02_BirdVisitsQC.Rmd

---
title: "Bird Visit QC"
author: "John Paul Schmit"
date: "5/18/2020"
output: html_document
---

```{r Events_Setup, include=F}
TotVisits<-nrow(QCVisits) #Total Number of visits checked

# 2.1.0
Visits_Bad_Unit<-QCVisits %>% 
   filter(!Admin_Unit_Code %in% c("ANTI", "CATO", "CHOH", "GWMP", "HAFE", "MANA", "MONO", "NACE", "PRWI", "ROCR", "WOTR")) %>% 
   select(Admin_Unit_Code, Point_Name)

#2.2.0
Visits_Missing_Point<-QCVisits %>% 
 filter(is.na(Point_Name) | Point_Name=="" | !Point_Name %in% QCPoints$Point_Name) %>% 
 select(Admin_Unit_Code, Point_Name, Year)
 
#2.3.0
Visits_No_Date<-QCVisits %>% left_join(QCPoints, by=c("Admin_Unit_Code","Point_Name")) %>%
 filter(is.na(EventDate) | EventDate=="")  %>%
 select(Admin_Unit_Code,Point_Name, Year, EventDate)

Visits_Date_Dupliacated<-QCVisits %>% 
  group_by(Admin_Unit_Code, Point_Name, Year, EventDate) %>% 
  summarise(Vists=n()) %>% 
  filter(Vists!=1)  %>%
  select(Admin_Unit_Code,Point_Name, Year, EventDate)

#2.4.0
Visits_Bad_Year<-QCVisits %>% filter(Year!=year(EventDate)) %>% 
   select(Admin_Unit_Code, Point_Name, EventDate, Year)
 
#2.5.0
Visits_Bad_StartTime<-QCVisits %>% 
  filter(is.na(StartTime) | StartTime=="" | !is.difftime(StartTime)) %>% 
  select(Admin_Unit_Code, Point_Name, EventDate, StartTime)

Visits_Bad_EndTime<-QCVisits %>% 
  filter(is.na(EndTime) | EndTime=="" | !is.difftime(EndTime)) %>% 
  select(Admin_Unit_Code, Point_Name, EventDate, EndTime)

Visits_Bad_Length <-QCVisits %>% 
  filter(EndTime- StartTime != 600) %>% 
  mutate(Length=EndTime - StartTime) %>% 
   select(Admin_Unit_Code, Point_Name, EventDate, StartTime, EndTime, Length)

#2.6.0
Visits_Bad_Visit<-QCVisits %>% 
  filter(!Visit %in% 1:3) %>% 
  select(Admin_Unit_Code, Point_Name, EventDate, Visit)

Visits_Duplicated_Visit<-QCVisits %>% 
  group_by(Admin_Unit_Code, Point_Name, Year, Visit) %>% 
  mutate(N=n()) %>% 
  filter(N!=1) %>% 
  select(Admin_Unit_Code,Point_Name, Year,Visit, EventDate)

Visits_Missing_Visit <-QCVisits %>% 
  group_by(Admin_Unit_Code, Point_Name, Year) %>% 
  filter(n()!=max(Visit)) %>% 
  select(Admin_Unit_Code,Point_Name, Year,Visit, EventDate) %>% 
  pivot_wider(id_cols=c(Admin_Unit_Code, Point_Name, Year), names_from=Visit, names_prefix="Visit ", names_sort=T, values_from=EventDate)

Visits_Bad_Order <-QCVisits %>% 
  group_by(Admin_Unit_Code, Point_Name, Year, Visit) %>% 
  mutate(Event_Order=rank(EventDate, ties.method = "average"),Visit_Order=rank(Visit, ties.method = "average")) %>% 
  filter(Event_Order!=Visit_Order) %>% 
  select(Admin_Unit_Code, Point_Name, Year, EventDate, Event_Order, Visit, Visit_Order)

#2.7.0
Visits_Bad_Temp<-QCVisits %>% 
  filter(is.na(Temperature) | Temperature=="" | Temperature < 7 | Temperature>37) %>% 
    select(Admin_Unit_Code, Point_Name, Year, EventDate, Temperature)

Visits_Big_Temp_Range<-QCVisits %>% 
  group_by(Admin_Unit_Code, Year, EventDate) %>% 
  summarise(Temp_Min=min(Temperature), Temp_Max=max(Temperature), Temp_Range=Temp_Max-Temp_Min) %>% 
  filter(Temp_Range>10) %>% 
  select(Admin_Unit_Code, Year, EventDate, Temp_Min, Temp_Max, Temp_Range)


#2.8.0
Visits_Bad_Humidity<-QCVisits %>% 
  filter(is.na(Humidity) | Humidity=="" | Humidity < 40 | Humidity > 100) %>% 
    select(Admin_Unit_Code, Point_Name, Year, EventDate, Humidity)

Visits_Big_Humidity_Range<-QCVisits %>% 
  group_by(Admin_Unit_Code, Year, EventDate) %>% 
  summarise(Humidity_Min=min(Humidity), Humidity_Max=max(Humidity), Humidity_Range=Humidity_Max-Humidity_Min) %>% 
  filter(Humidity_Range>20) %>% 
  select(Admin_Unit_Code, Year, EventDate, Humidity_Min, Humidity_Max, Humidity_Range)

#2.9.0
Visits_Bad_Survey<-QCVisits %>% 
  filter(!Survey_Type %in% c("Forest","Grassland")) %>% 
  select(Admin_Unit_Code, Year, EventDate, Survey_Type)

#2.10.0
Visits_Bad_Sky <-QCVisits %>% 
  filter(
    !(Sky_Condition ==0 & Sky =="Clear or Few Clouds") & !(Sky_Condition==1 & Sky== "Partly Cloudy") &
    !(Sky_Condition ==2 & Sky =="Cloudy/Overcast") & !(Sky_Condition ==3 & Sky=="Fog") &
    !(Sky_Condition ==4 & Sky =="Mist/Drizzle") & !(Sky_Condition ==5 & Sky == "Rain Showers")
  ) %>% 
  select(Admin_Unit_Code, Year, EventDate, Sky_Condition, Sky)

#2.11.0
Visits_Bad_Wind <-QCVisits %>% 
  filter(
    !(Wind_Code ==0 & Wind =="Calm (< 1 mph) smoke rises vertically") & !(Wind_Code==1 & Wind == "Light air movement (1-3 mph) smoke drifts") &
    !(Wind_Code ==2 & Wind =="Light breeze (4-7 mph) wind felt on face") & !(Wind_Code ==3 & Wind =="Gentle breeze (8-12 mph), leaves in motion") &
    !(Wind_Code ==4 & Wind =="Moderate breeze (13-18 mph), moves small branches") & !(Wind_Code ==5 & Wind == "Fresh breeze (19-24 mph), small trees sway")
  ) %>% 
  select(Admin_Unit_Code, Year, EventDate, Wind_Code, Wind)

#2.12.0
Visits_Bad_Disturbance <-QCVisits %>% 
  filter(
    !(Disturbance_Level ==0 & Disturbance =="No effect on count") &
    !(Disturbance_Level ==1 & Disturbance == "Slight effect on count") &
    !(Disturbance_Level ==2 & Disturbance =="Moderate effect on count") &
    !(Disturbance_Level ==3 & Disturbance =="Serious effect on count") 
  ) %>% 
  select(Admin_Unit_Code, Year, EventDate, Disturbance_Level, Disturbance)

#2.13.0
Visits_Bad_Observer <- QCVisits %>% 
  filter(is.na(Observer) | Observer == "") %>% 
  select(Admin_Unit_Code, Year, EventDate, Observer)  

