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Commit 39a610ba authored by Walmes Marques Zeviani's avatar Walmes Marques Zeviani
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Remove gap(), arruma ovos emergidos.

parent 84d5c522
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Showing with 31 additions and 36 deletions
vignettes/egg-parasitoid.Rmd
View file @ 39a610ba
......@@ -27,14 +27,6 @@ library(plyr)
library(doBy)
library(multcomp)
gap <- function(groups, gap = NULL) {
if (is.null(gap)) {
gap <- 0.5/nlevels(groups)
}
d <- 2 * ((as.numeric(groups) - 1)/(nlevels(groups) - 1)) - 1
return(gap * d)
}
# Versão da função apmc() para modelos que usam a matriz do modelo ao
# invés da formula.
apmc2 <- function(X,
......@@ -233,11 +225,14 @@ cap <-
"Estimated probability of surviving at 24h for each inseticide on two parasiods and two hosts. Segment is a confidence interval for the probability of surviving. Parasitoids estimates followed by the same lower letters in a insetice and host combination are not different at 5%. Inseticides estimates followed by the same lower letters in a parasitoid and host combination are not different at 5%."
cap <- fgn_("surv", cap)
pred$vjust <- -0.5
pred$vjust[pred$cld == "ABa"] <- 1.5
# Gráfico de segmentos.
segplot(I ~ lwr + upr | P,
centers = fit,
data = pred,
xlab = "Insticides",
xlab = "Insecticides",
ylab = "Probability of surviving a 24h period",
draw = FALSE,
horizontal = FALSE,
......@@ -253,20 +248,21 @@ segplot(I ~ lwr + upr | P,
layer({
a <- cld[which.max(nchar(cld))]
l <- cld[subscripts]
x <- as.integer(z)[subscripts] + gap(groups[subscripts], gap)
v <- pred$vjust[subscripts]
x <- as.integer(z)[subscripts] + centfac(groups[subscripts], gap)
y <- centers[subscripts]
# Usa símbolo unicode:
# http://www.alanwood.net/unicode/geometric_shapes.html
grid.text("\u25AE",
x = unit(x, "native"),
y = unit(y, "native"),
vjust = -0.5,
vjust = v,
gp = gpar(col = "white")
)
grid.text(l,
x = unit(x, "native"),
y = unit(y, "native"),
vjust = -0.5,
vjust = v,
gp = gpar(col = "black", fontsize = 10))
})
```
......@@ -307,7 +303,7 @@ comp <- vector(mode = "list", length = 2)
# Hospedeiros dentro de inseticida x parasitóide.
L <- by(lsm, INDICES = with(grid, interaction(I, P)), FUN = as.matrix)
L <- lapply(L, "rownames<-", levels(egg$H))
cmp <- lapply(L, apmc, model = m0, focus = "H")
cmp <- lapply(L, apmc2, model = m0, focus = "H")
pred <- ldply(cmp)
cmp <- ldply(strsplit(pred$.id, "\\."))
......@@ -320,7 +316,7 @@ comp[[1]] <- pred
# Inseticidas dentro de parasitóide e hospedeiro.
L <- by(lsm, INDICES = with(grid, interaction(H, P)), FUN = as.matrix)
L <- lapply(L, "rownames<-", levels(egg$I))
cmp <- lapply(L, apmc, model = m0, focus = "I", test = "fdr")
cmp <- lapply(L, apmc2, model = m0, focus = "I", test = "fdr")
pred <- ldply(cmp)
cmp <- ldply(strsplit(pred$.id, "\\."))
......@@ -378,11 +374,14 @@ cap <-
"Estimated proportion of of parasitated eggs for each inseticide on two parasiods and two hosts. Segment is a confidence interval for the probability of surviving. Parasitoids estimates followed by the same lower letters in a insetice and host combination are not different at 5%. Inseticides estimates followed by the same lower letters in a parasitoid and host combination are not different at 5%."
cap <- fgn_("opar", cap)
pred$vjust <- -0.5
pred$vjust[pred$cld == "ABCDa"] <- 1.5
# Gráfico de segmentos.
segplot(I ~ lwr + upr | P,
centers = fit,
data = pred,
xlab = "Insticides",
xlab = "Insecticides",
ylab = "Proportion of parasited eggs",
draw = FALSE,
horizontal = FALSE,
......@@ -395,28 +394,24 @@ segplot(I ~ lwr + upr | P,
cld = pred$cld,
panel = panel.groups.segplot,
pch = key$points$pch[as.integer(pred$H)]) +
# layer(panel.text(y = centers[subscripts],
# x = as.integer(z)[subscripts] +
# gap(groups[subscripts], gap),
# labels = round(centers[subscripts], 3),
# pos = 1)) +
layer({
a <- cld[which.max(nchar(cld))]
l <- cld[subscripts]
x <- as.integer(z)[subscripts] + gap(groups[subscripts], gap)
v <- pred$vjust[subscripts]
x <- as.integer(z)[subscripts] + centfac(groups[subscripts], gap)
y <- centers[subscripts]
# Usa símbolo unicode:
# http://www.alanwood.net/unicode/geometric_shapes.html
grid.text("\u25AE",
x = unit(x, "native"),
y = unit(y, "native"),
vjust = -0.5,
vjust = v,
gp = gpar(col = "white")
)
grid.text(l,
x = unit(x, "native"),
y = unit(y, "native"),
vjust = -0.5,
vjust = v,
gp = gpar(col = "black", fontsize = 10))
})
```
......@@ -431,7 +426,7 @@ segplot(I ~ lwr + upr | P,
ftable(xtabs(!is.na(oeme) ~ I + P + H, data = egg))
