P. S. Petraitis and S. R. Dudgeon. 2015. Variation in recruitment and the establishment of alternative community states. Ecology 96:31863196. http://dx.doi.org/10.1890/14-2107.1


Supplement

R script and data to run analyses presented in Tables A2 and A3 and to create Fig. A1.
Ecological Archives E096-274-S3.

Copyright


Authors
File list (downloads)
Description


Author(s)

P. S. Petraitis
Department of Biology
University of Pennsylvania
Philadelphia, PA 19104-6018, USA
E-mail: ppetrait@sas.upenn.edu

S. R. Dudgeon
Department of Biology
California State University
Northridge, CA 91330-8303, USA
E-mail: steve.dudgeon@csun.edu


File list

S3_Barnacle_code.R (MD5: 752b3184b93fe671188f5563f4cbb13e)

S3_Size_code.R (MD5: 77a6c0cc350dd857ecb630a4dafa15b2)

S3_CAP.R (MD5: 4f16767979c5d16ca2fc37d748197be2)

S3_Recruit_1997-2008_R_ready.csv (MD5: c0c848c7890c17fceccc0dd8fb8e907d)

Description

S3_Barnacle_code.R is R code to run 43 competing models to find the best-supported model for sources of variation in recruitment as presented in Table A2. Models were hierarchical, that is models lacking a particular main effect would not include interactions involving that effect. Code uses lmer() in the lme4 package and then model.sel() in the MuMIn package to obtain corrected AIC, deltas and AIC weights. Code provided is only for log transformed recruitment for barnacles. To run rockweed and mussel recruitment, replace logB_std with logF_std and logM_std, respectively. Code uses data file S3_Recruit_1997-2008_R_ready.csv.

S3_Size_code.R is R code to run competing models that look for thresholds in recruitment as presented in Table A3. Code uses lmer() in the lme4 package and then model.sel() in the MuMIn package to obtain corrected AIC, deltas and AIC weights. Four of the models tested for breaks or thresholds between different sized clearings. For example, the threshold in the first model was set between control plots and clearings of all sizes while the threshold in the fourth model was set between the eight meter clearings and all clearings that were smaller than eight meters. The fifth model tested for no effect due to clearing size (i.e., size was not included as a factor). For rockweeds, we added a sixth model in which tested for an exponential decline because Dudgeon and Petraitis (2001) reported this pattern for rockweeds. All models included time, bays, sites within bays, and interactions as random effects. Code uses data file S3_Recruit_1997-2008_R_ready.csv.

S3_CAP.R is R code to run the constrained analysis of proximities and create Fig. A1. Analysis was run using capscale() in the vegan package. Correlations of the recruitment with the CAP axes were determined using envfit(). Code uses data file S3_Recruit_1997-2008_R_ready.csv.

S3_Recruit_1997-2008_R_ready.csv contains data used in the analyses presented in the current paper and columns with intermediate steps and information about how the data were standardized. The standardizations are number per 1 sq cm per 56 days for A. nodosum, number per 100 sq cm per 56 days for S. balaniodes and number per 40 sq cm per 84 days for M. edulis. Data are in a format that can be easily loaded into R with variables being corrected identified by default as categorical or numeric. R convention of NA for missing data is used. Duration could not be determined for some entries because of missing information. In these cases, duration was inferred either from data from other plots at the same site in the same year or assumed to be the average duration for that year. Note that entry for Y2004-BO-S4-Barnacle is incorrect in Recruitment_data_97-07.txt and has been changed from 308 to 309.

Column label

Comment

Year

Year preceded by "Y" to insure read as categorical variable

Bay

Same as in Recruitment_data_97-07.txt

Site

Same as in Recruitment_data_97-07.txt

Size

Size preceded by "S" to insure read as categorical variable

Fucoid

Fucoid_T column from Recruitment_data_97-07.txt

Barnacle

Barnacle column from Recruitment_data_97-07.txt

Mussel

Sum of M_300 and M_425 columns from

Recruitment_data_97-07.txt

F-duration

Number of days from F_start to F_end in

Recruitment_data_97-07.txt

B-duration

Number of days from B_start to B_end in

Recruitment_data_97-07.txt

M-duration

Number of days from M_start to M_end in Recruitment_data_97-07.txt

F-infer

Logical variable if duration inferred; 0 = not inferred, 1 = inferred

B-infer

Logical variable if duration inferred; 0 = not inferred, 1 = inferred

M-infer

Logical variable if duration inferred; 0 = not inferred, 1 = inferred

F_std

Fucoid column standardized to number per 1 sq cm per 56 days

B_std

Barnacle column standardized to number per 100 sq cm per 56 days

M_std

Mussel column standardized to number per 40 sq cm per 84 days

logF_std

F_std column transformed as log10(x+1)

logB_std

F_std column transformed as log10(x+1)

logM_std

F_std column transformed as log10(x+1)

S0vs1248

Categorical variable defining two groups: SO vs Rest

S01vs248

Categorical variable defining two groups: SO, S1 vs S2, S4, S8

S012vs48

Categorical variable defining two groups: SO, S1, S2 vs S4, S8

S0124vs8

Categorical variable defining two groups: SO, S1, S2, S4 vs S8

Exp

Continuous variable defining exponential decline

References

Dudgeon, S., and P. S. Petraitis. 2001. Scale-dependent recruitment and divergence of intertidal communities. Ecology 82:991–1006.