#Breitnau-Neuhof.Roesch.2009
---
title: "Breitnau-Neuhof.Roesch.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 = 63
thisTS <- TS[which(udsn[i] == dsn)]
```
#Breitnau-Neuhof.Roesch.2009
Metadata {.sidebar}
-------------------------------------
[Download LiPD file](Breitnau-Neuhof.Roesch.2009.lpd)
[Edit LiPD file](http://lipd.net/playground?source=http://lipdverse.org/Temp12k/1_0_2/Breitnau-Neuhof.Roesch.2009.lpd)
[Download paleoData only (csv)](Breitnau-Neuhof.Roesch.2009.csv)
[Download chronData only (csv)](Breitnau-Neuhof.Roesch.2009-chron.csv)
[Report an issue (include dataset name)](https://github.com/nickmckay/LiPDverse/issues)
root
archiveType: Peat
originalDataUrl: 10.25921/4RY2-G808
lipdVersion: 1.3
dataContributor: Marsicek
pub
pub1
author: list(list(name = "Roesch, M."))
citeKey: XB5ULWSY
journal: Mitt. Ver. Forstl. Standortskunde u. Forstpflanzenzuechtung
volume: 46
pages: 15 24
title: Zur vorgeschichtlichen Besiedlung und Landnutzung im noerdlichen Schwarzwald aufgrund vegetationsgeschichtlicher Untersuchungen in zwei Karseen. [Prehistoric settlement and land use history of the Northern Black Forest as indicated by pollenanalytical investigations in two cirque lakes]
pub2
geo
latitude: 47.93
longitude: 8.07
elevation: 986
siteName: Breitnau-Neuhof
country: Germany
PaleoData columns
age (BP)
TSid: RV3cEBPKLrN
variableName: age
units: BP
depth (cm)
TSid: Rd5msPjFTdF
variableName: depth
units: cm
GDD5 (GDD5)
TSid: RARcblFICzL
variableName: GDD5
units: GDD5
interpretation
1
variable: GDD
direction: positive
seasonality: warm season
scope: climate
variableGroup: GDD
seasonalityOriginal: summer
seasonalityGeneral: summer
variableDetail: air@surface
temperature (degC)
TSid: R5TK1pF5QBE
variableName: temperature
units: degC
interpretation
1
variable: T
direction: positive
seasonality: coldest month
scope: climate
variableGroup: Temperature
variableOriginal: temperature
variableGroupOriginal: T
seasonalityGeneral: winter+
variableDetail: air@surface
variableGroupDirection: list("negative")
temperatureComposite (degC)
TSid: RQHbe4cH6UU
variableName: temperatureComposite
units: degC
interpretation
1
variable: T
direction: positive
seasonality: warmest + coldest months
scope: climate
variableGroup: Temperature
seasonalityOriginal: annual
variableOriginal: temperature
variableGroupOriginal: T
seasonalityGeneral: annual
variableDetail: air@surface
variableGroupDirection: list("negative")
precipitation (mm)
TSid: R9HguzMzOAE
variableName: precipitation
units: mm
interpretation
1
variable: M
direction: positive
seasonality: annual
scope: climate
variableGroup: M
seasonalityOriginal: 1 2 3 4 5 6 7 8 9 10 11 12
variableDetail: precip@surface
temperature (degC)
TSid: RBcRoisjDj1
variableName: temperature
units: degC
interpretation
1
variable: T
direction: positive
seasonality: warmest month
scope: climate
variableGroup: Temperature
variableOriginal: temperature
variableGroupOriginal: T
seasonalityGeneral: summer+
variableDetail: air@surface
variableGroupDirection: list("negative")
ChronData columns
depth (cm)
variableName: depth
units: cm
age (yr BP)
variableName: age
units: yr BP
ageHi (yr BP)
variableName: ageHi
units: yr BP
ageLow (yr BP)
variableName: ageLow
units: yr BP
age_type (unitless)
variableName: age_type
units: unitless
thickness (cm)
variableName: thickness
units: cm
labID (unitless)
variableName: labID
units: unitless
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}
-----------------------------------------------------------------------
### GDD5 (GDD5)
```{r}
plotCol(thisTS,ind = 3)
```
### temperature (degC)
```{r}
plotCol(thisTS,ind = 4)
```
### temperatureComposite (degC)
```{r}
plotCol(thisTS,ind = 5)
```
### precipitation (mm)
```{r}
plotCol(thisTS,ind = 6)
```
### temperature (degC)
```{r}
plotCol(thisTS,ind = 7)
```
Row {.tabset .tabset-fade}
-----------------------------------------------------------------------
### depth (cm)
```{r}
plotCol(chronTS,ind = 1)
```
### age (yr BP)
```{r}
plotCol(chronTS,ind = 4)
```
### ageHi (yr BP)
```{r}
plotCol(chronTS,ind = 5)
```
### ageLow (yr BP)
```{r}
plotCol(chronTS,ind = 6)
```
### age_type (unitless)
```{r}
plotCol(chronTS,ind = 7)
```
### thickness (cm)
```{r}
plotCol(chronTS,ind = 2)
```
### labID (unitless)
```{r}
plotCol(chronTS,ind = 3)
```