Re: [R-sig-eco] Recommended R package for analyzing community data set? - nested design, stratified random sampling, covariates
Dear Laura, David is certainly correct that vegan would provide a wealth of tools for the analysis of your data. More generally, if you go to CRAN and browse the environmetrics Task View you will see an review of many packages suitable for specific analyses you may be interested in. Dave Roberts On 01/15/2012 12:10 PM, Laura S wrote: Dear all: May you recommend an R package for analyzing this data set? I would greatly appreciate any thoughts you can provide. I. Study goals This study examines soil crust (lichens and bryophytes) recovery and succession in fields that underwent different levels of disturbance. II. Variables Response variables of interest: soil crust cover (categorical scale - described below), species richness, species composition Explanatory variable of interest: disturbance regime (categorical variable) Environmental variables measured (covariates - mix of categorical and numerical variables): cover of mineral soil, litter, vascular plant bases, stones, or rocks, slope, aspect III. Study sampling and design Eight research areas (BR, CB, CC, JL, PC, PL, SL, TR) Within each research area subplots were assigned six disturbance treatments (NC, NS, OC, OS, SC, SS) based on disturbance history A single transect was placed randomly in the center of each subplot and sampled in twenty 20 x 20 cm plots at 1 m intervals along the transect 47 of 48 possible treatment subplots were sampled (n=6 for 7 sites, n=5 for 1 site) Sampling cover scale: Scale valueRepresentative % cover 1= 1 21-4 34-10 410-25 525-50 650-75 775-95 895-100 There were three different sampling times (spread over two years), but time of sampling was not considered as a confounding factor given the way sampling was conducted with the particular communities studied (soil crust communities). Total species positively identified: 33 taxa (species and species groups), 15 of these were in four or more of 47 subplots (n=6 x 7, n=5 x 1) Unidentified collected taxa: less than 0.5% Approximate taxa pool (species observed in entire areas, but not necessarily in sample plots): 26 lichen + 21 bryophytes = 47 taxa Thank you for your time and consideration, Laura [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] Recommended R package for analyzing community data set? - nested design, stratified random sampling, covariates
Dear all: May you recommend an R package for analyzing this data set? I would greatly appreciate any thoughts you can provide. I. Study goals This study examines soil crust (lichens and bryophytes) recovery and succession in fields that underwent different levels of disturbance. II. Variables Response variables of interest: soil crust cover (categorical scale - described below), species richness, species composition Explanatory variable of interest: disturbance regime (categorical variable) Environmental variables measured (covariates - mix of categorical and numerical variables): cover of mineral soil, litter, vascular plant bases, stones, or rocks, slope, aspect III. Study sampling and design Eight research areas (BR, CB, CC, JL, PC, PL, SL, TR) Within each research area subplots were assigned six disturbance treatments (NC, NS, OC, OS, SC, SS) based on disturbance history A single transect was placed randomly in the center of each subplot and sampled in twenty 20 x 20 cm plots at 1 m intervals along the transect 47 of 48 possible treatment subplots were sampled (n=6 for 7 sites, n=5 for 1 site) Sampling cover scale: Scale value Representative % cover 1 = 1 2 1-4 3 4-10 4 10-25 5 25-50 6 50-75 7 75-95 8 95-100 There were three different sampling times (spread over two years), but time of sampling was not considered as a confounding factor given the way sampling was conducted with the particular communities studied (soil crust communities). Total species positively identified: 33 taxa (species and species groups), 15 of these were in four or more of 47 subplots (n=6 x 7, n=5 x 1) Unidentified collected taxa: less than 0.5% Approximate taxa pool (species observed in entire areas, but not necessarily in sample plots): 26 lichen + 21 bryophytes = 47 taxa Thank you for your time and consideration, Laura [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] Recommended R package for analyzing community data set? - nested design, stratified random sampling, covariates
Default packages of any installation of R can perform many types of regression (IMO regression can show you something). Your goal seems to wide for me, maybe you can provide more information like hypotheses? Any google query using community and R will show *vegan* (popular package for community analysis). ML is manly for discussion try to search for another resource first them here. Good luck 2012/1/15 Laura S les_e...@yahoo.com Dear all: May you recommend an R package for analyzing this data set? I would greatly appreciate any thoughts you can provide. I. Study goals This study examines soil crust (lichens and bryophytes) recovery and succession in fields that underwent different levels of disturbance. II. Variables Response variables of interest: soil crust cover (categorical scale - described below), species richness, species composition Explanatory variable of interest: disturbance regime (categorical variable) Environmental variables measured (covariates - mix of categorical and numerical variables): cover of mineral soil, litter, vascular plant bases, stones, or rocks, slope, aspect III. Study sampling and design Eight research areas (BR, CB, CC, JL, PC, PL, SL, TR) Within each research area subplots were assigned six disturbance treatments (NC, NS, OC, OS, SC, SS) based on disturbance history A single transect was placed randomly in the center of each subplot and sampled in twenty 20 x 20 cm plots at 1 m intervals along the transect 47 of 48 possible treatment subplots were sampled (n=6 for 7 sites, n=5 for 1 site) Sampling cover scale: Scale valueRepresentative % cover 1= 1 21-4 34-10 410-25 525-50 650-75 775-95 895-100 There were three different sampling times (spread over two years), but time of sampling was not considered as a confounding factor given the way sampling was conducted with the particular communities studied (soil crust communities). Total species positively identified: 33 taxa (species and species groups), 15 of these were in four or more of 47 subplots (n=6 x 7, n=5 x 1) Unidentified collected taxa: less than 0.5% Approximate taxa pool (species observed in entire areas, but not necessarily in sample plots): 26 lichen + 21 bryophytes = 47 taxa Thank you for your time and consideration, Laura [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- Currículo: http://lattes.cnpq.br/7541377569511492 [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
