#PalMod1_0_1

---
title: "PalMod1_0_1"
output: 
  flexdashboard::flex_dashboard:
    vertical_layout: scroll
    theme: bootstrap
    source_code: embed
    orientation: rows
---

```{r setup, include = FALSE}
library(flexdashboard)
library(maptools)
library(tidyverse)
library(purrr)
library(leaflet)
library(plotly)
library(lipdR)
library(dygraphs)
library(geoChronR)
library(lipdverseR)
#read functions
load("../../temp.Rdata")
load("../../chronTemp.Rdata")


#remove columns we don't want to plot
varNames <- sapply(TS, "[[","paleoData_variableName")

# good <- which(!(varNames %in% c("year","depth","age")))
# TS <- TS[good]



#All datasets
dsn <- lipdR::pullTsVariable(TS,"dataSetName")
ui <- which(!duplicated(dsn))
udsn <- dsn[ui]
lat <- lipdR::pullTsVariable(TS,"geo_latitude")[ui]
lon <- lipdR::pullTsVariable(TS,"geo_longitude")[ui]
elev <- lipdR::pullTsVariable(TS,"geo_elevation")[ui]


archiveType <- lipdR::pullTsVariable(TS,"archiveType")[ui]
link <- paste0(udsn,".html") %>%
  str_replace_all("'","_")


#Organize metadata for map
map.meta <- data.frame(dataSetName = udsn, #datasetname
                       lat = lat,#lat
                       lon = lon,#lon
                      # elev = elev,#elevation
                       archiveType = factor(archiveType),#archiveType
                       link = link)#Link


#set index number

i = 1
```
#PalMod1_0_1

Metadata {.sidebar}
-------------------------------------
[Download all LiPD files for PalMod1_0_1](PalMod1_0_1.zip)
            

[Download R serialization of all LiPD files for PalMod1_0_1](PalMod1_0_1.RData)
            

[Download matlab serialization of all LiPD files for PalMod1_0_1](PalMod1_0_1.mat)
            

[Download python (pickle) serialization of all LiPD files for PalMod1_0_1](PalMod1_0_1.pkl)
            

[Report an issue (include project name)](https://github.com/nickmckay/LiPDverse/issues)
            

[View changelog for PalMod1_0_1](metadataChangelog.html)


Row {.tabset .tabset-fade}
-----------------------------------------------------------------------

### Sitemap

```{r}
  map.meta.split <- split(map.meta, map.meta$archiveType)


factpal <- colorFactor("Paired",map.meta$archiveType)
buff <- 60
l <- leaflet() %>% 
  addTiles() %>% 
  fitBounds(map.meta$lon[i]-buff,map.meta$lat[i]-buff,map.meta$lon[i]+buff,map.meta$lat[i]+buff)
  

  
  
names(map.meta.split) %>%
  purrr::walk( function(df) {
    l <<- l %>%
      addMarkers(data=map.meta.split[[df]],
                 lng=~lon, lat=~lat,
                 label=~as.character(archiveType),
                 popup=~paste(str_c('Dataset: ',dataSetName,''),
                                 # str_c("Elevation: ",elev),
                                  str_c("Archive Type: ",archiveType),
                                  sep = "
"),
                 group = df,
                 clusterOptions = markerClusterOptions(removeOutsideVisibleBounds = F),
                 labelOptions = labelOptions(noHide = F,
                                             direction = 'auto'))
  })

l <- l %>%   addCircleMarkers(lng = map.meta$lon[i], lat = map.meta$lat[i],radius = 20,color = "red",fillColor = "none")

l %>%
  addLayersControl(position = "bottomleft",
    overlayGroups = names(map.meta.split),
    options = layersControlOptions(collapsed = FALSE,
                                   opacity = 0.8)
  )
```

### Search the LiPDverse (Beta! doesn't work well yet)
```{r}
#Add google search bar
htmltools::includeHTML("../../googleSearchChunk.html")
```