Package 'GerminaR' reference manual

Title:	Indices and Graphics for Assess Seed Germination Process
Description:	A collection of different indices and visualization techniques for evaluate the seed germination process in ecophysiological studies (Lozano-Isla et al. 2019) <doi:10.1111/1440-1703.1275>.
Authors:	Flavio Lozano-Isla [aut, cre] , Omar Benites Alfaro [aut] , Marcelo F. Pompelli [aut, ths] , Denise Garcia de Santana [aut], Marli A. Ranal [aut], Federal University of Pernambuco [cph] (Register of application), Federal Rural University of Pernambuco [cph] (Post Graduate Program), Inkaverse [ctb]
Maintainer:	Flavio Lozano-Isla <[email protected]>
License:	GPL-3 \| file LICENSE
Version:	2.1.4
Built:	2024-11-17 06:12:14 UTC
Source:	https://github.com/flavjack/germinar

Plot line or bar graphic

Description

Function use the dtsm function for plot the results

Usage

fplot(
  data,
  type = "bar",
  x,
  y,
  group = NA,
  xlab = NA,
  ylab = NA,
  glab = NA,
  ylimits = NA,
  xrotation = NA,
  xtext = NA,
  gtext = NA,
  legend = "top",
  sig = NA,
  sigsize = 3,
  error = NA,
  color = TRUE,
  opt = NA
)
fplot(
  data,
  type = "bar",
  x,
  y,
  group = NA,
  xlab = NA,
  ylab = NA,
  glab = NA,
  ylimits = NA,
  xrotation = NA,
  xtext = NA,
  gtext = NA,
  legend = "top",
  sig = NA,
  sigsize = 3,
  error = NA,
  color = TRUE,
  opt = NA
)

Arguments

`data`	Output from ger_testcomp function
`type`	Type of graphic. "bar" or "line"
`x`	Axis x variable
`y`	Axis y variable
`group`	Group variable
`xlab`	Title for the axis x
`ylab`	Title for the axis y
`glab`	Title for the legend
`ylimits`	limits of the y axis
`xrotation`	Rotation in x axis c(angle, h, v)
`xtext`	Text labels in x axis
`gtext`	Text labels in groups
`legend`	the position of legends ("none", "left", "right", "bottom", "top", or two-element numeric vector)
`sig`	Column with the significance
`sigsize`	Font size in significance letters
`error`	Show the error bar ("ste" or "std").
`color`	colored figure c(TRUE, FALSE) or vector with the color.
`opt`	Add news layer to the plot

Value

Line o bar plot

Examples

 

## Not run: 

library(GerminaR)
library(dplyr)

smr <- ger_summary(SeedN = "seeds"
                   , evalName = "D"
                   , data = prosopis) %>%
  mutate(across(rep:temp, as.factor))
  
av <- aov(grp ~ nacl*temp, smr)

anova(av)

mc <- ger_testcomp(aov = av
                   , comp = c("nacl", "temp"))
                   
plotdt <- mc$table
                    
plot <- fplot(data = plotdt
       , type = "bar"
       , x = "temp"
       , y = "grp"
       , group = "nacl"
       , sig = "sig"
       #, error = "ste"
       , color = T
       , ylimits = c(0, 120, 20)
       )
       
plot
       

## End(Not run) 

## Not run: 

library(GerminaR)
library(dplyr)

smr <- ger_summary(SeedN = "seeds"
                   , evalName = "D"
                   , data = prosopis) %>%
  mutate(across(rep:temp, as.factor))
  
av <- aov(grp ~ nacl*temp, smr)

anova(av)

mc <- ger_testcomp(aov = av
                   , comp = c("nacl", "temp"))
                   
plotdt <- mc$table
                    
plot <- fplot(data = plotdt
       , type = "bar"
       , x = "temp"
       , y = "grp"
       , group = "nacl"
       , sig = "sig"
       #, error = "ste"
       , color = T
       , ylimits = c(0, 120, 20)
       )
       
plot
       

## End(Not run)

ArcSin of Germination Percentage

Description

This function calculates the arcsin of germination percentage for normalization.

