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(dataIPMpackSuccisa)

Format

The format is: chr "dataIPMpackSuccisa"

Details

data-frame with headings:

- size: log of the product of the number of leaves and the maximum leaf length of rosette leaves at time t

- sizeNext: log of the product of the number of leaves and the maximum leaf length of rosette 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(dataIPMpackSuccisa)
print(head(dataIPMpackSuccisa))

Sp <- dataIPMpackSuccisa

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"
Copyright (C) 2016 The R Foundation for Statistical Computing
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/dataIPMpackSuccisa.csv.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dataIPMpackSuccisa
> ### Title: Succisa pratensis Dataset
> ### Aliases: dataIPMpackSuccisa
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(dataIPMpackSuccisa)
> print(head(dataIPMpackSuccisa))
      size sizeNext      stage  stageNext surv offspringNext fec1Bolt fec2Stem
1 6.282965 4.801939 continuous continuous    1          <NA>        0       NA
2 3.472842 5.376433 continuous continuous    1          <NA>        0       NA
3 4.902599 4.624504 continuous continuous    1          <NA>        0       NA
4 6.074348 6.588023 continuous continuous    1          <NA>        0       NA
5 7.218641 6.588023 continuous continuous    1          <NA>        0       NA
6 6.937394 6.703946 continuous continuous    1          <NA>        1        1
  fec3Head fec1BoltNext fec2StemNext fec3HeadNext cloning clonesNext
1       NA            1            2          1.5       0         NA
2       NA            0           NA           NA       0         NA
3       NA            0           NA           NA       0         NA
4       NA            1            2          3.0       0         NA
5       NA            1            2          3.5       0         NA
6        4            1            1          4.0       0         NA
> 
> Sp <- dataIPMpackSuccisa
> 
> 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 38 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 
>