vignettes/vignette.R
In jensharbers/agricolaeplotr: Visualization of Design of Experiments from the 'agricolae' Package
## ----setup, eval = FALSE------------------------------------------------------
# install.packages("agricolaeplotr")
## ----message=FALSE, warning=FALSE---------------------------------------------
library("ggplot2")
library("agricolae")
library("agricolaeplotr")
library("FielDHub")
library("raster")
## -----------------------------------------------------------------------------
library(agricolae) # origin of the needed design object
trt<-c(3,2) # factorial 3x2
outdesign <- design.ab(trt, r=3, serie=2,design = 'crd')
head(outdesign$book,10)
plot_design.factorial_crd(outdesign,ncols=7,nrows=3, width = 1, height = 1)
## ---- echo=TRUE, results='asis'-----------------------------------------------
plot_design.factorial_crd(outdesign,ncols=6,nrows=3, width = 1, height = 1, reverse_y = TRUE)
## ---- echo=TRUE, results='asis'-----------------------------------------------
plot_design.factorial_crd(outdesign,ncols=6,nrows=3, width = 1, height = 1, reverse_x = TRUE)
## ---- results='asis'----------------------------------------------------------
plot_design.factorial_crd(outdesign,ncols=6,nrows=3, width = 1, height = 1, reverse_x = TRUE,reverse_y = TRUE)
## ---- echo = TRUE, results='asis'---------------------------------------------
plot_design.factorial_crd(outdesign,ncols=6,nrows=3, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE)
## ---- echo = TRUE, results='asis'---------------------------------------------
plot_design.factorial_crd(outdesign,ncols=6,nrows=3, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE,space_width = 1,space_height = 1)
## ---- echo = TRUE, results='asis'---------------------------------------------
plot_design.factorial_crd(outdesign,ncols=6,nrows=3, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE,space_width = 0.7,space_height = 0.8)
## ---- echo = TRUE, results='asis'---------------------------------------------
plot_design.factorial_crd(outdesign,ncols=6,nrows=3, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE, factor_name = "B")
## ---- echo = TRUE, results='asis'---------------------------------------------
set.seed(129984)
trt<-c(3,2) # factorial 3x2
outdesign <- design.ab(trt, r=3, serie=2,design = 'crd')
plot_design.factorial_crd(outdesign,ncols=3,nrows=6, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE, factor_name = "B")
## ---- echo = TRUE, results='asis'---------------------------------------------
set.seed(129866478)
trt<-c(3,2) # factorial 3x2
outdesign <- design.ab(trt, r=3, serie=2,design = 'crd')
plot_design.factorial_crd(outdesign,ncols=3,nrows=6, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE, factor_name = "B") + theme_poster()
## ---- echo = TRUE, results='asis'---------------------------------------------
set.seed(12986)
trt<-c(3,2) # factorial 3x2
outdesign <- design.ab(trt, r=3, serie=2,design = 'crd')
plot_design.factorial_crd(outdesign,ncols=3,nrows=6, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE, factor_name = "B") + theme_pres()
## ---- echo = TRUE, results='asis'---------------------------------------------
trt<-c(3,2) # factorial 3x2
outdesign <- design.ab(trt, r=3, serie=2,design = 'crd')
plot_design.factorial_crd(outdesign,ncols=3,nrows=6, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE, factor_name = "B") + theme_pres() + scale_fill_viridis_d()
## -----------------------------------------------------------------------------
set.seed(23488833)
trt <-c(3,2)
outdesign<-design.ab(trt, serie=2, design="lsd",seed = 454555)
length_table <- dim(outdesign$book)[1] # length of the table
outdesign$book$yield <- sample(c(5:12,c(NA,NA,NA)), size = length_table, replace = TRUE)
plot_design.factorial_lsd(outdesign,factor_name = "yield") + scale_fill_viridis_c()
