#AMP112.vanderBilt.2016
---
title: "AMP112.vanderBilt.2016"
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 = 23
thisTS <- TS[which(udsn[i] == dsn)]
```
#AMP112.vanderBilt.2016
Metadata {.sidebar}
-------------------------------------
[Download LiPD file](AMP112.vanderBilt.2016.lpd)
[Edit LiPD file](http://lipd.net/playground?source=http://lipdverse.org/Temp12k/1_0_2/AMP112.vanderBilt.2016.lpd)
[Download paleoData only (csv)](AMP112.vanderBilt.2016.csv)
[Download chronData only (csv)](AMP112.vanderBilt.2016-chron.csv)
[Report an issue (include dataset name)](https://github.com/nickmckay/LiPDverse/issues)
root
archiveType: LakeSediment
originalDataUrl: 10.1594/PANGAEA.868935
lipdVersion: 1.3
pub
pub1
author: list(list(name = "van der Bilt, Willem G.M.; D'Andrea, William J.; Bakke, Jostein; Balascio, Nicholas L.; Werner, Johannes P.; Gjerde, Marthe; Bradley, Raymond S."))
citeKey: ECUUQ2NN
journal: Quaternary Science Reviews
volume: 183
pages: 204 213
title: Alkenone-based reconstructions reveal four-phase Holocene temperature evolution for high arctic Svalbard
funding
funding1
agency: Funding Agency
grant: Grant name or number
geo
latitude: 79.77
longitude: 10.74
elevation: 35
siteName: AMP112
PaleoData columns
year (AD)
TSid: WEBfa18cf11
variableName: year
units: AD
description: Year AD
age (BP)
TSid: WEBde76d47b
variableName: age
units: BP
description: Years before present (1950) BP
depth (m)
TSid: WEBcdb791a3
variableName: depth
units: m
description: depth
temperature (degC)
TSid: LPDdd0e97b8
variableName: temperature
units: degC
description: Temperature, relative [K] (T rel) * PI: van der Bilt, Willem G M (https://orcid.org/0000-0003-3157-451X, willemvanderbilt@gmail.com) * METHOD: Calculated from UK37 (D'Andrea et al., 2016) (URI: https://doi.org/10.1016/j.gca.2015.10.031) * COMMENT: Calculated using the Group I calibration slope presented by D'Andrea et al. (2016). As we could not calibrate UK37 values to in-situ temperature observations for this study (no overlap with instrumental period) - we present the relative values generating by this algorithm.
useInGlobalTemperatureAnalysis: FALSE
interpretation
1
interpDirection: positive
scope: climate
variable: T
variableOriginal: TRUE
variableGroup: Temperature
variableGroupOriginal: T
variableGroupDirection: list("negative")
temperature (degC)
TSid: LPDd2a984fe
variableName: temperature
units: degC
description: Temperature, relative [K] (T rel) * PI: van der Bilt, Willem G M (https://orcid.org/0000-0003-3157-451X, willemvanderbilt@gmail.com) * METHOD: Calculated from UK37 (D'Andrea et al., 2016) (URI: https://doi.org/10.1016/j.gca.2015.10.031) * COMMENT: Relative Temperature t.o.v. dataset mean, values have been weighted by the mean relative temperature value of the entire (Holocene) dataset
useInGlobalTemperatureAnalysis: TRUE
interpretation
1
scope: climate
variable: T
direction: positive
seasonality: 6,7,8
seasonalityOriginal: summer
isAnnual: FALSE
variableOriginal: TRUE
seasonalityGeneral: summer+
variableGroup: Temperature
variableGroupOriginal: T
variableDetail: lake@surface
variableGroupDirection: list("negative")
sampleID (unitless)
TSid: LPDa91ef31f
variableName: sampleID
units: unitless
useInGlobalTemperatureAnalysis: FALSE
Uk37 (unitless)
TSid: LPD7bedf5be
variableName: Uk37
units: unitless
useInGlobalTemperatureAnalysis: FALSE
ChronData columns
depth_top (cm)
TSid: LPD27c470ad
variableName: depth_top
units: cm
depth_bottom (cm)
TSid: LPDa5844c77
variableName: depth_bottom
units: cm
age (yr)
TSid: LPD6476bc5f
variableName: age
units: yr
age_type (unitless)
TSid: WEB36098da3
variableName: age_type
units: unitless
LabID (unitless)
TSid: LPDa18816cc
variableName: LabID
units: unitless
material (unitless)
TSid: LPDfc7c718d
variableName: material
units: unitless
1SD (yr)
TSid: LPD6315f935
variableName: 1SD
units: yr
d13C (per mil)
TSid: WEB6aa8c2fa
variableName: d13C
units: per mil
mass C (mg)
TSid: WEBc8fa2273
variableName: mass C
units: mg
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 = 6)
```
### temperature (degC)
```{r}
plotCol(thisTS,ind = 7)
```
### sampleID (unitless)
```{r}
plotCol(thisTS,ind = 1)
```
### Uk37 (unitless)
```{r}
plotCol(thisTS,ind = 5)
```
Row {.tabset .tabset-fade}
-----------------------------------------------------------------------
### depth_top (cm)
```{r}
plotCol(chronTS,ind = 2)
```
### depth_bottom (cm)
```{r}
plotCol(chronTS,ind = 3)
```
### age (yr)
```{r}
plotCol(chronTS,ind = 5)
```
### age_type (unitless)
```{r}
plotCol(chronTS,ind = 9)
```
### LabID (unitless)
```{r}
plotCol(chronTS,ind = 1)
```
### material (unitless)
```{r}
plotCol(chronTS,ind = 4)
```
### 1SD (yr)
```{r}
plotCol(chronTS,ind = 6)
```
### d13C (per mil)
```{r}
plotCol(chronTS,ind = 7)
```
### mass C (mg)
```{r}
plotCol(chronTS,ind = 8)
```