```

#### **Visits Checked:** `r TotVisits` ####


### Visits Unit Codes

```{r Visit_location, echo=FALSE, hold=FALSE, results="asis"}

cat("<br>**Missing or Incorrect Visits Unit Code**<br>")
if(nrow(Visits_Bad_Unit)==0) cat("All visits have a recoginized unit code.<br>") else {
errorText("Visits without a recognized unit code:"); NiceTable(Visits_Bad_Unit)}

```

---

### Visit Points

```{r Visit_Points, echo=FALSE, hold=FALSE, results="asis"}
cat("<br>**Missing or Incorrect Point Name**<br>")
if(nrow(Visits_Missing_Point)==0) cat("All visits have a point name that we use.<br>") else {
errorText("Visits without a point name, or from a point we don't monitor:"); NiceTable(Visits_Missing_Point)}

```


---

### Visit Date

```{r Visit_Date, echo=FALSE, hold=FALSE, results="asis"}

cat("<br>**Missing or Incorrect Event Date**<br>")
if(nrow(Visits_No_Date)==0) cat("All visits have an event date.<br>") else {
errorText("Visits with no date:"); NiceTable(Visits_No_Date)}

cat("<br>**Mulitple Visits to a Point on the Same Day**<br>")
if(nrow(Visits_Date_Dupliacated)==0) cat("No point was visited more than once on a single day.<br>") else {
errorText("Points with more than one visits on a single day:"); NiceTable(Visits_Date_Dupliacated)}
 
cat("<br>**Year should match Visit Date**<br>")
if(nrow(Visits_Bad_Year)==0) cat("All visit years match their event dates.<br>") else {
errorText("There is a mismach between year and event date:"); NiceTable(Visits_Bad_Year)}

```

---

### Visit Time

```{r Visit_Time, echo=FALSE, hold=FALSE, results="asis"}
cat("<br>**Missing or Incorrect Start Time**<br>")
if(nrow(Visits_Bad_StartTime)==0) cat("All visits have a start time.<br>") else {
errorText("Visits without a starting time:"); NiceTable(Visits_Bad_StartTime)}

cat("<br>**Missing or Incorrect End Time**<br>")
if(nrow(Visits_Bad_EndTime)==0) cat("All visits have an end time.<br>") else {
errorText("Visits without an ending time:"); NiceTable(Visits_Bad_EndTime)}

cat("<br>**Visits that lasted other than 10 minutes**<br>")
if(nrow(Visits_Bad_Length)==0) cat("All visits lasted 10 minutes.<br>") else {
errorText("Visits that were not 10 minutes long:"); NiceTable(Visits_Bad_Length)}

