nwcaLandownerReport_fromApp.Rmd

---
title: "National Wetland Condition Assessment Field Visit Summary"
author: ""
date: ""
params:
  userDataRMD: 'NULL'
output: html_document
---


```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
#suppressPackageStartupMessages(library(tidyverse))
suppressPackageStartupMessages(library(knitr))
suppressPackageStartupMessages(library(kableExtra))


```

```{r logo, echo=FALSE, fig.alt = 'NWCA logo'}

include_graphics("NWCA_logo_sm.jpg")

```

```{r verif, echo=FALSE}

verification_tbl <- subset(params[['userDataRMD']][['AA-1']][[1]], PARAMETER %in% c('SITE_ID','VISIT_NO', "ACTUAL_DATE","AA_LAT", "AA_LON", "HGM_CLASS"),
                       select = c('PARAMETER','RESULT'))

verification_tbl$PARAMETER[verification_tbl$PARAMETER=='SITE_ID'] <- 'Site ID'
verification_tbl$PARAMETER[verification_tbl$PARAMETER=='AA_LAT'] <- 'Latitude'
verification_tbl$PARAMETER[verification_tbl$PARAMETER=='AA_LON'] <- 'Longitude'
verification_tbl$PARAMETER[verification_tbl$PARAMETER=='VISIT_NO'] <- 'Visit Number'
verification_tbl$PARAMETER[verification_tbl$PARAMETER=='ACTUAL_DATE'] <- 'Sample Date'
verification_tbl$PARAMETER[verification_tbl$PARAMETER=='HGM_CLASS'] <- 'HGM Class'

pv1 <- subset(params[['userDataRMD']][['PV-1']][[1]], PARAMETER %in% c('SITESAMP'),
                       select = c('PARAMETER','RESULT'))
sampled <- subset(pv1, PARAMETER=='SITESAMP')$RESULT

```


```{r palt,echo=F}
## Physical Alteration - just list over all types observed in any plot
if(sampled=='Y' & !is.null(params[['userDataRMD']][['P-1']])){
  p1 <- subset(params[['userDataRMD']][['P-1']][[1]], str_detect(PARAMETER, 'WADSUB|WOBSTR|VEGREM|VEGREP|SOILHD|SOILMD') & str_detect(PARAMETER, 'NONE_PRESENT')==FALSE & !is.null(RESULT) & RESULT!='',
               select = c('PARAMETER')) 
  
  if(sampled=='Y' & nrow(p1)>0){
    p1$PATYPE <- with(p1, substring(PARAMETER, 1, 6)) 
    
  }
}

if(sampled=='Y' & !is.null(params[['userDataRMD']][['P-2']])){
  p2 <- subset(params[['userDataRMD']][['P-2']][[1]], str_detect(PARAMETER, 'WADSUB|WOBSTR|VEGREM|VEGREP|SOILHD|SOILMD') & str_detect(PARAMETER, 'NONE_PRESENT')==FALSE & !is.null(RESULT) & RESULT!='',
               select = c('PARAMETER')) 
  
  if(sampled=='Y' & nrow(p2)>0){
    p2$PATYPE <- with(p2, substring(PARAMETER, 1, 6))
    if(exists('p1') & nrow(p1)>0){
      p.all <- rbind(p1, p2)
      puniq <- unique(p.all)
    }
  }else if(sampled=='Y' & nrow(p1)>0){
    puniq <- unique(p1)

  }
  if(exists('puniq')){
    palt_tbl <- puniq
    palt_tbl$PATYPE[palt_tbl$PATYPE=='WADSUB'] <- "Water Addition or Substraction Alterations"
    palt_tbl$PATYPE[palt_tbl$PATYPE=='WOBSTR'] <- "Flow Obstruction Alterations"
    palt_tbl$PATYPE[palt_tbl$PATYPE=='SOILHD'] <- "Soil Hardening"
    palt_tbl$PATYPE[palt_tbl$PATYPE=='SOILMD'] <- "Surface Modification"
    palt_tbl$PATYPE[palt_tbl$PATYPE=='VEGREM'] <- "Vegetation Removal"
    palt_tbl$PATYPE[palt_tbl$PATYPE=='VEGREP'] <- "Vegetation Replacement"
   
    palt_tbl <- unique(subset(palt_tbl, select=c('PATYPE')))
  } else{
    palt_tbl <- data.frame(PATYPE=c("None Observed"),
                           stringsAsFactors=F)
  }

}



