Nothing
## ----setup, include=FALSE-----------------------------------------------------
source("https://raw.githubusercontent.com/Flavjack/inti/master/pkgdown/favicon/docs.r")
## ---- echo=TRUE---------------------------------------------------------------
# Install packages and dependencies
library(GerminaR)
library(dplyr)
# load data
fb <- prosopis %>%
mutate(across(c(nacl, temp, rep), as.factor))
# Prosopis data set
fb %>%
head(10) %>%
kable(caption = "Prosopis dataset")
## ---- echo=TRUE---------------------------------------------------------------
# germination analysis (ten variables)
gsm <- ger_summary(SeedN = "seeds"
, evalName = "D"
, data = fb
)
# Prosopis data set processed
gsm %>%
head(10) %>%
mutate(across(where(is.numeric), ~round(., 2))) %>%
kable(caption = "Function ger_summary performe ten germination indices")
## ---- echo=TRUE, fig.cap="Germination experiment with *Prosopis juliflor* under different osmotic potentials and temperatures. Bar graph with germination percentage in a factorial analisys"----
## Germination Percentage (GRP)
# analysis of variance
av <- aov(grp ~ nacl*temp + rep, data = gsm)
# mean comparison test
mc_grp <- ger_testcomp(aov = av
, comp = c("temp", "nacl")
, type = "snk"
)
# data result
mc_grp$table %>%
kable(caption = "Germination percentage mean comparision")
# bar graphics for germination percentage
grp <- mc_grp$table %>%
fplot(data = .
, type = "bar"
, x = "temp"
, y = "grp"
, group = "nacl"
, ylimits = c(0, 120, 30)
, ylab = "Germination ('%')"
, xlab = "Temperature"
, glab = "NaCl (MPa)"
, error = "ste"
, sig = "sig"
, color = F
)
grp
## ---- echo=TRUE, fig.cap="Germination experiment with *Prosopis juliflor* under different osmotic potentials and temperatures. Bar graph for mean germination time in a factorial analisys."----
## Mean Germination Time (MGT)
# analysis of variance
av <- aov(mgt ~ nacl*temp + rep, data = gsm)
# mean comparison test
mc_mgt <- ger_testcomp(aov = av
, comp = c("temp", "nacl")
, type = "snk")
# data result
mc_mgt$table %>%
kable(caption = "Mean germination time comparison")
# bar graphics for mean germination time
mgt <- mc_mgt$table %>%
fplot(data = .
, type = "bar"
, x = "temp"
, y = "mgt"
, group = "nacl"
, ylimits = c(0,10, 1)
, ylab = "Mean germination time (days)"
, xlab = "Temperature"
, glab = "NaCl (MPa)"
, sig = "sig"
, error = "ste"
, color = T
)
mgt
## ---- echo=TRUE, fig.cap="Germination experiment with *Prosopis juliflor* under different osmotic potentials and temperatures. Line graph from cumulative germination under different osmotic potentials."----
# data frame with percentage or relative germination in time by NaCl
git <- ger_intime(Factor = "nacl"
, SeedN = "seeds"
, evalName = "D"
, method = "percentage"
, data = fb
)
# data result
git %>%
head(10) %>%
kable(caption = "Cumulative germination by nacl factor")
# graphic germination in time by NaCl
nacl <- git %>%
fplot(data = .
, type = "line"
, x = "evaluation"
, y = "mean"
, group = "nacl"
, ylimits = c(0, 110, 10)
, ylab = "Germination ('%')"
, xlab = "Day"
, glab = "NaCl (MPa)"
, color = T
, error = "ste"
)
nacl
## ---- echo=TRUE, fig.cap="Germination experiment with *Prosopis juliflor* under different osmotic potentials and temperatures. Line graph from cumulative germination under different temperatures."----
# data frame with percentage or relative germination in time by temperature
git <- ger_intime(Factor = "temp"
, SeedN = "seeds"
, evalName = "D"
, method = "percentage"
, data = fb)
# data result
git %>%
head(10) %>%
kable(caption = "Cumulative germination by temperature factor")
# graphic germination in time by temperature
temp <- git %>%
fplot(data = .
, type = "line"
, x = "evaluation"
, y = "mean"
, group = "temp"
, ylimits = c(0, 110, 10)
, ylab = "Germination ('%')"
, xlab = "Day"
, glab = "Temperature"
, color = F
)
temp
## ---- echo=TRUE---------------------------------------------------------------
library(ggplot2)
git <- ger_intime(Factor = "temp"
, SeedN = "seeds"
, evalName = "D"
, method = "percentage"
, data = fb
)
ggplot <- git %>%
fplot(data = .
, type = "line"
, x = "evaluation"
, y = "mean"
, group = "temp"
, ylimits = c(0, 110, 10)
, ylab = "Germination ('%')"
, xlab = "Day"
, glab = "Temperature"
, color = T
) +
scale_x_continuous(n.breaks = 10, limits = c(0, 11))
ggplot
## ----references---------------------------------------------------------------
if(!file.exists("files/pkgs.bib")){write_bib(c(.packages()),'files/pkgs.bib')}
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