#TN062-0550.Barron.2018
---
title: "TN062-0550.Barron.2018"
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 = 640
thisTS <- TS[which(udsn[i] == dsn)]
```
#TN062-0550.Barron.2018
Metadata {.sidebar}
-------------------------------------
[Download LiPD file](TN062-0550.Barron.2018.lpd)
[Edit LiPD file](http://lipd.net/playground?source=http://lipdverse.org/Temp12k/1_0_2/TN062-0550.Barron.2018.lpd)
[Download paleoData only (csv)](TN062-0550.Barron.2018.csv)
[Download chronData only (csv)](TN062-0550.Barron.2018-chron.csv)
[Report an issue (include dataset name)](https://github.com/nickmckay/LiPDverse/issues)
root
archiveType: MarineSediment
originalDataUrl: www.ncdc.noaa.gov/paleo/study/27330
lipdVersion: 1.3
pub
pub1
author: list(list(name = "Barron, John A.; Bukry, David; Heusser, Linda E.; Addison, Jason A.; Alexander, Clark R."))
citeKey: S4IFMCS6
journal: Quaternary International
volume: 469
pages: 109 119
title: High-resolution climate of the past _7300 years of coastal northernmost California: Results from diatoms, silicoflagellates, and pollen
pub2
geo
latitude: 40.8656
longitude: -124.573
elevation: -569
siteName: TN062-0550
PaleoData columns
depthRange (cm) [1-1]
TSid: WEBe8c80314
variableName: depthRange
units: cm
depth (cm) [1-1]
TSid: WEB9bb9e2f9
variableName: depth
units: cm
description: composite depth
age (BP) [1-1]
TSid: WEB5bbb384d
variableName: age
units: BP
description: Original age in years before 1950 AD
Picea (percent) [1-1]
TSid: WEBe7dad2eb
variableName: Picea
units: percent
description: Picea = proxy for winter temp
useInGlobalTemperatureAnalysis: TRUE
interpretation
1
direction: positive
scope: climate
seasonality: winter
variable: T
isAnnual: FALSE
variableOriginal: TRUE
seasonalityGeneral: winterOnly
variableGroup: Temperature
variableGroupOriginal: T
variableDetail: air@surface
variableGroupDirection: list("negative")
Sequoia (percent) [1-1]
TSid: WEBa93dede4
variableName: Sequoia
units: percent
description: Sequoia = proxy for coastal fog (=upwelling) and has also been interpreted as coastal hydroclimate
useInGlobalTemperatureAnalysis: TRUE
interpretation
1
direction: positive
scope: climate
seasonality: annual
isAnnual: FALSE
variable: P-E
variableGroup: P-E
seasonalityGeneral: annual
variableOriginal: P-E
variableDetail: @surface
Quercus (percent) [1-1]
TSid: WEB49245d00
variableName: Quercus
units: percent
description: Quercus = warm, dry, mostly from interior. Effective moisture
useInGlobalTemperatureAnalysis: TRUE
interpretation
1
direction: negative
scope: climate
seasonality: summer
isAnnual: FALSE
variable: P-E
variableGroup: P-E
seasonalityGeneral: summerOnly
variableOriginal: P-E
variableDetail: @surface
Alnus (percent) [1-1]
TSid: WEBeb8b7a07
variableName: Alnus
units: percent
description: Anus (alder) = wet along river banks
useInGlobalTemperatureAnalysis: TRUE
interpretation
1
direction: positive
scope: climate
seasonality: annual
isAnnual: FALSE
variable: P-E
variableGroup: P-E
seasonalityGeneral: annual
variableOriginal: P-E
variableDetail: @surface
Calibrated (missing) [1-1]
TSid: WEB5f263302
variableName: Calibrated
units: missing
description: R for radiocarbon and CAL for calibrated age
useInGlobalTemperatureAnalysis: FALSE
depthRange (cm) [1-2]
TSid: WEB7439db68
variableName: depthRange
units: cm
depth (cm) [1-2]
TSid: WEB39869b05
variableName: depth
units: cm
description: composite depth
age (BP) [1-2]
TSid: WEB3b97d1b8
variableName: age
units: BP
description: calibarated years before 1950
Calibrated (missing) [1-2]
TSid: WEB1edd6bbb
variableName: Calibrated
units: missing
description: R for radiocarbon, CAL for calibrated age
useInGlobalTemperatureAnalysis: FALSE
Fragilariopsis (percent) [1-2]
TSid: WEB05d286cd
variableName: Fragilariopsis
units: percent
description: Fragilariopsis doliolus. Winter SST proxy
useInGlobalTemperatureAnalysis: FALSE
depthRange (cm) [1-3]
TSid: WEBafc93b60
variableName: depthRange
units: cm
depth (cm) [1-3]
TSid: WEB3e7e56fc
variableName: depth
units: cm
description: Composite depth
age (BP) [1-3]
TSid: WEB52b1937a
variableName: age
units: BP
description: original age
upwelling (percent) [1-3]
TSid: WEB47918ab8
variableName: upwelling