```
```{r v2, echo=FALSE}
## Plant species observed
if(sampled=='Y' & !is.null(params[['userDataRMD']][['V-2']])){
  spp <- subset(params[['userDataRMD']][['V-2']][[1]], select = c('SPECIES'))
  
  if(sampled=='Y' & nrow(spp)>0){
    spp <- subset(spp, !is.na(SPECIES))
    spp_tbl <- unique(spp)
    spp_tbl <- spp_tbl[order(spp_tbl$SPECIES),]
  }
}
```



```{r water, echo=FALSE}
if(sampled=='Y' & !is.null(params[['userDataRMD']][['W-1']])){
  # Pull DO, cond, pH, and temp of water
  field_tbl <- subset(params[['userDataRMD']][['W-1']][[1]], PARAMETER %in% c('WATER_TYPE','DO','CONDUCTIVITY','PH','TEMP'),
                 select = c('PARAMETER','RESULT'))
  
  field_tbl$group <- field_tbl$PARAMETER
  
  field_tbl$RESULT[field_tbl$PARAMETER == 'DO'] <- paste(field_tbl$RESULT[field_tbl$PARAMETER == 'DO'], 'mg/L', sep = ' ')
  field_tbl$RESULT[field_tbl$PARAMETER == 'TEMP'] <- paste(field_tbl$RESULT[field_tbl$PARAMETER == 'TEMP'], 'C', sep = ' ')
  field_tbl$RESULT[field_tbl$PARAMETER == 'CONDUCTIVITY'] <- paste(field_tbl$RESULT[field_tbl$PARAMETER == 'CONDUCTIVITY'], 'uS/cm', sep = ' ')
  
  field_tbl$group[field_tbl$group == 'TEMP'] <- 1
  field_tbl$group[field_tbl$group == 'DO'] <- 2
  field_tbl$group[field_tbl$group == 'PH'] <- 3
  field_tbl$group[field_tbl$group == 'CONDUCTIVITY'] <- 4
  field_tbl$group[field_tbl$group == 'WATER_TYPE'] <- 5
  
  field_tbl$PARAMETER[field_tbl$PARAMETER=='TEMP'] <- 'Temperature'
  field_tbl$PARAMETER[field_tbl$PARAMETER=='DO'] <- 'Dissolved Oxygen'
  field_tbl$PARAMETER[field_tbl$PARAMETER=='PH'] <- 'pH'
  field_tbl$PARAMETER[field_tbl$PARAMETER=='CONDUCTIVITY'] <- 'Conductivity'
  field_tbl$PARAMETER[field_tbl$PARAMETER=='WATER_TYPE'] <- 'Predominant Water Feature'
  
  field_tbl <- field_tbl[order(field_tbl$group),]
  field_tbl <- subset(field_tbl, select = -group)

}
```

#### About
This report provides landowners with preliminary data available after sampling. Additional information can be provided to you after laboratory analyses are completed. If you would like to be notified when this information is available, please contact the Crew Leader.


```{r row 1 tables, echo=F}  
kable(verification_tbl,col.names=c('Station Visit Information',''), row.names=FALSE, align=c('l','r')) %>%
  kable_styling(bootstrap_options = 'condensed', full_width = F, position = "float_left") %>%
  column_spec(1, border_right = T) %>%
  column_spec(2, width = "16em")
```

```{r row 1 b tables, echo=F}
if(sampled=='Y' & exists("field_tbl")){
  if(nrow(field_tbl)>0){
  kable(field_tbl,col.names=c('Field Water Quality Measurements',''), row.names=FALSE, align=c('l','r')) %>%
    kable_styling(bootstrap_options = 'condensed', full_width = F, position = "float_left") %>%
    column_spec(1, border_right = T, width = "20em") %>%
    column_spec(2, width = "16em")
  }
}
```

```{r row 1 c tables, echo=F}
if(sampled=='Y' & exists("palt_tbl")){
  if(nrow(palt_tbl)>0){

  kable(palt_tbl ,col.names=c('Types of Physical Alteration Observed'), 
        row.names =FALSE, align=c('l')) %>%
    kable_styling(bootstrap_options = 'condensed', full_width = F, position = "float_left") %>%
    column_spec(1, border_right = T, width = "30em") 
  }
}
```
```{r row 2 tables, echo=F}
if(sampled=='Y' & exists("spp_tbl")){
kable(spp_tbl ,col.names=c('Vascular Plant Species Observed'), row.names =FALSE, align=c('l')) %>%
  kable_styling(bootstrap_options = 'condensed', full_width = F, position = "float_left") %>%
  column_spec(1, border_right = T, width = "30em")
}
```