DOI: 10.5281/zenodo.4972084
title: Dataset from : Browsing is a strong filter for savanna tree seedlings in their first growing season

description: The data presented here were used to produce the following paper: Archibald, Twine, Mthabini, Stevens (2021) Browsing is a strong filter for savanna tree seedlings in their first growing season. J. Ecology. The project under which these data were collected is:<br> Mechanisms Controlling Species Limits in a Changing World. NRF/SASSCAL Grant number 118588 For information on the data or analysis please contact Sally Archibald:<br> sally.archibald@wits.ac.za Description of file(s): <br> File 1: cleanedData_forAnalysis.csv<br> (required to run the R code: "finalAnalysis_PostClipResponses_Feb2021_requires_cleanData_forAnalysis_.R" The data represent monthly survival and growth data for ~740 seedlings from 10 species under various levels of clipping. The data consist of one .csv file with the following column names: treatment Clipping treatment (1 - 5 months clip plus control unclipped)<br> plot_rep One of three randomised plots per treatment<br> matrix_no Where in the plot the individual was placed<br> species_code First three letters of the genus name, and first three letters of the species name uniquely identifies the species<br> species Full species name<br> sample_period Classification of sampling period into time since clip.<br> status Alive or Dead<br> standing.height Vertical height above ground (in mm)<br> height.mm Length of the longest branch (in mm)<br> total.branch.length Total length of all the branches (in mm)<br> stemdiam.mm Basal stem diameter (in mm)<br> maxSpineLength.mm Length of the longest spine<br> postclipStemNo Number of resprouting stems (only recorded AFTER clipping)<br> date.clipped date.clipped<br> date.measured date.measured<br> date.germinated date.germinated<br> Age.of.plant Date measured - Date germinated<br> newtreat Treatment as a numeric variable, with 8 being the control plot (for plotting purposes) File 2: Herbivory_SurvivalEndofSeason_march2017.csv<br> (required to run the R code: "FinalAnalysisResultsSurvival_requires_Herbivory_SurvivalEndofSeason_march2017.R" The data consist of one .csv file with the following column names: treatment Clipping treatment (1 - 5 months clip plus control unclipped)<br> plot_rep One of three randomised plots per treatment<br> matrix_no Where in the plot the individual was placed<br> species_code First three letters of the genus name, and first three letters of the species name uniquely identifies the species<br> species Full species name<br> sample_period Classification of sampling period into time since clip.<br> status Alive or Dead<br> standing.height Vertical height above ground (in mm)<br> height.mm Length of the longest branch (in mm)<br> total.branch.length Total length of all the branches (in mm)<br> stemdiam.mm Basal stem diameter (in mm)<br> maxSpineLength.mm Length of the longest spine<br> postclipStemNo Number of resprouting stems (only recorded AFTER clipping)<br> date.clipped date.clipped<br> date.measured date.measured<br> date.germinated date.germinated<br> Age.of.plant Date measured - Date germinated<br> newtreat Treatment as a numeric variable, with 8 being the control plot (for plotting purposes)<br> genus Genus<br> MAR Mean Annual Rainfall for that Species distribution (mm)<br> rainclass High/medium/low <br> File 3: allModelParameters_byAge.csv<br> (required to run the R code: "FinalModelSeedlingSurvival_June2021_.R" <br> Consists of a .csv file with the following column headings <br> Age.of.plant Age in days<br> species_code Species<br> pred_SD_mm Predicted stem diameter in mm<br> pred_SD_up top 75th quantile of stem diameter in mm<br> pred_SD_low bottom 25th quantile of stem diameter in mm<br> treatdate date when clipped<br> pred_surv Predicted survival probability<br> pred_surv_low Predicted 25th quantile survival probability<br> pred_surv_high Predicted 75th quantile survival probability<br> species_code species code<br> Bite.probability Daily probability of being eaten<br> max_bite_diam_duiker_mm Maximum bite diameter of a duiker for this species<br> duiker_sd standard deviation of bite diameter for a duiker for this species<br> max_bite_diameter_kudu_mm Maximum bite diameer of a kudu for this species<br> kudu_sd standard deviation of bite diameter for a kudu for this species<br> mean_bite_diam_duiker_mm mean etc<br> duiker_mean_sd standard devaition etc<br> mean_bite_diameter_kudu_mm mean etc<br> kudu_mean_sd standard deviation etc<br> genus genus<br> rainclass low/med/high <br> File 4: EatProbParameters_June2020.csv<br> (required to run the R code: "FinalModelSeedlingSurvival_June2021_.R" <br> Consists of a .csv file with the following column headings shtspec species name<br> species_code species code<br> genus genus<br> rainclass low/medium/high<br> seed mass mass of seed (g per 1000seeds) <br> Surv_intercept coefficient of the model predicting survival from age of clip for this species<br> Surv_slope coefficient of the model predicting survival from age of clip for this species<br> GR_intercept coefficient of the model predicting stem diameter from seedling age for this species<br> GR_slope coefficient of the model predicting stem diameter from seedling age for this species<br> species_code species code<br> max_bite_diam_duiker_mm Maximum bite diameter of a duiker for this species<br> duiker_sd standard deviation of bite diameter for a duiker for this species<br> max_bite_diameter_kudu_mm Maximum bite diameer of a kudu for this species<br> kudu_sd standard deviation of bite diameter for a kudu for this species<br> mean_bite_diam_duiker_mm mean etc<br> duiker_mean_sd standard devaition etc<br> mean_bite_diameter_kudu_mm mean etc<br> kudu_mean_sd standard deviation etc<br> AgeAtEscape_duiker[t] age of plant when its stem diameter is larger than a mean duiker bite<br> AgeAtEscape_duiker_min[t] age of plant when its stem diameter is larger than a min duiker bite<br> AgeAtEscape_duiker_max[t] age of plant when its stem diameter is larger than a max duiker bite<br> AgeAtEscape_kudu[t] age of plant when its stem diameter is larger than a mean kudu bite<br> AgeAtEscape_kudu_min[t] age of plant when its stem diameter is larger than a min kudu bite<br> AgeAtEscape_kudu_max[t] age of plant when its stem diameter is larger than a max kudu bite
description: The data represent monthly survival and growth data for ~740 seedlings from 10 species under various levels of clipping. Total data rows : 3287. These were from of four common savanna tree clades: Combretum, Vachellia, Senegalia, and Detarioideae. The species: Colophospermum_mopane Combretum_apiculatum Combretum_collinum Combretum_hereroense Combretum_molle Senegalia_caffra Senegalia_mellifera Senegalia_nigrescens Vachellia_davyi Vachellia_erioloba Vachellia_exuvialis Vachellia_karroo(rbay) Vachellia_sieberiana The study was carried out at the Wits Rural Facility (WRF), a 350 ha research station of the University of the Witwatersrand, in the central savanna Lowveld area of Limpopo Province, South Africa (∼31° 06E, 24°30 S) between (September 2016) and March 2017 approximately. Data was collected by Frank Nyathi in field work. Elizabeth Telford did excavating and weighing the below-ground biomass. Stephen Young, Zemijo Kimmie, Benko Kimmie, and Zaid Kimmie did observational data collection, measuring seedlings and watching impala. Mechanisms Controlling Species Limits in a Changing World. NRF/SASSCAL Grant number 118588