knitr::opts_chunk$set(echo = TRUE, warning = F, message = F)
box::use(
here[...],
ggplot2[...],
tidyr[...],
dplyr[...],
ggridges[...],
reactable[...],
lubridate[ymd, year],
stringr[str_wrap],
forcats[fct_reorder2],
htmltools[h5],
htmlwidgets[prependContent],
plotly[...]
)
source(here('R/funcs.R'))
load(file = here('data/vegdat.RData'))
load(file = here('data/treedat.RData'))
thm <- theme_minimal(base_size = 14) +
theme(
panel.grid.minor = element_blank()
)
vegdat <- vegdat %>%
filter(sample != 2)
# test args
site <- 'Big Bend - TECO'
sp <- 'Avicennia germinans'
Plot showing number of times a zone was identified across transects, dates.
zonecnt_plo(vegdat, thm)
Plot showing total distance zone was recorded across transect, dates.
zonedst_plo(vegdat, thm)
An example showing zones for two sample dates at one site.
sitezonedst_plo1(vegdat, site = site, zonefct = NULL, thm = thm)
To evaluate simple changes in zones over time, an estimate of total distance per zone between time points could be evaluated. This is also very similar to the previous plot.
sitezonedst_plo2(vegdat, site = site, zonefct = NULL, thm = thm)
The same site, but showing species data along the transect.
sitezonedst_plo3(vegdat, site, thm = thm)
An evaluation of a single species across all sites, can be shown as frequency occurrence across the transect or mean percent basal cover. This example shows frequency occurrence of Avicennia germinans.
sppsum_plo(vegdat, sp, var = 'fo', thm = thm)
And now average percent basal cover.
sppsum_plo(vegdat, sp, var = 'cover', thm = thm)
A table of species frequency occurrence by zone, over time:
sitezonesum_tab(vegdat, site = site)
Same thing but as percent basal cover.
sitezonesum_tab(vegdat, site = site, var = 'cover')
A plot of sum of percent basal cover by arbitrary meter markings, top species, and across zones.
sitesum_plo(vegdat, site, delim = 10, vegsel = 8, var = 'cover', thm = thm, delimtyp = 'Number')
A plot of mean percent basal cover by arbitrary meter markings, top species, and for select zones.
sitesum_plo(vegdat, site, delim = 10, vegsel = 8, var = 'cover', zonefct = c('A: Mangrove Fringe', 'G: Coastal Upland'), thm = thm, delimtyp = 'Number')
Tabular summary of tree data by site, species.
treesum_tab(treedat, site = site, byspecies = T, var = 'trees_ha')
Same table as above, but aggregated across species.
treesum_tab(treedat, site = site, byspecies = F, var = 'trees_ha')
Tree summary plot by site, species.
treesum_plo(treedat, site = site, byspecies = T, var = 'trees_ha', thm = thm)
Tree summary plot, but aggregated across species.
treesum_plo(treedat, site = site, byspecies = F, var = 'trees_ha', thm = thm)