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all-data.Rmd
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all-data.Rmd
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---
title: "Current Data"
output:
html_document:
toc: no
highlight: tango
editor_options:
chunk_output_type: console
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(echo = FALSE)
knitr::opts_chunk$set(dpi = 300)
knitr::opts_chunk$set(warning = FALSE)
knitr::opts_chunk$set(message = FALSE)
source(here::here('R', '00_vis_custom.R'))
source(here::here('R', '00_load-packages.R'))
```
```{r load-data, include = FALSE, results = FALSE}
source(here::here('R', '02.2_load_all_data.R')) # updated 2021-12-03
source(here::here('R', '04.1_all-figures.R'))
```
Contains all data from both ISCO and tank collection methods from all reserves that submitted data.
# TAL Sensor CHLA (RFU) vs. Extracted CHLA ($\mu$g/L) {.tabset .tabset-pills}
## All
```{r}
all_figure
```
## Reserve and Methods
Current Data with reserves and the methods pulled out.
```{r}
all_reserve_method_figure
```
## Reserve and Methods (Interactive)
**How to use the interactive plot:** Hover over interactive plot for the tools panel to appear in top-right corner. Tools include: save plot, zoom, select (lasso or box), and data compare. Hover your cursor over a point for more information. You can also double click on an item in the legend to isolate that data series in the plot!
```{r, dpi = 120}
m = list(
l = 80,
r = 150,
b = 80,
t = 50,
pad = 0
)
all_interactive <- ggplotly(
all %>%
ggplot(aes(x = chlorophyll_rfu, y = chla_ugl)) +
geom_point(aes(color = reserve_code, shape = method), position = "jitter") +
stat_smooth(method = "lm", color = "black", se = FALSE) +
scale_colour_manual(name = "Reserve", values = reservecolours) +
scale_shape_discrete(name = "Method") +
scale_y_continuous(expand = c(0,0)) +
theme_classic() +
labs(x = "Chlorophyll a (RFU) EXO",
y = "Chlorophyll a (ug/L) Extracted",
caption = "ISCO and tank experiments"),
tooltip = c("method", "chlorophyll_rfu", "chla_ugl", "reserve_code")
)
all_interactive %>% layout(margin = m)
rm(all_interactive, m)
```
## Tank vs ISCO
```{r}
tank_isco
```
{-}
***
# Summary Information
```{r tables-load, include = FALSE}
source(here::here('R', '06.1_tables-all.R'))
```
```{r summary-table, caption = ""}
sum_table_final %>%
# dplyr::select(-`temp*`, -`do_mgl*`) %>% # don't know where these columns come from (2021-08-13)
kbl(align = "c", caption = 'Summary information for all parameters (Min-Max (Mean \U00B1 Standard Dev)) from each participating reserve for the <i>in vivo</i> ISCO experiments.') %>%
kable_styling(fixed_thead = T) %>%
row_spec(0, bold = T) %>%
column_spec(1, border_right = T) %>%
column_spec(2, border_right = T) %>%
kable_classic(c('striped', 'hover'), html_font = "Open Sans", full_width = F)
```
***
# Interference Parameters {.tabset .tabset-pills}
These are the three parameters of interest in the interference testing studies. The following is the chlorophyll a fluorescence (RFU) from the EXO total algae sensor by the extracted $\mu$g/L with the three parameters of interest overlaid as color. Note: Data where the interference parameter (fDOM, turbidity, or temperature) is not available have been removed from the figures.
**How to use the interactive plot:** Hover over interactive plot for the tools panel to appear in top-right corner. Tools include: save plot, zoom, select (lasso or box), and data compare. Hover your cursor over a point for more information.
## fDOM
```{r fdom-interf-interact, dpi = 120}
interference_interact_all_fxn(param = fdom, interact = TRUE)
# interference_interact_all_fxn(param = fdom, interact = FALSE) # to make it a still
```
## Turbidity
Had to filter to remove turbidity values > 240 NTU due to an outlier.
```{r turb-interf-interact, dpi = 120}
interference_interact_all_fxn(param = turbidity, interact = TRUE)
# interference_interact_all_fxn(param = turbidity, interact = FALSE) # to make it a still
```
## Temperature
```{r temp-interf-interact, dpi = 120}
interference_interact_all_fxn(param = temperature, interact = TRUE)
# interference_interact_all_fxn(param = temperature, interact = FALSE) # to make it a still
```