01_BirdPointsQC.Rmd

---
title: "Bird Points QC"
author: "John Paul Schmit"
date: "8/3/2020"
output: html_document
---

```{r Plot_setup, include=F}

TotPlots<-nrow(QCPoints) #Total number of points being checked

# 1.1.0
Points_Bad_Unit<-QCPoints %>% 
   filter(!Admin_Unit_Code %in% c("ANTI", "CATO", "CHOH", "GWMP", "HAFE", "MANA", "MONO", "NACE", "PRWI", "ROCR", "WOTR")) %>% 
   select(Admin_Unit_Code, Point_Name)
 
#1.2.0
Points_No_Point_Name<-QCPoints %>% 
    filter(is.na(Point_Name) | Point_Name=="") %>% 
    select(Admin_Unit_Code, Point_Name)
 
Points_Duplicated<-QCPoints %>% 
  group_by(Point_Name) %>% 
  summarize(Point_Count=n()) %>% 
  filter(Point_Count !=1) %>% 
  select(Point_Name, Point_Count)


#1.3.0
Points_No_Coords<-QCPoints %>% 
  filter(is.na(Latitude)| is.na(Longitude)) %>% 
  select(Admin_Unit_Code, Point_Name, Latitude, Longitude)

Points_Bad_Coords<-QCPoints %>% 
  filter(Latitude < 37.7| Latitude > 40.36|Longitude<  -79.5  | Longitude > -76.1 ) %>% 
  select(Admin_Unit_Code, Point_Name, Latitude, Longitude)

Points_Duplicated_Coords<-QCPoints %>% 
  group_by(Latitude,Longitude) %>% 
  mutate(Point_Count=n()) %>% 
  filter(Point_Count!=1) %>% 
  select(Admin_Unit_Code, Point_Name, Latitude, Longitude, Point_Count)

#1.4.0
Points_Bad_GRTS <- QCPoints %>% 
  filter(!GRTS_Order %in% 1:4683) %>% 
  select(Admin_Unit_Code, Point_Name, GRTS_Order)


Points_Duplicated_GRTS<-QCPoints %>% 
  group_by(GRTS_Order) %>% 
  mutate(Point_Count=n()) %>% 
  filter(Point_Count!=1) %>% 
  select(Admin_Unit_Code, Point_Name, GRTS_Order, Point_Count)

```


#### **Points Checked:** `r TotPlots` ####

### Unit Codes

```{r Point_unit_Codes, echo=FALSE, hold=FALSE, results="asis"}
if(nrow(Points_Bad_Unit)==0) cat("All points have a recognized Unit Code.<br>") else {
   errortext("Points with a missing or unrecongized Unit Code:"); NiceTable(Plots_Bad_Unit)}
```

---

### Plot Names

```{r Points_point_names, echo=FALSE, hold=FALSE, results="asis"}
if(nrow(Points_No_Point_Name)==0) cat("All points have a point name.<br>") else {
  errortext("Points without a point name:"); NiceTable(Points_No_Ponit_Name)}

if(nrow(Points_Duplicated)==0) cat("All points have a unique point name.<br>") else {
  errortext("Points with a duplicated point name:"); NiceTable(Points_Duplicated)}
```

---

### Geographic Coordinates

```{r Points_geo_coords, echo=FALSE, hold=FALSE, results="asis"}
cat("<br>**Coordinates Present**<br>")
if(nrow(Points_No_Coords)==0) cat("All points have geographic coordinates.") else { 
  cat("Points with missing coordinates:"); NiceTable(Points_No_Coords)}

cat("<br>**Bounding Box**<br>")
if(nrow(Points_Bad_Coords)==0) cat("All points' latitude and longitude are within the NCRN bounding box.<br>") else {
  errorText("Points with lat/long outside bounding box:"); NiceTable(Points_Bad_Coords)}

cat("<br>**Unique Coordinates**<br>")
if(nrow(Points_Duplicated_Coords)==0) cat("No points have the same latitude and longitude.<br>") else {
  errorText("Points with duplicated latitude and longitude:"); NiceTable(Points_Duplicated_Coords)}

```

---

### GRTS Order

```{r Points_GRTS_Order, echo=FALSE, hold=FALSE, results="asis"}
cat("<br>**Points GRTS Order**<br>")
if(nrow(Points_Bad_GRTS)==0) cat("All points have a valid GRTS order.<br>") else {
  errorText("Plots without a GRTS order between 1 and 4683:"); NiceTable(Points_Bad_GRTS)}

cat("<br>**Unique GRTS Order**<br>")
if(nrow(Points_Duplicated_GRTS)==0) cat("No points have duplicaed GRTS orders.<br>") else {
  errorText("Points with duplicated GRTS orders:"); NiceTable(Points_Duplicated_GRTS)}

```