## -----------------------------------------------------------------------------
set.seed(23488833)
trt <-c(3,2)
outdesign<-design.ab(trt, serie=2, design="lsd",seed = 454555)
length_table <- dim(outdesign$book)[1] # length of the table
yield <- sample(c(5:20,c(NA,NA,NA)), size = length_table, replace = TRUE)
df <- cbind(plots=outdesign$book$plots,yield)
head(df,10)
outdesign$book <- merge(outdesign$book,df, by.x = "plots", by.y = "plots")
plot_design.factorial_lsd(outdesign,factor_name = "yield") + scale_fill_viridis_c()
## -----------------------------------------------------------------------------
set.seed(1298664)
plots <- as.factor(1:(8*6))
block <- as.factor((rep(1:6,each=8)))
A <- as.vector(replicate(8,sample(rep(1:2,times=3),6,replace=FALSE)))
outcome <- runif(48,20,100)
experiment <- cbind(plots,block,A,outcome)
experiment <- as.data.frame(experiment)
head(experiment)
experiment_design <- list()
experiment_design$parameters$design<- "factorial"
experiment_design$parameters$applied <- "rcbd"
experiment_design$book <- experiment
head(experiment_design)
plot_design.factorial_rcbd(experiment_design,factor_name = "A")
plot_design.factorial_rcbd(experiment_design,factor_name = "outcome")
## -----------------------------------------------------------------------------
set.seed(1298664)
t1<-c('a','b','c','d','e',"f","g","h")
t2<-c("u",'v','w','x','y',"z")
outdesign2 <- design.split(trt1=t1, trt2=t2, r=r,serie = 2,
seed = 0, kinds = 'Super-Duper',
randomization=TRUE,first=TRUE,design = 'lsd')
plot_split_lsd(outdesign2,factor_name_1 = "t1",factor_name_2 = "t2",width = 2,height = 2, subplots = FALSE,labels = "plots")
plot_split_lsd(outdesign2,width = 2,height = 2, subplots = TRUE, labels = "splots", factor_name_1 = "t1", factor_name_2 = "t2")
## -----------------------------------------------------------------------------
set.seed(1298664)
t1<-c('a','b','c','d','e','f','g')
t2<-c('v','w','x','y','z')
r <- 4
outdesign2 <- design.split(trt1=t1, trt2=t2, r=r,
serie = 2, seed = 0, kinds = 'Super-Duper',
randomization=TRUE,first=TRUE,design = 'crd')
plot_split_crd(outdesign2,ncols = 5,nrows=6, subplots = FALSE,
factor_name_1 = "t1",factor_name_2 = "t2")
plot_split_crd(outdesign2,ncols = 5,nrows=6, subplots = TRUE, labels="splots",factor_name_1 = "t1",factor_name_2 = "t2")
## -----------------------------------------------------------------------------
set.seed(1298664)
T1<-c('a','b','c','d','e',"f","g")
T2<-c("we",'v','w','x','y','z',"d")
r = 3
outdesign2 <- design.split(trt1=T1, trt2=T2, r=r,serie = 2,
seed = 0, kinds = 'Super-Duper',randomization=TRUE,
first=TRUE,design = 'rcbd')
plot_split_rcbd(outdesign2,width = 5,height = 5,subplots = FALSE,
factor_name_1 = "T1",factor_name_2 = "T2")
plot_split_rcbd(outdesign2,width = 5,height = 5,labels = "splots",
factor_name_1 = "T1",factor_name_2 = "T2")
## -----------------------------------------------------------------------------
SpatpREP1 <- FielDHub::partially_replicated(nrows = 25,
ncols = 8,
repGens = c(30,50,10,1,1),
repUnits = c(1,2,3,20,20),
planter = "cartesian",
plotNumber = 101,
seed = 77)
plot_fieldhub(SpatpREP1,
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = TRUE,
reverse_x = TRUE)
## -----------------------------------------------------------------------------
NAME <- paste("G", 1:492, sep = "")
repGens = c(108, 384);repUnits = c(2,1)
REPS <- rep(repUnits, repGens)
treatment_list <- data.frame(list(ENTRY = 1:492,
NAME = NAME,
REPS = REPS))
SpatpREP2 <- FielDHub::partially_replicated(nrows = 30,
ncols = 20,
planter = "serpentine",
plotNumber = 101,
seed = 41,
data = treatment_list)
SpatpREP2$infoDesign
plot_fieldhub(SpatpREP2,
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = TRUE,
reverse_x = TRUE)
