---
title: "Getting Started"
vignette: >
  %\VignetteIndexEntry{tbepreport}
  %\VignetteEngine{quarto::html}
  %\VignetteEncoding{UTF-8}
knitr:
  opts_chunk:
    collapse: true
    comment: '#>'
    echo: true
    warning: false
    message: false
---

```{r}
#| label: setup
#| include: false
library(tbepreport)
```

`tbepreport` builds the Tampa Bay Estuary Program's annual bay segment
report card.  Individual indicators are assigned a 0-1 outcome,
indicators are averaged into a score for each of four categories (Water
Quality, Sediment, Fish and Wildlife, Habitat), and the four category
scores are averaged into one overall score per bay segment and year. This
article shows a minimal workflow for creating the report card. See the
[Report Card Scoring](scoring.html) article for how each indicator is
calculated and scored.

## Compute Indicators

Every `anlz_*` indicator function takes raw monitoring data (mostly from
[tbeptools](https://tbep-tech.github.io/tbeptools/)) and returns a 0-1
outcome by bay segment and year.

```{r}
# water quality
wqattain <- anlz_wq_attain(epcdata)
wqthresh <- anlz_wq_thresh(epcdata)
totanndat <- util_rdataload("https://github.com/tbep-tech/load-estimates/raw/main/data/totanndat.RData")
wqload <- anlz_wq_load(totanndat)
wqtidalcreeks <- anlz_wq_tidalcreeks(tidalcreeks, iwrraw, yrs = 1990:2024)
wqfib <- anlz_wq_fib(enterodata)

# sediment
peltel <- anlz_sed_peltel(sedimentdata, yrs = 1993:2024)
tbbi <- anlz_sed_tbbi(benthicdata)

# fish and wildlife
tbni <- anlz_fw_tbni(fimdata)
nonnative_obs <- anlz_fw_nonnative_obs()
nonnative_abundance <- anlz_fw_nonnative_abundance(nonnative_obs)
nonnative_richness <- anlz_fw_nonnative_richness(nonnative_obs)

# habitat
trnsct <- anlz_hab_seagrass_transect(transect)
cov <- anlz_hab_seagrass_coverage(sgsegest)
```

## Combine Scores

`anlz_category()` averages a category's indicators into one score per bay
segment/year, and `anlz_score()` averages the four category scores into
one overall score.

```{r}
wqoverall <- anlz_category(
  wq_attain    = wqattain,
  thresh       = wqthresh,
  load         = wqload,
  tidal_creeks = wqtidalcreeks,
  fib          = wqfib
)

sedoverall <- anlz_category(sed_peltel = peltel, sed_tbbi = tbbi)

fwoverall <- anlz_category(
  tbni                = tbni,
  nonnative_abundance = nonnative_abundance,
  nonnative_richness  = nonnative_richness
)

haboverall <- anlz_category(
  seagrass_transect = trnsct,
  seagrass_coverage = cov
)

score <- anlz_score(wqoverall, sedoverall, fwoverall, haboverall)
```

## Visualize

`plot_score()` plots the full results for one bay segment and year.

```{r}
plot_score(wqoverall, sedoverall, fwoverall, haboverall, bay_segment = 'OTB', yr = 2024)
```

`plot_trend()` plots the same hierarchy across every year for
one bay segment.

```{r}
#| fig-height: 12
plot_trend(wqoverall, sedoverall, fwoverall, haboverall, bay_segment = 'OTB', yr_range = c(2000, 2024))
```