Nothing
inst/doc/ALFAM2-start.R
In ALFAM2: Dynamic Model of Ammonia Emission from Field-Applied Manure
## ----include=FALSE, cache=FALSE--------------------------------
library(knitr)
#opts_chunk$set(cache=FALSE,tidy=FALSE,highlight=FALSE)
knitr::opts_chunk$set(fig.width=12, fig.height=8, out.width='100%', out.height='100%')
opts_chunk$set(cache = FALSE, tidy = FALSE, fig.align = "center")
library(ALFAM2)
options(width=65)
## ----eval=FALSE------------------------------------------------
# install.packages('ALFAM2')
## --------------------------------------------------------------
library(ALFAM2)
## ----eval=FALSE------------------------------------------------
# vignette("ALFAM2-start")
## --------------------------------------------------------------
packageVersion("ALFAM2")
## --------------------------------------------------------------
args(alfam2)
## ----eval=FALSE------------------------------------------------
# ?alfam2
## --------------------------------------------------------------
packageVersion("ALFAM2")
## --------------------------------------------------------------
args(alfam2)
## --------------------------------------------------------------
alfam2pars03
## --------------------------------------------------------------
dat1 <- data.frame(ctime = 168, TAN.app = 50, man.dm = 8,
air.temp = 20, wind.sqrt = 2,
app.mthd = 'bc')
print(dat1)
## --------------------------------------------------------------
pred1 <- alfam2(dat1, app.name = 'TAN.app', time.name = 'ctime')
## --------------------------------------------------------------
print(pred1)
## --------------------------------------------------------------
dat1b <- data.frame(ctime = 168, TAN.app = 50, man.dm = 8,
air.temp = 20, wind.sqrt = 2,
app.mthd = 'Broadcast')
print(dat1b)
## --------------------------------------------------------------
pred1b <- alfam2(dat1, app.name = 'TAN.app', time.name = 'ctime')
## --------------------------------------------------------------
all.equal(pred1, pred1b)
## --------------------------------------------------------------
dat2 <- dat1
## --------------------------------------------------------------
dat2$incorp <- 'deep'
dat2$t.incorp <- 0.5
print(dat2)
## --------------------------------------------------------------
pred2 <- alfam2(dat2, app.name = "TAN.app", time.name = "ctime",
time.incorp = "t.incorp", warn = FALSE)
print(pred2)
## --------------------------------------------------------------
dat3 <- dat1
dat3$incorp <- 'shallow'
dat3$t.incorp <- 0.5
print(dat3)
## --------------------------------------------------------------
pred3 <- alfam2(dat3, app.name = "TAN.app", time.name = "ctime",
time.incorp = "t.incorp", warn = FALSE)
print(pred3)
## --------------------------------------------------------------
datr <- data.frame(ctime = 168)
print(datr)
## --------------------------------------------------------------
predr <- alfam2(datr, app.name = 'TAN.app', time.name = 'ctime')
predr
## --------------------------------------------------------------
predr$j * predr$dt
## --------------------------------------------------------------
dat4 <- data.frame(scenario = 1:5, ctime = 168, TAN.app = 50,
man.dm = 8, air.temp = 20, wind.sqrt = 2,
app.mthd = 'bc',
incorp = 'deep',
t.incorp = c(0.1, 1, 6, 24, NA))
print(dat4)