## -----------------------------------------------------------------------------
spatd <- FielDHub::diagonal_arrangement(nrows = 15, ncols = 20, lines = 270,
checks = 4,
plotNumber = 101,
kindExpt = "SUDC",
planter = "serpentine",
seed = 1987,
exptName = "20WRY1",
locationNames = "MINOT")
plot_fieldhub(spatd,
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = TRUE,
reverse_x = TRUE)
## -----------------------------------------------------------------------------
OptimAd1 <- FielDHub::optimized_arrangement(nrows = 20, ncols = 20, lines = 362,
amountChecks = 38,
checks = 1:5,
planter = "cartesian",
plotNumber = 101,
seed = 14,
exptName = "20RW1",
locationNames = "CASSELTON")
OptimAd1$infoDesign
plot_fieldhub(OptimAd1,
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
rectangularLattice1 <- FielDHub::rectangular_lattice(t = 20, k = 4, r = 6, l = 1,
plotNumber = 101,
locationNames = "FARGO",
seed = 126)
rectangularLattice1$infoDesign
plot_fieldhub(rectangularLattice1,
x = "REP",
y = "ENTRY",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
squareLattice1 <- FielDHub::square_lattice(t = 64, k = 8, r = 5, l = 2,
plotNumber = c(1001, 2001),
locationNames = c("FARGO", "MINOT"),
seed = 1986)
squareLattice1$infoDesign
plot_fieldhub(squareLattice1,
x = "REP",
y = "ENTRY",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
squareLattice1 <- FielDHub::square_lattice(t = 64, k = 8, r = 5, l = 2,
plotNumber = c(1001, 2001),
locationNames = c("FARGO", "MINOT"),
seed = 1986)
squareLattice1$infoDesign
plot_fieldhub(squareLattice1,
x = "REP",
y = "ENTRY",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
ARCBD1 <- FielDHub::RCBD_augmented(lines = 50, checks = 3, b = 6, l = 1,
planter = "cartesian",
plotNumber = c(1,1001),
seed = 23,
locationNames = "FARGO")
ARCBD1$infoDesign
plot_fieldhub(ARCBD1,
x = "ROW",
y = "COLUMN",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
ibd1 <- FielDHub::incomplete_blocks(t = 12,
k = 4,
r = 2,
seed = 1984)
ibd1$infoDesign
plot_fieldhub(ibd1,
x = "ENTRY",
y = "REP",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
fullFact <- FielDHub::full_factorial(setfactors = c(2,2,2), reps = 3,
l = 1, type = 2,
plotNumber = 101,
continuous = TRUE,
planter = "serpentine",
seed = 325,
locationNames = "FARGO")
fullFact$infoDesign
fullFact$fieldBook$COLUMN <- rep(seq_len(length(unique(fullFact$fieldBook$TRT_COMB))),times=max(fullFact$fieldBook$REP))
full_control_positions(fullFact$fieldBook,x="REP",y="COLUMN",
factor_name = "TRT_COMB ",
labels="PLOT", shift_x= -1,shift_y = -1)
plot_fieldhub(fullFact,x="REP",y="COLUMN",
factor_name = "TRT_COMB",
labels="PLOT",shift_x=3,shift_y = 5.5)
## ----message=FALSE, warning=FALSE---------------------------------------------
trt<-c(3,2) # factorial 3x2
outdesign <- design.ab(trt, r=3, serie=2,design = 'crd')
plt <- plot_design.factorial_crd(outdesign,ncols=3,nrows=6, width = 5, height = 7.5 , reverse_x = FALSE,reverse_y = TRUE, factor_name = "B") + theme_pres() + scale_fill_viridis_d()
spat_df <- make_polygons(plt,east = 3454206.89,
north = 5939183.21 ,
projection_output = '+init=EPSG:4326')
plot(spat_df["fill"],col=spat_df$fill)
# this part does not work well in a vignette
library(leaflet)
spat_df <- sf:::as_Spatial(spat_df)
spat_df <- sp::elide(spat_df,rotate = -90)
leaflet(spat_df) %>% addPolygons(
fillColor = spat_df$fill,
opacity=1,
color="black",
fillOpacity = 1) %>% addProviderTiles(provider = "OpenStreetMap.DE")
## -----------------------------------------------------------------------------
H <- paste("H", 1:4, sep = "")
V <- paste("V", 1:5, sep = "")
strip1 <- FielDHub::strip_plot(Hplots = H,
Vplots = V,
b = 1,
l = 1,
plotNumber = 101,
planter = "serpentine",
locationNames = "A",
seed = 333)
strip1$infoDesign
strip1$fieldBook$ROW <- as.numeric(ordered(strip1$fieldBook$VSTRIP, levels = unique(strip1$fieldBook$VSTRIP)))
