) # a list of harvest_point objects
 
     # Make sure certain inputs are character
     should_be_c <- list(
-        zero_when_missing = zero_when_missing
+        zero_when_missing = zero_when_missing,
+        other_columns = other_columns
     )
 
     c_bad <- sapply(should_be_c, function(x) {!is.character(x)})
@@ -48,18 +75,13 @@ biomass_table.harvest_point <- function(..., zero_when_missing = character()) {
         'SLA',
         'LMA',
         'LAI_from_LMA',
-        'LAI_from_planting_density',
-        'LAI_from_measured_population',
-        'agb_per_plant_row',
-        'agb_per_plant_partitioning',
-        'measured_population',
         'row_spacing',
         'plant_spacing',
         'planting_density'
     )
 
     cnames <-
-        c(initial_columns, all_components, final_columns, additional_arguments)
+        c(initial_columns, all_components, final_columns, other_columns, additional_arguments)
 
     # Form a data frame
     biomass <- stats::setNames(
@@ -75,7 +97,7 @@ biomass_table.harvest_point <- function(..., zero_when_missing = character()) {
     for (i in seq_along(x)) {
         hpp <- x[[i]]
 
-        for (name in c(initial_columns, final_columns)) {
+        for (name in c(initial_columns, final_columns, other_columns)) {
             if (name %in% names(hpp)) {
                 biomass[i, name] <- hpp[[name]]
             }

R/harvest_point.R

@@ -190,13 +190,15 @@ harvest_point <- function(
     # Do not allow a leaf with zero area but nonzero mass
     if (!is.na(partitioning_leaf_area) && partitioning_leaf_area == 0 &&
         !is.null(partitioning_component_weights[['leaf']]) &&
+        !is.na(partitioning_component_weights[['leaf']]) &&
             partitioning_component_weights[['leaf']] > 0) {
         stop("It is not possible for a leaf with zero area to have a nonzero mass")
     }
 
     # Do not allow a leaf with zero mass but nonzero area
     if (!is.na(partitioning_leaf_area) && partitioning_leaf_area > 0 &&
         !is.null(partitioning_component_weights[['leaf']]) &&
+        !is.na(partitioning_component_weights[['leaf']]) &&
             partitioning_component_weights[['leaf']] == 0) {
         stop("It is not possible for a leaf with zero mass to have a nonzero area")
     }

R/process.R

@@ -12,7 +12,9 @@ process.harvest_point <- function(x, leaf_name = 'leaf', ...) {
     # that we can handle incomplete information in the inputs.
 
     # The time (as specified in BioCro)
-    time <- x[['doy']] + x[['hour']] / 24.0
+    time_list <- list(doy = x[['doy']], hour = x[['hour']])
+    time_list <- BioCro::add_time_to_weather_data(time_list)
+    time <- time_list[['time']]
 
     # Above-ground biomass from the plants that were partitioned (in g)
     partitioning_agb_weight <- if (length(x[['agb_components']]) > 0) {

man/biomass_table.Rd

@@ -11,9 +11,33 @@
 }
 
 \usage{
-  biomass_table(\dots, zero_when_missing = character())
-
-  \method{biomass_table}{harvest_point}(\dots, zero_when_missing = character())
+  biomass_table(
+    \dots,
+    zero_when_missing = character(),
+    other_columns = c(
+        'leaf_area_per_plant',
+        'LAI_from_planting_density',
+        'LAI_from_measured_population',
+        'agb_per_area',
+        'agb_per_plant_row',
+        'agb_per_plant_partitioning',
+        'measured_population'
+    )
+  )
+
+  \method{biomass_table}{harvest_point}(
+    \dots,
+    zero_when_missing = character(),
+    other_columns = c(
+        'leaf_area_per_plant',
+        'LAI_from_planting_density',
+        'LAI_from_measured_population',
+        'agb_per_area',
+        'agb_per_plant_row',
+        'agb_per_plant_partitioning',
+        'measured_population'
+    )
+  )
 }
 
 \arguments{
@@ -26,6 +50,11 @@
     \code{pod} would be set to \code{NA} for these points, but it would make
     more sense to set it to 0.
   }
+
+  \item{other_columns}{
+    The names of variables to include as columns in addition to the default
+    columns (see below).
+  }
 }
 
 \details{
@@ -55,16 +84,6 @@
 
     \item \code{LAI_from_LMA}
 
-    \item \code{LAI_from_planting_density}
-
-    \item \code{LAI_from_measured_population}
-
-    \item \code{agb_per_plant_row}
-
-    \item \code{agb_per_plant_partitioning}
-
-    \item \code{measured_population}
-
     \item \code{row_spacing}
 
