Dataset from : Browsing is a strong filter for savanna tree seedlings in their first growing season

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