strip1$fieldBook$COLUMN <- as.numeric(ordered(strip1$fieldBook$HSTRIP, levels = unique(strip1$fieldBook$HSTRIP)))
plot_fieldhub(strip1,
x = "ROW",
y = "COLUMN",
labels = "HSTRIP",
factor_name = "HSTRIP",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
plot_fieldhub(strip1,
x = "ROW",
y = "COLUMN",
labels = "VSTRIP",
factor_name = "VSTRIP",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
latinSq1 <- FielDHub::latin_square(t = 4,
reps = 2,
plotNumber = 101,
planter = "cartesian",
seed = 1980)
latinSq1$infoDesign
latinSq1$fieldBook$ROW <- as.numeric(ordered(latinSq1$fieldBook$ROW, levels = unique(latinSq1$fieldBook$ROW)))
latinSq1$fieldBook$COLUMN <- as.numeric(ordered(latinSq1$fieldBook$COLUMN, levels = unique(latinSq1$fieldBook$COLUMN)))
# Unitl now: plotting only one replication at a time (here a SQUARE)
latinSq1$fieldBook <- latinSq1$fieldBook[latinSq1$fieldBook$SQUARE==1,]
plot_fieldhub(latinSq1,
x = "ROW",
y = "COLUMN",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
rowcold1 <- FielDHub::row_column(t = 36, nrows = 6, r = 3, l = 1,
plotNumber= 101,
locationNames = "Loc1",
seed = 21)
rowcold1$infoDesign
rowcold1$resolvableBlocks
# Unitl now: plotting only one replication
rowcold1$fieldBook <- rowcold1$fieldBook[rowcold1$fieldBook$REP==1,]
plot_fieldhub(rowcold1,
x = "ROW",
y = "COLUMN",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
rcbd1 <- FielDHub::RCBD(t = LETTERS[1:20], reps = 5, l = 3,
plotNumber = c(101,1001, 2001),
continuous = TRUE,
planter = "serpentine",
seed = 1020,
locationNames = c("FARGO", "MINOT", "CASSELTON"))
rcbd1$infoDesign
rcbd1$fieldBook$ROW <- rep(1:15,each=20)
rcbd1$fieldBook$COLUMN <- serpentine(n=20,times = 15)
plot_fieldhub(rcbd1,
x = "ROW",
y = "COLUMN",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = TRUE,
reverse_x = FALSE)
rcbd1 <- FielDHub::RCBD(t = LETTERS[1:20], reps = 5, l = 3,
plotNumber = c(101,1001, 2001),
continuous = TRUE,
planter = "cartesian",
seed = 1020,
locationNames = c("FARGO", "MINOT", "CASSELTON"))
rcbd1$infoDesign
rcbd1$fieldBook$ROW <- rep(1:20,times=15)
rcbd1$fieldBook$COLUMN <- rep(1:15,each=20)
plot_fieldhub(rcbd1,
x = "ROW",
y = "COLUMN",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = TRUE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
varieties<-c('perricholi','yungay','maria bonita','tomasa')
outdesign <-design.youden(varieties,r=2,serie=2,seed=23)
p <- plot_youden(outdesign, labels = 'varieties', width=4, height=3)
stats <- DOE_obj(p)
r <- to_table(stats,part = "net_plot", digits = 2)
r
r <- to_table(stats,part = "gross_plot", digits = 2)
r
r <- to_table(stats,part = "field", digits = 2)
r
r <- to_table(stats,part = "experiment", digits = 2)
r
r <- to_table(stats,part = "all", digits = 2)
r
## -----------------------------------------------------------------------------
varieties<-c('perricholi','yungay','maria bonita','tomasa')
outdesign <-design.youden(varieties,r=2,serie=2,seed=23)
design <- outdesign$book
design
p <- full_control_positions(design,"col","row","varieties","plots",
width=3,height=4.5,
space_width=1,space_height=1,
shift_x=-0.5*3,shift_y=-0.5*4.5)
p
p <- full_control_positions(design,"col","row","varieties","plots",
width=3,height=4.5,
space_width=0.93,space_height=0.945,
start_origin = TRUE)
p
## -----------------------------------------------------------------------------
crd1 <- FielDHub::CRD(t = 10,
reps = 5,
plotNumber = 101,
seed = 1987,
locationName = "Fargo")
crd1$infoDesign
crd1$fieldBook$ROW <- rep(1:10,each=5)
crd1$fieldBook$COLUMN <- serpentine(n=5,times = 10)
plot_fieldhub(crd1,
x = "ROW",
y = "COLUMN",
labels = "PLOT",
factor_name = "TREATMENT",
width = 12,
height = 10,
reverse_y = TRUE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
citation("agricolaeplotr")
jensharbers/agricolaeplotr documentation built on Feb. 3, 2025, 5:40 p.m.
