Merge branch 'develop' into prepare-for-release

_pkgdown.yml

@@ -144,3 +144,10 @@ reference:
     - '`notetaker_print_notes`'
     - '`notes_random_string`'
 
+  - title: Deprecated function names
+    desc: Functions that have been moved from traits.build to austraits and renamed. Deprecated names still work.
+    contents:
+    - '`build_combine`'
+    - '`util_df_to_list`'
+    - '`util_list_to_df1`'
+    - '`util_list_to_df2`'

inst/support/traits.build_schema.yml

@@ -24,6 +24,7 @@ value_type:
     range: Value is a range of values recorded for an entity.
     bin: Value for an entity falls within specified limits.
     standard_error: Value is the standard error of a mean of values recorded for an entity.
+    standard_deviation: Value is the standard deviation of a mean of values recorded for an entity.
     unknown: Not currently known.
 
 basis_of_value:

ontology/data/traits.build_resource.csv

@@ -11,4 +11,4 @@ Subject,Predicate,Object
 <https://w3id.org/traits.build>,<http://purl.org/dc/terms/creator>,"""Elizabeth Wenk"""
 <https://w3id.org/traits.build>,<http://purl.org/dc/terms/creator>,"""Sophie Yang"""
 <https://w3id.org/traits.build>,<http://purl.org/dc/terms/created>,"""01 February 2024^^<xsd:date>"""
-https://w3id.org/traits.build#traits.build-database,<http://www.w3.org/2004/02/skos/core#topConceptOf>,"""<https://w3id.org/traits.build>""^^<xsd:anyURI>"
+<https://w3id.org/traits.build#traits.build-database>,<http://www.w3.org/2004/02/skos/core#topConceptOf>,"""<https://w3id.org/traits.build>""^^<xsd:anyURI>"

tests/testthat/examples/Test_2023_2/data.csv

@@ -43,5 +43,5 @@ Psychotria dallachiana,psydal,Cape Tribulation,0.079,0.0177,2495,0.612,0.33,,429
 Quassia baileyana,quabai,Cape Tribulation,0.086,0.023,9624,0.501,0.42,,,5867,3216,5719,2,unknown,mean,adult,,Test_2022,,
 Rockinghamia angustifolia,rocang,Cape Tribulation,0.108,0.0158,10636,0.455,0.39,19.38,,5862,4611,6098,2,unknown,mean,adult,,Test_2022,,
 Syzygium gustavioides,syzgus,Cape Tribulation,0.167,0.0129,3590,0.521,0.59,48000,2833,3121,3047,6584,2,unknown,mean,adult,,Test_2022,,
-Syzygium sayeri,syzsay,Cape Tribulation,0.131,0.0137,2645,0.485,0.65,841,3929,5767,4939,9836,2,unknown,mean,adult,,Test_2022,,
-Trema aspera,treasp,Cape Tribulation,0.053,0.0299,2071,0.357,0.53,5.12,3578,5291,5440,6695,2,unknown,mean,adult,,Test_2022,,
+Syzygium sayeri,syzsay,Cape Tribulation,0.131,0.0137,2645,0.485,0.65,841,3929,5767,4939,9836,2,unknown,standard_deviation,adult,,Test_2022,,
+Trema aspera,treasp,Cape Tribulation,0.053,0.0299,2071,0.357,0.53,5.12,3578,5291,5440,6695,2,unknown,standard_error,adult,,Test_2022,,

