Data Package Metadata View Summary

California Blue Oak reproduction and recruitment, Sierra Foothills, 2005-2010

General Information

Data Package:

Local Identifier:

edi.1225.1

Title:

California Blue Oak reproduction and recruitment, Sierra Foothills, 2005-2010

Alternate Identifier:

DOI PLACE HOLDER

Abstract:

Our study examines these potential factors by quantifying reproductive success (numbers of new seedlings and their sizes) and survival and growth of the younger life stages (seedlings and saplings), and by exploring how the timing of grazing, topographical variables, and rainfall limit reproduction, growth, and survival for these life stages, helping to identify potential management and restoration strategies to enhance the population viability of blue oak. We followed a population of blue oak (Quercus douglasii) seedlings and saplings in the Sierra Nevada foothills, measuring adult seed production and initial seedling recruitment (number and size of new seedlings), seedling growth and survival, seedling recruitment to saplings (growing greater than 10 cm in height), and sapling growth and survival. We tested the impacts on these demographic processes of timing and intensity of grazing, light availability, water availability, and individual size. We published our analysis of these data as part of the 8th Oak Woodland Symposium. This data archive contains the underlying data for our analysis plus some data we did not include in our analysis (residual dry matter, photosynthetically active radiation, percent exotic/native cover), including raw data and R and Perl scripts used to format them for analysis, and additional information not included in the conference proceedings.

Publication Date:

2022-10-03

For more information:
Visit:	DOI PLACE HOLDER

Time Period

Begin:

2005

End:

2010

People and Organizations
Contact:	Suding, K. [ email ]
Creator:	Eitzel, M.V.
Creator:	Rodríguez-Buriticá, S.
Creator:	Harpole, W.S.
Creator:	Aicher, R.
Creator:	Larios, L.
Creator:	McClaran, M.
Creator:	Suding, K.

Data Entities
Data Table Name:	GrazingResults_2022edit
Description:	Grazing data for each field/pasture - each row corresponds to a particular grazing episode for a set number of days with a set number of animals. The processing code will simplify these into just "leaf on animal grazing effort" and "leaf off animal grazing effort". Note that the Water Year and Season were created manually using conditional formatting based on the definitions of water year and seasons given elsewhere in this archive and based on the year and month.
Data Table Name:	MonthlyDataCIMIS_2022edit
Description:	Precipitation in mm for each month, summarized by water year (october-september) and blue oak leaf-off and leaf-on season
Data Table Name:	SubPlotDB
Description:	Data on each subplot where seedlings were tagged and rechecked. Residual Dry Matter, Photosynthetically Active Radiation, and Exotic/Native percent cover were only measured once in 2006.
Data Table Name:	FocalTreeDB_Tabular
Description:	Reproductive status, soil type, and acorn count for adult focal trees around which seedlings and saplings were surveyed.
Data Table Name:	SaplingStatus
Description:	Data for running the statistical models examining sapling survival status
Data Table Name:	SaplingIncrement
Description:	Data required for statistical models examining sapling growth
Data Table Name:	NewSeedlings
Description:	Data needed to run statistical models exploring the size of new seedlings in a given year of the surveys
Data Table Name:	NumberSeedlings
Description:	Data needed for running statistical models exploring the number of seedlings that are newly tagged in a given year.
Data Table Name:	SeedlingIncrement
Description:	Data required to run statistical models exploring how seedlings grow from year to year
Data Table Name:	SeedlingStatus
Description:	Data required for running statistical models exploring seedling survival status
Other Name:	EitzelEtAl_BlueOakRecruitmentReproduction_8thOakSymposium_Final
Description:	Final draft of the paper for the conference proceedings of the 8th Oak Symposium that both describes the methods associated with this dataset and also uses the data in this dataset. This draft is not the version in the Conference Proceedings, but is the final draft created before obtaining a DOI for this dataset.
Other Name:	EitzelEtAl_BlueOakRecruitmentReproduction_8thOakSymposium_AdditionalInformation
Description:	Appendix/additional information describing conference paper analysis methods and giving data summaries and distributions (including variables not included in the conference paper).
Other Name:	SF_oaks_methods survey
Description:	Original draft describing survey methods
Other Name:	SFREC_FocalTrees_Buffer20m
Description:	GIS data with zonal calculations of Topographic Wetness Index and Insolation for each focal tree
Other Name:	SFREC_FocalTreesUsed_all
Description:	GIS file with data on Insolation and Topographical Wetness Index for each adult focal tree
Other Name:	SeedlingStudyAnalysis2022
Description:	R code that ingests the data tables given in this repository, plus the two dbf files listed as "other entities", assembles them and does a final round of quality control, and generates the results shared in the related conference proceedings paper.
Other Name:	RawDataAndPrepCode
Description:	Raw data from oak seedling/sapling surveys and code to create the versions used in the analysis and paper in this archive. PrepareOakData_2022.R assembles the majority of these files into versions that can be ingested by the analysis code. With these two exceptions: animaldays.pl Perl script that takes grazing data in the form provided by the Research and Extension Center (day in, day out, number of head, pasture) and separates it out by year and month so it can be aggregated into a total number of animal days per month, in the R code. OakProject_GrazingData.csv Raw grazing data from the Research and Extension Center with number of head, date in, and date out. animaldays.pl converts this into a form that can be aggregated by month in the R script SeedlingStudyAnalysis2022.R

