Plot period (seasonal) averages from fitted GAM

Usage

show_metseason(
  mod,
  metfun = mean,
  doystr = 1,
  doyend = 364,
  yrstr = 2000,
  yrend = 2019,
  yromit = NULL,
  ylab,
  width = 0.9,
  size = 1.5,
  nsim = 10000,
  useave = FALSE,
  base_size = 11,
  xlim = NULL,
  ylim = NULL,
  ...
)

Arguments

mod: input model object as returned by anlz_gam
metfun: function input for metric to calculate, e.g., mean, var, max, etc
doystr: numeric indicating start Julian day for extracting averages
doyend: numeric indicating ending Julian day for extracting averages
yrstr: numeric for starting year for trend model, see details
yrend: numeric for ending year for trend model, see details
yromit: optional numeric vector for years to omit from the plot, see details
ylab: chr string for y-axis label
width: numeric for width of error bars
size: numeric for point size
nsim: numeric indicating number of random draws for simulating uncertainty
useave: logical indicating if anlz_avgseason is used for the seasonal metric calculation, see details
base_size: numeric indicating base font size, passed to theme_bw
xlim: optional numeric vector of length two for x-axis limits
ylim: optional numeric vector of length two for y-axis limits
...: additional arguments passed to metfun, e.g., na.rm = TRUE

Value

A ggplot object

Details

Setting yrstr or yrend to NULL will suppress plotting of the trend line for the meta-analysis regression model.

The optional yromit vector can be used to omit years from the plot and trend assessment. This may be preferred if seasonal estimates for a given year have very wide confidence intervals likely due to limited data, which can skew the trend assessments.

Set useave = T to speed up calculations if metfun = mean. This will use anlz_avgseason to estimate the seasonal summary metrics using a non-stochastic equation.

Examples

library(dplyr)

# data to model
tomod <- rawdat %>%
  filter(station %in% 34) %>%
  filter(param %in% 'chl') %>% 
  filter(yr > 2015)
  
mod <- anlz_gam(tomod, trans = 'ident')

show_metseason(mod, doystr = 90, doyend = 180, yrstr = 2016, yrend = 2019, 
     ylab = 'Chlorophyll-a (ug/L)')


# \donttest{
# show seasonal metrics without annual trend
show_metseason(mod, doystr = 90, doyend = 180, yrstr = NULL, yrend = NULL, 
     ylab = 'Chlorophyll-a (ug/L)')

     
# omit years from the analysis
show_metseason(mod, doystr = 90, doyend = 180, yrstr = 2016, yrend = 2019,
     yromit = 2017, ylab = 'Chlorophyll-a (ug/L)')

# }