#LS13WASU

---
title: "LS13WASU"
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 = 320
thisTS <- TS[which(udsn[i] == dsn)]
```
#LS13WASU

Metadata {.sidebar}
-------------------------------------
[Download LiPD file](LS13WASU.lpd)
            

[Edit LiPD file](http://lipd.net/playground?source=http://lipdverse.org/iso2k/1_0_0/LS13WASU.lpd)
            

[Download paleoData only (csv)](LS13WASU.csv)
            

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


root
archiveType: LakeSediment
lipdVersion: 1.3


pub

pub1
author: list(list(name = "Wang, Z. , Liu, W. , Liu, Z. , Wang, H. , He, Y. , Zhang, F."))
journal: The Holocene
volume: 23
title: A 1700-year n-alkanes hydrogen isotope record of moisture changes in sediments from Lake Sugan in the Qaidam Basin, northeastern Tibetan Plateau



geo
latitude: 38.8667
longitude: 93.95
elevation: 2800
siteName: Lake Sugan


PaleoData columns

year (AD)
TSid: MAT7cbe87ad3a
variableName: year
units: AD
description: Year AD


depth (cm)
TSid: MAT0bb768872a
variableName: depth
units: cm
description: depth


d2H (permil)
TSid: LS13WASU01B
variableName: d2H
units: permil
description: terrestrial biomarker

interpretation

1
basis: The effective moisture (ratio of precipitation to evaporation) is considered as the main factor controlling the ?D values of lipid n-alkanes in terrestrial plants (Polissar and Freeman, 2010). In a previous study, the ?D record from a loess profile in the Chinese Loess Plateau displayed a strong correlation to changes in the magnetic susceptibility (MS) over the past 130 ka, and the isoto- pic variation was thought to be strongly affected by aridity (Liu and Huang, 2005). Furthermore, a humidity control experiment in the field verified the correlation between D enrichment and rela- tive humidity (McInerney et al., 2011). A study of lipids from the Santa Barbara Basin from the past 1400 years also revealed the ?D of mid-chain acids to be partially correlated with existing data of drought severity (Li et al., 2011).
interpDirection: increase
scope: climate
seasonality: growing season? (not stated)
variable: P/E
variableDetail: air@surface
direction: increase
variableDetailOriginal: air
variableGroup: P/E


2
basis: Variation in vegetation type (shrubs and grass) is the main factor influencing the [d2H of leaf waxes in] sediments of Lake Sugan, because of the dD values of Chenopodiceae shrubs are higher than those of grasses. We can still discuss the moisture history using the hydrogen-isotope record, because the vegetation type would be consistent with hydrological condition. [i.e., Chenopodiaceae shrubs tend to be more abundant in dry climates, and Chenopodiaceae shrubs have a smaller apparent fractionation, so dry climates would not only cause greater evaporative enrichment of plant source water, but more leaf waxes with relatively enriched d2H would be produced by Chenopodiaceae shrubs.] In the arid area of western China, vegetation type is controlled by moisture changes (Wu, 2011).  The authors conclude that variations in vegetation type (shrub or grass), which are caused by moisture changes, are the main factor controlling the δD records in the study area.
direction: negative
inferredMaterial: soil water
mathematicalRelation: linear
rank: 1
scope: isotope
seasonality: unknown
variable: P_E
variableGroup: EffectiveMoisture
variableGroupOriginal: P_E
variableGroupDirection: list("negative")


3
basis: The effective moisture (ratio of precipitation to evaporation) is considered as the main factor controlling the ?D values of lipid n-alkanes in terrestrial plants (Polissar and Freeman, 2010). In a previous study, the ?D record from a loess profile in the Chinese Loess Plateau displayed a strong correlation to changes in the magnetic susceptibility (MS) over the past 130 ka, and the isoto- pic variation was thought to be strongly affected by aridity (Liu and Huang, 2005). Furthermore, a humidity control experiment in the field verified the correlation between D enrichment and relative humidity (McInerney et al., 2011). A study of lipids from the Santa Barbara Basin from the past 1400 years also revealed the dD of mid-chain acids to be partially correlated with existing data of drought severity (Li et al., 2011).
direction: negative
mathematicalRelation: linear
rank: 2
scope: isotope
seasonality: unknown
variable: P_E
variableGroup: EffectiveMoisture
variableGroupOriginal: P_E
variableGroupDirection: list("negative")




d2H (permil)
TSid: LS13WASU01A
variableName: d2H
units: permil
description: terrestrial biomarker

interpretation

1
basis: The effective moisture (ratio of precipitation to evaporation) is considered as the main factor controlling the ?D values of lipid n-alkanes in terrestrial plants (Polissar and Freeman, 2010). In a previous study, the ?D record from a loess profile in the Chinese Loess Plateau displayed a strong correlation to changes in the magnetic susceptibility (MS) over the past 130 ka, and the isoto- pic variation was thought to be strongly affected by aridity (Liu and Huang, 2005). Furthermore, a humidity control experiment in the field verified the correlation between D enrichment and rela- tive humidity (McInerney et al., 2011). A study of lipids from the Santa Barbara Basin from the past 1400 years also revealed the ?D of mid-chain acids to be partially correlated with existing data of drought severity (Li et al., 2011).
interpDirection: increase
scope: climate
seasonality: growing season? (not stated)
variable: P/E
variableDetail: air@surface
variableDetailOriginal: air
variableGroup: P/E


2
basis: Variation in vegetation type (shrubs and grass) is the main factor influencing the [d2H of leaf waxes in] sediments of Lake Sugan, because of the dD values of Chenopodiceae shrubs are higher than those of grasses. We can still discuss the moisture history using the hydrogen-isotope record, because the vegetation type would be consistent with hydrological condition. [i.e., Chenopodiaceae shrubs tend to be more abundant in dry climates, and Chenopodiaceae shrubs have a smaller apparent fractionation, so dry climates would not only cause greater evaporative enrichment of plant source water, but more leaf waxes with relatively enriched d2H would be produced by Chenopodiaceae shrubs.] In the arid area of western China, vegetation type is controlled by moisture changes (Wu, 2011).  The authors conclude that variations in vegetation type (shrub or grass), which are caused by moisture changes, are the main factor controlling the δD records in the study area.
direction: negative
inferredMaterial: soil water
mathematicalRelation: linear
rank: 1
scope: isotope
seasonality: unknown
variable: P_E
variableGroup: EffectiveMoisture
variableGroupOriginal: P_E
variableGroupDirection: list("negative")


3
basis: The effective moisture (ratio of precipitation to evaporation) is considered as the main factor controlling the dD values of lipid n-alkanes in terrestrial plants (Polissar and Freeman, 2010). In a previous study, the dD record from a loess profile in the Chinese Loess Plateau displayed a strong correlation to changes in the magnetic susceptibility (MS) over the past 130 ka, and the isoto- pic variation was thought to be strongly affected by aridity (Liu and Huang, 2005). Furthermore, a humidity control experiment in the field verified the correlation between D enrichment and relative humidity (McInerney et al., 2011). A study of lipids from the Santa Barbara Basin from the past 1400 years also revealed the dD of mid-chain acids to be partially correlated with existing data of drought severity (Li et al., 2011).
direction: negative
mathematicalRelation: linear
rank: 2
scope: isotope
seasonality: unknown
variable: P_E
variableGroup: EffectiveMoisture
variableGroupOriginal: P_E
variableGroupDirection: list("negative")




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}
-----------------------------------------------------------------------

### d2H (permil)
```{r}
plotCol(thisTS,ind = 1)
```

### d2H (permil)
```{r}
plotCol(thisTS,ind = 4)
```