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1225/1/2ac3c99a9f1e74b6abf830ddb77b63e4
Name:	GrazingResults_2022edit
Description:	Grazing data for each field/pasture - each row corresponds to a particular grazing episode for a set number of days with a set number of animals. The processing code will simplify these into just "leaf on animal grazing effort" and "leaf off animal grazing effort". Note that the Water Year and Season were created manually using conditional formatting based on the definitions of water year and seasons given elsewhere in this archive and based on the year and month.
Number of Records:	89
Number of Columns:	8

Table Structure

Object Name:

GrazingResults_2022edit.csv

Size:

3982 byte

Authentication:

da826c2e79d1545a615e024bc39c0409 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	'

Table Column Descriptions

PastureID

YearAndMonth

Year

Month

GrazeDays

AnimalDays

WaterYear

Season

Column Name:

PastureID

YearAndMonth

Year

Month

GrazeDays

AnimalDays

WaterYear

Season

Definition:

Name of each pasture

Year and month for which grazing occurred

Year of grazing data

Month of grazing

Total number of days within that month period that were grazed for that particular episode of grazing

Number of animals multiplied by the days they were grazed within that month for that particular grazing episode

Water year (oct-sept)

The water year is divided into the oak leaf-off season and leaf-on season

Storage Type:

string

dateTime

string

float

string

Measurement Type:

nominal

dateTime

nominal

ratio

nominal

Measurement Values Domain:

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	K1-11
Definition	Summer/dormant season grazed pasture Koch 1-11
Source

Code Definition

Code	L2
Definition	Winter/growing season grazed pasture Lewis 2
Source

Format	YYYY-MM
Precision

Format	YYYY
Precision

Definition

Month of grazing

Unit	day
Type	integer

Unit	animal-days
Type	integer

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	2002-2003
Definition	oct 2002-sept 2003
Source

Code Definition

Code	2003-2004
Definition	oct 2003 - sept 2004
Source

Code Definition

Code	2004-2005
Definition	oct 2004 - sept 2005
Source

Code Definition

Code	2005-2006
Definition	oct 2005- sept 2006
Source

Code Definition

Code	2006-2007
Definition	oct 2006 -sept 2007
Source

Code Definition

Code	2007-2008
Definition	oct 2007 - sept 2008
Source

Code Definition

Code	2008-2009
Definition	oct 2008 - sept 2009
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Leaf-Off
Definition	October-March
Source

Code Definition

Code	Leaf-On
Definition	April-September
Source

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1225/1/880b5cde5ae0bc4e225e96838470fd05
Name:	MonthlyDataCIMIS_2022edit
Description:	Precipitation in mm for each month, summarized by water year (october-september) and blue oak leaf-off and leaf-on season
Number of Records:	101
Number of Columns:	3

Table Structure

Object Name:

MonthlyDataCIMIS_2022edit.csv

Size:

2190 byte

Authentication:

eb097fc3817b2ef518bf6a494886fe52 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	'

Table Column Descriptions

Total Precip (mm)

WaterYear

Season

Column Name:

Total Precip (mm)

WaterYear

Season

Definition:

Precipitation in mm by month categorized by leaf-off season or leaf-on season

Water year (oct-sept)