## --------------------------------------------------------------
dat4 <- data.frame(scenario = 1:5, ctime = 168, TAN.app = 50,
man.dm = 8, air.temp = 20, wind.sqrt = 2,
app.mthd = 'bc',
incorp = c(rep('deep', 4), 'none'),
t.incorp = c(0.1, 1, 6, 24, NA))
print(dat4)
## --------------------------------------------------------------
pred4 <- alfam2(dat4, app.name = "TAN.app", time.name = "ctime",
time.incorp = "t.incorp", group = "scenario",
warn = FALSE)
print(pred4)
## --------------------------------------------------------------
barplot(pred4$er, names.arg = paste(dat4$t.incorp), xlab = 't.incorp', ylab = 'er')
## --------------------------------------------------------------
dat5 <- data.frame(scenario = 1:3, ctime = 168, TAN.app = 50,
man.dm = 8, wind.sqrt = 2,
air.temp = c(15, 20, 25),
app.mthd = c('bc', 'bsth', 'os')
)
print(dat5)
## --------------------------------------------------------------
pred5 <- alfam2(dat5, app.name = "TAN.app", time.name = "ctime",
group = "scenario", warn = FALSE)
print(pred5)
## --------------------------------------------------------------
dat5b <- data.frame(scenario = 1:3, ctime = 168, TAN.app = 50,
man.dm = 8, wind.sqrt = 2,
air.temp = c(15, 20, 25),
app.mthd.bc = c(TRUE, FALSE, FALSE),
app.mthd.os = c(FALSE, FALSE, TRUE)
)
print(dat5b)
## --------------------------------------------------------------
pred5b <- alfam2(dat5b, app.name = "TAN.app", time.name = "ctime",
group = "scenario", warn = FALSE)
print(pred5b)
all.equal(pred5b$e, pred5$e)
## --------------------------------------------------------------
alfam2pars03[grepl('^incorp', names(alfam2pars03))]
## --------------------------------------------------------------
dat6 <- data.frame(scenario = 1:6, ctime = 168, TAN.app = 100,
man.dm = 5, man.ph = 7.2, air.temp = 10,
wind.sqrt = 2,
man.source = c(rep('Cattle', 2), rep('Pig', 4)),
app.mthd = rep(c('Broadcast', 'Trailing hose'),
each = 3),
incorp = rep(c('None', 'Shallow', 'Deep'), 2),
t.incorp = 4)
print(dat6)
## --------------------------------------------------------------
pred6 <- alfam2(dat6, app.name = "TAN.app", time.name = "ctime",
time.incorp = "t.incorp", group = "scenario",
warn = TRUE)
print(pred6)
## --------------------------------------------------------------
pred6b <- alfam2(dat6, app.name = "TAN.app", time.name = "ctime",
time.incorp = "t.incorp", group = "scenario",
warn = TRUE, add.incorp.rows = TRUE)
print(pred6b)
## --------------------------------------------------------------
set.seed(1201)
dat7 <- data.frame(ctime = 0:84*2, TAN.app = 100, man.dm = 8,
air.temp = 7 + 7*sin(0:84*2 * 2*pi/24) +
rnorm(85, 0, 2),
wind.sqrt = sqrt(1.5 + 0.4*sin(0:84*2 * 2*pi/24)) +
rnorm(85, 0, 0.12),
app.mthd = 'ts')
plot(air.temp ~ ctime, data = dat7, type = 's', col = 'gray45')
plot(wind.sqrt^2 ~ ctime, data = dat7, type = 's', col = 'blue')
## --------------------------------------------------------------
pred7 <- alfam2(dat7, app.name = 'TAN.app', time.name = 'ctime',
warn = FALSE)
## --------------------------------------------------------------
plot(e ~ ctime, data = pred7, type = 'o', xlab = 'Time (h)',
ylab = 'Cumulative emission (kg/ha)')
plot(j ~ ctime, data = pred7, type = 'S', col = 'red',
xlab = 'Time (h)', ylab = 'Average flux (kg/ha-h)')
## --------------------------------------------------------------
plot(j ~ ctime, data = pred7, type = 'S', col = 'red',