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## ----setup, eval = FALSE------------------------------------------------------
# install.packages("agricolaeplotr")
## ----message=FALSE, warning=FALSE---------------------------------------------
library("ggplot2")
library("agricolae")
library("agricolaeplotr")
library("FielDHub")
library("raster")
## -----------------------------------------------------------------------------
library(agricolae) # origin of the needed design object
trt<-c(3,2) # factorial 3x2
outdesign <- design.ab(trt, r=3, serie=2,design = 'crd')
head(outdesign$book,10)
plot_design.factorial_crd(outdesign,ncols=7,nrows=3, width = 1, height = 1)
## ---- echo=TRUE, results='asis'-----------------------------------------------
plot_design.factorial_crd(outdesign,ncols=6,nrows=3, width = 1, height = 1, reverse_y = TRUE)
## ---- echo=TRUE, results='asis'-----------------------------------------------
plot_design.factorial_crd(outdesign,ncols=6,nrows=3, width = 1, height = 1, reverse_x = TRUE)
## ---- results='asis'----------------------------------------------------------
plot_design.factorial_crd(outdesign,ncols=6,nrows=3, width = 1, height = 1, reverse_x = TRUE,reverse_y = TRUE)
## ---- echo = TRUE, results='asis'---------------------------------------------
plot_design.factorial_crd(outdesign,ncols=6,nrows=3, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE)
## ---- echo = TRUE, results='asis'---------------------------------------------
plot_design.factorial_crd(outdesign,ncols=6,nrows=3, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE,space_width = 1,space_height = 1)
## ---- echo = TRUE, results='asis'---------------------------------------------
plot_design.factorial_crd(outdesign,ncols=6,nrows=3, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE,space_width = 0.7,space_height = 0.8)
## ---- echo = TRUE, results='asis'---------------------------------------------
plot_design.factorial_crd(outdesign,ncols=6,nrows=3, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE, factor_name = "B")
## ---- echo = TRUE, results='asis'---------------------------------------------
set.seed(129984)
trt<-c(3,2) # factorial 3x2
outdesign <- design.ab(trt, r=3, serie=2,design = 'crd')
plot_design.factorial_crd(outdesign,ncols=3,nrows=6, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE, factor_name = "B")
## ---- echo = TRUE, results='asis'---------------------------------------------
set.seed(129866478)
trt<-c(3,2) # factorial 3x2
outdesign <- design.ab(trt, r=3, serie=2,design = 'crd')
plot_design.factorial_crd(outdesign,ncols=3,nrows=6, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE, factor_name = "B") + theme_poster()
## ---- echo = TRUE, results='asis'---------------------------------------------
set.seed(12986)
trt<-c(3,2) # factorial 3x2
outdesign <- design.ab(trt, r=3, serie=2,design = 'crd')
plot_design.factorial_crd(outdesign,ncols=3,nrows=6, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE, factor_name = "B") + theme_pres()
## ---- echo = TRUE, results='asis'---------------------------------------------
trt<-c(3,2) # factorial 3x2
outdesign <- design.ab(trt, r=3, serie=2,design = 'crd')
plot_design.factorial_crd(outdesign,ncols=3,nrows=6, width = 1, height = 2.5 , reverse_x = FALSE,reverse_y = TRUE, factor_name = "B") + theme_pres() + scale_fill_viridis_d()
## -----------------------------------------------------------------------------
set.seed(23488833)
trt <-c(3,2)
outdesign<-design.ab(trt, serie=2, design="lsd",seed = 454555)
length_table <- dim(outdesign$book)[1] # length of the table
outdesign$book$yield <- sample(c(5:12,c(NA,NA,NA)), size = length_table, replace = TRUE)
plot_design.factorial_lsd(outdesign,factor_name = "yield") + scale_fill_viridis_c()
