gcdata2<-read.csv(file.choose(), header = T)
gcdata2
#> Concentration Temp Rep Day01 Day02 Day03 Day04 Day05 Day06 Day07 Day08 Day09
#> 1 0.0 10 1 0 0 0 0 0 0 0 0 0
#> 2 0.5 10 1 0 0 0 0 0 0 0 0 0
#> 3 0.3 10 1 0 0 0 0 0 0 0 0 0
#> 4 0.1 10 1 0 0 0 0 0 0 0 0 0
#> 5 0.0 10 2 0 0 0 0 0 0 0 0 0
#> 6 0.5 10 2 0 0 0 0 0 0 0 0 0
#> 7 0.3 10 2 0 0 0 0 0 0 0 0 0
#> 8 0.1 10 2 0 0 0 0 0 0 0 0 0
#> 9 0.0 10 3 0 0 0 0 0 0 0 0 0
#> 10 0.5 10 3 0 0 0 0 0 0 0 0 0
#> 11 0.3 10 3 0 0 0 0 0 0 0 0 0
#> 12 0.1 10 3 0 0 0 0 0 0 0 0 0
#> 13 0.0 20 1 0 0 0 9 16 17 17 17 17
#> 14 0.5 20 1 0 0 0 9 11 16 18 19 19
#> 15 0.3 20 1 0 0 0 4 5 8 10 10 11
#> 16 0.1 20 1 0 0 0 8 17 20 21 21 21
#> 17 0.0 20 2 0 0 0 16 23 23 23 23 23
#> 18 0.5 20 2 0 0 0 9 11 17 17 17 18
#> 19 0.3 20 2 0 0 0 3 4 7 12 12 12
#> 20 0.1 20 2 0 0 0 10 17 19 20 20 20
#> 21 0.0 20 3 0 0 0 6 18 18 18 20 20
#> 22 0.5 20 3 0 0 0 5 6 11 11 11 12
#> 23 0.3 20 3 0 0 0 3 4 10 11 11 14
#> 24 0.1 20 3 0 0 0 10 16 20 22 22 22
#> 25 0.0 30 1 0 0 5 8 13 13 13 16 16
#> 26 0.5 30 1 0 0 5 8 9 10 10 10 10
#> 27 0.3 30 1 0 0 9 17 17 17 17 17 17
#> 28 0.1 30 1 0 0 6 11 11 12 12 12 12
#> 29 0.0 30 2 0 0 8 12 22 22 22 22 22
#> 30 0.5 30 2 0 0 4 12 12 13 13 13 13
#> 31 0.3 30 2 0 0 7 8 9 13 14 14 15
#> 32 0.1 30 2 0 0 7 14 15 15 15 16 16
#> 33 0.0 30 3 0 0 5 12 22 22 22 23 23
#> 34 0.5 30 3 0 0 5 8 9 9 9 9 9
#> 35 0.3 30 3 0 0 6 9 11 15 16 16 16
#> 36 0.1 30 3 0 0 6 13 13 13 13 14 14
#> Day10 Day11 Day12 Day13 Day14 Day15 Day16 Day17 Day18 Day19 Total.Seeds
#> 1 0 0 0 0 0 0 0 0 0 0 25
#> 2 8 8 8 8 8 8 8 8 8 8 25
#> 3 0 3 3 3 3 5 5 5 5 5 25
#> 4 1 1 2 2 2 3 3 3 3 3 25
#> 5 0 0 0 0 0 0 0 0 0 0 25
#> 6 6 6 6 8 8 8 9 9 9 9 25
#> 7 0 3 3 5 5 6 6 6 6 6 25
#> 8 4 4 4 4 4 4 4 4 4 4 25
#> 9 0 0 0 0 0 0 0 0 0 0 25
#> 10 4 4 5 5 8 8 8 8 8 8 25
#> 11 0 4 4 5 5 8 8 8 8 8 25
#> 12 5 5 5 5 5 5 5 5 5 5 25
#> 13 17 17 17 17 17 17 17 17 17 17 25
#> 14 19 19 20 20 20 20 20 20 20 20 25
#> 15 11 11 11 11 11 11 11 11 11 11 25
#> 16 21 21 21 21 21 21 21 21 21 21 25
#> 17 23 23 23 23 23 23 23 23 23 23 25
#> 18 18 18 18 18 18 18 18 18 18 18 25
#> 19 13 13 13 13 13 13 13 13 13 13 25
#> 20 20 20 20 20 20 20 20 20 20 20 25
#> 21 20 20 20 20 20 20 20 20 20 20 25
#> 22 12 12 12 12 12 12 12 12 12 12 25
#> 23 14 14 14 14 14 14 14 14 14 14 25
#> 24 22 23 23 23 23 23 23 23 23 23 25
#> 25 16 16 16 16 16 16 16 16 16 16 25
#> 26 10 10 10 10 10 10 10 10 10 10 25
#> 27 19 19 19 19 19 19 19 19 19 19 25
#> 28 12 12 12 12 12 12 12 12 12 12 25
#> 29 22 22 22 22 22 22 22 22 22 22 25
#> 30 13 13 13 13 13 13 13 13 13 13 25
#> 31 15 15 15 15 15 15 15 15 15 15 25
#> 32 16 16 16 16 16 16 16 16 16 16 25
#> 33 23 23 23 23 23 23 23 23 23 23 25
#> 34 9 9 9 9 9 9 9 9 9 9 25
#> 35 17 17 17 17 17 17 17 17 17 17 25
#> 36 14 14 14 14 14 14 14 14 14 14 25
or
#> Error in eval(expr, envir, enclos): object 'or' not found
rm(list = ls())
library(germinationmetrics)
#>
#> --------------------------------------------------------------------------------
#> Welcome to germinationmetrics version 0.1.5
#>
#>
#> # To know how to use this package type:
#> browseVignettes(package = 'germinationmetrics')
#> for the package vignette.
