TCStemplate.Rmd

---
title: ""
output: pdf_document
params:
  data: NA
  siteCol: NA
  dateCol: NA
  varsCol: NA
  dataFormat: NA
  Sites: NA
  rendered_by_shiny: FALSE
---
```{r eval=TRUE,echo=FALSE,warning=FALSE}
df <- params$data
df$Month <- factor(month.name[df$Month], levels=month.name[1:12])
s <- params$siteCol
d <- params$dateCol
dform <- params$dataFormat
v <- params$varsCol
if (dform == "Wide"){
  vcols <- which(colnames(df)%in% v)
}
mcol <- which(colnames(df)== "Month")
ycol <- which(colnames(df)== "Year")
site <- unique(df[,s])[1]

```
# Temporal Coverage Summary Report: `r site `

```{r eval=TRUE,echo=FALSE,warning=FALSE,message=FALSE,error=FALSE}
ggplot(data = df, aes(x = Month)) + geom_bar(aes(fill=Year)) + theme_bw() + xlab("Month") + ylab("Number of Observations") + ggtitle(paste("Observation Counts by Month"))
```

```{r eval=TRUE,echo=FALSE,warning=FALSE,message=FALSE,error=FALSE}
ggplot(data = df, aes(x = Year)) + geom_bar(aes(fill=Month)) + theme_bw() + xlab("Month") + ylab("Number of Observations") + ggtitle(paste("Observation Counts by Year"))
```

```{r eval=TRUE,echo=FALSE,warning=FALSE,message=FALSE,error=FALSE}
library(dplyr)

if (dform == "Wide"){
  new <- df
  new <- new[,c(ycol,mcol,vcols)]
  new <- new %>% group_by(Year) %>% dplyr::summarise(Count = dplyr::n())

}
if (dform =="Long")
{
  groups <- c("Year",v)
 new <- df %>% group_by_at(groups) %>% dplyr::summarise(n = dplyr::n())
 
}
knitr::kable(new, caption="Observation Counts")
```


```{r,echo=FALSE}
if (params$rendered_by_shiny)
  shiny::setProgress(0.5)  # set progress to 50%
```



```{r,echo=FALSE}
if (params$rendered_by_shiny)
  shiny::setProgress(0.75)  # set progress to 75%
```




```{r,echo=FALSE}
if (params$rendered_by_shiny)
  shiny::setProgress(1)  # set progress to 100%
```