Correcting minor errors in dataset metadata files (#562)

A review by Isaac Towers (@itowers1) of AusTraits seed mass data identified a number of values that were off by many orders of magnitude (in comparison to other data for the same species).

Some of the biggest errors were tracked down. In many cases, it seems values in `mg` and `g` were mixed together (generally in big compilations). In others the decimal point was omitted. These have been corrected through a combination of custom_R_code and edits to spreadsheets. Adding a notes/multiplier column to the data.csv sheet would be better, but for after-the-fact edits, we're using custom_R_code or direct editing the data.csv file.

Seed mass edits include:
Ooi_2007
*  filter outliers
*  correct few values where decimal points mistakenly omitted
* fix typo in custom_R_code

Jurado_1991
* filter out seed_mass values that are identical to Leishman_1992

ANBG_2019, Catford_2014
* directly edit a few outlier seed mass values

Other minor errors corrected in this commit:
* fixed typo in Apgaua_2015; had mis-calculated vessel_diameter
* Dong_2017: omit leaf_area and leaf_mass as traits, since the values appear to apply to bulked samples

data/ANBG_2019/metadata.yml

@@ -51,7 +51,7 @@ dataset:
     comprehensively recorded and voucher specimens of the species are catalogued in
     the Australian National Herbarium.
   original_file: 4 files in raw data folder
-  notes: .na
+  notes: There are a few species whose seed masses are almost certainly incorrect. They've been compared to other AusTraits entries. These values have been manually adjusted in AusTraits, 15-02-2022, E Wenk
 sites:
   Adelaide Botanic Gardens.:
     latitude (deg): .na.real

data/Apgaua_2015/metadata.yml

@@ -62,7 +62,7 @@ config:
   variable_match:
     taxon_name: Species
     site_name: Study site
-  custom_R_code: data %>% mutate(vessel_diameter = sqrt(`Vessel Area (um2)`/3.14159))
+  custom_R_code: data %>% mutate(vessel_diameter = 2*sqrt(`Vessel Area (um2)`/3.14159))
 traits:
 - var_in: Theoretical Specific Conductivity (kg s-1 MPa-1)
   unit_in: 10^6 x kg/m/s/MPa