units: percent
description: proxy for subtropical water
useInGlobalTemperatureAnalysis: TRUE
interpretation
1
direction: negative
scope: climate
seasonality: summer
isAnnual: FALSE
variable: upwelling
variableGroup: upwelling
variableDetail: upwelling@surface
seasonalityGeneral: summerOnly
Dc_stapedia_aspinosa (percent) [1-3]
TSid: WEB5e293c85
variableName: Dc_stapedia_aspinosa
units: percent
description: Dc. stapedia aspinosa proxy for subtropical water
useInGlobalTemperatureAnalysis: FALSE
interpretation
1
direction: negative
scope: climate
seasonality: Summer
isAnnual: FALSE
variable: upwelling
variableGroup: upwelling
upwelling (percent) [1-3]
TSid: WEBfd6711c4
variableName: upwelling
units: percent
description: Dc. stapedia spinosa proxy for subtropical water
useInGlobalTemperatureAnalysis: TRUE
interpretation
1
direction: negative
scope: climate
seasonality: summer
isAnnual: FALSE
variable: upwelling
variableGroup: upwelling
variableDetail: upwelling@surface
seasonalityGeneral: summerOnly
upwelling (percent) [1-3]
TSid: WEB773c247c
variableName: upwelling
units: percent
description: total Dc. stapedia proxy for subtropical water
useInGlobalTemperatureAnalysis: TRUE
interpretation
1
direction: negative
scope: climate
seasonality: summer
isAnnual: FALSE
variable: upwelling
variableGroup: upwelling
variableDetail: upwelling@surface
seasonalityGeneral: summerOnly
upwelling (percent) [1-3]
TSid: WEBd49b515b
variableName: upwelling
units: percent
description: S..speculum var. minutus proxy for cold upwelling water
useInGlobalTemperatureAnalysis: TRUE
interpretation
1
direction: positive
scope: climate
seasonality: summer
isAnnual: FALSE
variable: upwelling
variableGroup: upwelling
variableDetail: upwelling@surface
seasonalityGeneral: summerOnly
Calibrated (missing) [1-3]
TSid: WEB173a177b
variableName: Calibrated
units: missing
description: R for radiocarbon and CAL for calibrated age
useInGlobalTemperatureAnalysis: FALSE
ChronData columns
age (yr)
TSid: WEB51d59bc7
variableName: age
units: yr
description: average depth of each sample
depth (cm)
TSid: WEB48a410bd
variableName: depth
units: cm
description: composite depth
age (yrBP)
TSid: WEBced593fd
variableName: age
units: yrBP
description: calibrated (surface) and radiocarbon ages
age_type (NA)
TSid: WEBef2ac056
variableName: age_type
units: NA
Core (NA)
TSid: WEBb221d41a
variableName: Core
units: NA
material (NA)
TSid: WEB438ba399
variableName: material
units: NA
uncertainty_young (yr)
TSid: WEBd6a33c16
variableName: uncertainty_young
units: yr
uncertainty_old (yr)
TSid: WEBe217a565
variableName: uncertainty_old
units: yr
rejected (NA)
TSid: WEB686af35e
variableName: rejected
units: NA
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}
-----------------------------------------------------------------------
### Picea (percent)
```{r}
plotCol(thisTS,ind = 5)
```
### Sequoia (percent)
```{r}
plotCol(thisTS,ind = 6)
```
### Quercus (percent)
```{r}
plotCol(thisTS,ind = 7)
```
### Alnus (percent)
```{r}
plotCol(thisTS,ind = 8)
```
### Calibrated (missing)
```{r}
plotCol(thisTS,ind = 4)
```
### Calibrated (missing)
```{r}
plotCol(thisTS,ind = 12)
```
### Fragilariopsis (percent)
```{r}
plotCol(thisTS,ind = 13)
```
### upwelling (percent)
```{r}
plotCol(thisTS,ind = 18)
```
### Dc_stapedia_aspinosa (percent)
```{r}
plotCol(thisTS,ind = 19)
```
### upwelling (percent)
```{r}
plotCol(thisTS,ind = 20)
```
### upwelling (percent)
```{r}
plotCol(thisTS,ind = 21)
```
### upwelling (percent)
```{r}
plotCol(thisTS,ind = 22)
```
### Calibrated (missing)
```{r}
plotCol(thisTS,ind = 17)
```
Row {.tabset .tabset-fade}
-----------------------------------------------------------------------
### age (yr)
```{r}
plotCol(chronTS,ind = 3)
```
### depth (cm)
```{r}
plotCol(chronTS,ind = 4)
```
### age (yrBP)
```{r}
plotCol(chronTS,ind = 5)
```
### age_type (NA)
```{r}
plotCol(chronTS,ind = 8)
```
### Core (NA)
```{r}
plotCol(chronTS,ind = 1)
```
### material (NA)
```{r}
plotCol(chronTS,ind = 2)
```
### uncertainty_young (yr)
```{r}
plotCol(chronTS,ind = 6)
```
### uncertainty_old (yr)
```{r}
plotCol(chronTS,ind = 7)
```
### rejected (NA)
```{r}
plotCol(chronTS,ind = 9)
```