PSUBDBC {AgroR}

Analysis: DBC experiments in split-plot

Description

Analysis of an experiment conducted in a randomized block design in a split-plot scheme using fixed effects analysis of variance.

Usage

PSUBDBC(
  f1,
  f2,
  block,
  response,
  norm = "sw",
  alpha.f = 0.05,
  alpha.t = 0.05,
  quali = c(TRUE, TRUE),
  names.fat = c("F1", "F2"),
  mcomp = "tukey",
  grau = c(NA, NA),
  grau12 = NA,
  grau21 = NA,
  transf = 1,
  constant = 0,
  geom = "bar",
  theme = theme_classic(),
  ylab = "Response",
  xlab = "",
  xlab.factor = c("F1", "F2"),
  color = "rainbow",
  textsize = 12,
  labelsize = 4,
  dec = 3,
  legend = "Legend",
  errorbar = TRUE,
  addmean = TRUE,
  ylim = NA,
  point = "mean_se",
  fill = "lightblue",
  angle = 0,
  family = "sans",
  posi = "right",
  angle.label = 0
)

Arguments

f1

Numeric or complex vector with plot levels

f2

Numeric or complex vector with subplot levels

block

Numeric or complex vector with blocks

response

Numeric vector with responses

norm

Error normality test (default is Shapiro-Wilk)

alpha.f

Level of significance of the F test (default is 0.05)

alpha.t

Significance level of the multiple comparison test (default is 0.05)

quali

Defines whether the factor is quantitative or qualitative (qualitative)

names.fat

Name of factors

mcomp

Multiple comparison test (Tukey (default), LSD, Scott-Knott and Duncan)

grau

Polynomial degree in case of quantitative factor (default is 1). Provide a vector with three elements.

grau12

Polynomial degree in case of quantitative factor (default is 1). Provide a vector with n levels of factor 2, in the case of interaction f1 x f2 and qualitative factor 2 and quantitative factor 1.

grau21

Polynomial degree in case of quantitative factor (default is 1). Provide a vector with n levels of factor 1, in the case of interaction f1 x f2 and qualitative factor 1 and quantitative factor 2.

transf

Applies data transformation (default is 1; for log consider 0)

constant

Add a constant for transformation (enter value)

geom

Graph type (columns or segments (For simple effect only))

theme

ggplot2 theme (default is theme_classic())

ylab

Variable response name (Accepts the expression() function)

xlab

Treatments name (Accepts the expression() function)

xlab.factor

Provide a vector with two observations referring to the x-axis name of factors 1 and 2, respectively, when there is an isolated effect of the factors. This argument uses 'parse'.

color

When the columns are different colors (Set fill-in argument as "trat")

textsize

Font size (default is 12)

labelsize

Font size (default is 4)

dec

Number of cells (default is 3)

legend

Legend title name

errorbar

Plot the standard deviation bar on the graph (In the case of a segment and column graph) - default is TRUE

addmean

Plot the average value on the graph (default is TRUE)

ylim

y-axis limit

point

This function defines whether the point must have all points ("all"), mean ("mean"), standard deviation (default - "mean_sd") or mean with standard error ("mean_se") if quali= FALSE. For quali=TRUE, 'mean_sd' and 'mean_se' change which information will be displayed in the error bar.

fill

Defines chart color (to generate different colors for different treatments, define fill = "trat")

angle

x-axis scale text rotation

family

Font family (default is sans)

posi

Legend position

angle.label

Label angle

Value

The table of analysis of variance, the test of normality of errors (Shapiro-Wilk, Lilliefors, Anderson-Darling, Cramer-von Mises, Pearson and Shapiro-Francia), the test of homogeneity of variances (Bartlett), the test of multiple comparisons (Tukey, LSD, Scott-Knott or Duncan) or adjustment of regression models up to grade 3 polynomial, in the case of quantitative treatments. The column chart for qualitative treatments is also returned. The function also returns a standardized residual plot.

Note

The order of the chart follows the alphabetical pattern. Please use 'scale_x_discrete' from package ggplot2, 'limits' argument to reorder x-axis. The bars of the column and segment graphs are standard deviation.

In the final output when transformation (transf argument) is different from 1, the columns resp and respo in the mean test are returned, indicating transformed and non-transformed mean, respectively.

Author(s)

Gabriel Danilo Shimizu

References

Principles and procedures of statistics a biometrical approach Steel, Torry and Dickey. Third Edition 1997

Multiple comparisons theory and methods. Departament of statistics the Ohio State University. USA, 1996. Jason C. Hsu. Chapman Hall/CRC.

Practical Nonparametrics Statistics. W.J. Conover, 1999

Ramalho M.A.P., Ferreira D.F., Oliveira A.C. 2000. Experimentacao em Genetica e Melhoramento de Plantas. Editora UFLA.

Scott R.J., Knott M. 1974. A cluster analysis method for grouping mans in the analysis of variance. Biometrics, 30, 507-512.

Examples

#==============================
# Example tomate
#==============================
library(AgroR)
data(tomate)
with(tomate, PSUBDBC(parc, subp, bloco, resp, ylab="Dry mass (g)"))

#==============================
# Example orchard
#==============================
library(AgroR)
data(orchard)
with(orchard, PSUBDBC(A, B, Bloco, Resp, ylab="CBM"))