xlab = 'Time (h)', ylab = 'Average flux (kg/ha-h)')
points(jinst ~ ctime, data = pred7, col = 'blue')
## --------------------------------------------------------------
dat8 <- dat7
dat8$incorp <- "deep"
dat8$t.incorp <- 6.5
## --------------------------------------------------------------
pred8 <- alfam2(dat8, app.name = 'TAN.app', time.name = 'ctime',
time.incorp = 't.incorp', warn = FALSE,
add.incorp.rows = TRUE)
## --------------------------------------------------------------
plot(e ~ ctime, data = pred8, type = 'o', xlab = 'Time (h)',
ylab = 'Cumulative emission (kg/ha)')
abline(v = 6.5, col = 'blue', lty = 2)
plot(j ~ ctime, data = pred8, type = 'S', col = 'red',
xlab = 'Time (h)', ylab = 'Average flux (kg/ha-h)')
abline(v = 6.5, col = 'blue', lty = 2)
## ----eval=FALSE------------------------------------------------
# set.seed(0812)
# dat9 <- expand.grid(field = 1:1000, ct = 1:168,
# TAN.app = 100, man.dm = 8,
# app.rate.ni = 30, man.source = "pig",
# man.ph = 7, rain.rate = 0,
# app.mthd = "bsth")
#
# dat9$air.temp <- 7 + 7*sin(dat9$ct * 2 * pi / 24) +
# rnorm(1000, 0, 2)
# dat9$wind.sqrt <- sqrt(1.5 + 0.4*sin(dat9$ct * 2 * 2 * pi / 24)) +
# rnorm(1000, 0, 0.1)
# dat9 <- dat9[order(dat9$field, dat9$ct), ]
## ----eval=FALSE------------------------------------------------
# head(dat9)
# dim(dat9)
## ----eval=FALSE------------------------------------------------
# system.time(
# pred9 <- alfam2(dat9, app.name = 'TAN.app', time.name = 'ct',
# group = 'field', warn = FALSE)
# )
## ----eval=FALSE------------------------------------------------
# pred9sub <- subset(pred9, field %in% 1:100)
# pred9sub <- pred9sub[order(pred9sub$field), ]
# pred9sub[pred9sub$ct == 168, c('er', 'j')] <- NA
## ----eval=FALSE------------------------------------------------
# plot(j ~ ct, data = pred9sub, type = 'S', col = 'red',
# xlab = 'Time (h)', ylab = 'Average flux (kg/ha-h)')
## ----eval=FALSE------------------------------------------------
# system.time(
# alfam2(dat9, app.name = 'TAN.app', time.name = 'ct',
# group = 'field', check = FALSE, warn = FALSE)
# )
## ----eval=FALSE------------------------------------------------
# dat9b <- dat9
# dat9b$incorp <- 'shallow'
# dat9b$t.incorp <- 4
## ----eval=FALSE------------------------------------------------
# system.time(
# pred9b <- alfam2(dat9b, app.name = 'TAN.app', time.name = 'ct',
# time.incorp = "t.incorp", group = 'field',
# warn = FALSE)
# )
## ----eval=FALSE------------------------------------------------
# dat9c <- alfam2(dat9b, app.name = 'TAN.app', time.name = 'ct',
# time.incorp = 't.incorp', group = 'field',
# warn = FALSE, value = 'incorp')
# head(dat9c)
## ----eval=FALSE------------------------------------------------
# system.time(
# pred9c <- alfam2(dat9c, app.name = 'TAN.app', time.name = 'ct',
# time.incorp = "t.incorp", group = 'field',
# warn = FALSE, prep.dum = FALSE, prep.incorp = FALSE,
# check = FALSE)
# )
## ----eval=FALSE------------------------------------------------
# head(pred9b)
# head(pred9c)
# all.equal(pred9b$e, pred9c$e)
## --------------------------------------------------------------
set.seed(2609)
dat10 <- data.frame(ctime = 0:84*2, TAN.app = 100, man.dm = 8,
air.temp = 7 + 7*sin(0:84*2 * 2*pi/24) +
rnorm(85, 0, 2),
wind.sqrt = sqrt(1.5 + 0.4*sin(0:84*2 * 2*pi/24)) +
rnorm(85, 0, 0.12),
app.mthd = 'bsth')
