Description:

Four SAFE seedling plot censuses including measurement after the 2015-16 El Nino drought and leaf trait data

Project: This dataset was collected as part of the following SAFE research project: Resilience of Tropical Forest Ecosystem Processes to the Interactive Effects of El Nino and Forest Disturbance

XML metadata: GEMINI compliant metadata for this dataset is available here

Files: This consists of 1 file: Seedling_data_for_SAFE_upload_2_Aug_2018.xlsx

Seedling_data_for_SAFE_upload_2_Aug_2018.xlsx

This file contains dataset metadata and 3 data tables:

1. SAFE seedling plot censuses (described in worksheet Censuses)

   Description: In each of the 84 SAFE vegetation plot a 5 m x 5 m seedling plot was established in 2012. All tree and liana seedlings >= 50 cm height and <= 1 cm DBH were tagged mapped and identified. At the centre of the 5 m x 5 m plot a subplot of 2 m x 2 m was marked out where all seedlings >= 10 cm height were included. Censuses 1&2 in 2012 were carried out by Hamzah Bin Tangki (PhD thesis 2014); census 3 in 2015 was carried out by Michael Massam (MSc thesis 2015); census 4 in 2017 was carried out by Elizabeth Telford. Diameter was measured at 20 cm from ground. Height was measured for tree seedlings (not measured if stem was snapped). A number of stems are missing diameter and height records in earlier censuses but considered alive at those times based on information from census 4 -- these data rows are kept and NA values assigned. Species id were done by SAFE field botanists. 2017 recruits stems have less complete identification. 11 seedling plots were not measured due to disturbances, mainly logging road and landslide.

   Number of fields: 12

   Number of data rows: 7376

   Fields:

   • census: census number (Field type: ID)
   • Plot: SAFE project plot number (Field type: Location)
   • tag: seedling tag number (Field type: ID)
   • North: coordinate within seedling plot: northing (Field type: Numeric)
   • East: coordinate within seedling plot: easting (Field type: Numeric)
   • type: growth form of seedling: tree or vine (liana) (Field type: Categorical)
   • species: species (Field type: Taxa)
   • Da: diameter measurement 1 (Field type: Numeric)
   • Db: diameter measurement 2 (Field type: Numeric)
   • height: seedling height (Field type: Numeric)
   • snapped: stem snapped or not (Field type: Categorical)
   • remark: remark (Field type: Comments)

2. Germination count (described in worksheet Germination)

   Description: At census 3 and 4, newly germinated seedlings were counted for the 2 m x 2 m seedling subplot. These were not tagged, mapped or identified.

   Number of fields: 4

   Number of data rows: 168

   Fields:

   • Plot: SAFE project plot number (Field type: Location)
   • census: census number (Field type: ID)
   • count: count of newly germinated seedlings (Field type: Abundance)
   • remark: remark (Field type: Comments)

3. Seedling leaf traits (described in worksheet Leaf traits)

   Description: At census 4, for each seedling in the plots which was deemed big enough, the fifth youngest leaf counting from the top shoot was collected. If damaged, the nearest alternative was taken Leaf petiole was removed and leaf was photographed while fresh. Fresh weight and oven dry weight were measured. Leaf area was calculated from photographs using ImageJ. These measurements were used to calculate seedling CSR trait values (Piece, S., et al. 2017 Functional Ecology)

   Number of fields: 5

   Number of data rows: 1072

   Fields:

   • Plot: SAFE project plot number (Field type: Location)
   • tag: seedling tag number (Field type: ID)
   • Fresh.Weight: leaf fresh weight (Field type: Numeric)
   • Dry.Weight: leaf dry weight (Field type: Numeric)
   • Leaf.Area: leaf area (Field type: Numeric)

Date range: 2012-06-01 to 2017-12-31

Latitudinal extent: 4.6882 to 4.7714

Longitudinal extent: 116.9477 to 117.7028

Taxonomic coverage:
All taxon names are validated against the GBIF backbone taxonomy. If a dataset uses a synonym, the accepted usage is shown followed by the dataset usage in brackets. Taxa that cannot be validated, including new species and other unknown taxa, morphospecies, functional groups and taxonomic levels not used in the GBIF backbone are shown in square brackets.