The season the month is in (leaf-off or leaf-on)

Storage Type:

float

string

Measurement Type:

ratio

nominal

Measurement Values Domain:

Unit	millimeter
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	2001-2002
Definition	oct 2001-sept 2002
Source

Code Definition

Code	2002-2003
Definition	oct 2002-sept 2003
Source

Code Definition

Code	2003-2004
Definition	oct 2003 - sept 2004
Source

Code Definition

Code	2004-2005
Definition	oct 2004 - sept 2005
Source

Code Definition

Code	2005-2006
Definition	oct 2005- sept 2006
Source

Code Definition

Code	2006-2007
Definition	oct 2006 -sept 2007
Source

Code Definition

Code	2007-2008
Definition	oct 2007- sept 2008
Source

Code Definition

Code	2008-2009
Definition	oct 2008 - sept 2009
Source

Code Definition

Code	2009-2010
Definition	oct 2009 - sept 2010
Source

Code Definition

Code	2010-2011
Definition	oct 2010- sept 2011
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Leaf-Off
Definition	October-March
Source

Code Definition

Code	Leaf-On
Definition	April-September
Source

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1225/1/9ee135d0683d8150f0a04f6d7201c036
Name:	SubPlotDB
Description:	Data on each subplot where seedlings were tagged and rechecked. Residual Dry Matter, Photosynthetically Active Radiation, and Exotic/Native percent cover were only measured once in 2006.
Number of Records:	480
Number of Columns:	11

Table Structure

Object Name:

SubPlotDB.csv

Size:

18916 byte

Authentication:

9d9903ffa2db06d192ce37d86943b13d Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

PlotID

native

exotic

direction

distance

tree

RDM

Grass.par

Litter.par

Tree.par

CanopyPos

Column Name:

PlotID

native

exotic

direction

distance

tree

RDM

Grass.par

Litter.par

Tree.par

CanopyPos

Definition:

Subplot seedling is found in; most PlotIDs are formatted as TreeIDDistanceDirection, with some exceptions

Percent cover that is native (see additional information on how species were identified) - only measured in 2006

Percent cover that is exotic (see additional information on how species were identified) - only measured in 2006

Cardinal direction from the adult focal tree

Distance from the focal tree in meters

Unique ID for each adult focal tree

Residual Dry Matter in grams/square foot (only measured in 2006)

Photosynthetically Active Radiation measured under the herbaceous canopy but above the litter (only measured in 2006)

Photosynthetically Active Radiation measured under the litter at the soil surface (only measured in 2006)

Photosynthetically Active Radiation measured under the tree canopy but above the herbaceous canopy (only measured in 2006)

Canopy Position ( only recorded in 2006)

Storage Type:

string

float

string

float

string

float

string

Measurement Type:

nominal

ratio

nominal

ratio

nominal

ratio

nominal

Measurement Values Domain:

Definition

Subplot seedling is found in; most PlotIDs are formatted as TreeIDDistanceDirection, with some exceptions

Unit	percent
Type	real

Unit	percent
Type	integer

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	E
Definition	East
Source

Code Definition

Code	N
Definition	North
Source

Code Definition

Code	S
Definition	South
Source

Code Definition

Code	W
Definition	West
Source

Unit	meter
Type	real

Definition

Unique ID for each adult focal tree

Unit	grams/square foot
Type	real

Unit	micromoles per square meter per second
Type	real

Unit	micromoles per square meter per second
Type	real

Unit	micromoles per square meter per second
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	O
Definition	Outside the focal tree canopy
Source

Code Definition

Code	U
Definition	Under focal tree canopy
Source

Missing Value Code:

Code	NA
Expl	Not measured

Code	NA
Expl	Not measured

Code	NA
Expl	Not measured

Code	NA
Expl	Not measured

Code	NA
Expl	Not measured

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1225/1/207bdfb7734974f1c92b14248475c565
Name:	FocalTreeDB_Tabular
Description:	Reproductive status, soil type, and acorn count for adult focal trees around which seedlings and saplings were surveyed.
Number of Records:	180
Number of Columns:	6

Table Structure

Object Name:

FocalTreeDB_Tabular.csv

Size:

4288 byte

Authentication:

9151c7f638d0c7c798039a5d7be4d285 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	'

