Merge pull request #12 from biocro/na-leaf

Allow partitioned leaf mass to be `NA`

Author: eloch216

.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: 0.3.0-0
+Version: 0.3.0-1
 Title: Tools for BioCro Field Data
 Description: A collection of tools for processing field data related to BioCro
     crop growth simulations.
@@ -12,7 +12,7 @@ Authors@R: c(
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-Depends: R (>= 4.0.0)
+Depends: R (>= 4.1.0)
 Imports:
     rmarkdown,
     BioCro

NEWS.md

@@ -22,6 +22,8 @@ for the next release.
   `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
 

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")
     }

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)
+    )
+})

tests/testthat/test-process.R

@@ -122,6 +122,8 @@ test_that("LMA is calculated only when possible", {
     expect_na(hpp$LMA)
 
     expect_na(process(harvest_point(partitioning_leaf_area = 1))$LMA)
+    
+    expect_na(process(harvest_point(partitioning_component_weights = list(leaf = NA), partitioning_leaf_area = 1))$LMA)
 
     expect_na(process(harvest_point(partitioning_component_weights = list(leaf = 1)))$LMA)