carlson.germination {agridat} | R Documentation

## Germination of alfalfa seeds at various salt concentrations

### Description

Germination of alfalfa seeds at various salt concentrations

### Usage

    data("carlson.germination")

### Format

A data frame with 120 observations on the following 3 variables.

`gen`

  genotype factor, 15 levels

`germ`

  germination percent, 0-100

`nacl`

  salt concentration percent, 0-2

### Details

Data are means averaged over 5, 10, 15, and 20 day counts. Germination is expressed as a percent of the no-salt control to account for differences in germination among the cultivars.

### Source

Carlson, JR and Ditterline, RL and Martin, JM and Sands, DC and Lund, RE. (1983). Alfalfa Seed Germination in Antibiotic Agar Containing NaCl. Crop science, 23, 882-885. http://doi.org/10.2135/cropsci1983.0011183X002300050016x

### Examples

    data(carlson.germination)
    dat <- carlson.germination
    dat$germ <- dat$germ/100 # Convert to percent

    # Separate response curve for each genotype.
    # Really, we should use a glmm with random int/slope for each genotype
    m1 <- glm(germ~ 0 + gen*nacl, data=dat, family=quasibinomial)

    # Plot data and fitted model
    if(require(latticeExtra)){
      newd <- data.frame(expand.grid(gen=levels(dat$gen), nacl=seq(0,2,length=100)))
      newd$pred <- predict(m1, newd, type="response")
      xyplot(germ~nacl|gen, dat, as.table=TRUE, main="carlson.germination",
             xlab="Percent NaCl", ylab="Fraction germinated") +
      xyplot(pred~nacl|gen, newd, type='l', grid=list(h=1,v=0))
    }

    # Calculate LD50 values.  Note, Carlson et al used quadratics, not glm.
    # MASS::dose.p cannot handle multiple slopes, so do a separate fit for
    # each genotype.  Results are vaguely similar to Carlson table 5.
    if(require(MASS)){
      for(ii in unique(dat$gen)){
        cat("\n", ii, "\n")
        mm <- glm(germ ~ 1 + nacl, data=dat, subset=gen==ii, family=quasibinomial(link="probit"))
        print(dose.p(mm))
      }
      ##              Dose         SE
      ## Anchor    1.445728  0.05750418
      ## Apollo    1.305804  0.04951644
      ## Baker     1.444153  0.07653989
      ## Drylander 1.351201  0.03111795
      ## Grimm     1.395735  0.04206377
    }

[Package agridat version 1.16 Index]