#Holzmaar.Litt.2009
---
title: "Holzmaar.Litt.2009"
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 = 238
thisTS <- TS[which(udsn[i] == dsn)]
```
#Holzmaar.Litt.2009
Metadata {.sidebar}
-------------------------------------
[Download LiPD file](Holzmaar.Litt.2009.lpd)
[Edit LiPD file](http://lipd.net/playground?source=http://lipdverse.org/Temp12k/1_0_2/Holzmaar.Litt.2009.lpd)
[Download paleoData only (csv)](Holzmaar.Litt.2009.csv)
[Download chronData only (csv)](Holzmaar.Litt.2009-chron.csv)
[Report an issue (include dataset name)](https://github.com/nickmckay/LiPDverse/issues)
root
archiveType: LakeSediment
originalDataUrl: 10.25921/4RY2-G808
lipdVersion: 1.3
pub
pub1
author: list(list(name = "Litt, Thomas; SchÌŠlzel, Christian; K _hl, Norbert; Brauer, Achim"))
citeKey: 8N3KPUMY
journal: Boreas
volume: 38
pages: 679 690
title: Vegetation and climate history in the Westeifel Volcanic Field (Germany) during the past 11 000 years based on annually laminated lacustrine maar sediments
geo
latitude: 50.1167
longitude: 6.8833
elevation: 425
siteName: Holzmaar
country: Germany
PaleoData columns
age (Calibrated)
TSid: Ra0Hhlx7RH0
variableName: age
units: Calibrated
temperature (degC)
TSid: RBFjUCSs1ez
variableName: temperature
units: degC
interpretation
1
variable: T
direction: positive
scope: climate
seasonality: 1
seasonalityGeneral: winter+
variableGroup: Temperature
variableGroupOriginal: T
variableDetail: air@surface
variableGroupDirection: list("negative")
temperature (degC)
TSid: RiOf362hfE8
variableName: temperature
units: degC
interpretation
1
variable: T
direction: positive
scope: climate
seasonality: 7
seasonalityGeneral: summer+
variableGroup: Temperature
variableGroupOriginal: T
variableDetail: air@surface
variableGroupDirection: list("negative")
temperatureComposite (degC)
TSid: RiqkBNqHL3T
variableName: temperatureComposite
units: degC
useInGlobalTemperatureAnalysis: TRUE
interpretation
1
variable: T
direction: positive
scope: climate
seasonality: 1,8
seasonalityGeneral: annual
variableGroup: Temperature
variableGroupOriginal: T
variableDetail: air@surface
variableGroupDirection: list("negative")
uncertaintyHigh (missing)
TSid: RrCiXqpbi9y
variableName: uncertaintyHigh
units: missing
uncertaintyLow (missing)
TSid: RRNQN45y0Xu
variableName: uncertaintyLow
units: missing
ReliabIeYN1 (missing)
TSid: R4rMuznN1oR
variableName: ReliabIeYN1
units: missing
uncertaintyHigh (missing)
TSid: RSvFx9SdidF
variableName: uncertaintyHigh
units: missing
uncertaintyLow (missing)
TSid: RsGnBMUx3Aa
variableName: uncertaintyLow
units: missing
ReliabIeYN2 (missing)
TSid: RWOLZG4SOzC
variableName: ReliabIeYN2
units: missing
ChronData columns
age_type ()
TSid: RRmVAPoayNm
variableName: age_type
age ()
TSid: RnZUJCLVKhI
variableName: age
IncludeYN ()
TSid: RAuuiK92BDW
variableName: IncludeYN
Row {.tabset .tabset-fade}
-----------------------------------------------------------------------
### Sitemap
```{r}
map.meta.split <- split(map.meta, map.meta$archiveType)
factpal <- colorFactor("Paired",map.meta$archiveType)
buff <- 15
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")
```
Row {.tabset .tabset-fade}
-----------------------------------------------------------------------
### temperature (degC)
```{r}
plotCol(thisTS,ind = 2)
```
### temperature (degC)
```{r}
plotCol(thisTS,ind = 6)
```
### temperatureComposite (degC)
```{r}
plotCol(thisTS,ind = 10)
```
### uncertaintyHigh (missing)
```{r}
plotCol(thisTS,ind = 3)
```
### uncertaintyLow (missing)
```{r}
plotCol(thisTS,ind = 4)
```
### ReliabIeYN1 (missing)
```{r}
plotCol(thisTS,ind = 5)
```
### uncertaintyHigh (missing)
```{r}
plotCol(thisTS,ind = 7)
```
### uncertaintyLow (missing)
```{r}
plotCol(thisTS,ind = 8)
```
### ReliabIeYN2 (missing)
```{r}
plotCol(thisTS,ind = 9)
```
Row {.tabset .tabset-fade}
-----------------------------------------------------------------------
### age_type ()
```{r}
plotCol(chronTS,ind = 1)
```
### age ()
```{r}
plotCol(chronTS,ind = 2)
```
### IncludeYN ()
```{r}
plotCol(chronTS,ind = 3)
```