Succisa pratensis Dataset

Description

Subset of multiple years of demographic data of Succisa pratensis collected at the "Bennekomse Meent" site in the Netherlands. Details are described in Jongejans and de Kroon (2005). More information: E.Jongejans@science.ru.nl

Usage

data(dataIPMpackSuccisa2)

Format

The format is: chr "dataIPMpackSuccisa2"

Details

data-frame with headings:

- size: log of the sum of the products of the number of leaves and the maximum leaf length for rosette and stem leaves at time t

- sizeNext: log of the sum of the products of the number of leaves and the maximum leaf length for rosette and stem leaves at time t+1

- stage: stage of the individual ('continuous' means the plant has a size; NA = not recruited yet) at time t

- stageNext: stage of the individual ('continuous' means the plant has a size; 'dead' = dead) at time t+1

- surv: survival (0 = dead, 1= alive, NAs if not yet recruited)

- offspringNext: type of new recruit ('sexual' = seedling, 'clonal' = side-rosette, NA = not a recruit) at time t+1

- fec1Bolt: whether stems are produced (0 = no stems, 1 = at least 1 stem, NA = not recruited yet) at time t

- fec2Stem: number of stems when stems are produced (NA when fec1Bolt = NA or 0) at time t

- fec3Head: mean number of flower heads per stem when stems are produced (NA when fec1Bolt = NA or 0) at time t

- fec1BoltNext: whether stems are produced (0 = no stems, 1 = at least 1 stem, NA = not recruited yet) at time t+1

- fec2StemNext: number of stems when stems are produced (NA when fec1BoltNext = NA or 0) at time t+1

- fec3HeadNext: mean number of flower heads per stem when stems are produced (NA when fec1BoltNext = NA or 0) at time t+1

- cloning: whether clonal offspring (side-rosettes) are produced by this individual (NA for plants that were not recruited yet at time t)

- clonesNext: number of clonal offspring (side-rosettes) produced when at least on side-rosette is produced (NA when 'cloning' = 0 or NA)

Author(s)

Eelke Jongejans & Hans de Kroon

References

Jongejans, E. and de Kroon, H. (2005) Space versus time variation in the population dynamics of three co-occurring perennial herbs. Journal of Ecology, 93, 681-692.

Examples

data(dataIPMpackSuccisa2)
print(head(dataIPMpackSuccisa2))

Sp <- dataIPMpackSuccisa2

fo<-makeFecObj(Sp, Formula = list(fec1Bolt ~ size+size2, 
    fec2Stem ~ size, fec3Head ~ size), 
        Family = c("binomial","poisson","poisson"), 
            Transform=c("none","-1","none"), 
            fecConstants = data.frame(seedsPerHead=50,
            seedlingEstablishmentRate= 0.02))

co<-makeClonalObj(Sp, Formula = list(cloning ~ size, clonesNext ~ size), 
    Family = c("binomial","poisson"), Transform=c("none","-1"), 
       offspringSizeExplanatoryVariables = "size")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(IPMpack)
Loading required package: Matrix
Loading required package: MASS
Loading required package: nlme
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/IPMpack/dataIPMpackSuccisa2.csv.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dataIPMpackSuccisa2
> ### Title: Succisa pratensis Dataset
> ### Aliases: dataIPMpackSuccisa2
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(dataIPMpackSuccisa2)
> print(head(dataIPMpackSuccisa2))
      size sizeNext      stage  stageNext surv offspringNext fec1Bolt fec2Stem
1       NA 6.824145       <NA> continuous   NA        sexual       NA       NA
2       NA 5.255197       <NA> continuous   NA        sexual       NA       NA
3 5.756455 5.575728 continuous continuous    1          <NA>        0       NA
4 3.231931       NA continuous       dead    0          <NA>        0       NA
5 6.733190 7.171465 continuous continuous    1          <NA>        1        1
6 5.478644 5.957354 continuous continuous    1          <NA>        0       NA
  fec3Head fec1BoltNext fec2StemNext fec3HeadNext cloning clonesNext
1       NA            0           NA           NA      NA         NA
2       NA            0           NA           NA      NA         NA
3       NA            1            1            1       0         NA
4       NA           NA           NA           NA       0         NA
5        3            0           NA           NA       0         NA
6       NA            0           NA           NA       0         NA
> 
> Sp <- dataIPMpackSuccisa2
> 
> fo<-makeFecObj(Sp, Formula = list(fec1Bolt ~ size+size2, 
+     fec2Stem ~ size, fec3Head ~ size), 
+         Family = c("binomial","poisson","poisson"), 
+             Transform=c("none","-1","none"), 
+             fecConstants = data.frame(seedsPerHead=50,
+             seedlingEstablishmentRate= 0.02))
There were 42 warnings (use warnings() to see them)
> 
> co<-makeClonalObj(Sp, Formula = list(cloning ~ size, clonesNext ~ size), 
+     Family = c("binomial","poisson"), Transform=c("none","-1"), 
+        offspringSizeExplanatoryVariables = "size")
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>