Usage

ger_ASG(SeedN, evalName, data)
ger_ASG(SeedN, evalName, data)

Arguments

`SeedN`	Name of the column with the number of seeds sown.
`evalName`	Prefix of the names of the periods of evaluation.
`data`	The name of the data frame containing the data.

Value

It returns an vector with the ArcSin of Germination values

Examples

library(GerminaR)
dfr <- prosopis
gas <- ger_ASG(SeedN = "seeds", evalName = "D", data = dfr)
gas
library(GerminaR)
dfr <- prosopis
gas <- ger_ASG(SeedN = "seeds", evalName = "D", data = dfr)
gas

Boxplot graphic

Description

Function use the raw data for made a boxplot graphic

Usage

ger_boxp(
  data,
  x,
  y,
  group = NULL,
  xlab = NULL,
  ylab = NULL,
  glab = NULL,
  ylimits = NULL,
  xrotation = NULL,
  legend = "top",
  xtext = NULL,
  gtext = NULL,
  opt = NULL
)
ger_boxp(
  data,
  x,
  y,
  group = NULL,
  xlab = NULL,
  ylab = NULL,
  glab = NULL,
  ylimits = NULL,
  xrotation = NULL,
  legend = "top",
  xtext = NULL,
  gtext = NULL,
  opt = NULL
)

Arguments

`data`	raw data
`x`	Axis x variable
`y`	Axis y variable
`group`	Group variable
`xlab`	Title for the axis x
`ylab`	Title for the axis y
`glab`	Title for the legend
`ylimits`	Limitis and break of the y axis c(init, end, brakes)
`xrotation`	Rotation in x axis c(angle, h, v)
`legend`	the position of legends ("none", "left", "right", "bottom", "top", or two-element numeric vector)
`xtext`	Text labels in x axis
`gtext`	Text labels in groups
`opt`	Add news layer to the plot

Value

boxplot

Examples


## Not run: 

library(GerminaR)

fb <- ger_summary(SeedN = "seeds", evalName = "D", data = prosopis)

ger_boxp(data = fb
         , x =  "nacl"
         , y = "grp"
         , group = "temp"
         )


## End(Not run)

## Not run: 

library(GerminaR)

fb <- ger_summary(SeedN = "seeds", evalName = "D", data = prosopis)

ger_boxp(data = fb
         , x =  "nacl"
         , y = "grp"
         , group = "temp"
         )


## End(Not run)

Coefficient of Variance of the Mean Germination Time

Description

This function calculates the coefficient of variation of the mean germination time

Usage

ger_CVG(evalName, data)
ger_CVG(evalName, data)

Arguments

`evalName`	Prefix of the names of the periods of evaluation.
`data`	The name of the data frame containing the data.

Value

It returns an vector with the values of Coefficient of Variance of germination

Examples

library(GerminaR)
dfr <- prosopis
cvg <- ger_CVG(evalName = "D", data = dfr)
cvg
library(GerminaR)
dfr <- prosopis
cvg <- ger_CVG(evalName = "D", data = dfr)
cvg

Germination Seed Percentage

Description

This function calculates the germination percentage related at total seed sown for experimental unit.

Usage

ger_GRP(SeedN, evalName, data)
ger_GRP(SeedN, evalName, data)

Arguments

`SeedN`	Name of the column with the number of seeds sown.
`evalName`	Prefix of the names of the periods of evaluation.
`data`	The name of the data frame containing the data.

Details

According GOUVEA LABOURIAU (1983), the germinability of a sample of is the percentage of seeds in which the seed germination process comes to an end, in experimental conditions by the seminal intrauterine growth resulting protrusion (or emergence) of a living embryo.

Value

It returns an vector with the percentage of seed germinated.

References

LABOURIAU, L. G.; VALADARES, M. E. B. The germination of seeds. OEA, Washington, DC, 1983.

Examples


library(GerminaR)
dt <- prosopis
grp <- ger_GRP(SeedN = "seeds",evalName = "D", data = dt)
grp
library(GerminaR)
dt <- prosopis
grp <- ger_GRP(SeedN = "seeds",evalName = "D", data = dt)
grp

Germinated Seed Number

Description

This function calculates the number of seed germinated.

