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:
Mechanisms Controlling Species Limits in a Changing World. NRF/SASSCAL Grant number 118588
For information on the data or analysis please contact Sally Archibald:
sally.archibald@wits.ac.za
Description of file(s):
File 1: cleanedData_forAnalysis.csv
(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)
plot_rep One of three randomised plots per treatment
matrix_no Where in the plot the individual was placed
species_code First three letters of the genus name, and first three letters of the species name uniquely identifies the species
species Full species name
sample_period Classification of sampling period into time since clip.
status Alive or Dead
standing.height Vertical height above ground (in mm)
height.mm Length of the longest branch (in mm)
total.branch.length Total length of all the branches (in mm)
stemdiam.mm Basal stem diameter (in mm)
maxSpineLength.mm Length of the longest spine
postclipStemNo Number of resprouting stems (only recorded AFTER clipping)
date.clipped date.clipped
date.measured date.measured
date.germinated date.germinated
Age.of.plant Date measured - Date germinated
newtreat Treatment as a numeric variable, with 8 being the control plot (for plotting purposes)
File 2: Herbivory_SurvivalEndofSeason_march2017.csv
(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)
plot_rep One of three randomised plots per treatment
matrix_no Where in the plot the individual was placed
species_code First three letters of the genus name, and first three letters of the species name uniquely identifies the species
species Full species name
sample_period Classification of sampling period into time since clip.
status Alive or Dead
standing.height Vertical height above ground (in mm)
height.mm Length of the longest branch (in mm)
total.branch.length Total length of all the branches (in mm)
stemdiam.mm Basal stem diameter (in mm)
maxSpineLength.mm Length of the longest spine
postclipStemNo Number of resprouting stems (only recorded AFTER clipping)
date.clipped date.clipped
date.measured date.measured
date.germinated date.germinated
Age.of.plant Date measured - Date germinated
newtreat Treatment as a numeric variable, with 8 being the control plot (for plotting purposes)
genus Genus
MAR Mean Annual Rainfall for that Species distribution (mm)
rainclass High/medium/low
File 3: allModelParameters_byAge.csv
(required to run the R code: "FinalModelSeedlingSurvival_June2021_.R"
Consists of a .csv file with the following column headings
Age.of.plant Age in days
species_code Species
pred_SD_mm Predicted stem diameter in mm
pred_SD_up top 75th quantile of stem diameter in mm
pred_SD_low bottom 25th quantile of stem diameter in mm
treatdate date when clipped
pred_surv Predicted survival probability
pred_surv_low Predicted 25th quantile survival probability
pred_surv_high Predicted 75th quantile survival probability
species_code species code
Bite.probability Daily probability of being eaten
max_bite_diam_duiker_mm Maximum bite diameter of a duiker for this species
duiker_sd standard deviation of bite diameter for a duiker for this species
max_bite_diameter_kudu_mm Maximum bite diameer of a kudu for this species
kudu_sd standard deviation of bite diameter for a kudu for this species
mean_bite_diam_duiker_mm mean etc
duiker_mean_sd standard devaition etc
mean_bite_diameter_kudu_mm mean etc
kudu_mean_sd standard deviation etc
genus genus
rainclass low/med/high
File 4: EatProbParameters_June2020.csv
(required to run the R code: "FinalModelSeedlingSurvival_June2021_.R"
Consists of a .csv file with the following column headings
shtspec species name
species_code species code
genus genus
rainclass low/medium/high
seed mass mass of seed (g per 1000seeds)
Surv_intercept coefficient of the model predicting survival from age of clip for this species
Surv_slope coefficient of the model predicting survival from age of clip for this species
GR_intercept coefficient of the model predicting stem diameter from seedling age for this species
GR_slope coefficient of the model predicting stem diameter from seedling age for this species
species_code species code
max_bite_diam_duiker_mm Maximum bite diameter of a duiker for this species
duiker_sd standard deviation of bite diameter for a duiker for this species
max_bite_diameter_kudu_mm Maximum bite diameer of a kudu for this species
kudu_sd standard deviation of bite diameter for a kudu for this species
mean_bite_diam_duiker_mm mean etc
duiker_mean_sd standard devaition etc
mean_bite_diameter_kudu_mm mean etc
kudu_mean_sd standard deviation etc
AgeAtEscape_duiker[t] age of plant when its stem diameter is larger than a mean duiker bite
AgeAtEscape_duiker_min[t] age of plant when its stem diameter is larger than a min duiker bite
AgeAtEscape_duiker_max[t] age of plant when its stem diameter is larger than a max duiker bite
AgeAtEscape_kudu[t] age of plant when its stem diameter is larger than a mean kudu bite
AgeAtEscape_kudu_min[t] age of plant when its stem diameter is larger than a min kudu bite
AgeAtEscape_kudu_max[t] age of plant when its stem diameter is larger than a max kudu bite