Table Column Descriptions

TreeID

DBH.cm

Soil

Year

Acorn

Reproductive

Column Name:

TreeID

DBH.cm

Soil

Year

Acorn

Reproductive

Definition:

Unique ID for each adult focal tree

Diameter at Breast Height of adult blue oak focal tree

Soil type listed in SSURGO database

Year acorns were counted

Quantity of acorns counted within 15 seconds using the naked eye or binoculars

Whether the adult tree had acorns or not

Storage Type:

float

string

dateTime

float

string

Measurement Type:

ratio

nominal

dateTime

ratio

nominal

Measurement Values Domain:

Unit	Unitless ID
Type	real

Unit	centimeter
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	235
Definition	Sobrante Gravelly Loam 3-8 percent slopes
Source

Code Definition

Code	236
Definition	Sobrante Gravelly Loam 8-15 percent slopes
Source

Code Definition

Code	241
Definition	Sobrante-Timbuctoo Complex 30-50 percent slopes
Source

Format	YYYY
Precision

Unit	Count
Type	integer

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	FALSE
Definition	Tree did not have acorns
Source

Code Definition

Code	TRUE
Definition	Tree did have acorns
Source

Code Definition

Code	NA
Definition	Tree's reproductive status was not assessed
Source

Missing Value Code:

Code	NA
Expl	Diameter was not measured for this tree

Code	NA
Expl	Acorns were not counted for this tree/year

Code	NA
Expl	Reproductive status was not noted for this tree

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1225/1/775152cf4b72d543c00a3769472c9b90
Name:	SaplingStatus
Description:	Data for running the statistical models examining sapling survival status
Number of Records:	534
Number of Columns:	8

Table Structure

Object Name:

SaplingStatus.csv

Size:

18137 byte

Authentication:

71bc6e4aae63a6aacb7e84261874591f Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	'

Table Column Descriptions

IndID

TreeID

Year

Diam.mm

Height

Status

Dist

Dir

Column Name:

IndID

TreeID

Year

Diam.mm

Height

Status

Dist

Dir

Definition:

Individual sapling ID

Unique ID for each adult focal tree

The year the status was observed

Basal diameter in mm

Height in cm

Sapling survival status

Distance from the focal tree in meters

Direction, measured in degrees from North, from the focal tree

Storage Type:

string

dateTime

float

string

float

Measurement Type:

nominal

dateTime

ratio

nominal

ratio

Measurement Values Domain:

Definition

Individual sapling ID

Definition

Unique ID for each adult focal tree

Format	YYYY
Precision

Unit	millimeter
Type	real

Unit	centimeter
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	Dead
Source

Code Definition

Code	1
Definition	Alive
Source

Unit	meter
Type	real

Unit	degree
Type	integer

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1225/1/70fb17c2d699543cd1d8fde16e30e2bf
Name:	SaplingIncrement
Description:	Data required for statistical models examining sapling growth
Number of Records:	525
Number of Columns:	12

Table Structure

Object Name:

SaplingIncrement.csv

Size:

29365 byte

Authentication:

f3a34e70e4e882a6befc1734e7b2000f Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	'

Table Column Descriptions

IndID

TreeID

Year

Diam.mm

Diam2

Year2

Increment.G

Height

Height2

Increment.H

Dist

Dir

Column Name:

IndID

TreeID

Year

Diam.mm

Diam2

Year2

Increment.G

Height

Height2

Increment.H

Dist

Dir

Definition:

Individual sapling ID

Unique ID for each adult focal tree

Year of previous measurement

Basal diameter in mm in the first year

Basal diameter in mm in the second year

Year of the second measurement

Growth increment in diameter between Year 1 and Year 2

Height of sapling in cm in the first year

Height of sapling in cm in the second year

Growth increment in height between Year 1 and Year 2

Distance from the focal tree in meters

Direction, measured in degrees from North, from the focal tree

Storage Type:

string

dateTime

float

dateTime

float

Measurement Type:

nominal

dateTime

ratio

dateTime

ratio

Measurement Values Domain:

Definition

Individual sapling ID

Definition

Unique ID for each adult focal tree

Format	YYYY
Precision

Unit	millimeter
Type	real

Unit	millimeter
Type	real

Format	YYYY
Precision

Unit	millimeter
Type	real

Unit	centimeter
Type	real

Unit	centimeter
Type	real

Unit	centimeter
Type	real

Unit	meter
Type	real

Unit	degree
Type	integer

Missing Value Code:

