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StatsTemplate.Rmd
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---
title: ""
output: pdf_document
params:
data: NA
siteCol: NA
dateCol: NA
varsCol: NA
dataFormat: NA
Sites: NA
sumpar: NA
valuecol: NA
rendered_by_shiny: FALSE
---
---
```{r eval=TRUE,echo=FALSE,warning=FALSE}
df <- params$data
s <- params$siteCol
d <- params$dateCol
dform <- params$dataFormat
v <- params$sumpar
if (dform == "Wide"){
vcol <- which(colnames(df)== v)
}
if (dform == "Long"){
valscol <- which(colnames(df)==params$valuecol)
varscol <- which(colnames(df)== params$varsCol)
df <- subset(df,df[,varscol] == v)
}
mcol <- which(colnames(df)== "Month")
ycol <- which(colnames(df)== "Year")
site <- unique(df[,s])[1]
```
# Parameter Report for `r site `: `r params$sumpar `
```{r eval=TRUE,echo=FALSE,warning=FALSE,collapse=FALSE}
if (dform == "Wide"){
if ((nrow(df) - 2 > sum(is.na(df[,v])))){
n <- nrow(df) - sum(is.na(df[,v]))
twfth <- quantile(mean(df[,v]),c(0.25),na.rm = T)
min <- min(df[,v],na.rm = T)
mean <- mean(df[,v],na.rm = T)
median <- median(df[,v],na.rm = T)
svfth <- quantile(mean(df[,v]),c(0.75),na.rm = T)
max <- max(df[,v],na.rm = T)
na <- sum(is.na(df[,v]))
Table <- data.frame("Count" = n, "Minimum" = min,"Mean" = mean,"Median"= median, "Maximum" = max, "NAs" = na) %>% mutate_if(is.numeric, round, digits=2)
knitr::kable(Table, caption="Summary Statistics")
}}
if (dform == "Long"){
if ((nrow(df) - 2 > sum(is.na(df[,valscol])))){
n <- nrow(df) - sum(is.na(df[,valscol]))
twfth <- quantile(mean(df[,valscol]),c(0.25),na.rm = T)
min <- min(df[,valscol],na.rm = T)
mean <- mean(df[,valscol],na.rm = T)
median <- median(df[,valscol],na.rm = T)
svfth <- quantile(mean(df[,valscol]),c(0.75),na.rm = T)
max <- max(df[,valscol],na.rm = T)
na <- sum(is.na(df[,valscol]))
Table <- data.frame("Count" = n, "Minimum" = min,"Mean" = mean,"Median"= median, "Maximum" = max, "NAs" = na) %>% mutate_if(is.numeric, round, digits=2)
knitr::kable(Table, caption="Summary Statistics")
}}
```
```{r eval=TRUE,echo=FALSE,warning=FALSE,collapse=TRUE}
if (dform == "Wide"){
if ((nrow(df) - 2 > sum(is.na(df[,v])))){
boxplot(df[,vcol],main=paste("All Observations"))
}
}
if (dform == "Long"){
if ((nrow(df) - 2 > sum(is.na(df[,valscol])))){
boxplot(df[,valscol],main=paste("All Observations"))
}
}
```
```{r eval=TRUE,echo=FALSE,warning=FALSE,collapse=TRUE}
if (dform == "Wide"){
if ((nrow(df) - 2 > sum(is.na(df[,v])))){
ggplot(data=df,aes(x=df$Month,y=df[,vcol])) + theme_bw() + ggtitle(paste("Monthly Observations - ",params$sumpar,", ",site)) +geom_boxplot() + theme(axis.text.x = element_text(angle=90, vjust=0.5, size=10)) + xlab("Month") +ylab(params$sumpar)
}
}
if (dform == "Long"){
if ((nrow(df) - 2 > sum(is.na(df[,valscol])))){
ggplot(data=df,aes(x=df$Month,y=df[,valscol])) + theme_bw() + ggtitle(paste("Monthly Observations - ",params$sumpar,", ",site)) +geom_boxplot() + theme(axis.text.x = element_text(angle=90, vjust=0.5, size=10)) + xlab("Month") +ylab(params$sumpar)
}
}
```
```{r eval=TRUE,echo=FALSE,warning=FALSE,collapse=TRUE}
if (dform == "Wide"){
if ((nrow(df) - 2 > sum(is.na(df[,v])))){
ggplot(data=df,aes(x=df$Year,y=df[,vcol])) + theme_bw() + ggtitle(paste("Yearly Observations - ",params$sumpar,", ",site)) +geom_boxplot() + theme(axis.text.x = element_text(angle=90, vjust=0.5, size=10)) + xlab("Year") +ylab(params$sumpar)
}
}
if (dform == "Long"){
if ((nrow(df) - 2 > sum(is.na(df[,valscol])))){
ggplot(data=df,aes(x=df$Year,y=df[,valscol])) + theme_bw() + ggtitle(paste("Yearly Observations - ",params$sumpar,", ",site)) +geom_boxplot() + theme(axis.text.x = element_text(angle=90, vjust=0.5, size=10)) + xlab("Year") +ylab(params$sumpar)
}
}
```