date: '22 November, 2019' output: html_document: keep_md: yes
climproxyrecords
The climproxyrecords
package supplies published proxy climate record data and
compilations. So far it includes data from:
the Marcott et al (2013) and Shakun et al (2012) compilation
the GISP2 Ice Core Temperature and Accumulation Data from Alley (2000)
Uk'37 based proxy for core MD99-2275 from Sicre et al (2011)
Alkenone based reconstruction for core ODP846 from Herbert et al (2010)
Alkenone based reconstruction for core U1313 from Naafs et al (2012)
For the two compilations the package contains three dataframes: proxies
,
dating
, and metadata
(e.g. marcott.proxies
). These
contain the proxy data, associated carbon dating information, and metadata
respectively.
For the individual proxies there are similar dataframes.
alley.accumulation
alley.temperature
sicre.2011.MD99_2275.age.model
sicre.2011.MD99_2275.metadata
sicre.2011.MD99_2275.temperature
naafs.U1313.temperature
naafs.U1313.metadata
herbert.ODP846.temperature
herbert.ODP846.metadata
climproxyrecords
can be installed from github like this:
if (!require("devtools")) {
install.packages("devtools")
}
devtools::install_github("EarthSystemDiagnostics/climproxyrecords")
For the compilations, please cite both the compilaton papers (Marcott et al 2013, Shakun et al
2012), and the original sources from which the data were extracted. A full
list of sources can be found in the metadata dataframes, e.g. marcott.metadata
.
For the other records please cite the original papers. See the help files e.g.
help(sicre.2011.MD99_2275.temperature)
for the correct citations.
climproxyrecords
data packageAfter loading the package with library(climproxyrecords)
, all included data has been "lazy loaded". Data are not in memory yet, but are available when the name of an object is passed to the R interpreter.
library(climproxyrecords)
library(dplyr)
## Warning: package 'dplyr' was built under R version 3.6.1
marcott.proxies
## # A tibble: 13,134 x 13
## Number ID Core.location Proxy.type Proxy.value Published.tempe~
## <int> <chr> <chr> <fct> <dbl> <dbl>
## 1 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## 2 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## 3 1 GeoB~ GeoB5844-2 Uk'37 0.954 26.9
## 4 1 GeoB~ GeoB5844-2 Uk'37 0.937 26.4
## 5 1 GeoB~ GeoB5844-2 Uk'37 0.94 26.5
## 6 1 GeoB~ GeoB5844-2 Uk'37 0.957 27
## 7 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## 8 1 GeoB~ GeoB5844-2 Uk'37 0.937 26.4
## 9 1 GeoB~ GeoB5844-2 Uk'37 0.937 26.4
## 10 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## # ... with 13,124 more rows, and 7 more variables: Proxy.depth.type <chr>,
## # Proxy.depth <dbl>, Published.age <dbl>, Age.model.error <dbl>,
## # depth.flag <lgl>, Age.type <chr>, Age <dbl>
For each proxy compilation, all records are stored in a single dataframe. To access subsets of proxies use either base R's subsetting
subset(marcott.proxies, Proxy.type == "Uk'37")
## # A tibble: 3,222 x 13
## Number ID Core.location Proxy.type Proxy.value Published.tempe~
## <int> <chr> <chr> <fct> <dbl> <dbl>
## 1 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## 2 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## 3 1 GeoB~ GeoB5844-2 Uk'37 0.954 26.9
## 4 1 GeoB~ GeoB5844-2 Uk'37 0.937 26.4
## 5 1 GeoB~ GeoB5844-2 Uk'37 0.94 26.5
## 6 1 GeoB~ GeoB5844-2 Uk'37 0.957 27
## 7 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## 8 1 GeoB~ GeoB5844-2 Uk'37 0.937 26.4
## 9 1 GeoB~ GeoB5844-2 Uk'37 0.937 26.4
## 10 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## # ... with 3,212 more rows, and 7 more variables: Proxy.depth.type <chr>,
## # Proxy.depth <dbl>, Published.age <dbl>, Age.model.error <dbl>,
## # depth.flag <lgl>, Age.type <chr>, Age <dbl>
or dplyr::filter
