gcdata {germinationmetrics}

Germination count data

Description

An example germination count dataset. It includes germination count data over 14 days from five genotypes (G1 to G5) in three replications

Usage

gcdata

Format

A data frame with 17 columns:

Genotype

The genotype.

Rep

Replication.

Day01

Number of seeds that germinated (germination counts) on Day 1.

Day02

Number of seeds that germinated (germination counts) on Day 2.

Day03

Number of seeds that germinated (germination counts) on Day 3.

Day04

Number of seeds that germinated (germination counts) on Day 4.

Day05

Number of seeds that germinated (germination counts) on Day 5.

Day06

Number of seeds that germinated (germination counts) on Day 6.

Day07

Number of seeds that germinated (germination counts) on Day 7.

Day08

Number of seeds that germinated (germination counts) on Day 8.

Day09

Number of seeds that germinated (germination counts) on Day 9.

Day10

Number of seeds that germinated (germination counts) on Day 10.

Day11

Number of seeds that germinated (germination counts) on Day 11.

Day12

Number of seeds that germinated (germination counts) on Day 12.

Day13

Number of seeds that germinated (germination counts) on Day 13.

Day14

Number of seeds that germinated (germination counts) on Day 14.

Total Seeds

Total number of seeds tested.

Examples

data(gcdata)
library(ggplot2)
library(reshape2)

# Plot partial germination counts over time
#----------------------------------------------------------------------------
# Convert wide-from to long-form
gcdatamelt <- melt(gcdata[, !names(gcdata) %in% c("Total Seeds")],
                   id.vars = c("Genotype", "Rep"))

ggplot(gcdatamelt, aes(x = variable, y = value,
                       group = interaction(Genotype, Rep),
                       colour = Genotype)) +
  geom_point(alpha = 0.7) +
  geom_line(alpha = 0.7) +
  ylab("Germination count (Partial)") +
  xlab("Intervals") +
  theme_bw()

# Plot partial germination counts over time
#----------------------------------------------------------------------------

# Convert wide-from to long-form
# Compute cumulative germination counts
gcdata2 <- gcdata
gcdata2[, !names(gcdata2) %in% c("Genotype", "Rep", "Total Seeds")] <-
  t(apply(gcdata2[, !names(gcdata2) %in% c("Genotype", "Rep", "Total Seeds")], 1, cumsum))


gcdatamelt2 <- melt(gcdata2[, !names(gcdata2) %in% c("Total Seeds")],
                    id.vars = c("Genotype", "Rep"))

ggplot(gcdatamelt2, aes(x = variable, y = value,
                        group = interaction(Genotype, Rep),
                        colour = Genotype)) +
  geom_point(alpha = 0.7) +
  geom_line(alpha = 0.7) +
  ylab("Germination count (Cumulative)") +
  xlab("Intervals") +
  theme_bw()

# Compute germination indices
#----------------------------------------------------------------------------

counts.per.intervals <- c("Day01", "Day02", "Day03", "Day04", "Day05",
                          "Day06", "Day07", "Day08", "Day09", "Day10",
                          "Day11", "Day12", "Day13", "Day14")
germination.indices(gcdata, total.seeds.col = "Total Seeds",
                    counts.intervals.cols = counts.per.intervals,
                    intervals = 1:14, partial = TRUE, max.int = 5)