     \item \code{plant_spacing}
@@ -76,6 +95,9 @@
 
     \item Any additional arguments (such as comments) that were passed to
           \code{\link{harvest_point}} when creating the data points
+
+    \item Any additional variables specified in the \code{other_columns} input
+          argument
   }
 
   See \code{\link{harvest_point}} and \code{\link{process}} for more information

man/generate_crop_guide.Rd

@@ -88,7 +88,7 @@
   LaTeX installation, you may need to use the \code{TinyTex} package. To do
   this, make sure the package is installed and then run
   \code{tinytex::install_tinytex()}. \code{TinyTex} can be installed from CRAN
-  by typing code{install.packages('TinyTex')}.
+  by typing \code{install.packages('TinyTex')}.
 }
 
 \value{

man/process.Rd

@@ -38,8 +38,8 @@
 
   The detailed calculations are as follows:
   \itemize{
-    \item \code{time}: In BioCro, the time is specified as a fractional day of
-          the year calculated by \code{time = doy + hour / 24.0}.
+    \item \code{time}: The time as determined from the \code{doy} and
+          \code{hour} using \code{\link[BioCro]{add_time_to_weather_data}}.
 
     \item \code{measured_population}: The number of plants per unit ground area
           (in \code{plants / acre} can be estimated from the row spacing and the

tests/testthat/test-add_seed_biomass.R

@@ -50,3 +50,19 @@ test_that("Seed biomass is properly added to tables", {
         2.47
     )
 })
+
+test_that("Time is calculated the same was as in `process`", {
+    doy = 12
+    hour = 3
+
+    biomass_df <- add_seed_biomass(
+        biomass_table(process(harvest_point(doy = doy, hour = hour))),
+        doy = doy,
+        hour = hour
+    )
+
+    expect_equal(
+        biomass_df$time[1],
+        biomass_df$time[2]
+    )
+})

tests/testthat/test-biomass_table.R

@@ -24,3 +24,55 @@ test_that("Additional harvest_point arguments are included in the final table",
 
     expect_identical(biomass$stem_comment, c('blah', NA))
 })
+
+test_that("Some table columns are specified by the user", {
+    essential_columns <- c(
+        'crop',
+        'variety',
+        'location',
+        'plot',
+        'year',
+        'doy',
+        'hour',
+        'time',
+        'SLA',
+        'LMA',
+        'LAI_from_LMA',
+        'row_spacing',
+        'plant_spacing',
+        'planting_density'
+    )
+
+    optional_columns <- c(
+        'LAI_from_planting_density',
+        'LAI_from_measured_population',
+        'agb_per_area',
+        'agb_per_plant_row',
+        'agb_per_plant_partitioning',
+        'measured_population'
+    )
+
+    hp <- process(harvest_point())
+
+    # Use default arguments
+    biomass_table_1 <- biomass_table(hp)
+
+    expect_true(
+        all(essential_columns %in% colnames(biomass_table_1))
+    )
+
+    expect_true(
+        all(optional_columns %in% colnames(biomass_table_1))
+    )
+
+    # Don't include any extra columns
+    biomass_table_2 <- biomass_table(hp, other_columns = character())
+
+    expect_true(
+        all(essential_columns %in% colnames(biomass_table_2))
+    )
+
+    expect_true(
+        all(!optional_columns %in% colnames(biomass_table_2))
+    )
+})

tests/testthat/test-harvest_point.R

@@ -156,12 +156,12 @@ test_that("Missing density parameters are automatically calculated", {
         harvest_point(row_spacing = 0.75, plant_spacing = 0.2)$planting_density,
         26980
     )
-    
+
     expect_equal(
         harvest_point(row_spacing = 0.75, planting_density = 26980)$plant_spacing,
         0.2
     )
-    
+
     expect_equal(
         harvest_point(plant_spacing = 0.2, planting_density = 26980)$row_spacing,
         0.75
@@ -218,3 +218,9 @@ test_that("Additional arguments must have length 1 and be numeric, character, or
         "The following inputs should have length 1, but do not: construct"
     )
 })
+
+test_that("Partitioned leaf mass can be NA when leaf area is numeric", {
+    expect_no_error(
+        harvest_point(partitioning_component_weights = list(leaf = NA), partitioning_leaf_area = 1)
+    )
+})