data/Catford_2014/data.csv

@@ -22,7 +22,7 @@ Calystegia sepium,,1,,1,1,,,1,1,,,1,,,0,,,1,2,4,25.58,,,,,,,,
 Carex gaudichaudiana,,,1,,,,1,1,1,,,1,,,1,,1,,0.1,0.9,0.93,,,,32.27133333,17.67323841,0.1826,,
 Carex inversa,,,1,1,,1,,,1,1,,1,,,1,,1,,0.1,0.5,0.37,,,,1.406,11.1,0.0127,dry,
 Carex tereticaulis,,,1,,,,1,1,1,,,1,,,1,,1,,0.4,1.2,1.46,,,,22.592,2.559130041,0.8828,,
-Centella cordifolia,,1,,1,1,,,1,1,,,1,,,1,1,,1,,0.2,0.0049,Water,,,12.33833333,22.81355932,0.0541,wet,
+Centella cordifolia,,1,,1,1,,,1,1,,,1,,,1,1,,1,,0.2,4.9,Water,,,12.33833333,22.81355932,0.0541,wet,
 Centipeda cunninghamii,,1,,,,,1,,1,1,,1,,,0,,,,,0.2,0.05,,,,0.577333333,21.65,0.0027,dry,
 Cirsium vulgare,,1,,1,,1,,,,,1,,1,,0,,,,,1.5,2.9,wind,,,,9.99780569,,dry,
 Conyza bonariensis,,1,,1,1,,,,,,1,,,1,0,,,,,1,0.1,wind,,,0.785,11.71641791,0.0067,wet,
@@ -36,10 +36,10 @@ Cyperus fulvus cf,,,1,,,,1,1,1,,,1,,,1,,1,,0.25,0.5,0.35,,,,,13.92,,,
 Cyperus gunnii,,,1,,,,1,1,1,,,1,,,1,,1,,,1.5,0.19,,,,,13.92,,,
 Cyperus sp1,,,1,1,1,,,,,,,1,,,,,,,,1.2,0.35,,,,50.83,13.50963455,0.3763,,
 Deyeuxia sp1,,,1,1,,,,,,,,,,,,,,,,0.5,0.3,,,,1.231666667,18.475,,,
-Dichondra repens,,1,,1,,1,,1,1,,,1,,,1,1,,,,0.1,0.0025,,,,145.868,24.90429268,,dry,
+Dichondra repens,,1,,1,,1,,1,1,,,1,,,1,1,,,,0.1,2.5,,,,145.868,24.90429268,,dry,
 Dysphania littoralis cf,,1,,1,,,,,,,,,1,1,,,,1,,0.1,,,,,,,,,
 Echium plantagineum,,1,,1,,1,,,,,1,,,1,,,,,,1.2,4.2,,,,,12.52201652,,dry,
-Eclipta platyglossa,,1,,1,1,,,,1,1,,,1,1,1,1,,1,,0.3,6.92E-04,water,,,,26.27781818,,wet,
+Eclipta platyglossa,,1,,1,1,,,,1,1,,,1,1,1,1,,1,,0.3,6.92E-01,water,,,,26.27781818,,wet,
 Elatine gratioloides,,1,,,,,1,1,1,,,,,1,1,1,,1,,0,0.05,,,,,,,,
 Eleocharis acuta,,,1,,,,1,1,1,,,1,,,1,,1,,0.1,0.6,0.56,,,,8.75,7.109967497,0.1231,,
 Eleocharis atricha,,,1,,,,1,1,1,,,1,,,1,,1,,0.03,0.4,0.59,,,,,7.109967497,,,
@@ -59,10 +59,10 @@ Hypochaeris glabra,,1,,1,,1,,,,,1,,,1,0,,,,0.1,0.4,0.69,wind,,,31.49266667,24.71
 Hypochaeris radicata,,1,,1,,1,,,,,1,,,1,0,,,,0.15,0.8,0.8,wind,,,16.945,25.4047976,0.0667,dry,
 Isotoma fluviatalis subsp. australis,,1,,,,,1,1,1,,,1,,,1,1,,1,,0.1,0.04,,,,,35.60466667,,,
 Juncus acuminatus,,,1,1,1,,,,,,1,1,,,1,,1,,0.25,0.6,0.04,,,,,3.209876928,,wet,
-Juncus aridicola,,,1,1,1,,,,1,1,,1,,,1,,1,,0.55,1.2,5.00E-05,,,,14.35833333,2.675465839,0.5367,wet,
-Juncus flavidus,,,1,1,1,,,1,1,,,1,,,1,,1,,0.25,0.9,5.00E-05,,,,7.623333333,4.160703457,0.1832,wet,
+Juncus aridicola,,,1,1,1,,,,1,1,,1,,,1,,1,,0.55,1.2,5.00E-02,,,,14.35833333,2.675465839,0.5367,wet,
+Juncus flavidus,,,1,1,1,,,1,1,,,1,,,1,,1,,0.25,0.9,5.00E-02,,,,7.623333333,4.160703457,0.1832,wet,
 Juncus fockei,,,1,,,,,,,,,1,,,1,,1,,0.08,0.5,0.01,,,,,3.21,,,
-Juncus gregiflorus,,,1,1,1,,,1,1,,,1,,,1,,1,,1.1,3,5.00E-05,,,,6.531153846,3.319194683,0.1899,wet,
+Juncus gregiflorus,,,1,1,1,,,1,1,,,1,,,1,,1,,1.1,3,5.00E-02,,,,6.531153846,3.319194683,0.1899,wet,
 Juncus holoschoenus,,,1,1,1,,,1,1,,,1,,,1,,1,,0.25,0.8,0.04,,,,,3.21,,wet,
 Juncus ingens,,,1,,,,1,1,1,,,1,,,1,,1,,1.2,4,0.001,,,,,1.862274628,,,
 Juncus sp1,,,1,1,1,,,1,1,,,1,,,1,,1,,,1.1,0.07,animal??,,,,3.21,,,
@@ -128,7 +128,7 @@ Sagittaria platyphylla,,1,,,,,1,,,,1,1,,,1,,1,,0.5,1,0.69,water,animal,,,,,,
 Salix x rubens,1,,,1,1,,,,,,1,1,,,,,,,,16,0.164,,,,,,,,
 Senecio quadridentatus,,1,,1,,1,,1,1,,,1,,,,,,,0.4,1,0.173,wind,,,,,,,
 Senecio tenuiflorus cf,,1,,1,,1,,1,1,,,,1,1,,,,,0.3,0.8,1.054,,,,,,,,
-Solanum physalifolium var. nitidibaccatum,,1,,1,,1,,,,,1,,,1,,,,,,0.5,0.002133333,,,,10.43533333,25.74506579,0.0405,dry,
+Solanum physalifolium var. nitidibaccatum,,1,,1,,1,,,,,1,,,1,,,,,,0.5,2.133333,,,,10.43533333,25.74506579,0.0405,dry,
 Spergularia rubra,,1,,1,,1,,,,,1,,1,1,,,,,0.05,0.3,0.07,wind,,,,,,,
 Spirodela punctata,,1,,,,,1,,1,1,,,,,,,,1,,0,,,,,,,,,
 Stellaria angustifolia,,1,,,,,1,1,1,,,1,,,,,,1,,0.1,0.42,,,,,25.80766667,,,
@@ -141,7 +141,7 @@ Trifolium glomeratum,,1,,1,1,,,,,,1,,,1,,,,,,0.4,0.4,,,,,23.50680625,,wet,
 Trifolium repens var. repens,,1,,1,1,,,,,,1,,,1,,,,,,0.3,0.6,animal,,,0,19.86643895,,wet,
 Trifolium striatum,,1,,1,1,,,,,,1,,,1,,,,,,0.3,1.9,wind,,,,23.51,,wet,
 Triglochin dubia,,,1,,,,1,1,1,,,1,,,1,,1,,0.3,0.8,4.26,,,,23.92846154,16.1343361,0.1483,,
-Triglochin procera,,,1,,,,1,1,1,,,1,,,1,,1,,,2,0.001,,,,48.27692308,10.77424893,0.4481,,
+Triglochin procera,,,1,,,,1,1,1,,,1,,,1,,1,,,2,1,,,,48.27692308,10.77424893,0.4481,,
 Triticum aestivum,,,1,1,,1,,,,,1,,,1,,,,,,1,35.96,,,,,35.91371602,,dry,
 Typha orientalis,,,1,,,,1,,1,1,,1,,,1,,1,,,4,0.2,,,,,6.004399415,,,
 Verbena bonariensis,,1,,1,,1,,,,,1,1,,,,,,,0.6,2,0.17,,,,13.49333333,10.14028056,,dry,