marcott.proxies %>%
filter(Proxy.type == "Uk'37")
## # A tibble: 3,222 x 13
## Number ID Core.location Proxy.type Proxy.value Published.tempe~
## <int> <chr> <chr> <fct> <dbl> <dbl>
## 1 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## 2 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## 3 1 GeoB~ GeoB5844-2 Uk'37 0.954 26.9
## 4 1 GeoB~ GeoB5844-2 Uk'37 0.937 26.4
## 5 1 GeoB~ GeoB5844-2 Uk'37 0.94 26.5
## 6 1 GeoB~ GeoB5844-2 Uk'37 0.957 27
## 7 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## 8 1 GeoB~ GeoB5844-2 Uk'37 0.937 26.4
## 9 1 GeoB~ GeoB5844-2 Uk'37 0.937 26.4
## 10 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## # ... with 3,212 more rows, and 7 more variables: Proxy.depth.type <chr>,
## # Proxy.depth <dbl>, Published.age <dbl>, Age.model.error <dbl>,
## # depth.flag <lgl>, Age.type <chr>, Age <dbl>
or make a list of dataframes, each a separate proxy record
lst <- plyr::dlply(marcott.proxies, "ID")
lapply(lst[1:2], head)
## $`17940 Uk'37`
## Number ID Core.location Proxy.type Proxy.value
## 1 49 17940 Uk'37 17940 Uk'37 0.929
## 2 49 17940 Uk'37 17940 Uk'37 0.932
## 3 49 17940 Uk'37 17940 Uk'37 0.925
## 4 49 17940 Uk'37 17940 Uk'37 0.926
## 5 49 17940 Uk'37 17940 Uk'37 0.933
## 6 49 17940 Uk'37 17940 Uk'37 0.927
## Published.temperature Proxy.depth.type Proxy.depth Published.age
## 1 26.821 Proxy depth (cm) 0 13.5
## 2 26.922 Proxy depth (cm) 9 174.0
## 3 26.711 Proxy depth (cm) 17 326.0
## 4 26.725 Proxy depth (cm) 21 396.0
## 5 26.950 Proxy depth (cm) 27 492.0
## 6 26.752 Proxy depth (cm) 37 635.0
## Age.model.error depth.flag Age.type Age
## 1 NA TRUE Marine09 age (yr BP) 0.00000
## 2 90.18293 FALSE Marine09 age (yr BP) 74.96323
## 3 96.58324 FALSE Marine09 age (yr BP) 139.87508
## 4 88.40831 FALSE Marine09 age (yr BP) 171.82024
## 5 108.50835 FALSE Marine09 age (yr BP) 242.60834
## 6 116.74236 FALSE Marine09 age (yr BP) 370.76723
##
## $`18287-3 Uk'37`
## Number ID Core.location Proxy.type Proxy.value
## 1 28 18287-3 Uk'37 18287-3 Uk'37 0.9631
## 2 28 18287-3 Uk'37 18287-3 Uk'37 0.9662
## 3 28 18287-3 Uk'37 18287-3 Uk'37 0.9662
## 4 28 18287-3 Uk'37 18287-3 Uk'37 0.9662
## 5 28 18287-3 Uk'37 18287-3 Uk'37 0.9631
## 6 28 18287-3 Uk'37 18287-3 Uk'37 0.9631
## Published.temperature Proxy.depth.type Proxy.depth Published.age
## 1 28.1 Proxy depth (cm) 5 3389
## 2 28.2 Proxy depth (cm) 15 3751
## 3 28.2 Proxy depth (cm) 25 4114
## 4 28.2 Proxy depth (cm) 35 4476
## 5 28.1 Proxy depth (cm) 45 4838
## 6 28.1 Proxy depth (cm) 55 5200
## Age.model.error depth.flag Age.type Age
## 1 377.0880 FALSE Marine09 age (yr BP) 1776.787
## 2 184.3612 FALSE Marine09 age (yr BP) 3746.217
## 3 285.4207 FALSE Marine09 age (yr BP) 4105.665
## 4 346.4947 FALSE Marine09 age (yr BP) 4466.036
## 5 387.1881 FALSE Marine09 age (yr BP) 4826.850
## 6 413.6232 FALSE Marine09 age (yr BP) 5187.967
Core.location does not identify a unique proxy record (for the Marcott data at least) because some cores have multiple proxies measured on them.
