Incorporating a few of the Paraty fixes

[dsrivast]

We made a lot of progress at Paraty, it would be nice sometime to have these incorporated into the BWGtools pkg as we now have snippets of code on some papers' R scripts and not others. Only when you have time @aammd !

(1) make site a factor within BWGtools (I need to do it manually outside)
(2) make this summarize code below part of the hydro function, not having it in the function threw me for a loop by creating duplication of rownames (as two leaves per bromeliad) in the final fulldata:
mean_hydro <- hydro %>%
ungroup %>%
select(c(2,7:17, long_dry, long_wet, n_driedout, n_overflow)) %>%
group_by(site_brom.id) %>%
summarise_each(funs(median(., na.rm = TRUE))) %>%
replace_na(list(long_dry = 0, long_wet = 0, n_driedout = 0, n_overflow = 0))

when_last <- hydro %>%
ungroup %>%
select(site_brom.id, last_dry, last_wet) %>%
group_by(site_brom.id) %>%
summarise_each(funs(min(., na.rm = TRUE))) %>%
replace_na(list(last_dry = 65, last_wet = 65))

brom_hydro <- mean_hydro %>% left_join(when_last)

(3) adding this code to summarize the ibutton data, which I think is not yet part of BWGtools:
ibuttons <- combine_tab(sheetname = "bromeliad.ibuttons")
ibutton_data <- ibuttons %>%
group_by(site, site_brom.id) %>%
summarise(mean_max = mean(max.temp, na.rm = TRUE), mean_min = mean(min.temp, na.rm = TRUE),
mean_mean = mean(mean.temp, na.rm = TRUE), sd_max = sd(max.temp, na.rm = TRUE),
sd_min = sd(min.temp, na.rm = TRUE), sd_mean = sd(mean.temp, na.rm = TRUE),
cv_max = 100_(sd_max/mean_max), cv_min = 100_(sd_min/mean_min),
cv_mean = 100*(sd_mean/mean_mean)) %>%
ungroup %>%
gather(variable, observed, 3:11) %>%
replace_na(list(observed = "NA")) %>%
select(-site) %>%
spread(variable, observed, fill = 0) %>%
rename(max_temp = mean_max, min_temp = mean_min, mean_temp = mean_mean,
sd_max_temp = sd_max, sd_min_temp = sd_min, sd_mean_temp = sd_mean,
cv_max_temp = cv_max, cv_min_temp = cv_min, cv_mean_temp = cv_mean)