05-insects-sol.Rmd

# Soil invertebrates


```{r setup_insect_sol}
# confirm that the only variable recorded here is "abondance"
microfaunes$var %>% unique %>% {stopifnot(. == "abondance")}


## are sites nested in cells? 

microfaunes %>% 
  select(site_code, cell_code) %>% distinct %>% 
  group_by(cell_code) %>% tally
# no, here we have one survey per cell
```

```{r make_rank_abundance_insect_sol}

rank_abundance <- microfaunes %>% 
  filter(val>0) %>% 
  left_join(select(cells, cell_code, name)) %>% 
  group_by(cell_code, name, site_code) %>% 
  mutate(rank = row_number(desc(count)))
```

```{r fig_rank_abd_insects_sol}
rank_abundance %>% 
  ggplot(aes(x = rank, y = count, group = site_code)) + 
  geom_point() + 
  geom_line() + 
  facet_wrap(~name) + 
  coord_trans(y = "log") + 
  theme_bw()
```

## Questions

Why are some site names NA? do those sites not have names? 

Should 0 values be uploaded into Coleo?