#>
#> # To know whats new in this version type:
#> news(package='germinationmetrics')
#> for the NEWS file.
#>
#> # To cite the methods in the package type:
#> citation(package='germinationmetrics')
#>
#> # To suppress this message use:
#> suppressPackageStartupMessages(library(germinationmetrics))
#> --------------------------------------------------------------------------------
setwd("D:/GERMIN/")
gcdata1<-read.csv("gcdata1.csv", header = T)
#> Warning in file(file, "rt"): cannot open file 'gcdata1.csv': No such file or
#> directory
#> Error in file(file, "rt"): cannot open the connection
#data(gcdata)
counts.per.intervals <- c("Day01", "Day02", "Day03", "Day04", "Day05",
"Day06", "Day07", "Day08", "Day09", "Day10",
"Day11", "Day12", "Day13", "Day14", "Day15",
"Day16", "Day17", "Day18", "Day19")
reindices<-germination.indices(gcdata1, total.seeds.col = "Total.Seeds",
counts.intervals.cols = counts.per.intervals,
intervals = 1:19, partial = FALSE, max.int = 5)
#> Error in is.data.frame(data): object 'gcdata1' not found
outliers::rm.outlier(gcdata1, fill = FALSE, median = FALSE, opposite = FALSE)
#> Error in outliers::rm.outlier(gcdata1, fill = FALSE, median = FALSE, opposite = FALSE): object 'gcdata1' not found
x_out_rm<-x[!x%in%plot.stats(x)$out]
#> Error in eval(expr, envir, enclos): object 'x' not found
fits<-FourPHFfit.bulk(gcdata1, total.seeds.col = "Total.Seeds",
counts.intervals.cols = counts.per.intervals,
intervals = 1:19, partial = FALSE,
fix.y0 = TRUE, fix.a = FALSE,
tmax = 10, tries = 3, umax = 70, umin = 10)
#> Error in is.data.frame(data): object 'gcdata1' not found
write.csv(indices,"indices.csv" )
#> Error in is.data.frame(x): object 'indices' not found
write.csv(fits,"fits.csv" )
#> Error in is.data.frame(x): object 'fits' not found
a<-plot(fits, group.col = "Concentration")
#> Error in plot(fits, group.col = "Concentration"): object 'fits' not found
b<-plot(fits, group.col = "Temp")
#> Error in plot(fits, group.col = "Temp"): object 'fits' not found
ggsave("a.jpg",a, units="in", width=8, height=5, dpi=300)
#> Error in ggsave("a.jpg", a, units = "in", width = 8, height = 5, dpi = 300): could not find function "ggsave"
ggsave("b.jpg",b, units="in", width=8, height=5, dpi=300)
#> Error in ggsave("b.jpg", b, units = "in", width = 8, height = 5, dpi = 300): could not find function "ggsave"
c<-plot(fits, rog = TRUE, group.col = "Concentration")
#> Error in plot(fits, rog = TRUE, group.col = "Concentration"): object 'fits' not found
d<-plot(fits, rog = TRUE, group.col = "Temp")
#> Error in plot(fits, rog = TRUE, group.col = "Temp"): object 'fits' not found
ggsave("c.jpg",c, units="in", width=8, height=5, dpi=300)
#> Error in ggsave("c.jpg", c, units = "in", width = 8, height = 5, dpi = 300): could not find function "ggsave"
ggsave("d.jpg",d, units="in", width=8, height=5, dpi=300)
#> Error in ggsave("d.jpg", d, units = "in", width = 8, height = 5, dpi = 300): could not find function "ggsave"
plot(fits, group.col = "Concentration", annotate = "t50.germ")
#> Error in plot(fits, group.col = "Concentration", annotate = "t50.germ"): object 'fits' not found
plot(fits, group.col = "Concentration", annotate = "tmgr")
#> Error in plot(fits, group.col = "Concentration", annotate = "tmgr"): object 'fits' not found
plot(fits, group.col = "Concentration", annotate = "mgt")
#> Error in plot(fits, group.col = "Concentration", annotate = "mgt"): object 'fits' not found
plot(fits, group.col = "Concentration", annotate = "uniformity")
#> Error in plot(fits, group.col = "Concentration", annotate = "uniformity"): object 'fits' not found
Created on 2021-11-30 by the reprex package (v2.0.1)