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Mt Hehuan treeline ecotone change
No full textThis dataset details landcover change interpreted from historic aerial photography from the treeline ecotone of Mt. Hehuan, Taiwan, enabling change in the position and area of montane forest to be calculated at the elevational limit of the montane forest of Taiwan. The associated R files can be run to calculate change statistics presented in the paper 'Montane forest expansion at high elevations drives rapid reduction in non-forest area despite no change in mean forest elevation.' published in Journal of Biogeography - DOI: 10.1111/JBI.13951.The dataset is interpreted from four sets of aerial photography (P1-4) collected in 1963(P1), 1980(P2), 2001(P3) and 2016(P4) across a study are measuring 4072 ha from the Mt hehuan area of the Taiwanese Central Mountain Range. A proportional stratified random sampling design was used to assess change in forest distribution at the treeline ecotone. Sample plots were created that measure 15 x 15 m and slope orientation was used as a basis for stratification using 12 categories of slope aspect and incline attributes calculated from a high-resolution TanDEM-X Digital Elevation Model. Strata were based on four cardinal compass directions (± 45° in either direction) and three inclination classes (0-20°, 21-45° and > 46°). The number of samples taken in each stratum was proportional to the area of the study region occupied by the aspect-incline combination and a total of 2,785 sample plots were interpreted, equivalent to 1.54 % of the study area. Each sample is assigned one of four vegetation classes for each year in the change survey. Areas that meet the FAO Global Forest Resources Assessment (2018) criterion of a forest as an area with at least 10 % canopy cover and trees greater than 5 m in height are classified here as forest. Areas with small trees present within the plot that do not meet the thresholds of a forest as set out by the FAO definition were categorised as establishing forest. The scale of the aerial photography (≤0.5 m pixel size) is sufficient to discriminate differences in tree size based on crown size. Areas with partial removal of the forest canopy between time periods are categorised as disturbed and treeless areas are categorised here as non-forest areas. The R files provided carry out the change assessment for the results presented in the paper publised in Journal of Biogeography (DOI: 10.1111/JBI.13951 ). R files should be run from the master script to as this will set up the change analysis to account for the stratification of sample plots and will then subsequently calculate change statistics for the study area as a whole and by each aspect or incline class
What drives the quality and decay of soil detritivore faeces: the ingested litter quality, or the animal identity?
No full textLitter-feeding soil animals play a dominant role on litter decomposition by ingesting large amount of plant litter and returning most of it to the soil as faeces. Despite the prevalence of this pathway, the consequences of this transformation on organic matter physicochemical characteristics and decomposition rates are largely unknown. Here, we assessed these consequences for distinct detritivore species (six species) feeding on contrasted litter quality (six litter species). We did so by collected leaf litter and soil animals from diverse species in Scotland. We then fed all soil animal species with litter from all litter species, separately, in all possible combinations. We collected the 36 resulting faeces type, and the 6 intact litter as controls. We then measured a range of physicochemical characteristics (C:N ratio, tannins concentrations, water-holding capacity, specific area, NMR spectra) for all 42 substrates. We also incubated all substrates for 180 days under controlled conditions and measured their respective rates of C and N loss. All methods associated with the collection of these datasets will be available in the resulting manuscript.faeces_litter_decomposition.xlsx : this file contains the decomposition rates (C and N loss) for all substrate types (36 faeces and 6 intact litter)
faeces_litter_NMR.xlsx : this file contains the relative abundance of distinct regions of 13C NMR spectra for all substrate types (36 faeces and 6 intact litter)
faeces_litter_quality.xlsx: this file contains the physicochemical characteristics for all substrate types (36 faeces and 6 intact litter
Menstrual waste generation and management in urban Malawi
No full textMenstrual waste is a socio-culturally sensitive material that is usually concealed from public view, and therefore its interactions with urban sanitation and waste management infrastructure are hidden. This dataset was produced from a questionnaire survey with 258 women in Blantyre, Malawi, and contains information on the menstrual absorbents used at their last period, how they disposed of them, socio-economic characteristics, and toilet and solid waste services.Excel file containing dataset and category coding labelsIn this dataset, age is collapsed into a categorical variable. A copy of the dataset with age as a continuous variable can be requested by emailing the dataset creator with an explanation of why it is needed and what it will be used for
Supplementary data for "Are flowers tuned to buzzing pollinators? Variation in natural frequency of stamens with different morphologies and its relationship to bee vibrations"
No full textCode and data used in Nunes, Nevard, Montealegre-Zapata & Vallejo-Marin (2020) preprint at https://doi.org/10.1101/2020.05.19.104422 . Abstract: During buzz pollination, bees use vibrations to remove pollen from flowers. Vibrations at the natural frequency of pollen-carrying stamens are amplified through resonance, resulting in higher-amplitude vibrations. Because pollen release depends on vibration amplitude, bees could increase pollen removal by vibrating at the natural frequency of stamens. Yet, few studies have characterized the natural frequencies of stamens and compared them to frequencies of buzz-pollinating bees. Here we use laser Doppler vibrometry to characterise natural frequencies of stamens of six buzz-pollinated Solanum taxa of contrasting stamen morphology. We also compare the fundamental frequency of bumblebee buzzes produced on two Solanum species with different natural frequencies. We found that stamen morphology and plant identity explain variation in natural frequency of stamens. Our results show that medium-sized pollinators, such as bumblebees, produce buzzes of frequencies higher than the natural frequency of most (5/6) of the Solanum species we studied. However, the observed natural frequency of Solanum stamens is at the low end of the range of frequencies produced by other buzz-pollinating bees. Thus, our findings suggest that in some buzz pollination interactions, but not others, stamen resonance may play a role in mediating pollen release.From the ReadMe file. This folder contains code and data necessary to replicate our data analysis.