name.type <- marcott.proxies %>%
select(Core.location, Proxy.type) %>%
distinct()
name.type %>%
group_by(Core.location) %>%
mutate(n = n_distinct(Proxy.type)) %>%
filter(n > 1)
## # A tibble: 9 x 3
## # Groups: Core.location [3]
## Core.location Proxy.type n
## <chr> <fct> <int>
## 1 MD79-257 Foram T.F. (warm season) 3
## 2 GIK23258-2 Foram T.F. (warm season) 3
## 3 MD79-257 Foram T.F. (cold season) 3
## 4 GIK23258-2 Foram T.F. (cold season) 3
## 5 TN057-17 Diatom T.F. (warm season) 3
## 6 TN057-17 Diatom T.F. (cold season) 3
## 7 MD79-257 Foram T.F. (mean; deg C) 3
## 8 GIK23258-2 Foram T.F. (mean; deg C) 3
## 9 TN057-17 Diatom T.F. (mean; deg C) 3
At present, things like the names of proxy types have been taken "as is" from the supplementary data to the publications. There may be multiple spellings of the same type.
To get additional metadata for the proxies, look at corresponding metadata
dataframe and reference/join by ID
dplyr::left_join(marcott.proxies, marcott.metadata)
## Joining, by = c("Number", "Core.location", "Proxy.type")
## # A tibble: 13,134 x 22
## Number ID Core.location Proxy.type Proxy.value Published.tempe~
## <int> <chr> <chr> <fct> <dbl> <dbl>
## 1 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## 2 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## 3 1 GeoB~ GeoB5844-2 Uk'37 0.954 26.9
## 4 1 GeoB~ GeoB5844-2 Uk'37 0.937 26.4
## 5 1 GeoB~ GeoB5844-2 Uk'37 0.94 26.5
## 6 1 GeoB~ GeoB5844-2 Uk'37 0.957 27
## 7 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## 8 1 GeoB~ GeoB5844-2 Uk'37 0.937 26.4
## 9 1 GeoB~ GeoB5844-2 Uk'37 0.937 26.4
## 10 1 GeoB~ GeoB5844-2 Uk'37 0.950 26.8
## # ... with 13,124 more rows, and 16 more variables:
## # Proxy.depth.type <chr>, Proxy.depth <dbl>, Published.age <dbl>,
## # Age.model.error <dbl>, depth.flag <lgl>, Age.type <chr>, Age <dbl>,
## # Proxy.type.detail <chr>, Temperature.cali.ref <chr>, Lat <dbl>,
## # Lon <dbl>, Elevation <int>, Resolution <int>, Pub.seas.interp <chr>,
## # Reference <chr>, Seasonality.comment <chr>
marcott.metadata %>%
filter(Core.location == "GeoB5844-2")
## # A tibble: 1 x 12
## Number Core.location Proxy.type Proxy.type.deta~ Temperature.cal~ Lat
## <int> <chr> <fct> <chr> <chr> <dbl>
## 1 1 GeoB5844-2 Uk'37 UK’37 Müller et al., ~ 27.7
## # ... with 6 more variables: Lon <dbl>, Elevation <int>, Resolution <int>,
## # Pub.seas.interp <chr>, Reference <chr>, Seasonality.comment <chr>
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