Add new study: Drake_2011 #753
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* Adding 7 studies with morphological trait data extracted from 7 state and national floras: "SAH_2023", "WAH_2023_1", "WAH_2023_2", "ABRS_2023", "RBGV_2023", "NHNSW_2023", "NTH_2023" * 30 traits added * trait values mostly mapped to those developed in vocabulary workshops, but a few additional terms were needed, especially for traits like leaf_base for which we previously had very little data * branch also includes some preliminary work on fire response traits and edits to water use/hydraulics traits --------- Co-authored-by: David Coleman <https://github.com/dcol2804> Co-authored-by: Sophie Yang <78716301+yangsophieee@users.noreply.github.com>
Add large dataset on fire response, seed longevity and reproductive maturity of most taxa in the Northern Territory Herbarium database, compiled from the literature and expert review. Lizzy emailed the report to the author but he's on leave so merging now! --------- Co-authored-by: ehwenk <ehwenk@gmail.com>
Add 3 new studies from Nadia Santini looking at water relations Contributor has submitted her raw data files and reviewed all reports --------- Co-authored-by: Sophie Yang <78716301+yangsophieee@users.noreply.github.com>
Add study examining how resprouting and propagule persistence are associated with grassland and shrubland habitats and other environmental and biotic variables. Lizzy has emailed the author and we are awaiting a response. --------- Co-authored-by: ehwenk <ehwenk@gmail.com>
Add study with seed storage location and fire response data (both resprouting and seedling recruitment) at the plot level after experimental fire treatments. The study also investigated density changes after fire, which I have not mapped. --------- Co-authored-by: ehwenk <ehwenk@gmail.com>
* edits to traits related to fire response and plant regeneration following one of the AusTraits vocabulary workshops * major change is renaming all `fire_response` related traits to `resprouting_capacity` * removing several derived traits that can be recreated from other trait values; in the coming 6 months we will create some scripts showing how current data can be analysed * remap values for some traits in NSWFRD_2014 to capture more data --------- Co-authored-by: Sophie Yang <78716301+yangsophieee@users.noreply.github.com>
* add new study: Mitchell_2008 * no contact with data collector * some problems with archived data - for instance Kl data are identical to Ks, so not used. --------- Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
* add new study: Kocacinar_2003 * contacted authors for additional traits and individual-level data, but haven't heard back, so merging in data that are available in the manuscript --------- Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
* old study and data extracted from tables and figures in paper --------- Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
* add new study * data transcribed from manuscript & author not contacted --------- Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
* Add new study: Britton_1994 * First study with recruitment_time * transcribed data from manuscript; no contact with author --------- Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
* Add new study: Cowling_1987 * data on germination & flowering relative to fire for 4 WA Banksia species * data transcribed from manuscript; no contact with author --------- Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
* Add new study: Auld_2000 * dataset with seedbank longevity half-lives --------- Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
* edit metadata_create_template to add proper fields for data_collectors * Tweak and add tests --------- Co-authored-by: Daniel Falster <daniel.falster@unsw.edu.au>
* Add new study: Tsakalos_2022 * large dataset documenting clonal spread mechanisms and bud bank locations for WA taxa * dataset available online, but will contact author --------- Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
* Add new study: Brodribb_2000 * data transcribed from manuscript * author not contacted, as this is an older study --------- Co-authored-by: GillianKowalick Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
* Add new study: Collette_2021 * Large study looking at seed dormancy across Australia * Data from supplementary material; authors have not yet responded to email --------- Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
* add new study * data transcribed from paper --------- Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
Add study on growth and storage traits of post-fire seedlings in Mediterranean ecosystems of south-western Australia. I originally transcribed it in long format because that was easiest, but I changed it into wide format (see Pate_1990_extra_R_code.R) because there were some warning messages associated with it being in long format. --------- Co-authored-by: ehwenk <ehwenk@gmail.com>
* Flora data fixes Covering 2022 traits which are in the current release and 2023 traits which will be in the next version. * Aligned the growth form and woodiness to correct version
* script to generate traits.yml from APD data files (APD_traits.csv & APD_categorical_values.csv)
* APD files are pulled directly from github APD repository
* use script to updates traits.yml from APD version 1.0.0
ensure in final version of traits.yml (in the future):
- ''' (3 single quotes) don't exist; should be ' (1 single quote)
