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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,19 +1,20 @@ | ||
| Package: labdsv | ||
| Version: 1.6-1 | ||
| Date: 2013-09-13 | ||
| Version: 1.7-0 | ||
| Date: 2015-05-04 | ||
| Title: Ordination and Multivariate Analysis for Ecology | ||
| Author: David W. Roberts <droberts@montana.edu> | ||
| Maintainer: David W. Roberts <droberts@montana.edu> | ||
| Depends: R (>= 2.10), mgcv, MASS | ||
| Suggests: rgl, optpart | ||
| Imports: rgl, cluster | ||
| Suggests: optpart, fso | ||
| Description: A variety of ordination and community analyses | ||
| useful in analysis of data sets in community ecology. | ||
| Includes many of the common ordination methods, with | ||
| graphical routines to facilitate their interpretation, | ||
| as well as several novel analyses. | ||
| License: GPL (>= 2) | ||
| URL: http://ecology.msu.montana.edu/labdsv/R | ||
| Packaged: 2013-09-13 17:50:42 UTC; dvrbts | ||
| Packaged: 2015-05-04 22:05:02 UTC; dvrbts | ||
| NeedsCompilation: yes | ||
| Repository: CRAN | ||
| Date/Publication: 2013-09-13 22:20:43 | ||
| Date/Publication: 2015-05-05 00:12:11 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,42 +1,48 @@ | ||
| abuocc <- function(taxa,minabu=0) | ||
| abuocc <- function (taxa, minabu = 0, panel='all') | ||
| { | ||
| if (!is.data.frame(taxa)) taxa <- data.frame(taxa) | ||
|
|
||
| spc.plt <- apply(taxa>minabu,1,sum) | ||
| plt.spc <- apply(taxa>minabu,2,sum) | ||
|
|
||
| if (minabu==0) { | ||
| mean.abu <- apply(taxa,2,sum)/plt.spc | ||
| if (!is.data.frame(taxa)) | ||
| taxa <- data.frame(taxa) | ||
| spc.plt <- apply(taxa > minabu, 1, sum) | ||
| plt.spc <- apply(taxa > minabu, 2, sum) | ||
| if (minabu == 0) { | ||
| mean.abu <- apply(taxa, 2, sum)/plt.spc | ||
| } else { | ||
| mean.abu <- rep(0,ncol(taxa)) | ||
| mean.abu <- rep(0, ncol(taxa)) | ||
| for (i in 1:ncol(taxa)) { | ||
| mask <- taxa[,i]>minabu | ||
| mean.abu[i] <- sum(taxa[mask,i]) / max(1,plt.spc[i]) | ||
| mask <- taxa[, i] > minabu | ||
| mean.abu[i] <- sum(taxa[mask, i])/max(1, plt.spc[i]) | ||
| } | ||
| } | ||
| mean.abu[is.na(mean.abu)] <- 0 | ||
|
|
||
| plot(rev(sort(plt.spc[plt.spc>minabu])),log="y",xlab="Species Rank",ylab="Number of Plots", | ||
| main="Species Occurrence") | ||
| readline("Press return for next plot ") | ||
|
|
||
| plot(rev(sort(spc.plt)),xlab="Plot Rank",ylab="Number of Species", | ||
| main="Species/Plot") | ||
| readline("Press return for next plot ") | ||
|
|
||
| plot(plt.spc[mean.abu>minabu],mean.abu[mean.abu>minabu],log="y",xlab="Number of Plots",ylab="Mean Abundance", | ||
| main="Abundance vs Occurrence") | ||
| yorn <- readline("Do you want to identify individual species? Y/N : ") | ||
| if (yorn == 'Y' || yorn == 'y') | ||
| identify(plt.spc[mean.abu>minabu],mean.abu[mean.abu>minabu],names(taxa)[mean.abu>minabu]) | ||
| readline("Press return for next plot ") | ||
|
|
||
| plot(spc.plt,apply(taxa,1,sum),xlab="Number of Species/Plot", | ||
| ylab="Total Abundance") | ||
| yorn <- readline("Do you want to identify individual plots? Y/N : ") | ||
| if (yorn == 'Y' || yorn == 'y') | ||
| identify(spc.plt,apply(taxa,1,sum),labels=row.names(taxa)) | ||
|
|
||
| invisible(list(spc.plt=spc.plt,plt.spc=plt.spc,mean=mean.abu)) | ||
| if (panel=='all' || panel==1) { | ||
| plot(rev(sort(plt.spc[plt.spc > minabu])), log = "y", xlab = "Species Rank", | ||
| ylab = "Number of Plots", main = "Species Occurrence") | ||
| if (panel == 'all') readline("Press return for next plot ") | ||
| } | ||
| if (panel=='all' || panel==2) { | ||
| plot(rev(sort(spc.plt)), xlab = "Plot Rank", ylab = "Number of Species", | ||
| main = "Species/Plot") | ||
| if (panel=='all') readline("Press return for next plot ") | ||
| } | ||
| if (panel=='all' || panel==3) { | ||
| plot(plt.spc[mean.abu > minabu], mean.abu[mean.abu > minabu], | ||
| log = "y", xlab = "Number of Plots", ylab = "Mean Abundance", | ||
| main = "Abundance vs Occurrence") | ||
| yorn <- readline("Do you want to identify individual species? Y/N : ") | ||
| if (yorn == "Y" || yorn == "y") | ||
| identify(plt.spc[mean.abu > minabu], mean.abu[mean.abu > | ||
| minabu], names(taxa)[mean.abu > minabu]) | ||
| if (panel=='all') readline("Press return for next plot ") | ||
| } | ||
| if (panel=='all' || panel==4) { | ||
| plot(spc.plt, apply(taxa, 1, sum), xlab = "Number of Species/Plot", | ||
| ylab = "Total Abundance") | ||
| yorn <- readline("Do you want to identify individual plots? Y/N : ") | ||
| if (yorn == "Y" || yorn == "y") | ||
| identify(spc.plt, apply(taxa, 1, sum), labels = row.names(taxa)) | ||
| } | ||
| out <- list(spc.plt = spc.plt, plt.spc = plt.spc, mean = mean.abu) | ||
| attr(out,'call') <- match.call() | ||
| attr(out,'taxa') <- deparse(substitute(taxa)) | ||
| invisible(out) | ||
| } | ||
|
|
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