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leg
MRDCr
Commits
09eb537d
Commit
09eb537d
authored
Apr 27, 2016
by
Walmes Marques Zeviani
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Adiciona arquivos da vinheta no inst/doc. Ignora no Rmd la.
parent
9591be4c
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#3515
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.gitignore
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inst/doc/01_poisson.R
inst/doc/01_poisson.R
+182
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inst/doc/01_poisson.html
inst/doc/01_poisson.html
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09eb537d
...
...
@@ -4,3 +4,4 @@ vignettes/*.html
!vignettes/_before_body.html
!vignettes/_after_body.html
!vignettes/_MathJax.html
inst/doc/*.Rmd
inst/doc/01_poisson.R
0 → 100644
View file @
09eb537d
## ----setup, include=FALSE-----------------------------------------
source
(
"_setup.R"
)
## ---- include=FALSE-----------------------------------------------
library
(
devtools
)
if
(
!
suppressWarnings
(
require
(
MRDCr
)))
{
switch
(
Sys.info
()[
"user"
],
"walmes"
=
{
load_all
(
"~/repos/MRDCr"
)
},
"eduardo"
=
NULL
,
"cesar"
=
NULL
)
}
ls
(
"package:MRDCr"
)
## ---- eval=FALSE--------------------------------------------------
# library(MRDCr)
# help(soja)
## -----------------------------------------------------------------
ls
(
"package:MRDCr"
)
library
(
lattice
)
data
(
soja
)
str
(
soja
)
xtabs
(
~
umid
+
K
,
data
=
soja
[
-75
,
])
xyplot
(
nvag
+
ngra
~
K
,
groups
=
umid
,
outer
=
TRUE
,
data
=
soja
[
-74
,
],
type
=
c
(
"p"
,
"a"
),
scales
=
"free"
,
ylab
=
NULL
,
xlab
=
expression
(
"Nível de potássio aplicado"
~
(
mg
~
dm
^
{
-3
})),
auto.key
=
list
(
title
=
"Umidade do solo (%)"
,
cex.title
=
1
,
columns
=
3
),
strip
=
strip.custom
(
factor.levels
=
c
(
"Número de vagens"
,
"Número de grãos"
)))
soja
<-
soja
[
-74
,
]
## ---- message=FALSE-----------------------------------------------
# Considerar K categórico.
soja
<-
transform
(
soja
,
K
=
factor
(
K
))
m0
<-
glm
(
nvag
~
bloc
+
umid
*
K
,
data
=
soja
,
family
=
poisson
)
par
(
mfrow
=
c
(
2
,
2
))
plot
(
m0
);
layout
(
1
)
#-----------------------------------------------------------------------
deviance
(
m0
)
df.residual
(
m0
)
summary
(
m0
)
anova
(
m0
,
test
=
"Chisq"
)
#-----------------------------------------------------------------------
# Predição com intervalos de confiança.
library
(
doBy
)
library
(
multcomp
)
X
<-
LSmatrix
(
m0
,
effect
=
c
(
"umid"
,
"K"
))
pred
<-
attr
(
X
,
"grid"
)
pred
<-
transform
(
pred
,
K
=
as.integer
(
as.character
(
K
)),
umid
=
factor
(
umid
))
# Quantil normal para fazer um IC de 95%.
qn
<-
qnorm
(
0.975
)
*
c
(
lwr
=
-1
,
fit
=
0
,
upr
=
1
)
