BrookTrout: Salmon Survival in the Presence of Brook Trout

In abd: The Analysis of Biological Data

Description

Total numbers of salmon released (salmon.released) and surviving (salmon.surviving) in 12 streams, 6 with brook trout present and 6 with brook trout absent. The proportion of salmon surviving (proportion.surviving) is given for each stream.

Format

BrookTrout is a data frame with 12 observations on the following 4 variables. BrookTrout2 is a different summary of the same study and gives survival rates for chinook in different years.

trout

a factor with levels absent and present indicating whether brook trout are absent or present in the stream

salmon.released

a numeric vector of the total number of salmon released

salmon.surviving

a numeric vector of the number of salmon surviving

proportion.surviving

a numeric vector of the proportion of salmon surviving

Source

Levin, P.S., S. Achord, B.E. Fiest, and R.W. Zabel. 2002. Non-indigenous brook trout and the demise of Pacific salmon: a forgotten threat? Proceedings of the Royal Society of London, Series B, Biological Sciences 269: 1663-1670.

Examples

str(BrookTrout)
str(BrookTrout2)

bwplot(proportion.surviving ~ trout, BrookTrout)

aggregate(proportion.surviving ~ trout, BrookTrout, FUN = favstats)
summary(proportion.surviving ~ trout, BrookTrout, fun = favstats)

Example output

Loading required package: nlme
Loading required package: lattice
Loading required package: grid
Loading required package: mosaic
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:nlme':

    collapse

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: ggformula
Loading required package: ggplot2
Loading required package: ggstance

Attaching package: 'ggstance'

The following objects are masked from 'package:ggplot2':

    GeomErrorbarh, geom_errorbarh


New to ggformula?  Try the tutorials: 
	learnr::run_tutorial("introduction", package = "ggformula")
	learnr::run_tutorial("refining", package = "ggformula")
Loading required package: mosaicData
Loading required package: Matrix

The 'mosaic' package masks several functions from core packages in order to add 
additional features.  The original behavior of these functions should not be affected by this.

Note: If you use the Matrix package, be sure to load it BEFORE loading mosaic.

Attaching package: 'mosaic'

The following object is masked from 'package:Matrix':

    mean

The following object is masked from 'package:ggplot2':

    stat

The following objects are masked from 'package:dplyr':

    count, do, tally

The following objects are masked from 'package:stats':

    IQR, binom.test, cor, cor.test, cov, fivenum, median, prop.test,
    quantile, sd, t.test, var

The following objects are masked from 'package:base':

    max, mean, min, prod, range, sample, sum

'data.frame':	12 obs. of  4 variables:
 $ trout               : Factor w/ 2 levels "absent","present": 2 1 2 2 1 2 1 2 1 1 ...
 $ salmon.survived     : int  166 180 136 153 178 103 326 173 7 120 ...
 $ salmon.released     : int  820 467 960 700 959 545 1029 769 27 998 ...
 $ proportion.surviving: num  0.202 0.385 0.142 0.219 0.186 ...
'data.frame':	12 obs. of  9 variables:
 $ trout                : Factor w/ 2 levels "absent","present": 2 1 2 2 1 2 1 2 1 1 ...
 $ chinook.survival.1998: num  0.202 0.385 0.142 0.219 0.186 0.189 0.317 0.225 0.259 0.12 ...
 $ chinook.survival.1993: num  0.215 0.294 0.12 0.158 0.168 0.105 0.259 0.183 0.2 0.134 ...
 $ chinook.survival.1999: num  0.197 0.353 0.188 0.212 0.201 0.151 0.237 0.147 NA 0.13 ...
 $ mean.chinook.survival: num  0.194 0.339 0.134 0.176 0.176 ...
 $ chinook.survival.1992: num  0.16 0.325 0.086 0.116 0.15 0.228 0.347 0.133 0.48 0.152 ...
 $ arcsin               : num  0.466 0.669 0.386 0.487 0.446 ...
 $ survivors            : int  166 180 136 153 178 103 326 173 7 120 ...
 $ num.released         : int  820 467 960 700 959 545 1029 769 27 998 ...
    trout proportion.surviving
1  absent            0.1202405
2 present            0.1416667
Warning message:
In format.data.frame(x, digits = digits, na.encode = FALSE) :
  corrupt data frame: columns will be truncated or padded with NAs
 Length   Class    Mode 
      3 formula    call 

abd documentation built on May 2, 2019, 2:14 p.m.