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Effects of forest management on acorn production, weevil infestation, and removal by predators
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data
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README.md
analysis_production.R
analysis_removal.R
analysis_weevils.R
function_crown_areas.R
function_removal_parse.R

README.md

hee-oak-mast

Analyses associated with mast (i.e., oak acorn) production and predation and small mammals and insects. Data were collected from ~113 black and white oak trees at the Hardwood Ecosystem Experiment (south-central Indiana) both before and after timber harvest.

The project was broken into three separate experiments conducted at each oak tree:

  1. Mast production - yearly counts of acorns that fell into 2 mast traps under the crown of each tree.

  2. Weevil infestation - collected acorns from each tree were x-rayed to determine weevil infestation status.

  3. Acorn removal - marked acorns that fell into a system of semipermeable exclosures were tracked throughout each fall over 8 sampling occasions to determine if and when they were removed by seed predators.

The pre-harvest results are published in the following U.S. Forest Service GTR chapter:

Kellner, Kenneth F.; Riegel, Jeffery K.; Lichti, Nathanael I.; Swihart, Robert K. 2013. Oak mast production and animal impacts on acorn survival in the central hardwoods. In: Swihart, Robert K.; Saunders, Michael R.; Kalb, Rebecca A.; Haulton, G. Scott; Michler, Charles H., eds. 2013. The Hardwood Ecosystem Experiment: a framework for studying responses to forest management. Gen. Tech. Rep. NRS (2013): 108

Pre vs. post harvest results (6 total years) are published in the following article:

Kellner, Kenneth F.; Riegel, Jeffery K.; Swihart, Robert K. 2014. Effects of silvicultural disturbance on acorn infestation and removal. New Forests 45: 265-281

Metadata

The analysis_hee_[ ].R files contain the framework of the Bayesian analysis in JAGS for each of the three project components listed above. The corresponding figures_[ ].R files contain code for figures associated with each analysis. Both sets of R scripts are heavily commented within.

The function_[ ].R files contain functions used to parse the raw HEE data and generate the datasets used in the analyses.

The models subfolder contains the model description (in the BUGS language) for each JAGS analysis.

The figures subfolder contains code for each figure in the New Forests paper.

The data subfolder contains CSV files for the first six years of data collection on this project. These data files are distilled versions of the full HEE mast project datasets. I do not currently have permission to publish the data. The metadata of each file are described below, and I have provided corresponding example CSV files for each (containing scrambled data) to help visualize their structure.

  1. hee_acorn_covs.csv contains covariates for the acorns monitored in the removal study:
    a. acorn ID (acornno) b. HEE experimental unit, mast tree of origin full name and id code (unit/treeno/treecode) c. year of the study in which the acorn was monitored both as a single column and series of indicator variable columns (yearno/y1-y6) d. acorn species with 0=black oak and 1=white oak e. the exclosure type in which the acorn was placed (open/deer/squirrel with baseline=no access to any animals) f. the first and last sampling occasions that the acorn was monitored (first/last) g. If the acorn was ultimately removed by predators across all sampling occasions (rem=1) or not (rem=0)

  2. hee_acorn_eh.csv contains encounter histories for acorns monitored in the removal study: a. acorn ID (acornno) b. acorn 'survival' (i.e., non-removal) encounter history (surv1-8) c. acorn weevil infestation status in each sampling period based on weevil exit hole presence (weev1-8) d. acorn damage status (brok1-8) e. acorn germination status (germ1-8)

  3. hee_mast_sampledates.csv contains information about when the mast trees were sampled and how long the time between samples was. Since all trees within a given unit were sampled at the same time, the data is summarized by unit and year. NAs indicate occasions when the units were not sampled. a. Experimental unit (unit) b. Julian date on which sampling occurred for each occasion (p1-8) c. Number of days since the previous sampling occasion (l1-8) d. Year of the study from 1-6 (year)

  4. hee_production.csv is a matrix (# of trees x # of sample years) containin the total number of acorns collected in traps under each tree in each year. The row number is equal to the tree id (treecode) and the column number is the year of the study (1-6).

  5. hee_treedata.csv contains detailed characteristics of the mast trees in this experiment: a. The unit and treeid for each tree (unit/treecode) b. The tree species (0=black oak, 1=white oak) c. The tree height (in meters), crown length from the top to bottom of hte crown (in meters) and dbh (in cm); (height/dbh/llc) d. Radial distance measurements in meters in the 8 cardinal directions from the tree to the edge of the canopy, in meters (N,NE,E,SE,S,SW,W,NW) and the length of the longest axis based on these measurements (length) e. Crown area in square meters based on these radii, calculated using Greenberg CH (2000) Individual variation in acorn production by five species of southern Appalachian oaks. For Ecol Manag 132:199–210 (crownarea) d. Crown volume in meters^3 based on llc and length, not especially precise (volume) e. Silvicultural treatment: shelterwood (shelter=1), opening edge (edge=1), or control (shelter=0 & edge=0) f. Index providing the years in which a given tree was sampled, to account for missing values for some trees in BUGS (syr1-syr6) g. Index of available mast at each tree each year for use in the weevil removal study (mast1-mast6)

  6. hee_weevils.csv contains information about the characteristics and weevil infestation status of acorns included in the weevil study: a. Experimental unit, full tree name, and tree id of the source tree (unit, tree, treecode) b. Acorn species (species=1 for white oak and species=0 for black oak) c. Year in which the acorn was collected as a single column (year) and series of indicator variable columns (y1-y6) d. Infestation status of the acorn (infest=1 if weevil damage was present, infest=0 if not)

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