## --------------------------------------------------------------
pred10 <- alfam2(dat10, app.name = 'TAN.app', time.name = 'ctime',
warn = FALSE)
head(pred10)
## --------------------------------------------------------------
predci1 <- alfam2(dat10, app.name = 'TAN.app', time.name = 'ctime',
warn = FALSE, conf.int = 0.90)
head(predci1)
## --------------------------------------------------------------
plot(er ~ ctime, data = predci1, type = 'l',
ylim = c(0, max(predci1$er.upr)))
lines(er.lwr ~ ctime, data = predci1, type = 'l', col = 'blue')
lines(er.upr ~ ctime, data = predci1, type = 'l', col = 'red')
## --------------------------------------------------------------
predci2 <- alfam2(dat10, app.name = 'TAN.app', time.name = 'ctime',
warn = FALSE, conf.int = 0.90, var.ci = c('er', 'j', 'r1'))
head(predci2)
## --------------------------------------------------------------
dat11 <- data.frame(ctime = 168, TAN.app = 50,
app.mthd = 'bc',
man.dm = 1:10, air.temp = 20, wind.sqrt = 2)
## --------------------------------------------------------------
predci3 <- alfam2(dat11, app.name = 'TAN.app', time.name = 'ctime',
group = 'man.dm', conf.int = 0.90)
print(predci3)
## --------------------------------------------------------------
plot(dat11$man.dm, predci3$er, type = 'o',
ylim = c(0, max(predci3$er.upr)))
lines(dat11$man.dm, predci3$er.lwr, col = 'blue')
lines(dat11$man.dm, predci3$er.upr, col = 'blue')
## --------------------------------------------------------------
dim(alfam2pars03var)
## --------------------------------------------------------------
datuc1 <- data.frame(group = 1:100, ctime = 168, TAN.app = 50,
app.mthd = 'bc',
man.dm = rnorm(100, mean = 8, sd = 2),
air.temp = 20, wind.sqrt = 2)
quantile(datuc1$man.dm)
## --------------------------------------------------------------
preduc1 <- alfam2(datuc1, app.name = 'TAN.app', time.name = 'ctime',
group = 'group', conf.int = 'all')
head(preduc1)
dim(preduc1)
## --------------------------------------------------------------
quantile(preduc1$er, c(0.05, 0.95))
## --------------------------------------------------------------
datuc2 <- data.frame(group = 1, ctime = 168, TAN.app = 50,
app.mthd = 'bc',
man.dm = 8,
air.temp = 20, wind.sqrt = 2)
## --------------------------------------------------------------
preduc2 <- alfam2(datuc2, app.name = 'TAN.app',
time.name = 'ctime', group = 'group',
conf.int = 0.9)
print(preduc2)
## ----eval=FALSE------------------------------------------------
# write.csv(pred7, 'pred7.csv', row.names = FALSE)
## ----eval=FALSE------------------------------------------------
# library(data.table)
# library(ALFAM2)
# dat1b <- data.table(ctime = 168, TAN.app = 50, man.dm = 8,
# air.temp = 20, wind.sqrt = 2,
# app.mthd = 'bc')
# dat1b
## ----eval=FALSE------------------------------------------------
# pred1b <- alfam2(dat1b, app.name = 'TAN.app', time.name = 'ctime')
# pred1b
# class(pred1b)
# setDT(pred1b)
# class(pred1b)
## ----eval=FALSE------------------------------------------------
# library(tibble)
# dat1c <- tibble(ctime = 168, TAN.app = 50, man.dm = 8,
# air.temp = 20, wind.sqrt = 2,
# app.mthd.bc = TRUE)
# dat1c
# class(dat1c)
## ----eval=FALSE------------------------------------------------
# pred1c <- alfam2(dat1c, app.name = 'TAN.app', time.name = 'ctime')
# class(pred1c)
# pred1c <- as_tibble(pred1c)
# class(pred1c)
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## ----include=FALSE, cache=FALSE--------------------------------