PlotQA is a VQA dataset with 28.9 million question-answer pairs grounded over 224,377 plots on data from real-world sources and questions based on crowd-sourced question templates. Existing synthetic datasets (FigureQA, DVQA) for reasoning over plots do not contain variability in data labels, real-valued data, or complex reasoning questions. Consequently, proposed models for these datasets do not fully address the challenge of reasoning over plots. In particular, they assume that the answer comes either from a small fixed size vocabulary or from a bounding box within the image. However, in practice this is an unrealistic assumption because many questions require reasoning and thus have real valued answers which appear neither in a small fixed size vocabulary nor in the image. In this work, we aim to bridge this gap between existing datasets and real world plots by introducing PlotQA. Further, 80.76% of the out-of-vocabulary (OOV) questions in PlotQA have answers that are not in a fixed vocabulary.

This dataset consists of growth and yield data for each season when winter wheat (Triticum aestivum L.) was grown for grain at the USDA-ARS Conservation and Production Laboratory (CPRL), Soil and Water Management Research Unit (SWMRU) research weather station, Bushland, Texas (Lat. 35.186714°, Long. -102.094189°, elevation 1170 m above MSL). In each season, winter wheat was grown for grain on two large, precision weighing lysimeters, each in the center of a 4.44 ha square field. The square fields are themselves arranged in a larger square with the fields in four adjacent quadrants of the larger square. Fields and lysimeters within each field are thus designated northeast (NE), southeast (SE), northwest (NW), and southwest (SW). Irrigation was by linear move sprinkler system. Irrigation protocols described as full were managed to replenish soil water used by the crop on a weekly or more frequent basis as determined by soil profile water content readings made with a neutron probe to 2.4-m depth in the field. Irrigation protocols described as deficit typically involved irrigations to establish the crop early in the season, followed by reduced or absent irrigations later in the season (typically in the later winter and spring). The growth and yield data include plant population density, height (except in 1989-1990), plant row width, leaf area index, growth stage, total above-ground biomass, leaf and stem biomass, head mass (when present), kernel number, and final yield. Data are from replicate samples in the field and non-destructive (except for final harvest) measurements on the weighing lysimeters. In most cases yield data are available from both manual sampling on replicate plots in each field and from machine harvest. These datasets originate from research aimed at determining crop water use (ET), crop coefficients for use in ET-based irrigation scheduling based on a reference ET, crop growth, yield, harvest index, and crop water productivity as affected by irrigation method, timing, amount (full or some degree of deficit), agronomic practices, cultivar, and weather. Prior publications have focused on winter wheat ET, crop coefficients, and crop water productivity. Crop coefficients have been used by ET networks. The data have utility for testing simulation models of crop ET, growth, and yield and have been used by the Agricultural Model Intercomparison and Improvement Project (AgMIP) and by many others for testing, and calibrating models of ET that use satellite and/or weather data. Resources in this dataset:Resource Title: 1989-1990 Bushland, TX, west winter wheat growth and yield data. File Name: 1989-1990_West_Wheat_Growth_and_Yield.xlsxResource Description: This dataset consists of growth and yield data the 1989-1990 winter wheat (Triticum aestivum L.) season at the USDA-ARS Conservation and Production Laboratory (CPRL), Soil and Water Management Research Unit (SWMRU) research weather station, Bushland, Texas (Lat. 35.186714°, Long. -102.094189°, elevation 1170 m above MSL). Winter wheat was grown on two large, precision weighing lysimeters, each in the center of a 4.44 ha square field. The two square fields were themselves arranged with one directly north of and contiguous with the other. Fields and lysimeters within each field were designated northwest (NW), and southwest (SW). Irrigation was by linear move sprinkler system. Irrigations described as full were managed to replenish soil water used by the crop on a weekly or more frequent basis as determined by soil profile water content readings made with a neutron probe to 2.4-m depth in the field. Irrigation described as deficit typically involved irrigation to establish the crop in the autumn followed by reduced or no irrigation later in the late winter or spring. The growth and yield data include plant height (except in 1989-1990), leaf area index, growth stage, total above-ground biomass, leaf and stem biomass, hea biomass, and final yield. Data are from replicate samples in the field and non-destructive (except for final harvest) measurements on the weighing lysimeters. In most cases yield data are available from both manual sampling on replicate plots in each field and from machine harvest. There is a single spreadsheet for the west (NW and SW) lysimeters and fields. The spreadsheets contain tabs for data and corresponding tabs for data dictionaries. Typically, there are separate data tabs and corresponding dictionaries for plant growth during the season, crop growth stage, plant population, manual harvest from replicate plots in each field and from lysimeter surfaces, and