Code	NA
Expl	miss

Code	NA
Expl	missing

Code	NA
Expl	missing

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1225/1/caa9ab4dc954ce7c1a88be534df9d134
Name:	NewSeedlings
Description:	Data needed to run statistical models exploring the size of new seedlings in a given year of the surveys
Number of Records:	349
Number of Columns:	7

Table Structure

Object Name:

NewSeedlings.csv

Size:

14138 byte

Authentication:

a0e2e5cdc404ced254cfc119a351b3b3 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	'

Table Column Descriptions

IndID

PlotID

TreeID

Diam.mm

Field

Year

DBH.cm

Column Name:

IndID

PlotID

TreeID

Diam.mm

Field

Year

DBH.cm

Definition:

Individual seedling ID

Subplot seedling is found in; most PlotIDs are formatted as TreeIDDistanceDirection, with some exceptions

Unique ID for each adult focal tree

Basal diameter in mm

Which pasture the seedling is found in

Year that the seedling was newly tagged

Diameter at Breast Height of adult blue oak focal tree

Storage Type:

string

float

string

dateTime

float

Measurement Type:

nominal

ratio

nominal

dateTime

ratio

Measurement Values Domain:

Definition

Individual seedling ID

Definition

Subplot seedling is found in; most PlotIDs are formatted as TreeIDDistanceDirection, with some exceptions

Definition

Unique ID for each adult focal tree

Unit	millimeter
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Koch 1-11
Definition	Summer/dormant season grazed pasture
Source

Code Definition

Code	Koch 1-21
Definition	Ungrazed pasture
Source

Code Definition

Code	Lewis 2
Definition	Winter/growing season grazed pasture
Source

Format	YYYY
Precision

Unit	centimeter
Type	real

Missing Value Code:

Code	NA
Expl	missing seedling

Code	NA
Expl	Missing measurement

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1225/1/ec6dabb325b7c5d4f31e8ce3973667fa
Name:	NumberSeedlings
Description:	Data needed for running statistical models exploring the number of seedlings that are newly tagged in a given year.
Number of Records:	1392
Number of Columns:	4

Table Structure

Object Name:

NumberSeedlings.csv

Size:

24020 byte

Authentication:

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Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	'

Table Column Descriptions

TreeID

Count

Year

PlotID

Column Name:

TreeID

Count

Year

PlotID

Definition:

Unique ID for each adult focal tree

Number of new seedlings in a subplot

Year that the seedlings were newly tagged

Subplot seedling is found in; most PlotIDs are formatted as TreeIDDistanceDirection, with some exceptions

Storage Type:

string

float

dateTime

string

Measurement Type:

nominal

ratio

dateTime

nominal

Measurement Values Domain:

Definition

Unique ID for each adult focal tree

Unit	count (unitless)
Type	integer

Format	YYYY
Precision

Definition

Subplot seedling is found in; most PlotIDs are formatted as TreeIDDistanceDirection, with some exceptions

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1225/1/ce610d81f72a2a2690fc492788dd5372
Name:	SeedlingIncrement
Description:	Data required to run statistical models exploring how seedlings grow from year to year
Number of Records:	709
Number of Columns:	6

Table Structure

Object Name:

SeedlingIncrement.csv

Size:

23230 byte

Authentication:

7e7fbd794b2d540746ad1b8cb5431f24 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	'

Table Column Descriptions

IndID

TreeID

Year

Diam.mm

Increment

PlotID

Column Name:

IndID

TreeID

Year

Diam.mm

Increment

PlotID

Definition:

Individual seedling ID

Unique ID for each adult focal tree

Year of previous measurement

Basal diameter in mm in the first year

Growth increment in diameter since the previous year

Subplot seedling is found in; most PlotIDs are formatted as TreeIDDistanceDirection, with some exceptions

Storage Type:

string

dateTime

float

string

Measurement Type:

nominal

dateTime

ratio

nominal

Measurement Values Domain:

Definition

Individual seedling ID

Definition

Unique ID for each adult focal tree

Format	YYYY
Precision

Unit	millimeter
Type	real

Unit	millimeter
Type	real

Definition

Subplot seedling is found in; most PlotIDs are formatted as TreeIDDistanceDirection, with some exceptions