## -----------------------------------------------------------------------------
set.seed(23488833)
trt <-c(3,2)
outdesign<-design.ab(trt, serie=2, design="lsd",seed = 454555)
length_table <- dim(outdesign$book)[1] # length of the table
yield <- sample(c(5:20,c(NA,NA,NA)), size = length_table, replace = TRUE)
df <- cbind(plots=outdesign$book$plots,yield)
head(df,10)
outdesign$book <- merge(outdesign$book,df, by.x = "plots", by.y = "plots")
plot_design.factorial_lsd(outdesign,factor_name = "yield") + scale_fill_viridis_c()
## -----------------------------------------------------------------------------
set.seed(1298664)
plots <- as.factor(1:(8*6))
block <- as.factor((rep(1:6,each=8)))
A <- as.vector(replicate(8,sample(rep(1:2,times=3),6,replace=FALSE)))
outcome <- runif(48,20,100)
experiment <- cbind(plots,block,A,outcome)
experiment <- as.data.frame(experiment)
head(experiment)
experiment_design <- list()
experiment_design$parameters$design<- "factorial"
experiment_design$parameters$applied <- "rcbd"
experiment_design$book <- experiment
head(experiment_design)
plot_design.factorial_rcbd(experiment_design,factor_name = "A")
plot_design.factorial_rcbd(experiment_design,factor_name = "outcome")
## -----------------------------------------------------------------------------
set.seed(1298664)
t1<-c('a','b','c','d','e',"f","g","h")
t2<-c("u",'v','w','x','y',"z")
outdesign2 <- design.split(trt1=t1, trt2=t2, r=r,serie = 2,
seed = 0, kinds = 'Super-Duper',
randomization=TRUE,first=TRUE,design = 'lsd')
plot_split_lsd(outdesign2,factor_name_1 = "t1",factor_name_2 = "t2",width = 2,height = 2, subplots = FALSE,labels = "plots")
plot_split_lsd(outdesign2,width = 2,height = 2, subplots = TRUE, labels = "splots", factor_name_1 = "t1", factor_name_2 = "t2")
## -----------------------------------------------------------------------------
set.seed(1298664)
t1<-c('a','b','c','d','e','f','g')
t2<-c('v','w','x','y','z')
r <- 4
outdesign2 <- design.split(trt1=t1, trt2=t2, r=r,
serie = 2, seed = 0, kinds = 'Super-Duper',
randomization=TRUE,first=TRUE,design = 'crd')
plot_split_crd(outdesign2,ncols = 5,nrows=6, subplots = FALSE,
factor_name_1 = "t1",factor_name_2 = "t2")
plot_split_crd(outdesign2,ncols = 5,nrows=6, subplots = TRUE, labels="splots",factor_name_1 = "t1",factor_name_2 = "t2")
## -----------------------------------------------------------------------------
set.seed(1298664)
T1<-c('a','b','c','d','e',"f","g")
T2<-c("we",'v','w','x','y','z',"d")
r = 3
outdesign2 <- design.split(trt1=T1, trt2=T2, r=r,serie = 2,
seed = 0, kinds = 'Super-Duper',randomization=TRUE,
first=TRUE,design = 'rcbd')
plot_split_rcbd(outdesign2,width = 5,height = 5,subplots = FALSE,
factor_name_1 = "T1",factor_name_2 = "T2")
plot_split_rcbd(outdesign2,width = 5,height = 5,labels = "splots",
factor_name_1 = "T1",factor_name_2 = "T2")
## -----------------------------------------------------------------------------
SpatpREP1 <- FielDHub::partially_replicated(nrows = 25,
ncols = 8,
repGens = c(30,50,10,1,1),
repUnits = c(1,2,3,20,20),
planter = "cartesian",
plotNumber = 101,
seed = 77)
plot_fieldhub(SpatpREP1,
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = TRUE,
reverse_x = TRUE)
## -----------------------------------------------------------------------------
NAME <- paste("G", 1:492, sep = "")
repGens = c(108, 384);repUnits = c(2,1)
REPS <- rep(repUnits, repGens)
treatment_list <- data.frame(list(ENTRY = 1:492,
NAME = NAME,
REPS = REPS))
SpatpREP2 <- FielDHub::partially_replicated(nrows = 30,
ncols = 20,
planter = "serpentine",
plotNumber = 101,
seed = 41,
data = treatment_list)
SpatpREP2$infoDesign
plot_fieldhub(SpatpREP2,
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = TRUE,
reverse_x = TRUE)
## -----------------------------------------------------------------------------
spatd <- FielDHub::diagonal_arrangement(nrows = 15, ncols = 20, lines = 270,