tests/testthat/examples/Test_2023_2/output/traits.csv

@@ -439,25 +439,25 @@ Test_2023_2,Syzygium gustavioides,097,leaf_N_per_dry_mass,12.9,mg/g,species,mean
 Test_2023_2,Syzygium gustavioides,097,leaf_area,3590,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Syzygium gustavioides
 Test_2023_2,Syzygium gustavioides,097,leaf_mass_per_area,167,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Syzygium gustavioides
 Test_2023_2,Syzygium gustavioides,097,wood_density,0.521,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Syzygium gustavioides
-Test_2023_2,Syzygium sayeri,098,branch_mass_fraction,0.65,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Syzygium sayeri
-Test_2023_2,Syzygium sayeri,098,huber_value,0.000254517688979384,mm2{sapwood}/mm2{leaf},population,mean,unknown,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Syzygium sayeri
-Test_2023_2,Syzygium sayeri,098,huber_value,0.000173400381480839,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Syzygium sayeri
-Test_2023_2,Syzygium sayeri,098,huber_value,0.000202470135654991,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Syzygium sayeri
+Test_2023_2,Syzygium sayeri,098,branch_mass_fraction,0.65,mg/mg,population,standard_deviation,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Syzygium sayeri
 Test_2023_2,Syzygium sayeri,098,huber_value,0.000101667344448963,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Syzygium sayeri
 Test_2023_2,Syzygium sayeri,098,huber_value,0.000101667344448963,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Syzygium sayeri
-Test_2023_2,Syzygium sayeri,098,seed_dry_mass,841,mg,population,mean,unknown,unknown,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Syzygium sayeri
-Test_2023_2,Syzygium sayeri,099,leaf_N_per_dry_mass,13.7,mg/g,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Syzygium sayeri
-Test_2023_2,Syzygium sayeri,099,leaf_area,2645,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Syzygium sayeri
-Test_2023_2,Syzygium sayeri,099,leaf_mass_per_area,131,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Syzygium sayeri
-Test_2023_2,Syzygium sayeri,099,wood_density,0.485,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Syzygium sayeri
-Test_2023_2,Trema tomentosa var. aspera,100,branch_mass_fraction,0.53,mg/mg,population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Trema aspera
-Test_2023_2,Trema tomentosa var. aspera,100,huber_value,0.000279485746226942,mm2{sapwood}/mm2{leaf},population,mean,unknown,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Trema aspera
-Test_2023_2,Trema tomentosa var. aspera,100,huber_value,0.000189000189000189,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Trema aspera
-Test_2023_2,Trema tomentosa var. aspera,100,huber_value,0.000183823529411765,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Trema aspera
+Test_2023_2,Syzygium sayeri,098,huber_value,0.000254517688979384,mm2{sapwood}/mm2{leaf},population,standard_deviation,unknown,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Syzygium sayeri
+Test_2023_2,Syzygium sayeri,098,huber_value,0.000173400381480839,mm2{sapwood}/mm2{leaf},population,standard_deviation,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Syzygium sayeri
+Test_2023_2,Syzygium sayeri,098,huber_value,0.000202470135654991,mm2{sapwood}/mm2{leaf},population,standard_deviation,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Syzygium sayeri
+Test_2023_2,Syzygium sayeri,098,seed_dry_mass,841,mg,population,standard_deviation,unknown,unknown,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Syzygium sayeri
+Test_2023_2,Syzygium sayeri,099,leaf_N_per_dry_mass,13.7,mg/g,species,standard_deviation,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Syzygium sayeri
+Test_2023_2,Syzygium sayeri,099,leaf_area,2645,mm2,species,standard_deviation,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Syzygium sayeri
+Test_2023_2,Syzygium sayeri,099,leaf_mass_per_area,131,g/m2,species,standard_deviation,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Syzygium sayeri
+Test_2023_2,Syzygium sayeri,099,wood_density,0.485,mg/mm3,species,standard_deviation,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Syzygium sayeri
+Test_2023_2,Trema tomentosa var. aspera,100,branch_mass_fraction,0.53,mg/mg,population,standard_error,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Trema aspera
 Test_2023_2,Trema tomentosa var. aspera,100,huber_value,0.000149365197908887,mm2{sapwood}/mm2{leaf},population,mean,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Trema aspera
 Test_2023_2,Trema tomentosa var. aspera,100,huber_value,0.000149365197908887,mm2{sapwood}/mm2{leaf},population,maximum,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,04,,Trema aspera
-Test_2023_2,Trema tomentosa var. aspera,100,seed_dry_mass,5.12,mg,population,mean,unknown,unknown,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Trema aspera
-Test_2023_2,Trema tomentosa var. aspera,101,leaf_N_per_dry_mass,29.9,mg/g,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera
-Test_2023_2,Trema tomentosa var. aspera,101,leaf_area,2071,mm2,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera
-Test_2023_2,Trema tomentosa var. aspera,101,leaf_mass_per_area,53,g/m2,species,mean,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera
-Test_2023_2,Trema tomentosa var. aspera,101,wood_density,0.357,mg/mm3,species,mean,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera
+Test_2023_2,Trema tomentosa var. aspera,100,huber_value,0.000279485746226942,mm2{sapwood}/mm2{leaf},population,standard_error,unknown,7,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Trema aspera
+Test_2023_2,Trema tomentosa var. aspera,100,huber_value,0.000189000189000189,mm2{sapwood}/mm2{leaf},population,standard_error,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,02,,Trema aspera
+Test_2023_2,Trema tomentosa var. aspera,100,huber_value,0.000183823529411765,mm2{sapwood}/mm2{leaf},population,standard_error,unknown,2,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,03,,Trema aspera
+Test_2023_2,Trema tomentosa var. aspera,100,seed_dry_mass,5.12,mg,population,standard_error,unknown,unknown,field_experiment,juvenile,02,,,,Test_2022,02,,,,2002/2003,Made-up measurement remarks for Cape Tribulation,01,,Trema aspera
+Test_2023_2,Trema tomentosa var. aspera,101,leaf_N_per_dry_mass,29.9,mg/g,species,standard_error,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera
+Test_2023_2,Trema tomentosa var. aspera,101,leaf_area,2071,mm2,species,standard_error,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera
+Test_2023_2,Trema tomentosa var. aspera,101,leaf_mass_per_area,53,g/m2,species,standard_error   ,measurement,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera
+Test_2023_2,Trema tomentosa var. aspera,101,wood_density,0.357,mg/mm3,species,standard_error,unknown,2,field,adult,,,,,Test_2022,,,,,,,01,,Trema aspera