Currently the folder is at the final state, with all data processed and analysed.
The spreadsheet "new_file_list.txt" lists the flower measurements and sample data with the .txt files from vibration measurements
with Fast Fourier Transform (FFT) spectra in .txt files in separate folders for data obtained
with Doppler laser vibrometer from stamens (vib_data) and
with a accelerometer attached to the shaker platform (ref_data),
obtained simultaneously with the data acquisition software VibSoft 20 (Polytec, Waldbronn, Germany).
Files with the same number in their name refer to the same sampling event or the same measured stamen.
To visually check and explore the data, you can use the code in "nat_freqs_shaker.pdf".
The markdown codes "obtaining_fn_single_values.pdf" were used to retrieve the first natural frequency from files in folder "vib_data".
To replicate data processing of the natural frequency data, use "obtaining_fn_single_values.pdf".
To replicate the analysis of stamen natural frequencies,
you can use the code from "fn_stats.pdf" after running the code from "obtaining_fn_single_values.pdf" in your R environment.
To replicate the generation of plots used in the figures,
you can use the code from "MS_figure_plots.pdf" after running the code in "obtaining_fn_single_values.pdf" in your R environment.
The spreadsheet "ColonyA1cit_to_het.csv" refers to data on the peak frequencies from bee buzzes
obtained with the free Software Audacity (Audacity Team 2019)
as described in the paper Methods.
Both pdfs and Rmarkdown files from the codes are included in this folder.
Proper UnZip software is recommended for accessing the dataset, for instance, IZArc
Predicting the ecological consequences of mega hydroelectric dams on vertebrate assemblages in lowland tropical forests
No full textDataset (tree saplings) to accompany Jones et al. "Instability of insular tree communities in an Amazonian mega-dam is driven by impaired recruitment and altered species composition" accepted for publication in the Journal of Applied Ecology, November 2018. Dataset contains tree sapling species abundance per surveyed site in the Balbina Dam, Brazilian Amazon. Data were collected in 2014 as part of Jones’ PhD at the University of Stirling.Tree_Saplings_Site_Abundance_Jones_etal.csv: CSV file containing tree sapling species abundance per surveyed sit
The Cartography of Computational Search Spaces
No full textThe dataset contains all symmetric TSP instances, performance results and features sets for "Rigorous Performance Analysis of State-of-the-art TSP Heuristic Solvers", P. McMenemy, N. Veerapen, J. Adair, G. Ochoa. The 18th European Conference on Evolutionary Computation in Combinatorial Optimisation (EvoCOP 2018), 24 - 26 April 2019, Leipzig, Germany. The dataset contains .tsp format files for all 1893 instances used in the study, as well as the performance data for each TSP instance for the 3 TSP heuristics analysed. Full details are given in the README.txt file.The dataset contains all symmetric TSP instances, performance results and features sets for "Rigorous Performance Analysis of State-of-the-art TSP Heuristic Solvers", P. McMenemy, N. Veerapen, J. Adair, G. Ochoa. The 18th European Conference on Evolutionary Computation in Combinatorial Optimisation (EvoCOP 2018), 24 - 26 April 2019, Leipzig, Germany. The dataset contains tsp format files for all 1893 instances used in the study, as well as the performance data for each TSP instance for the 3 TSP heuristics analysed. Full TOC details are given in the README.txt file
Towards a better understanding of mirror-symmetry coding in human vision
No full textMotion-direction does not contribute to symmetry perception, but limiting the lifetime of pattern elements improves symmetry detection1. Here we examine whether symmetry mechanisms are tuned to motion speed and if there are speed-selective symmetry channels. Stimuli were dynamic dot patterns containing varying amounts of symmetry. We measured symmetry detection thresholds for stimuli in which symmetric and noise elements moved at the same or different speeds and compared them to those obtained with static and limited-lifetime static patterns. In a second experiment, we measured percentage correct in two conditions: segregated – symmetric and noise elements drifted at different speeds, and non-segregated – symmetric elements drifted at two different speeds, as did the noise elements. We found that (i) performance was worse when symmetric and noise elements had the same speed and improved gradually as the speed difference increased, (ii) thresholds were comparable for all limited-lifetime static conditions, (iii) performance was improved in segregated compared to non-segregated conditions, (iv) modelling suggests that there are speed-selective channels that combine their outputs using probability summation. In conclusion, symmetry mechanisms are tuned to speed, and there are speed-selective symmetry channels, (v) better performance for moving compared to static patterns.SpeedPredictions.xlsx – probability summation predictions
VelocitySummary1.xlsx – summary of results
Code (folder) – all experimental code
Experiment 1 (folder) – raw data from Experiment 1
Experiment 2 (folder) – raw data from Experiment
Structure, function and resilience of avian communities in tropical ecosystems
