3_estimate_indicators.Rmd

---
title: "Estimate indicators"
output: html_document
---

## Packages and functions

Load required libraries:

```{r, warning=FALSE, message=FALSE}
library(tidyr)
library(dplyr)
```

Load required functions. These custom fuctions are available at: https://github.com/AliciaMstt/GeneticIndicators

```{r source}
source("estimate_indicatorNe.R")
```

Other custom functions:
```{r custom_funs}
### not in
'%!in%' <- function(x,y)!('%in%'(x,y))

```


## Get data 
Get clean data (output of step 2) ready to estimate the indicators:

```{r, echo=TRUE}
# Get data:
indNe_data<-read.csv("indNe_data.csv")
indPM_data<-read.csv("indPM_data.csv")
indDNAbased_data<-read.csv("indDNAbased_data.csv")
metadata<-read.csv("metadata.csv")
```


## Estimate the indicators

### Ne 500 indicator 

The Ne 500 indicator es estimated by dividing  "the number of populations whithin a species with Ne > 500" over "the number of populations within a species with data to estimate Ne".

Here the indicator is estimated not by taxon but by X_uuid (unique record of a taxon), because a single taxon could be assessed by different countries or more than once with different parameters)  

See the function to estimate the indicator:

```{r}
estimate_indicatorNe
```

```{r}
indicatorNe<-estimate_indicatorNe(indNe_data=indNe_data)
```
### PM indicator 

The Proportion of Maintained populations (PM indicator) is the he proportion of populations within species which are maintained. This can be estimated based on the ´n_extant_populations´ and ´n_extinct_populations´, as follows:

```{r}
# create a copy of the PM data
indicatorPM<-indPM_data

# calculate the indicator and save it as a new column along with the rest of the PM data
indicatorPM$indicatorPM<-indicatorPM$n_extant_populations / (indicatorPM$n_extant_populations + indicatorPM$n_extinct_populations)

```

Example output selecting the most relevant columns:

```{r}
indicatorPM %>% select(country_assessment, taxon, n_extant_populations, n_extinct_populations, indicatorPM)
```

### DNA-based genetic monitoring indicator 

This indicator refers to the number (count) of taxa by country in which genetic monitoring based on DNA-methods is occurring. This is stored in the variable ´temp_gen_monitoring´ as a “yes/no” answer for each taxon, so to estimate the indicator, we only need to count how many said “yes”, keeping only one of the records when the taxon was multiassessed.


```{r}
indicatorDNAbased<-indDNAbased_data %>%
                 # keep only one record if the taxon was assessed more than once within the country
                 select(country_assessment, taxon, temp_gen_monitoring) %>%
                 filter(!duplicated(.)) %>%

                 # count "yes" in tem_gen_monitoring by country
                 filter(temp_gen_monitoring=="yes") %>%
                 group_by(country_assessment) %>%
                 summarise(n_taxon_gen_monitoring= n())
```

Example output
```{r}
head(indicatorDNAbased)
```

## Join indicators and metadata in a single table

It is useful to have the PM and Ne 500 indicators and the metadata in a single large table, in which each row is a taxon assessed.

```{r}
indicators_full<-left_join(metadata, indicatorNe) %>% 
                     left_join(indicatorPM)
```
Save this file as an output
```{r}
write.csv(indicators_full, "indicators_full.csv", row.names = FALSE)
```