data/Catford_2014/metadata.yml

@@ -82,7 +82,7 @@ dataset:
   original_file: Data extracted from two worksheets in the file 'Catford_River Murray
     wetland plants_260215_contributed to AusTraits.xls'. The two sheets were combined
     using some custom R code saved in the Austraits project.
-  notes: .na
+  notes: There are a few species whose seed masses are almost certainly in grams (instead of mg), as their seed mass values are on the order of 10^3 smaller than other AusTraits entries. These values have been manually adjusted in AusTraits, 15-02-2022, E Wenk
 sites:
   Yarrawonga:
     longitude (deg): 145.99973
@@ -122,7 +122,7 @@ config:
     %>% na_if(""), life_history = stringr::str_squish(life_history) %>% na_if(""),
     growth_habit = stringr::str_squish(growth_habit) %>% na_if(""), aquatic_terrestrial_detailed
     = stringr::str_squish(aquatic_terrestrial_detailed) %>% na_if(""), dispersal_syndrome
-    = stringr::str_squish(dispersal_syndrome) %>% na_if("") )
+    = stringr::str_squish(dispersal_syndrome) %>% na_if(""))
 traits:
 - var_in: Leaf size (cm^2)
   unit_in: cm2
@@ -159,7 +159,7 @@ traits:
   replicates: .na
   methods: Information about species' seed mass was sourced from available databases
     (Liu et al. 2008, Kew Seed Database (http://data.kew.org/sid/) or from field collections
-    (9 species). For the field collected species, 2-30 seeds were collected.
+    (9 species). For the field collected species, 2-30 seeds were collected. [Note from AusTraits data processors, there are 9 species with values that seem to be in grams and the remaining species are in mg. A column has been added to tentatively adjust some species values.]
 - var_in: plant height min (m)
   unit_in: m
   trait_name: .na

data/Dong_2017/metadata.yml

@@ -365,24 +365,24 @@ config:
 traits:
 - var_in: dry.mg
   unit_in: mg
-  trait_name: leaf_dry_mass
+  trait_name: .na
   value_type: raw_value
   replicates: 1
   methods: Mature outer-canopy leaves of each species were sampled during the growing
     season using the AusPlots methodology (White et al., 2012). (Note that in denser
     vegetation many species sampled are in the understorey, so their "outcanopy" leaves
     are still shaded by the overstorey. Leaf area was determined by scanning the leaves.
-    The value is a bulked value based on collections from 5-6 individuals.
+    The value is a bulked value based on collections from 5-6 individuals. [Removed from AusTraits 2021-10-28. These appear to be bulked numbers including multiple leaves.]
 - var_in: leafarea(m2)
   unit_in: m2
-  trait_name: leaf_area
+  trait_name: .na
   value_type: raw_value
   replicates: 1
   methods: Mature outer-canopy leaves of each species were sampled during the growing
     season using the AusPlots methodology (White et al., 2012). (Note that in denser
     vegetation many species sampled are in the understorey, so their "outcanopy" leaves
     are still shaded by the overstorey. Leaf area was determined by scanning the leaves.
-    The value is a bulked value based on collections from 5-6 individuals.
+    The value is a bulked value based on collections from 5-6 individuals. [Removed from AusTraits 2021-10-28. These appear to be bulked numbers including multiple leaves.]
 - var_in: d13c
   unit_in: per mille
   trait_name: leaf_delta13C