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1225/1/9b13ceced5a2743a2f49f414ae55b3ef
Name:	SeedlingStatus
Description:	Data required for running statistical models exploring seedling survival status
Number of Records:	771
Number of Columns:	6

Table Structure

Object Name:

SeedlingStatus.csv

Size:

22701 byte

Authentication:

18fb3a0b6852216753cf1be07765526e Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

IndID

TreeID

Year

Diam.mm

Status

PlotID

Column Name:

IndID

TreeID

Year

Diam.mm

Status

PlotID

Definition:

Individual seedling ID

Unique ID for each adult focal tree

Year that the seedling's survival status was checked

Basal diameter in mm

Seedling survival status

Subplot seedling is found in; most PlotIDs are formatted as TreeIDDistanceDirection, with some exceptions

Storage Type:

string

dateTime

float

string

Measurement Type:

nominal

dateTime

ratio

nominal

Measurement Values Domain:

Definition

Individual seedling ID

Definition

Unique ID for each adult focal tree

Format	YYYY
Precision

Unit	millimeter
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	Dead
Source

Code Definition

Code	1
Definition	Alive
Source

Definition

Subplot seedling is found in; most PlotIDs are formatted as TreeIDDistanceDirection, with some exceptions

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Non-Categorized Data Resource

Name:

EitzelEtAl_BlueOakRecruitmentReproduction_8thOakSymposium_Final

Entity Type:

pdf

Description:

Final draft of the paper for the conference proceedings of the 8th Oak Symposium that both describes the methods associated with this dataset and also uses the data in this dataset. This draft is not the version in the Conference Proceedings, but is the final draft created before obtaining a DOI for this dataset.

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EitzelEtAl_BlueOakRecruitmentReproduction_8thOakSymposium_Final.pdf

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EitzelEtAl_BlueOakRecruitmentReproduction_8thOakSymposium_AdditionalInformation

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pdf

Description:

Appendix/additional information describing conference paper analysis methods and giving data summaries and distributions (including variables not included in the conference paper).

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EitzelEtAl_BlueOakRecruitmentReproduction_8thOakSymposium_AdditionalInformation.pdf

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SF_oaks_methods survey

Entity Type:

doc

Description:

Original draft describing survey methods

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Name:

SFREC_FocalTrees_Buffer20m

Entity Type:

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Description:

GIS data with zonal calculations of Topographic Wetness Index and Insolation for each focal tree

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Entity Type:

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Description:

GIS file with data on Insolation and Topographical Wetness Index for each adult focal tree

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Name:

SeedlingStudyAnalysis2022

Entity Type:

Description:

R code that ingests the data tables given in this repository, plus the two dbf files listed as "other entities", assembles them and does a final round of quality control, and generates the results shared in the related conference proceedings paper.

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Name:

RawDataAndPrepCode

Entity Type:

zip

Description:

Raw data from oak seedling/sapling surveys and code to create the versions used in the analysis and paper in this archive. PrepareOakData_2022.R assembles the majority of these files into versions that can be ingested by the analysis code. With these two exceptions: animaldays.pl Perl script that takes grazing data in the form provided by the Research and Extension Center (day in, day out, number of head, pasture) and separates it out by year and month so it can be aggregated into a total number of animal days per month, in the R code. OakProject_GrazingData.csv Raw grazing data from the Research and Extension Center with number of head, date in, and date out. animaldays.pl converts this into a form that can be aggregated by month in the R script SeedlingStudyAnalysis2022.R

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Data Package Usage Rights

This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.

Keywords

By Thesaurus:
LTER Controlled Vocabulary	recruitment, reproduction, regeneration, grazing, precipitation, growth, survival
(No thesaurus)	light availability, seedling, sapling, acorn, moisture availability

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package

Description:

See additional documentation for descriptions of methods.