# ATTENTION: Com os 7 inseticidas dá cela perdida.
useOuterStrips(xyplot(oeme/otot ~ I | H + P,
useOuterStrips(xyplot(oeme/opar ~ I | H + P,
data = egg[!is.na(egg$oeme), ],
jitter.x = TRUE,
type = c("p", "a")))
......@@ -439,7 +434,7 @@ useOuterStrips(xyplot(oeme/otot ~ I | H + P,
#-----------------------------------------------------------------------
# Ajuste do modelo.
m0 <- glm(cbind(oeme, otot - oeme) ~ I * P * H,
m0 <- glm(cbind(oeme, opar - oeme) ~ I * P * H,
data = egg,
family = quasibinomial)
......@@ -542,7 +537,7 @@ key <- list(points = list(pch = c(1, 19)),
#-----------------------------------------------------------------------
ab <- aggregate(cbind(emerg = oeme/otot) ~ I + H + P,
ab <- aggregate(cbind(emerg = oeme/opar) ~ I + H + P,
data = egg,
FUN = mean)
......@@ -557,7 +552,7 @@ cap <- fgn_("oeme", cap)
segplot(I ~ lwr + upr | P,
centers = fit,
data = pred,
xlab = "Insticides",
xlab = "Insecticides",
ylab = "Probability of egg emergency",
draw = FALSE,
horizontal = FALSE,
......@@ -572,13 +567,13 @@ segplot(I ~ lwr + upr | P,
pch = key$points$pch[as.integer(pred$H)]) +
# layer(panel.text(y = centers[subscripts],
# x = as.integer(z)[subscripts] +
# gap(groups[subscripts], gap),
# centfac(groups[subscripts], gap),
# labels = round(centers[subscripts], 3),
# pos = 1)) +
layer({
a <- cld[which.max(nchar(cld))]
l <- cld[subscripts]
x <- as.integer(z)[subscripts] + gap(groups[subscripts], gap)
x <- as.integer(z)[subscripts] + centfac(groups[subscripts], gap)
y <- centers[subscripts]
# Usa símbolo unicode:
# http://www.alanwood.net/unicode/geometric_shapes.html
......@@ -697,13 +692,13 @@ segplot(P ~ lwr + upr,
panel = panel.groups.segplot,
pch = key$points$pch[as.integer(pred$H)]) +
# layer(panel.text(y = centers[subscripts],
# x = as.integer(z)[subscripts] + gap(groups, gap),
# x = as.integer(z)[subscripts] + centfac(groups, gap),
# labels = pred$cld[subscripts],
# adj = -0.25 * c(1, 1)))
layer({
a <- cld[which.max(nchar(cld))]
l <- cld[subscripts]
x <- as.integer(z)[subscripts] + gap(groups[subscripts], gap)
x <- as.integer(z)[subscripts] + centfac(groups[subscripts], gap)
y <- centers[subscripts]
# Usa símbolo unicode:
# http://www.alanwood.net/unicode/geometric_shapes.html
......@@ -847,7 +842,7 @@ cap <- fgn_("pemer", cap)
segplot(I ~ lwr + upr | P,
centers = fit,
data = pred,
xlab = "Insticides",
xlab = "Insecticides",
ylab = "Proportion of parasitoid emergency",
draw = FALSE,
horizontal = FALSE,
......@@ -862,13 +857,13 @@ segplot(I ~ lwr + upr | P,
pch = key$points$pch[as.integer(pred$H)]) +
# layer(panel.text(y = centers[subscripts],
# x = as.integer(z)[subscripts] +
# gap(groups[subscripts], gap),
# centfac(groups[subscripts], gap),
# labels = cld[subscripts],
# adj = -0.25 * c(1, 1)))
layer({
a <- cld[which.max(nchar(cld))]
l <- cld[subscripts]
x <- as.integer(z)[subscripts] + gap(groups[subscripts], gap)
x <- as.integer(z)[subscripts] + centfac(groups[subscripts], gap)
y <- centers[subscripts]
# Usa símbolo unicode:
# http://www.alanwood.net/unicode/geometric_shapes.html
......@@ -1006,7 +1001,7 @@ cap <- fgn_("tot", cap)
segplot(I ~ lwr + upr | P,
centers = fit,
data = pred,
xlab = "Insticides",
xlab = "Insecticides",
ylab = "Total of parasitoids",
draw = FALSE,
horizontal = FALSE,
......@@ -1022,7 +1017,7 @@ segplot(I ~ lwr + upr | P,
layer({
a <- cld[which.max(nchar(cld))]
l <- cld[subscripts]
x <- as.integer(z)[subscripts] + gap(groups[subscripts], gap)
x <- as.integer(z)[subscripts] + centfac(groups[subscripts], gap)
y <- centers[subscripts]
# Usa símbolo unicode:
# http://www.alanwood.net/unicode/geometric_shapes.html
......
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