library(knitr)
#opts_chunk$set(cache=FALSE,tidy=FALSE,highlight=FALSE)
knitr::opts_chunk$set(fig.width=12, fig.height=8, out.width='100%', out.height='100%')
opts_chunk$set(cache = FALSE, tidy = FALSE, fig.align = "center")
library(ALFAM2)
options(width=65)
## ----eval=FALSE------------------------------------------------
# install.packages('ALFAM2')
## --------------------------------------------------------------
library(ALFAM2)
## ----eval=FALSE------------------------------------------------
# vignette("ALFAM2-start")
## --------------------------------------------------------------
packageVersion("ALFAM2")
## --------------------------------------------------------------
args(alfam2)
## ----eval=FALSE------------------------------------------------
# ?alfam2
## --------------------------------------------------------------
packageVersion("ALFAM2")
## --------------------------------------------------------------
args(alfam2)
## --------------------------------------------------------------
alfam2pars03
## --------------------------------------------------------------
dat1 <- data.frame(ctime = 168, TAN.app = 50, man.dm = 8,
air.temp = 20, wind.sqrt = 2,
app.mthd = 'bc')
print(dat1)
## --------------------------------------------------------------
pred1 <- alfam2(dat1, app.name = 'TAN.app', time.name = 'ctime')
## --------------------------------------------------------------
print(pred1)
## --------------------------------------------------------------
dat1b <- data.frame(ctime = 168, TAN.app = 50, man.dm = 8,
air.temp = 20, wind.sqrt = 2,
app.mthd = 'Broadcast')
print(dat1b)
## --------------------------------------------------------------
pred1b <- alfam2(dat1, app.name = 'TAN.app', time.name = 'ctime')
## --------------------------------------------------------------
all.equal(pred1, pred1b)
## --------------------------------------------------------------
dat2 <- dat1
## --------------------------------------------------------------
dat2$incorp <- 'deep'
dat2$t.incorp <- 0.5
print(dat2)
## --------------------------------------------------------------
pred2 <- alfam2(dat2, app.name = "TAN.app", time.name = "ctime",
time.incorp = "t.incorp", warn = FALSE)
print(pred2)
## --------------------------------------------------------------
dat3 <- dat1
dat3$incorp <- 'shallow'
dat3$t.incorp <- 0.5
print(dat3)
## --------------------------------------------------------------
pred3 <- alfam2(dat3, app.name = "TAN.app", time.name = "ctime",
time.incorp = "t.incorp", warn = FALSE)
print(pred3)
## --------------------------------------------------------------
datr <- data.frame(ctime = 168)
print(datr)
## --------------------------------------------------------------
predr <- alfam2(datr, app.name = 'TAN.app', time.name = 'ctime')
predr
## --------------------------------------------------------------
predr$j * predr$dt
## --------------------------------------------------------------
dat4 <- data.frame(scenario = 1:5, ctime = 168, TAN.app = 50,
man.dm = 8, air.temp = 20, wind.sqrt = 2,
app.mthd = 'bc',
incorp = 'deep',
t.incorp = c(0.1, 1, 6, 24, NA))
print(dat4)
## --------------------------------------------------------------
dat4 <- data.frame(scenario = 1:5, ctime = 168, TAN.app = 50,