```

---

### Visit Number

```{r Visits_visit_mumber, echo=FALSE, hold=FALSE, results="asis"}
cat("<br>**Missing or Incorrect Visit Number**<br>")
if(nrow(Visits_Bad_Visit)==0) cat("All visits have a valid visit number.<br>") else {
errorText("Visits without a valid visit number:"); NiceTable(Visits_Bad_Visit)}

cat("<br>**Duplicated Visit Numbers**<br>")
if(nrow(Visits_Duplicated_Visit)==0) cat("No visit numbers were duplicated at a point in a single year.<br>") else {
errorText("Duplicated Visit Numbers:"); NiceTable(Visits_Duplicated_Visit)}

cat("<br>**Missing Visits**<br>")
if(nrow(Visits_Missing_Visit)==0) cat("No visit numbers were skipped at a point in a single year.<br>") else {
errorText("Groups of visits with a missing visit number:"); NiceTable(Visits_Missing_Visit)}

cat("<br>**Visit Order vs Event Date Order**<br>")
if(nrow(Visits_Bad_Order)==0) cat("All visit numbers are in the same order as their event dates.<br>") else {
errorText("Viis numnber that are in a different order than their event dates:"); NiceTable(Visits_Bad_Order)}
```

---

### Temperature

```{r Visit_Temperature, echo=FALSE, hold=FALSE, results="asis"}
cat("<br>**Missing or Suspicious Temperatures**<br>")
if(nrow(Visits_Bad_Temp)==0) cat("All visits have a temperature between 7 and 37 C.<br>") else {
errorText("Visits without temperature between 7 and 37 C:"); NiceTable(Visits_Bad_Temp)}

cat("<br>**Big Temperature Range**<br>")
if(nrow(Visits_Big_Temp_Range)==0) cat("All dates have a temperature range of less than 10 degrees C.<br>") else {
errorText("Event dates where the temperature range is 10 or more degrees C:"); NiceTable(Visits_Big_Temp_Range)}

```

---

### Humidity

```{r Visit_Humidity, echo=FALSE, hold=FALSE, results="asis"}
cat("<br>**Missing or Suspicious Humidity**<br>")
if(nrow(Visits_Bad_Humidity)==0) cat("All visits have a humidity between 40 and 100%.<br>") else {
errorText("Visits without humidity between 40 and 100%:"); NiceTable(Visits_Bad_Humidity)}

 cat("<br>**Big Humidity Range**<br>")
 if(nrow(Visits_Big_Humidity_Range)==0) cat("All dates have a humidity range of less than 20 %.<br>") else {
 errorText("Event dates where the humidity range is 20 or more %:"); NiceTable(Visits_Big_Humidity_Range)}

```

---

### Survey Type

```{r Visit_Survey, echo=FALSE, hold=FALSE, results="asis"}
cat("<br>**Missing or Incorrect Survey Type**<br>")
if(nrow(Visits_Bad_Survey)==0) cat("All visits have a survey type of Forest or Grassland.<br>") else {
errorText("Visits with a survey type that is not Forest or Grassalnd:"); NiceTable(Visits_Bad_Survey)}

```

---

### Sky Conditions

```{r Visit_Sky, echo=FALSE, hold=FALSE, results="asis"}
cat("<br>**Missing or Incorrect Sky Conditions**<br>")
if(nrow(Visits_Bad_Sky)==0) cat("All visits have valid Sky and Sky Condidtion values <br>") else {
errorText("Visits with Sky or Sky Condition values we don't use:"); NiceTable(Visits_Bad_Sky)}

```

---

### Wind

```{r Visit_Wind, echo=FALSE, hold=FALSE, results="asis"}
cat("<br>**Missing or Incorrect Wind**<br>")
if(nrow(Visits_Bad_Wind)==0) cat("All visits have valid Wind and Wind Code values <br>") else {
errorText("Visits with Wind or Wind Code values we don't use:"); NiceTable(Visits_Bad_Wind)}

```

---

### Distrubance

```{r Visit_Disturbance, echo=FALSE, hold=FALSE, results="asis"}
cat("<br>**Missing or Incorrect Disturbance**<br>")
if(nrow(Visits_Bad_Disturbance)==0) cat("All visits have valid Disturbance and Distrubance Level values <br>") else {
errorText("Visits with Disturbance or Disturbance Level values we don't use:"); NiceTable(Visits_Bad_Disturbance)}

```


---

### Observers

```{r Visit_Observers, echo=FALSE, hold=FALSE, results="asis"}
cat("<br>**Missing Observers**<br>")
if(nrow(Visits_Bad_Observer)==0) cat("All visits have an Observer.<br>") else {
errorText("Visits that are missing an Observer:"); NiceTable(Visits_Bad_Observer)}

```