# Preditos pela Poisson.
# aux <- predict(m0, newdata = pred$pois, se.fit = TRUE)
# aux <- exp(aux$fit + outer(aux$se.fit, qn, FUN = "*"))
# pred$pois <- cbind(pred$pois, aux)
aux
<-
confint
(
glht
(
m0
,
linfct
=
X
),
calpha
=
univariate_calpha
())
$
confint
colnames
(
aux
)[
1
]
<-
"fit"
pred
<-
cbind
(
pred
,
exp
(
aux
))
str
(
pred
)
urls
<-
paste0
(
"https://raw.githubusercontent.com/walmes/wzRfun/master/R/"
,
c
(
"prepanel.cbH.R"
,
"panel.cbH.R"
))
sapply
(
urls
,
source
)
xyplot
(
fit
~
K
|
umid
,
data
=
pred
,
layout
=
c
(
NA
,
1
),
as.table
=
TRUE
,
ylab
=
"Número de vagens por vaso"
,
xlab
=
expression
(
"Nível de potássio aplicado"
~
(
mg
~
dm
^
{
-3
})),
xlim
=
extendrange
(
range
(
pred
$
K
),
f
=
0.1
),
ly
=
pred
$
lwr
,
uy
=
pred
$
upr
,
cty
=
"bars"
,
length
=
0
,
prepanel
=
prepanel.cbH
,
panel
=
panel.cbH
)
#-----------------------------------------------------------------------
# Comparações múltiplas.
urls
<-
paste0
(
"https://raw.githubusercontent.com/walmes/wzRfun/master/R/"
,
c
(
"apc.R"
))
sapply
(
urls
,
source
)
L
<-
by
(
X
,
INDICES
=
pred
$
umid
,
FUN
=
as.matrix
)
names
(
L
)
<-
levels
(
soja
$
umid
)
L
<-
lapply
(
L
,
"rownames<-"
,
levels
(
soja
$
K
))
K
<-
lapply
(
L
,
apc
)
apc
(
L
[[
1
]])
lapply
(
K
,
FUN
=
function
(
k
)
{
summary
(
glht
(
model
=
m0
,
linfct
=
k
),
test
=
adjusted
(
type
=
"fdr"
))
})
## ---- message=FALSE-----------------------------------------------
m1
<-
glm
(
ngra
~
bloc
+
umid
*
K
,
data
=
soja
,
family
=
poisson
)
par
(
mfrow
=
c
(
2
,
2
))
plot
(
m1
);
layout
(
1
)
#-----------------------------------------------------------------------
deviance
(
m1
)
df.residual
(
m1
)
summary
(
m1
)
anova
(
m1
,
test
=
"Chisq"
)
#-----------------------------------------------------------------------
# Predição com intervalos de confiança.
X
<-
LSmatrix
(
m1
,
effect
=
c
(
"umid"
,
"K"
))
pred
<-
attr
(
X
,
"grid"
)
pred
<-
transform
(
pred
,
K
=
as.integer
(
as.character
(
K
)),
umid
=
factor
(
umid
))
# Quantil normal para fazer um IC de 95%.
qn
<-
qnorm
(
0.975
)
*
c
(
lwr
=
-1
,
fit
=
0
,
upr
=
1
)
aux
<-
confint
(
glht
(
m1
,
linfct
=
X
),
calpha
=
univariate_calpha
())
$
confint
colnames
(
aux
)[
1
]
<-
"fit"
pred
<-
cbind
(
pred
,
exp
(
aux
))
str
(
pred
)
xyplot
(
fit
~
K
|
umid
,
data
=
pred
,
layout
=
c
(
NA
,
1
),
as.table
=
TRUE
,
ylab
=
"Número de grãos por vaso"
,
xlab
=
expression
(
"Nível de potássio aplicado"
~
(
mg
~
dm
^
{
-3
})),
xlim
=
extendrange
(
range
(
pred
$
K
),
f
=
0.1
),
ly
=
pred
$
lwr
,
uy
=
pred
$
upr
,
cty
=
"bars"
,
length
=
0
,
prepanel
=
prepanel.cbH
,
panel
=
panel.cbH
)
#-----------------------------------------------------------------------
# Comparações múltiplas.
L
<-
by
(
X
,
INDICES
=
pred
$
umid
,
FUN
=
as.matrix
)
names
(
L
)
<-
levels
(
soja
$
umid
)
L
<-
lapply
(
L
,
"rownames<-"
,
levels
(
soja
$
K
))
K
<-
lapply
(
L
,
apc
)
apc
(
L
[[
1
]])
lapply
(
K
,
FUN
=
function
(
k
)
{
summary
(
glht
(
model
=
m1
,
linfct
=
k
),
test
=
adjusted
(
type
=
"fdr"
))
})
## -----------------------------------------------------------------
sessionInfo
()
inst/doc/01_poisson.html
0 → 100644
View file @
09eb537d
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