man.dm = 8, air.temp = 20, wind.sqrt = 2,
app.mthd = 'bc',
incorp = c(rep('deep', 4), 'none'),
t.incorp = c(0.1, 1, 6, 24, NA))
print(dat4)
## --------------------------------------------------------------
pred4 <- alfam2(dat4, app.name = "TAN.app", time.name = "ctime",
time.incorp = "t.incorp", group = "scenario",
warn = FALSE)
print(pred4)
## --------------------------------------------------------------
barplot(pred4$er, names.arg = paste(dat4$t.incorp), xlab = 't.incorp', ylab = 'er')
## --------------------------------------------------------------
dat5 <- data.frame(scenario = 1:3, ctime = 168, TAN.app = 50,
man.dm = 8, wind.sqrt = 2,
air.temp = c(15, 20, 25),
app.mthd = c('bc', 'bsth', 'os')
)
print(dat5)
## --------------------------------------------------------------
pred5 <- alfam2(dat5, app.name = "TAN.app", time.name = "ctime",
group = "scenario", warn = FALSE)
print(pred5)
## --------------------------------------------------------------
dat5b <- data.frame(scenario = 1:3, ctime = 168, TAN.app = 50,
man.dm = 8, wind.sqrt = 2,
air.temp = c(15, 20, 25),
app.mthd.bc = c(TRUE, FALSE, FALSE),
app.mthd.os = c(FALSE, FALSE, TRUE)
)
print(dat5b)
## --------------------------------------------------------------
pred5b <- alfam2(dat5b, app.name = "TAN.app", time.name = "ctime",
group = "scenario", warn = FALSE)
print(pred5b)
all.equal(pred5b$e, pred5$e)
## --------------------------------------------------------------
alfam2pars03[grepl('^incorp', names(alfam2pars03))]
## --------------------------------------------------------------
dat6 <- data.frame(scenario = 1:6, ctime = 168, TAN.app = 100,
man.dm = 5, man.ph = 7.2, air.temp = 10,
wind.sqrt = 2,
man.source = c(rep('Cattle', 2), rep('Pig', 4)),
app.mthd = rep(c('Broadcast', 'Trailing hose'),
each = 3),
incorp = rep(c('None', 'Shallow', 'Deep'), 2),
t.incorp = 4)
print(dat6)
## --------------------------------------------------------------
pred6 <- alfam2(dat6, app.name = "TAN.app", time.name = "ctime",
time.incorp = "t.incorp", group = "scenario",
warn = TRUE)
print(pred6)
## --------------------------------------------------------------
pred6b <- alfam2(dat6, app.name = "TAN.app", time.name = "ctime",
time.incorp = "t.incorp", group = "scenario",
warn = TRUE, add.incorp.rows = TRUE)
print(pred6b)
## --------------------------------------------------------------
set.seed(1201)
dat7 <- data.frame(ctime = 0:84*2, TAN.app = 100, man.dm = 8,
air.temp = 7 + 7*sin(0:84*2 * 2*pi/24) +
rnorm(85, 0, 2),
wind.sqrt = sqrt(1.5 + 0.4*sin(0:84*2 * 2*pi/24)) +
rnorm(85, 0, 0.12),
app.mthd = 'ts')
plot(air.temp ~ ctime, data = dat7, type = 's', col = 'gray45')
plot(wind.sqrt^2 ~ ctime, data = dat7, type = 's', col = 'blue')
## --------------------------------------------------------------
pred7 <- alfam2(dat7, app.name = 'TAN.app', time.name = 'ctime',
warn = FALSE)
## --------------------------------------------------------------
plot(e ~ ctime, data = pred7, type = 'o', xlab = 'Time (h)',
ylab = 'Cumulative emission (kg/ha)')
plot(j ~ ctime, data = pred7, type = 'S', col = 'red',
xlab = 'Time (h)', ylab = 'Average flux (kg/ha-h)')
## --------------------------------------------------------------
plot(j ~ ctime, data = pred7, type = 'S', col = 'red',
xlab = 'Time (h)', ylab = 'Average flux (kg/ha-h)')
