Nothing
## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----eval = T, message = F, warning = F---------------------------------------
library(WRTDStidal)
## -----------------------------------------------------------------------------
# import data
data(chldat)
# data format
str(chldat)
## ----eval = F-----------------------------------------------------------------
# # load a fitted model, quantiles
# data(tidfit)
#
# # load a fitted model, mean
# data(tidfitmean)
#
# # or recreate the quanitile models from chldat
# tidfit <- modfit(chldat, tau = c(0.1, 0.5, 0.9))
#
# # or recreate the mean model from chldat
# tidfitmean <- modfit(chldat, resp_type = 'mean')
## ----fig.height = 6, fig.width = 8--------------------------------------------
# create a tidal object from a data frame, or use tidalmean function
tidobj <- tidal(chldat)
# plot the raw data
obsplot(tidobj)
## -----------------------------------------------------------------------------
# data
head(tidobj)
# names of the attributes
names(attributes(tidobj))
# load a fitted tidal object, or use tidfitmean
data(tidfit)
# fitted data
head(tidfit)
# fitted attributes
names(attributes(tidfit))
## ----message = FALSE, cache = TRUE--------------------------------------------
# get wrtds results, quantile model
mod <- modfit(chldat)
# get wrtds mean model
mod <- modfit(chldat, resp_type = 'mean')
## ----message = FALSE, eval = FALSE--------------------------------------------
# # this is equivalent to running modfit
# # modfit is a wrapper for tidal, wrtds, respred, and resnorm functions
#
# # pipes from the dplyr (magrittr) package are used for simplicity
# library(dplyr)
#
# # quantile model
# mod <- tidal(chldat) %>% # creates a tidal object
# wrtds %>% # creates wrtds interpolation grids
# respred %>% # get predictions from grids
# resnorm # get normalized predictions from grids
#
# # mean model
# mod <- tidalmean(chldat) %>% # creates a tidal object
# wrtds %>% # creates wrtds interpolation grids
# respred %>% # get predictions from grids
# resnorm # get normalized predictions from grids
## ----eval = FALSE-------------------------------------------------------------
# ## fit the model and get predicted/normalized chlorophyll data
# # default median fit, quantile model
# # grids predicted across salinity range with ten values
# mod <- modfit(chldat)
#
# ## fit different quantiles and smaller interpolation grid
# mod <- modfit(chldat, tau = c(0.2, 0.8), flo_div = 5)
#
# ## fit with different window widths
# # half-window widths of one day, five years, and 0.3 salinity
# mod <- modfit(chldat, wins = list(1, 5, 0.3))
#
# ## suppress console output
# mod <- modfit(chldat, trace = FALSE)
## ----fig.height=4, fig.width=8, message=FALSE, warning=FALSE------------------
# load data from the package for the example
data(tidfit)
# plot using fitplot function
fitplot(tidfit)
# plot non-aggregated results
fitplot(tidfit, annuals = FALSE)
## ----fig.height=4, fig.width=8, message=FALSE, warning=FALSE------------------
# plot january, july as defaults
sliceplot(tidfit)
## ----fig.height=6, fig.width=8, message=FALSE, warning=FALSE------------------
# fits by month, normalized
fitmoplot(tidfit, predicted = F)
## ----fig.height=4, fig.width=8, message=FALSE, warning=FALSE------------------
seasplot(tidfit)
## ----fig.height=4, fig.width=8, message=FALSE, warning=FALSE------------------
seasyrplot(tidfitmean, predicted = F)
## ----fig.height=4, fig.width=8, message=FALSE, warning=FALSE------------------
# plot predicted, normalized results for each quantile
prdnrmplot(tidfit)
# plot as monthly values
prdnrmplot(tidfit, annuals = FALSE)
## ----fig.height=6, fig.width=8, message=FALSE, warning=FALSE------------------
# plot using defaults
# defaults to the fiftieth quantile
dynaplot(tidfit)
## ----fig.height=6, fig.width=8, message=FALSE, warning=FALSE------------------
# create a gridded plot
# defaults to the fiftieth quantile
gridplot(tidfit)
gridplot(tidfit, month = 'all')
## ----fig.height=6, fig.width=8, message=FALSE, warning=FALSE------------------
library(dplyr)
library(plotly)
dat <- attr(tidfitmean, 'fits') %>%
.[[1]] %>%
select(-date, -year, -month, -day) %>%
as.matrix
scene <- list(
aspectmode = 'manual',
aspectratio = list(x = 0.5, y = 1, z = 0.3),
xaxis = list(title = 'Salinity'),
yaxis = list(title = 'Time'),
zaxis = list(title = 'log-Chl')
)
p <- plot_ly(z = ~dat) %>%
add_surface(colors = rev(RColorBrewer::brewer.pal(11, 'Spectral'))) %>%
layout(scene = scene)
p
## ----fig.height=7, fig.width=7, message=FALSE, warning=FALSE------------------
# wt plot
wtsplot(tidfit, ref = '1995-07-01')
## ----fig.height=3, fig.width=5, message=FALSE, warning=FALSE------------------
# create a nobsplot
nobsplot(tidfit)
## -----------------------------------------------------------------------------
wrtdsperf(tidfit)
# setup month, year categories for trend summaries
mobrks <- list(c(1, 2, 3), c(4, 5, 6), c(7, 8, 9), c(10, 11, 12))
yrbrks <- c(-Inf, 1985, 1994, 2003, Inf)
molabs <- c('JFM', 'AMJ', 'JAS', 'OND')
yrlabs <- c('1974-1985', '1986-1994', '1995-2003', '2004-2012')
wrtdstrnd(tidfit, mobrks, yrbrks, molabs, yrlabs)
## -----------------------------------------------------------------------------
wrtdstrnd_sk(tidfit, mobrks, yrbrks, molabs, yrlabs)
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