checks = 4,
plotNumber = 101,
kindExpt = "SUDC",
planter = "serpentine",
seed = 1987,
exptName = "20WRY1",
locationNames = "MINOT")
plot_fieldhub(spatd,
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = TRUE,
reverse_x = TRUE)
## -----------------------------------------------------------------------------
OptimAd1 <- FielDHub::optimized_arrangement(nrows = 20, ncols = 20, lines = 362,
amountChecks = 38,
checks = 1:5,
planter = "cartesian",
plotNumber = 101,
seed = 14,
exptName = "20RW1",
locationNames = "CASSELTON")
OptimAd1$infoDesign
plot_fieldhub(OptimAd1,
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
rectangularLattice1 <- FielDHub::rectangular_lattice(t = 20, k = 4, r = 6, l = 1,
plotNumber = 101,
locationNames = "FARGO",
seed = 126)
rectangularLattice1$infoDesign
plot_fieldhub(rectangularLattice1,
x = "REP",
y = "ENTRY",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
squareLattice1 <- FielDHub::square_lattice(t = 64, k = 8, r = 5, l = 2,
plotNumber = c(1001, 2001),
locationNames = c("FARGO", "MINOT"),
seed = 1986)
squareLattice1$infoDesign
plot_fieldhub(squareLattice1,
x = "REP",
y = "ENTRY",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
squareLattice1 <- FielDHub::square_lattice(t = 64, k = 8, r = 5, l = 2,
plotNumber = c(1001, 2001),
locationNames = c("FARGO", "MINOT"),
seed = 1986)
squareLattice1$infoDesign
plot_fieldhub(squareLattice1,
x = "REP",
y = "ENTRY",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
ARCBD1 <- FielDHub::RCBD_augmented(lines = 50, checks = 3, b = 6, l = 1,
planter = "cartesian",
plotNumber = c(1,1001),
seed = 23,
locationNames = "FARGO")
ARCBD1$infoDesign
plot_fieldhub(ARCBD1,
x = "ROW",
y = "COLUMN",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
ibd1 <- FielDHub::incomplete_blocks(t = 12,
k = 4,
r = 2,
seed = 1984)
ibd1$infoDesign
plot_fieldhub(ibd1,
x = "ENTRY",
y = "REP",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
fullFact <- FielDHub::full_factorial(setfactors = c(2,2,2), reps = 3,
l = 1, type = 2,
plotNumber = 101,
continuous = TRUE,
planter = "serpentine",
seed = 325,
locationNames = "FARGO")
fullFact$infoDesign
fullFact$fieldBook$COLUMN <- rep(seq_len(length(unique(fullFact$fieldBook$TRT_COMB))),times=max(fullFact$fieldBook$REP))
full_control_positions(fullFact$fieldBook,x="REP",y="COLUMN",
factor_name = "TRT_COMB ",
labels="PLOT", shift_x= -1,shift_y = -1)
plot_fieldhub(fullFact,x="REP",y="COLUMN",
factor_name = "TRT_COMB",
labels="PLOT",shift_x=3,shift_y = 5.5)
## ----message=FALSE, warning=FALSE---------------------------------------------
trt<-c(3,2) # factorial 3x2
outdesign <- design.ab(trt, r=3, serie=2,design = 'crd')
plt <- plot_design.factorial_crd(outdesign,ncols=3,nrows=6, width = 5, height = 7.5 , reverse_x = FALSE,reverse_y = TRUE, factor_name = "B") + theme_pres() + scale_fill_viridis_d()
spat_df <- make_polygons(plt,east = 3454206.89,
north = 5939183.21 ,
projection_output = '+init=EPSG:4326')
plot(spat_df["fill"],col=spat_df$fill)
# this part does not work well in a vignette
library(leaflet)
spat_df <- sf:::as_Spatial(spat_df)
spat_df <- sp::elide(spat_df,rotate = -90)
leaflet(spat_df) %>% addPolygons(
fillColor = spat_df$fill,
opacity=1,
color="black",
fillOpacity = 1) %>% addProviderTiles(provider = "OpenStreetMap.DE")
## -----------------------------------------------------------------------------
H <- paste("H", 1:4, sep = "")
V <- paste("V", 1:5, sep = "")
strip1 <- FielDHub::strip_plot(Hplots = H,
Vplots = V,
b = 1,
l = 1,
plotNumber = 101,
planter = "serpentine",
locationNames = "A",
seed = 333)
strip1$infoDesign
strip1$fieldBook$ROW <- as.numeric(ordered(strip1$fieldBook$VSTRIP, levels = unique(strip1$fieldBook$VSTRIP)))
strip1$fieldBook$COLUMN <- as.numeric(ordered(strip1$fieldBook$HSTRIP, levels = unique(strip1$fieldBook$HSTRIP)))