points(jinst ~ ctime, data = pred7, col = 'blue')
## --------------------------------------------------------------
dat8 <- dat7
dat8$incorp <- "deep"
dat8$t.incorp <- 6.5
## --------------------------------------------------------------
pred8 <- alfam2(dat8, app.name = 'TAN.app', time.name = 'ctime',
time.incorp = 't.incorp', warn = FALSE,
add.incorp.rows = TRUE)
## --------------------------------------------------------------
plot(e ~ ctime, data = pred8, type = 'o', xlab = 'Time (h)',
ylab = 'Cumulative emission (kg/ha)')
abline(v = 6.5, col = 'blue', lty = 2)
plot(j ~ ctime, data = pred8, type = 'S', col = 'red',
xlab = 'Time (h)', ylab = 'Average flux (kg/ha-h)')
abline(v = 6.5, col = 'blue', lty = 2)
## ----eval=FALSE------------------------------------------------
# set.seed(0812)
# dat9 <- expand.grid(field = 1:1000, ct = 1:168,
# TAN.app = 100, man.dm = 8,
# app.rate.ni = 30, man.source = "pig",
# man.ph = 7, rain.rate = 0,
# app.mthd = "bsth")
#
# dat9$air.temp <- 7 + 7*sin(dat9$ct * 2 * pi / 24) +
# rnorm(1000, 0, 2)
# dat9$wind.sqrt <- sqrt(1.5 + 0.4*sin(dat9$ct * 2 * 2 * pi / 24)) +
# rnorm(1000, 0, 0.1)
# dat9 <- dat9[order(dat9$field, dat9$ct), ]
## ----eval=FALSE------------------------------------------------
# head(dat9)
# dim(dat9)
## ----eval=FALSE------------------------------------------------
# system.time(
# pred9 <- alfam2(dat9, app.name = 'TAN.app', time.name = 'ct',
# group = 'field', warn = FALSE)
# )
## ----eval=FALSE------------------------------------------------
# pred9sub <- subset(pred9, field %in% 1:100)
# pred9sub <- pred9sub[order(pred9sub$field), ]
# pred9sub[pred9sub$ct == 168, c('er', 'j')] <- NA
## ----eval=FALSE------------------------------------------------
# plot(j ~ ct, data = pred9sub, type = 'S', col = 'red',
# xlab = 'Time (h)', ylab = 'Average flux (kg/ha-h)')
## ----eval=FALSE------------------------------------------------
# system.time(
# alfam2(dat9, app.name = 'TAN.app', time.name = 'ct',
# group = 'field', check = FALSE, warn = FALSE)
# )
## ----eval=FALSE------------------------------------------------
# dat9b <- dat9
# dat9b$incorp <- 'shallow'
# dat9b$t.incorp <- 4
## ----eval=FALSE------------------------------------------------
# system.time(
# pred9b <- alfam2(dat9b, app.name = 'TAN.app', time.name = 'ct',
# time.incorp = "t.incorp", group = 'field',
# warn = FALSE)
# )
## ----eval=FALSE------------------------------------------------
# dat9c <- alfam2(dat9b, app.name = 'TAN.app', time.name = 'ct',
# time.incorp = 't.incorp', group = 'field',
# warn = FALSE, value = 'incorp')
# head(dat9c)
## ----eval=FALSE------------------------------------------------
# system.time(
# pred9c <- alfam2(dat9c, app.name = 'TAN.app', time.name = 'ct',
# time.incorp = "t.incorp", group = 'field',
# warn = FALSE, prep.dum = FALSE, prep.incorp = FALSE,
# check = FALSE)
# )
## ----eval=FALSE------------------------------------------------
# head(pred9b)
# head(pred9c)
# all.equal(pred9b$e, pred9c$e)
## --------------------------------------------------------------
set.seed(2609)
dat10 <- data.frame(ctime = 0:84*2, TAN.app = 100, man.dm = 8,
air.temp = 7 + 7*sin(0:84*2 * 2*pi/24) +
rnorm(85, 0, 2),
wind.sqrt = sqrt(1.5 + 0.4*sin(0:84*2 * 2*pi/24)) +
rnorm(85, 0, 0.12),
app.mthd = 'bsth')
## --------------------------------------------------------------
pred10 <- alfam2(dat10, app.name = 'TAN.app', time.name = 'ctime',
