Create Q_SPECIE.Rmd

---
title: "Create Q_SPECIE"
author: "Sander Devisscher"
date: "15 februari 2018"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r libraries}
library(readr)
library(foreign)
library(dplyr)
```
```{r read existing Q_Specie}
Q_Specie <- read_csv("G://Mijn Drive/INBOPRJ-10217 - Monitoring exoten ikv EU- verordening IAS  Coördinatie, voorbereiding, implementatie en opvolging/EASIN/Data/EASIN files/Q_SPECIE.csv")

```


```{r T0_Species}
T0 <- read_csv2("./Output/GRID10kData_Source_20_02_18_Export_20_02_18.csv")
T0$X <- NULL

SPEC_T0 <- unique(T0$species)

T0_Species <- data.frame(SPEC_T0)
T0_Species$SPEC_T0 <- as.character(T0_Species$SPEC_T0)
T0_Species$SPEC <- gsub(" ", "_", T0_Species$SPEC_T0)
T0_Species$SPEC <- gsub(".", "_", T0_Species$SPEC, fixed = T )
T0_Species$SPEC <- gsub(",", "_", T0_Species$SPEC, fixed = T )
T0_Species$SPEC <- gsub("&", "_", T0_Species$SPEC, fixed = T )
T0_Species$SPEC <- gsub("(", "_", T0_Species$SPEC, fixed = T ) 
T0_Species$SPEC <- gsub(")", "_", T0_Species$SPEC, fixed = T )

```

```{r EASIN_Species}
Batchnummer <- 2
EASIN_NEW <- read.dbf("G://Mijn Drive/INBOPRJ-10217 - Monitoring exoten ikv EU- verordening IAS  Coördinatie, voorbereiding, implementatie en opvolging/EASIN/Data/EASIN files/Tweede batch/EASIN check/EASIN baseline check.dbf")
SPEC_EASIN <- unique(EASIN_NEW$Species)
EASIN_Species <- data.frame(SPEC_EASIN)
EASIN_Species$Batch <- as.integer(Batchnummer)
EASIN_Species$SPEC_EASIN <- as.character(EASIN_Species$SPEC_EASIN)

#Check for species not yet present in Q_Specie
temp <- anti_join(EASIN_Species, Q_Specie, by = "SPEC_EASIN")

if(nrow(temp)>0){
  temp_species <- unique(temp$SPEC_EASIN)
  for(s in temp_species){
    temp2 <- subset(Q_Specie, pmatch(x = SPEC_T0, y = s, duplicates.ok = F ))
    if(nrow(temp2)>0){
    Q_Specie$SPEC_EASIN <- s
    Q_Specie$Batch <- as.integer(Batchnummer)
    }else{
      print(s, " is not present in T0 Sourcedata")
    }
  }
}

Q_Specie$Batch <- ifelse(is.na(Q_Specie$SPEC_EASIN), NA, Q_Specie$Batch)

```
```{r Merge}

```

```{r Export}
write_csv(Q_Specie, "G://Mijn Drive/INBOPRJ-10217 - Monitoring exoten ikv EU- verordening IAS  Coördinatie, voorbereiding, implementatie en opvolging/EASIN/Data/EASIN files/Q_SPECIE.csv")
```