Usage

ger_GRS(evalName, data)
ger_GRS(evalName, data)

Arguments

`evalName`	Prefix of the names of the periods of evaluation.
`data`	The name of the data frame containing the data.

Value

Number of seed germinated

Examples


library(GerminaR)
dt <- prosopis
grs <- ger_GRS(evalName = "D", data = dt)
grs
library(GerminaR)
dt <- prosopis
grs <- ger_GRS(evalName = "D", data = dt)
grs

Germination Speed

Description

This function calculates the Germination Speed according at the time lapse of the evaluations.

Usage

ger_GSP(evalName, data)
ger_GSP(evalName, data)

Arguments

`evalName`	Prefix of the names of the periods of evaluation.
`data`	The name of the data frame containing the data.

Value

It returns an vector with the Germination Speed

Examples

library(GerminaR)
dfr <- prosopis
gsp <- ger_GSP(evalName = "D", data = dfr)
gsp
library(GerminaR)
dfr <- prosopis
gsp <- ger_GSP(evalName = "D", data = dfr)
gsp

Cumulative sum of germination by period of time for line graphic

Description

This function makes a data table with the cumulative sum of values of germination by days.

Usage

ger_intime(Factor, SeedN, evalName, method = "percentage", data)
ger_intime(Factor, SeedN, evalName, method = "percentage", data)

Arguments

`Factor`	Factor which will be graph in time
`SeedN`	Name of the column with the seed numbers
`evalName`	Prefix of the evaluation variable
`method`	Type of cumulative germination. "percentage" or "relative"
`data`	Data with the germination evaluation process

Details

Need a summary by factor before use it with function SummaryBy.

Value

Data frame with the germination by period

Examples


## Not run: 

library(GerminaR)
data <- prosopis
grt <- ger_intime(Factor = "temp"
                  , SeedN = "seeds"
                  , evalName = "D"
                  , method = "rel"
                  , data = data)
                   
head(grt, 10)
 
fplot(data = grt
      , type = "line"
      , x = "evaluation"
      , y = "mean"
      , groups = "temp"
      , sig = NULL) 
      

## End(Not run)
      
## Not run: 

library(GerminaR)
data <- prosopis
grt <- ger_intime(Factor = "temp"
                  , SeedN = "seeds"
                  , evalName = "D"
                  , method = "rel"
                  , data = data)
                   
head(grt, 10)
 
fplot(data = grt
      , type = "line"
      , x = "evaluation"
      , y = "mean"
      , groups = "temp"
      , sig = NULL) 
      

## End(Not run)

Mean Germination Rate

Description

This function calculates the mean germination rate of the germination.

Usage

ger_MGR(evalName, data)
ger_MGR(evalName, data)

Arguments

`evalName`	Prefix of the names of the periods of evaluation.
`data`	The name of the data frame containing the data.

Details

The average speed of germination is defined as the reciprocal of the average time germination (RANAL; SANTANA, 2006).

Value

It returns an vector with the values of Mean Germination Rate

References

RANAL, M. A.; SANTANA, D. G. DE. How and why to measure the germination process? Revista Brasileira de Botanica, v. 29, n. 1, p. 1-11, mar. 2006.

Examples

library(GerminaR)
dfr <- prosopis
mgr <- ger_MGR(evalName = "D", data = dfr)
mgr
library(GerminaR)
dfr <- prosopis
mgr <- ger_MGR(evalName = "D", data = dfr)
mgr

Mean Germination Time

Description

This function calculates the mean germination time of germination according at the time lapse of the evaluations.

Usage

ger_MGT(evalName, data)
ger_MGT(evalName, data)

Arguments

`evalName`	Prefix of the names of the periods of evaluation.
`data`	The name of the data frame containing the data.

Details

It was proposed by Haberlandt in 1875. It is calculated as the weighted average germination time. The number of germinated seeds at the intervals established for the collection of data is used as weight. It is expressed in terms of the same units of time used in the germination count (CZABATOR, 1962).

Value

It returns an vector with the values of Mean Germination Time.

References

CZABATOR, F. J. Germination value: an index combining speed and completeness of pine seed germination. Forest Science, v. 8, n. 4, p. 386-396, 1962.