No full textPredicted species extinctions caused by the destruction and degradation of tropical primary forest may be at least partially mitigated by the expansion of regenerating secondary forest. However, the conservation value of secondary forest remains controversial, and potentially underestimated, since most previous studies have focused on young, single-aged, or isolated stands. Here we use point count surveys to compare tropical forest bird communities in 20–120-yr-old secondary forest and primary forest stands in central Panama, with varying connectivity between secondary forest sites and extensive primary forest. We found that species richness and other metrics of ecological diversity, as well as the combined population density of all birds, reached a peak in younger (20-yr-old) secondary forests, and appeared to decline in older secondary forest stands. This counter-intuitive result can be explained by the greater connectivity between younger secondary forests and extensive primary forests at our study site, compared with older secondary forests that are either (1) more isolated, or (2) connected to primary forests that are themselves small and isolated. Our results suggest that connectivity with extensive primary forest is a more important determinant of avian species richness and community structure than forest age, and highlight the vital contribution secondary forests can make in conserving tropical bird diversity, so long as extensive primary habitats are adjacent and spatially connected.Mayhew et al._Panama Bird Data_20190105.csv - dataset to accompany manuscript 'Connectivity with primary forest determines the value of secondary tropical forests for bird conservation'
GABON: maintain long-standing scientific profile
No full textSince 1984, researchers at the Station d’Études des Gorilles and Chimpanzées (SEGC) in Lopé National Park, Gabon have recorded weather data (temperature, rainfall and humidity) using various types of equipment at two locations: a savanna site (the research station; 11.605E, -0.201N) and a forest site (800m from the research station and approximately 10m from the savanna/forest edge; 11.605E, -0.206N). More recently solar radiation and wind speed (as well as temperature, rainfall and humidity) have been recorded using automatic weather stations (2012-2016). Analyses of these data can be found in the accompanying peer-reviewed paper: https://peerj.com/articles/8732/Humidity_daily_v.2018-03-14.csv - Daily absolute humidity record from Lopé NP (1984-2018), Gabon; Humidity_daily_v.2018-03-14_metadata.pdf - Metadata for "Humidity_daily_v.2018-03-14.csv";
Rainfall_daily_v.2017-12-31.csv - Daily rainfall record from Lopé NP, Gabon (1984-2018); Rainfall_daily_v.2017-12-31_metadata.pdf - Metadata for "Rainfall_daily_v.2017-12-31.csv"; Solar_daily_v.2015-10-30.csv - Daily solar radiation record from Lopé NP, Gabon (2012-2016); Solar_daily_v.2015-10-30_metadata.pdf - Metadata for "Solar_daily_v.2015-10-30.csv "; Temperature_daily_v.2018-03-13.csv - Daily maximum and minimum temperature record from Lopé NP, Gabon (1984-2018); Temperature_daily_v.2018-03-13_metadata.pdf - Metadata for "Temperature_daily_v.2018-03-13.csv"; Wind_daily_v.2016-07-01.csv - Daily wind speed record from Lopé NP, Gabon (2012-2016); Wind_daily_v.2016-07-01_metadata.pdf - Metadata for "Wind_daily_v.2016-07-01.csv";1.
Supplementary Model for 'The Sustainability Conundrum of Fishmeal Substitution by Plant Ingredients in Shrimp Feeds'
No full textCurrent knowledge suggests that aquaculture growth and its increasing demand for plant ingredients in aquafeed could affect agricultural supply and its resources, such as land, freshwater, and fertilizer. However, the quantitative impact is relatively unknown.
Therefore, we modeled the natural resource demands of a transition to plant-based ingredients in shrimp feed formulations. In this study, feed formulation algorithms were used to create unique feed formulations per shrimp species, with intermediate declining steps of 20% fishmeal substitution by plant ingredients while accounting for the dietary requirements of individual shrimp species. These diets were modeled in combination with a comprehensive multifactorial assessment of marine and terrestrial resource demand for agricultural crop production and processed ingredients.
For a detailed description, the secondary data used, feed formulations, resource demand dataset and equations, consult the Materials and Methods of the paper (open access) ‘The Sustainability Conundrum of Fishmeal Substitution by Plant Ingredients in Shrimp Feeds’; https://doi.org/10.3390/su11041212. The methodology for the feed formulations and data input is explained in Section 3.1. This is followed up (Section 3.2) by a detailed explanation of the marine and terrestrial resource demand dataset for each ingredient, which was based on FAO data and scientific literature. The last (Section 3.3) explains the model simulations and runs and includes an overview of the modeled feed formulations, ingredients, and their respective resource demand values (Table 1). These data are modeled in order to calculate the range in resource demands of the combined ingredients in the feed formulation with the equation explained at the end of Section 3.3.The table of contents of the model is explained on the first tab of the Excel sheet