machine (combine) harvest, An Introduction tab explains the tab names and contents, lists the authors, explains conventions, and lists some relevant references.Resource Title: 1991-1992 Bushland, TX, east winter wheat growth and yield data. File Name: 1991-1992_East_Wheat_Growth_and_Yield.xlsxResource Description: This dataset consists of growth and yield data the 1991-1992 winter wheat (Triticum aestivum L.) season at the USDA-ARS Conservation and Production Laboratory (CPRL), Soil and Water Management Research Unit (SWMRU) research weather station, Bushland, Texas (Lat. 35.186714°, Long. -102.094189°, elevation 1170 m above MSL). Winter wheat was grown on two large, precision weighing lysimeters, each in the center of a 4.44 ha square field. The two square fields were themselves arranged with one directly north of and contiguous with the other. Fields and lysimeters within each field were designated northeast (NE), and southeast (SE). Irrigation was by linear move sprinkler system. Irrigations described as full were managed to replenish soil water used by the crop on a weekly or more frequent basis as determined by soil profile water content readings made with a neutron probe to 2.4-m depth in the field. Irrigation described as deficit typically involved irrigation to establish the crop in the autumn followed by reduced or no irrigation later in the late winter or spring. The growth and yield data include plant height, leaf area index, growth stage, total above-ground biomass, leaf and stem biomass, hea biomass, and final yield. Data are from replicate samples in the field and non-destructive (except for final harvest) measurements on the weighing lysimeters. In most cases yield data are available from both manual sampling on replicate plots in each field and from machine harvest. There is a single spreadsheet for the east (NE and SE) lysimeters and fields. The spreadsheets contain tabs for data and corresponding tabs for data dictionaries. Typically, there are separate data tabs and corresponding dictionaries for plant growth during the season, crop growth stage, plant population, manual harvest from replicate plots in each field and from lysimeter surfaces, and machine (combine) harvest, An Introduction tab explains the tab names and contents, lists the authors, explains conventions, and lists some relevant references.Resource Title: 1992-1993 Bushland, TX, west winter wheat growth and yield data. File Name: 1992-1993_W_Wheat_Growth_and_Yield.xlsxResource Description: This dataset consists of growth and yield data the 1992-1993 winter wheat (Triticum aestivum L.) season at the USDA-ARS Conservation and Production Laboratory (CPRL), Soil and Water Management Research Unit (SWMRU) research weather station, Bushland, Texas (Lat. 35.186714°, Long. -102.094189°, elevation 1170 m above MSL). Winter wheat was grown on two large, precision weighing lysimeters, each in the center of a 4.44 ha square field. The two square fields were themselves arranged with one directly north of and contiguous with the other. Fields and lysimeters within each field were designated northwest (NW), and southwest (SW). Irrigation was by linear move sprinkler system. Irrigations described as full were managed to replenish soil water used by the crop on a weekly or more frequent basis as determined by soil profile water content readings made with a neutron probe to 2.4-m depth in the field. Irrigation described as deficit typically involved irrigation to establish the crop in the autumn followed by reduced or no irrigation later in the late winter or spring. The growth and yield data include plant height, leaf area index, growth stage, total above-ground biomass, leaf and stem biomass, hea biomass, and final yield. Data are from replicate samples in the field and non-destructive (except for final harvest) measurements on the weighing lysimeters. In most cases yield data are available from both manual sampling on replicate plots in each field and from machine harvest. There is a single spreadsheet for the west (NW and SW) lysimeters and fields. The spreadsheets contain tabs for data and corresponding tabs for data dictionaries. Typically, there are separate data tabs and corresponding dictionaries for plant growth during the season, crop growth stage, plant population, manual harvest from replicate plots in each field and from lysimeter surfaces, and machine (combine) harvest, An Introduction tab explains the tab names and contents, lists the authors, explains conventions, and lists some relevant references.

Chest ImaGenome is a dataset with a scene graph data structure to describe 242,072 images. Local annotations are automatically produced using a joint rule-based natural language processing (NLP) and atlas-based bounding box detection pipeline. Through a radiologist constructed CXR ontology, the annotations for each CXR are connected as an anatomy-centered scene graph, useful for image-level reasoning and multimodal fusion applications. Overall, the following are provided: i) 1256 combinations of relation annotations between 29 CXR anatomical locations (objects with bounding box coordinates) and their attributes, structured as a scene graph per image, ii) over 670,000 localized comparison relations (for improved, worsened, or no change) between the anatomical locations across sequential exams, as well as ii) a manually annotated gold standard scene graph dataset from 500 unique patients.

Description from: Chest ImaGenome Dataset for Clinical Reasoning

Data used in box plots or bar charts that are not presented in S1–S6 Tables are shown. (XLSX)