Examples


library(GerminaR)
dfr <- prosopis
mgt <- ger_MGT(evalName = "D", data = dfr)
mgt
library(GerminaR)
dfr <- prosopis
mgt <- ger_MGT(evalName = "D", data = dfr)
mgt

Standard deviation of the Mean Germination Time

Description

This function calculates the standard deviation of the mean germination time

Usage

ger_SDG(evalName, data)
ger_SDG(evalName, data)

Arguments

`evalName`	Prefix of the names of the periods of evaluation.
`data`	The name of the data frame containing the data.

Value

It returns an vector with the values of Standard deviation of germination

Examples

library(GerminaR)
dfr <- prosopis
sdg <- ger_SDG(evalName = "D", data = dfr)
sdg
library(GerminaR)
dfr <- prosopis
sdg <- ger_SDG(evalName = "D", data = dfr)
sdg

Summary of Germination indices

Description

This function makes a data table with the result of germination indices for each experimental unit.

Usage

ger_summary(SeedN, evalName, data)
ger_summary(SeedN, evalName, data)

Arguments

`SeedN`	Name of the column with the seed numbers
`evalName`	Prefix of the evaluation variable
`data`	The name of the data frame containing the data.

Value

Data frame with the summary values of germination variables.

Examples


library(GerminaR)
fb <- prosopis
smr <- ger_summary(SeedN = "seeds", evalName = "D", data = fb)
smr
library(GerminaR)
fb <- prosopis
smr <- ger_summary(SeedN = "seeds", evalName = "D", data = fb)
smr

Germination Synchronization Index

Description

This function calculates the germination synchronization of the germination process.

Usage

ger_SYN(evalName, data)
ger_SYN(evalName, data)

Arguments

`evalName`	Prefix of the names of the periods of evaluation.
`data`	The name of the data frame containing the data.

Details

The Synchory Index Z has been proposed to assess the degree of overlap between flowering individuals in a population. By adopting the idea expressed by PRIMACK, R.B. (1980) the synchrony of one seed with other included in the same replication. Z = 1 when germination of all the seeds occurs at the same time and Z = 0 when at least two seeds can germinate one each time. Z produces a number if and only if there are two seeds finishing the seed germination process at the same time. Thus, the value of Z assessments is the grade of overlap between seed germination.

Value

It returns an vector with the values of Germination synchrony

References

RANAL, M. A.; SANTANA, D. G. DE. How and why to measure the germination process? Revista Brasileira de Botanica, v. 29, n. 1, p. 1-11, mar. 2006.

Examples

library(GerminaR)
dfr <- prosopis
syn <- ger_SYN(evalName = "D", data = dfr)
syn
library(GerminaR)
dfr <- prosopis
syn <- ger_SYN(evalName = "D", data = dfr)
syn

Multiple comparison test

Description

Function analysis of variance for summary data.

Usage

ger_testcomp(aov, comp, type = "snk", sig = 0.05)
ger_testcomp(aov, comp, type = "snk", sig = 0.05)

Arguments

`aov`	lm o aov result function.
`comp`	treatments will be compared.
`type`	method for made comparison analysis: c("snk", "tukey", "duncan").
`sig`	significance level. Default 0.05

Value

Table with complete data for graphics

Examples

 

## Not run: 

library(GerminaR)
library(dplyr)

gdata <- prosopis %>% mutate(across(c(nacl, temp, rep), as.factor))

smr <- ger_summary(SeedN = "seeds", evalName = "D", data = gdata)

av <- aov(grp ~ rep + nacl*temp, smr)

mc <- ger_testcomp(aov = av
                   , comp = c("nacl", "temp")
                   )
                   

## End(Not run) 
## Not run: 

library(GerminaR)
library(dplyr)

gdata <- prosopis %>% mutate(across(c(nacl, temp, rep), as.factor))

smr <- ger_summary(SeedN = "seeds", evalName = "D", data = gdata)

av <- aov(grp ~ rep + nacl*temp, smr)

mc <- ger_testcomp(aov = av
                   , comp = c("nacl", "temp")
                   )
                   

## End(Not run)

Germination Uncertainty

Description

This function calculates the germination uncertainty in the germination process.

