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compute various germination indices from cumulative germination counts and Plot cumulative germination counts over time #5

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zahrahesabi opened this issue Nov 30, 2021 · 0 comments
Open

compute various germination indices from cumulative germination counts and Plot cumulative germination counts over time #5

zahrahesabi opened this issue Nov 30, 2021 · 0 comments

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@zahrahesabi
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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)
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