warn = FALSE)
head(pred10)
## --------------------------------------------------------------
predci1 <- alfam2(dat10, app.name = 'TAN.app', time.name = 'ctime',
warn = FALSE, conf.int = 0.90)
head(predci1)
## --------------------------------------------------------------
plot(er ~ ctime, data = predci1, type = 'l',
ylim = c(0, max(predci1$er.upr)))
lines(er.lwr ~ ctime, data = predci1, type = 'l', col = 'blue')
lines(er.upr ~ ctime, data = predci1, type = 'l', col = 'red')
## --------------------------------------------------------------
predci2 <- alfam2(dat10, app.name = 'TAN.app', time.name = 'ctime',
warn = FALSE, conf.int = 0.90, var.ci = c('er', 'j', 'r1'))
head(predci2)
## --------------------------------------------------------------
dat11 <- data.frame(ctime = 168, TAN.app = 50,
app.mthd = 'bc',
man.dm = 1:10, air.temp = 20, wind.sqrt = 2)
## --------------------------------------------------------------
predci3 <- alfam2(dat11, app.name = 'TAN.app', time.name = 'ctime',
group = 'man.dm', conf.int = 0.90)
print(predci3)
## --------------------------------------------------------------
plot(dat11$man.dm, predci3$er, type = 'o',
ylim = c(0, max(predci3$er.upr)))
lines(dat11$man.dm, predci3$er.lwr, col = 'blue')
lines(dat11$man.dm, predci3$er.upr, col = 'blue')
## --------------------------------------------------------------
dim(alfam2pars03var)
## --------------------------------------------------------------
datuc1 <- data.frame(group = 1:100, ctime = 168, TAN.app = 50,
app.mthd = 'bc',
man.dm = rnorm(100, mean = 8, sd = 2),
air.temp = 20, wind.sqrt = 2)
quantile(datuc1$man.dm)
## --------------------------------------------------------------
preduc1 <- alfam2(datuc1, app.name = 'TAN.app', time.name = 'ctime',
group = 'group', conf.int = 'all')
head(preduc1)
dim(preduc1)
## --------------------------------------------------------------
quantile(preduc1$er, c(0.05, 0.95))
## --------------------------------------------------------------
datuc2 <- data.frame(group = 1, ctime = 168, TAN.app = 50,
app.mthd = 'bc',
man.dm = 8,
air.temp = 20, wind.sqrt = 2)
## --------------------------------------------------------------
preduc2 <- alfam2(datuc2, app.name = 'TAN.app',
time.name = 'ctime', group = 'group',
conf.int = 0.9)
print(preduc2)
## ----eval=FALSE------------------------------------------------
# write.csv(pred7, 'pred7.csv', row.names = FALSE)
## ----eval=FALSE------------------------------------------------
# library(data.table)
# library(ALFAM2)
# dat1b <- data.table(ctime = 168, TAN.app = 50, man.dm = 8,
# air.temp = 20, wind.sqrt = 2,
# app.mthd = 'bc')
# dat1b
## ----eval=FALSE------------------------------------------------
# pred1b <- alfam2(dat1b, app.name = 'TAN.app', time.name = 'ctime')
# pred1b
# class(pred1b)
# setDT(pred1b)
# class(pred1b)
## ----eval=FALSE------------------------------------------------
# library(tibble)
# dat1c <- tibble(ctime = 168, TAN.app = 50, man.dm = 8,
# air.temp = 20, wind.sqrt = 2,
# app.mthd.bc = TRUE)
# dat1c
# class(dat1c)
## ----eval=FALSE------------------------------------------------
# pred1c <- alfam2(dat1c, app.name = 'TAN.app', time.name = 'ctime')
# class(pred1c)
# pred1c <- as_tibble(pred1c)
# class(pred1c)
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