Usage

ger_UNC(evalName, data)
ger_UNC(evalName, data)

Arguments

`evalName`	Prefix of the names of the periods of evaluation.
`data`	The name of the data frame containing the data.

Details

The uncertainty index u is an adaptation of Shannon index measures the degree of uncertainty in predicting the informational entropy or uncertainty associated with the distribution of the relative frequency of germination (GOUVEA LABOURIAU 1983; LABOURIAU; VALADARES, 1983). Low values of u indicate frequencies with short peaks, i.e. the more concentrated the germination in time. Just a germinated seed changes the value of u. This means that u measures the degree of germination scattering.

Value

It returns an vector with the values of Germination Uncertainty.

References

GOUVEA LABOURIAU, L. L. G. L. A germinacao das sementes. Washington. LABOURIAU, L. G.; VALADARES, M. E. B. The germination of seeds. OEA, Washington, DC, 1983.

Examples

library(GerminaR)
dfr <- prosopis
unc <- ger_UNC(evalName = "D", data = dfr)
unc
library(GerminaR)
dfr <- prosopis
unc <- ger_UNC(evalName = "D", data = dfr)
unc

Variance of the Mean Germination Time

Description

This function calculates the variance of the mean germination time.

Usage

ger_VGT(evalName, data)
ger_VGT(evalName, data)

Arguments

`evalName`	Prefix of the names of the periods of evaluation.
`data`	The name of the data frame containing the data.

Value

It returns an vector with the values of Variance of Germination

Examples

library(GerminaR)
dfr <- prosopis
vgt <- ger_VGT(evalName = "D", data = dfr)
vgt
library(GerminaR)
dfr <- prosopis
vgt <- ger_VGT(evalName = "D", data = dfr)
vgt

GerminaQuant for R

Description

GermiQuant for R app allows make the calculation for the germination indices incredibly easy in a interactive applications build in base a GerminaR R package and Shiny. GermiQuant app is live!. Outputs change instantly as users modify inputs, without requiring a reload the app. The principal features of the application allow calculate the principal germination indices, statistical analysis and easy way to plot the results.

Usage

GerminaQuant(dependencies = FALSE)
GerminaQuant(dependencies = FALSE)

Arguments

dependencies

Install package dependencies for run the app

Source

Lozano-Isla, F., Benites Alfaro, O., & Pompelli, M. F. (2016). GerminaQuant for R (Patent No. BR 51 2016 001327-3). https://flavjack.shinyapps.io/germinaquant/

GerminaQuant data analysis

Description

Function analysis of variance for summary data.

Usage

gquant_analysis(
  data,
  response,
  factors,
  block = NA,
  comparison = NA,
  type = "snk",
  sig = 0.05
)
gquant_analysis(
  data,
  response,
  factors,
  block = NA,
  comparison = NA,
  type = "snk",
  sig = 0.05
)

Arguments

`data`	data from ger_summary() function
`response`	germination indices to analyse
`factors`	factor as vector or factor model as string
`block`	block factor for RCBD
`comparison`	treatments will be compared.
`type`	method for made comparison analysis: c("snk", "tukey", "duncan").
`sig`	significance level. Default 0.05

Details

Function for the analysis module in the app

Value

list

Examples

 

## Not run: 

library(GerminaR)

smr <- ger_summary(SeedN = "seeds", evalName = "D", data = prosopis)

mc <- gquant_analysis(data = smr
                      , response = "grp"
                      , factors = c("nacl", "temp")
                      , block = "rep"
                      , comparison = c("nacl", "temp")
                      )
                      
mc


## End(Not run) 

## Not run: 

library(GerminaR)

smr <- ger_summary(SeedN = "seeds", evalName = "D", data = prosopis)

mc <- gquant_analysis(data = smr
                      , response = "grp"
                      , factors = c("nacl", "temp")
                      , block = "rep"
                      , comparison = c("nacl", "temp")
                      )
                      
mc


## End(Not run)

Osmotic potential calculator

Description

Function to calculate the grams of salt or PEG-6000 needed for determinated osmotic potential

Usage

osmp(type = "salt", vol, pres, temp, mw, ki)
osmp(type = "salt", vol, pres, temp, mw, ki)

Arguments

`type`	Salt or PEG-6000 c("salt", "peg6000"). Default: "salt".
`vol`	volume (liters)
`pres`	Pressure (Mpa) in negative values. 1 bar = 0.1 Mpa
`temp`	Temperature (centigrade)
`mw`	Molecular weight
`ki`	Salt dissociation constant (NaCl = 1.8)

Value

Numeric value (grams)

Germination under different osmotic potentials and temperatures.