- there are no instances of `allowed_values_levels: {}`
closes issue #727
---------
Co-authored-by: Daniel Falster <daniel.falster@unsw.edu.au>
add study - seed germination data from Kings Park, WA botanic garden --------- Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
- Added additional raw data files from Caroline Nano for NT fire response - Filtered out duplicate taxa for `resprouting_capacity` data from Simpson_2021 (where it cites Crowley_2007) --------- Co-authored-by: ehwenk <ehwenk@gmail.com>
Small dataset of bark thickness index values. There is a lot more raw data supposedly in the study but we decided to not contact the author. --------- Co-authored-by: Elizabeth Wenk <ehwenk@gmail.com>
* add 3 traits to scraped data files, `plant_photosynthetic_organ`, `leaf_lamina_posture` and `leaf_margin_posture` to scraped flora data files --------- Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
Small study looking at reproductive characteristics of 3 Banksia species in relation to fire --------- Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
* Add new study: Wilson_2004 * resprouting capacity & time to flowering data for WA taxa --------- Co-authored-by: yangsophieee <sophie.yang917@gmail.com>
* add 2 Canham studies * reports reviewed by author --------- Co-authored-by: Sophie Yang <78716301+yangsophieee@users.noreply.github.com>
* study with Banksia resprouting capacity, bud bank location, and serotiny data * data extracted from phylogenetic trees with character states
* Ignore allow column names that are the same as values for entity_type and value_type * Add other entity_type fixes to branch --------- Co-authored-by: ehwenk <ehwenk@gmail.com>
Add large dataset containing resprouting capacity and post-fire regeneration times for 826 taxa. See table below for new taxa for AusTraits. trait_name taxa_before taxa_with_study new_taxa 1 resprouting_capacity 11300 11364 64 2 fire_time_from_fire_to_50_percent_flowering 21 38 17 3 reproductive_maturity 7589 7623 34 4 fire_time_from_fire_to_flowering 1823 2155 332 5 fire_time_from_fire_to_peak_flowering 26 124 98 6 dispersal_unit 20 21 1 7 fire_time_from_fire_to_fruiting 101 578 477 8 seed_germination_time 2136 2344 208 --------- Co-authored-by: ehwenk <ehwenk@gmail.com>
* Add new study: Pate_1998 New taxa added for various traits: leaf_delta13C 50 leaf_delta15N 55 nitrogen_fixing 23 photosynthetic_pathway 16 plant_succulence 34 --------- Co-authored-by: GillianKowalick <z5242422@ad.unsw.edu.au>
Add new study: DeCampos_2013 Add new study with leaf P, dead leaf P for 8 taxa --------- Co-authored-by: GillianKowalick <z5242422@ad.unsw.edu.au>
* Add contexts to floras so they pivot wider In the floras there are often replicate trait values for certain taxa, because the same "trait" is measured on slightly different entities (primary leaflets vs secondary leaflets). This information had been read in as measurement remarks, but is now a context. There is now significant custom_R_code to condense the categories into more sensible contexts, remove duplicates, and add replicate observation counters to the remaining (true) duplicates. --------- Co-authored-by: dcol2804 <50344360+dcol2804@users.noreply.github.com>
Codecov ReportPatch and project coverage have no change.
Additional details and impacted files@@ Coverage Diff @@
## develop #753 +/- ##
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Hits 1231 1231
Misses 317 317 ☔ View full report in Codecov by Sentry. |
* add new study,Togashi_2015 * compilation of Huber value values from many resources * some datasets exist in AusTraits as stand-alone datasets and these have been filtered out of Togashi * remaining datasets also linked to their source_id's --------- Co-authored-by: GillianKowalick <z5242422@ad.unsw.edu.au>
edits following review
* add new study: Grigg_2008 * Hydraulic traits and traits on nutrient composition --------- Co-authored-by: ehwenk <ehwenk@gmail.com>
ehwenk
reviewed
Jun 28, 2023
| entity_type: population | ||
| value_type: raw | ||
| basis_of_value: measurement | ||
| replicates: 1 |
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I think this should be 1, but I'm not sure. There were 9 months x 4 samples/month, and these 36 samples were used to generate a single curve, from which the value is extracted.
ehwenk
approved these changes
Jun 28, 2023
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This looks good. However, as this researcher is still active and has several additional datasets we should include in AusTraits (https://orcid.org/0000-0002-1329-180X) I suggest we keep this on a branch until we contact him directly.
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This dataset has been reviewed and could be merged into AusTraits, but as this researcher is still active and has several additional datasets we should include in AusTraits (https://orcid.org/0000-0002-1329-180X) I suggest we keep this on a branch until we contact him directly. |
* Dataset with nutrient contents for many different plant tissues --------- Co-authored-by: ehwenk <ehwenk@gmail.com>
Small dataset of transpiration and water potential traits. --------- Co-authored-by: ehwenk <ehwenk@gmail.com>
Closes #620 Tidyselect 1.2.0 has changed what is allowed in dplyr::select, currently spitting warnings --------- Co-authored-by: Becca-90 <z3378134@ad.unsw.edu.au>
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hydraulic conductivity and photosynthetic traits