From ca392fb1cf2ee600c9406928bc64d96b95d6b1bf Mon Sep 17 00:00:00 2001 From: Elizabeth Wenk Date: Fri, 20 Dec 2024 08:50:47 +1100 Subject: [PATCH 1/2] Add standard deviation to allowed value types (#187) * Add standard deviation to allowed value types Although SE mostly reported today, older manuscripts often document SD instead --- inst/support/traits.build_schema.yml | 1 + tests/testthat/examples/Test_2023_2/data.csv | 4 +-- .../examples/Test_2023_2/output/traits.csv | 36 +++++++++---------- 3 files changed, 21 insertions(+), 20 deletions(-) diff --git a/inst/support/traits.build_schema.yml b/inst/support/traits.build_schema.yml index b3e95191..47abc2a2 100644 --- a/inst/support/traits.build_schema.yml +++ b/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: diff --git a/tests/testthat/examples/Test_2023_2/data.csv b/tests/testthat/examples/Test_2023_2/data.csv index 62085e56..59c6bdd4 100644 --- a/tests/testthat/examples/Test_2023_2/data.csv +++ b/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,, diff --git a/tests/testthat/examples/Test_2023_2/output/traits.csv b/tests/testthat/examples/Test_2023_2/output/traits.csv index 1911c42e..748872f1 100644 --- a/tests/testthat/examples/Test_2023_2/output/traits.csv +++ b/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 From 8367483f61b2ecd430a248df8d1bea72a6238ae0 Mon Sep 17 00:00:00 2001 From: Elizabeth Wenk Date: Fri, 20 Dec 2024 08:56:37 +1100 Subject: [PATCH 2/2] edit pkgdown.yml, add "<" (#188) Two fixes: - needed to add deprecated/renamed functions to pkgdown.yml since they are still valid function names output by traits.build - missed a pair of brackets in ontology --- _pkgdown.yml | 7 +++++++ ontology/data/traits.build_resource.csv | 2 +- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 5c989b09..df9f6aa2 100644 --- a/_pkgdown.yml +++ b/_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`' diff --git a/ontology/data/traits.build_resource.csv b/ontology/data/traits.build_resource.csv index f26a5a83..e6ef9f6a 100644 --- a/ontology/data/traits.build_resource.csv +++ b/ontology/data/traits.build_resource.csv @@ -11,4 +11,4 @@ Subject,Predicate,Object ,,"""Elizabeth Wenk""" ,,"""Sophie Yang""" ,,"""01 February 2024^^""" -https://w3id.org/traits.build#traits.build-database,,"""""^^" +,,"""""^^"