plot_fieldhub(strip1,
x = "ROW",
y = "COLUMN",
labels = "HSTRIP",
factor_name = "HSTRIP",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
plot_fieldhub(strip1,
x = "ROW",
y = "COLUMN",
labels = "VSTRIP",
factor_name = "VSTRIP",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
latinSq1 <- FielDHub::latin_square(t = 4,
reps = 2,
plotNumber = 101,
planter = "cartesian",
seed = 1980)
latinSq1$infoDesign
latinSq1$fieldBook$ROW <- as.numeric(ordered(latinSq1$fieldBook$ROW, levels = unique(latinSq1$fieldBook$ROW)))
latinSq1$fieldBook$COLUMN <- as.numeric(ordered(latinSq1$fieldBook$COLUMN, levels = unique(latinSq1$fieldBook$COLUMN)))
# Unitl now: plotting only one replication at a time (here a SQUARE)
latinSq1$fieldBook <- latinSq1$fieldBook[latinSq1$fieldBook$SQUARE==1,]
plot_fieldhub(latinSq1,
x = "ROW",
y = "COLUMN",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
rowcold1 <- FielDHub::row_column(t = 36, nrows = 6, r = 3, l = 1,
plotNumber= 101,
locationNames = "Loc1",
seed = 21)
rowcold1$infoDesign
rowcold1$resolvableBlocks
# Unitl now: plotting only one replication
rowcold1$fieldBook <- rowcold1$fieldBook[rowcold1$fieldBook$REP==1,]
plot_fieldhub(rowcold1,
x = "ROW",
y = "COLUMN",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = FALSE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
rcbd1 <- FielDHub::RCBD(t = LETTERS[1:20], reps = 5, l = 3,
plotNumber = c(101,1001, 2001),
continuous = TRUE,
planter = "serpentine",
seed = 1020,
locationNames = c("FARGO", "MINOT", "CASSELTON"))
rcbd1$infoDesign
rcbd1$fieldBook$ROW <- rep(1:15,each=20)
rcbd1$fieldBook$COLUMN <- serpentine(n=20,times = 15)
plot_fieldhub(rcbd1,
x = "ROW",
y = "COLUMN",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = TRUE,
reverse_x = FALSE)
rcbd1 <- FielDHub::RCBD(t = LETTERS[1:20], reps = 5, l = 3,
plotNumber = c(101,1001, 2001),
continuous = TRUE,
planter = "cartesian",
seed = 1020,
locationNames = c("FARGO", "MINOT", "CASSELTON"))
rcbd1$infoDesign
rcbd1$fieldBook$ROW <- rep(1:20,times=15)
rcbd1$fieldBook$COLUMN <- rep(1:15,each=20)
plot_fieldhub(rcbd1,
x = "ROW",
y = "COLUMN",
labels = "PLOT",
factor_name = "PLOT",
width = 12,
height = 10,
reverse_y = TRUE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
varieties<-c('perricholi','yungay','maria bonita','tomasa')
outdesign <-design.youden(varieties,r=2,serie=2,seed=23)
p <- plot_youden(outdesign, labels = 'varieties', width=4, height=3)
stats <- DOE_obj(p)
r <- to_table(stats,part = "net_plot", digits = 2)
r
r <- to_table(stats,part = "gross_plot", digits = 2)
r
r <- to_table(stats,part = "field", digits = 2)
r
r <- to_table(stats,part = "experiment", digits = 2)
r
r <- to_table(stats,part = "all", digits = 2)
r
## -----------------------------------------------------------------------------
varieties<-c('perricholi','yungay','maria bonita','tomasa')
outdesign <-design.youden(varieties,r=2,serie=2,seed=23)
design <- outdesign$book
design
p <- full_control_positions(design,"col","row","varieties","plots",
width=3,height=4.5,
space_width=1,space_height=1,
shift_x=-0.5*3,shift_y=-0.5*4.5)
p
p <- full_control_positions(design,"col","row","varieties","plots",
width=3,height=4.5,
space_width=0.93,space_height=0.945,
start_origin = TRUE)
p
## -----------------------------------------------------------------------------
crd1 <- FielDHub::CRD(t = 10,
reps = 5,
plotNumber = 101,
seed = 1987,
locationName = "Fargo")
crd1$infoDesign
crd1$fieldBook$ROW <- rep(1:10,each=5)
crd1$fieldBook$COLUMN <- serpentine(n=5,times = 10)
plot_fieldhub(crd1,
x = "ROW",
y = "COLUMN",
labels = "PLOT",
factor_name = "TREATMENT",
width = 12,
height = 10,
reverse_y = TRUE,
reverse_x = FALSE)
## -----------------------------------------------------------------------------
citation("agricolaeplotr")
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