Description

Dataset containing information from germination experiment with Prosopis juliflor under different osmotic potentials and temperatures.

rep a numeric vector, repetitions or replications.
nacl a numeric vector, NaCl osmotic potentials levels in Mpa to be evaluated.
temp a numeric vector, temperature levels in centigrades to be evelauted.
seeds a numeric vector, number of seed used for experimental unit.
D0-D10 numeric vectors, ten evaluations days performed in the germination experiment.

Usage

prosopis
prosopis

Format

A data frame with 15 columns and 80 rows.

Source

LEV-UFRPE

References

MIRANDA, R. D. Q.; CORREIA, R. M.; DE ALMEIDA-CORTEZ, J. S.; POMPELLI, M. F. Germination of Prosopis juliflora (Sw.) D.C. seeds at different osmotic potentials and temperatures. Plant Species Biology, v. 29, n. 3, p. E9-E20, set. 2014.

Repeated Rows in a data matrix

Description

This function made a data table with the evaluation days of germination

Usage

rep_row(Rseq, Nrow)
rep_row(Rseq, Nrow)

Arguments

`Rseq`	Row sequence for the data matrix
`Nrow`	Number of rows for the data matrix

Value

Data Matrix with day of the germination

Colourise text for display in the terminal.

Description

If R is not currently running in a system that supports terminal colours the text will be returned unchanged.

Usage

textcolor(text, fg = "red", bg = NULL)
textcolor(text, fg = "red", bg = NULL)

Arguments

`text`	character vector
`fg`	foreground colour, defaults to white
`bg`	background colour, defaults to transparent

Details

Allowed colours are: black, blue, brown, cyan, dark gray, green, light blue, light cyan, light gray, light green, light purple, light red, purple, red, white, yellow

Author(s)

testthat package

Examples


print(textcolor("Red", "red"))
cat(textcolor("Red", "red"), "\n")
cat(textcolor("White on red", "white", "red"), "\n")

print(textcolor("Red", "red"))
cat(textcolor("Red", "red"), "\n")
cat(textcolor("White on red", "white", "red"), "\n")

Web table

Description

Web table

Usage

webTable(
  data,
  caption = NULL,
  digits = 3,
  rnames = FALSE,
  buttons = NULL,
  file_name = NULL,
  scrolly = NULL
)
webTable(
  data,
  caption = NULL,
  digits = 3,
  rnames = FALSE,
  buttons = NULL,
  file_name = NULL,
  scrolly = NULL
)

Arguments

`data`	Dataset.
`caption`	Title for the table.
`digits`	Digits number in the table exported.
`rnames`	Row names.
`buttons`	Buttons: "excel", "copy" or "none". Default c("excel", "copy")
`file_name`	Excel file name
`scrolly`	Windows height to show the table

Package 'GerminaR'

Help Index

Plot line or bar graphic

Description

Usage

Arguments

Value

Examples

ArcSin of Germination Percentage

Description

Usage

Arguments

Value

Examples

Boxplot graphic

Description

Usage

Arguments

Value

Examples

Coefficient of Variance of the Mean Germination Time

Description

Usage

Arguments

Value

Examples

Germination Seed Percentage

Description

Usage

Arguments

Details

Value

References

Examples

Germinated Seed Number

Description

Usage

Arguments

Value

Examples

Germination Speed

Description

Usage

Arguments

Value

Examples

Cumulative sum of germination by period of time for line graphic

Description

Usage

Arguments

Details

Value

Examples

Mean Germination Rate

Description

Usage

Arguments

Details

Value

References

Examples

Mean Germination Time

Description

Usage

Arguments

Details

Value

References

Examples

Standard deviation of the Mean Germination Time

Description

Usage

Arguments

Value

Examples

Summary of Germination indices

Description

Usage

Arguments

Value