People and Organizations

Publishers:

Organization:

Environmental Data Initiative

Email Address:

info@edirepository.org

Web Address:

https://edirepository.org

Id:

https://ror.org/0330j0z60

Creators:

Individual:

M.V. Eitzel

Email Address:

mveitzel@gmail.com

Id:

https://orcid.org/0000-0002-3877-1551

Individual:

S. Rodríguez-Buriticá

Individual:

W.S. Harpole

Individual:

R. Aicher

Individual:

L. Larios

Individual:

M. McClaran

Individual:

K. Suding

Email Address:

Katharine.Suding@colorado.edu

Contacts:

Individual:

K. Suding

Email Address:

Katharine.Suding@colorado.edu

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period

Begin:

2005

End:

2010

Geographic Region:

Description:

Sierra Foothills Research and Extension Center

Bounding Coordinates:

Northern:	39.30006	Southern:	39.27478
Western:	-121.31177	Eastern:	-121.285

Taxonomic Range:

Classification:

Rank Name:

Kingdom

Rank Value:

Viridiplantae

Common Name:

green plants

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 33090 (Viridiplantae)

Classification:

Rank Name:

Phylum

Rank Value:

Streptophyta

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 35493 (Streptophyta)

Classification:

Rank Name:

Subphylum

Rank Value:

Streptophytina

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 131221 (Streptophytina)

Classification:

Rank Name:

Class

Rank Value:

Magnoliopsida

Common Name:

flowering plants

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 3398 (Magnoliopsida)

Classification:

Rank Name:

Order

Rank Value:

Fagales

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 3502 (Fagales)

Classification:

Rank Name:

Family

Rank Value:

Fagaceae

Common Name:

beech family

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 3503 (Fagaceae)

Classification:

Rank Name:

Genus

Rank Value:

Quercus

Identifer:

National Center for Biotechnology Information - Taxonomy (NCBI)
Info for ID: 3511 (Quercus)

Classification:

Rank Name:	Species
Rank Value:	Quercus douglasii
Identifer:	National Center for Biotechnology Information - Taxonomy (NCBI) Info for ID: 465759 (Quercus douglasii)

Project

Parent Project Information:

Title:

Reproduction and Recruitment of Blue Oak in the Sierra Nevada Foothills of California

Personnel:

Individual:	M.V. Eitzel
Role:	Paper author, analyst

Individual:	K. Suding
Role:	Principal Investigator

Abstract:

California oaks suffer from recruitment problems due to a number of climate and management-related factors, including timing and presence of grazing. Our study examines these potential factors by quantifying reproductive success (numbers of new seedlings and their sizes) and survival and growth of the younger life stages (seedlings and saplings), and by exploring how the timing of grazing, topographical variables, and rainfall limit reproduction, growth, and survival for these life stages, helping to identify potential management and restoration strategies to enhance the population viability of blue oak. We followed a population of blue oak (Quercus douglasii) seedlings and saplings in the Sierra Nevada foothills, measuring adult seed production and initial seedling recruitment (number and size of new seedlings), seedling growth and survival, seedling recruitment to saplings (growing greater than 10 cm in height), and sapling growth and survival. We tested the impacts on these demographic processes of timing and intensity of grazing, light availability, water availability, and individual size. Seedlings were more sensitive to moisture availability while saplings were more sensitive to light availability. Individual level variables such as the previous year’s size impacted adult trees as well as seedlings and saplings, pointing to individual characteristics as an important component of demography. Grazing had a negative impact on seedling survival, sapling growth, and numbers of new seedlings, but the timing of the grazing mattered. High-quality, larger adult trees in good locations could be key in enabling early life stage transitions, though density-dependence and competition with the adult may mediate that beneficial effect. Future studies could examine the impact of competition with invasive exotic grasses and also how fire severity impacts these benefits of adult trees on early life stages. Ultimately a population model is needed to synthesize these data with information on other demographic transitions in order to establish population persistence.

Maintenance

Maintenance:

Description:	This dataset is complete as of 2010.
Frequency:

Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'unitList'
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Count'
        |     |     |     |  \___attribute 'name' = 'Count'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Unitless ID'
        |     |     |     |  \___attribute 'name' = 'Unitless ID'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'day'
        |     |     |     |  \___attribute 'name' = 'day'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'animal-days'
        |     |     |     |  \___attribute 'name' = 'animal-days'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'count (unitless)'
        |     |     |     |  \___attribute 'name' = 'count (unitless)'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'grams/square foot'
        |     |     |     |  \___attribute 'name' = 'grams/square foot'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'micromoles per square meter per second'
        |     |     |     |  \___attribute 'name' = 'micromoles per square meter per second'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n        '
        |     |     |___text '\n      '
        |     |___text '\n    '
        |___text '\n  '

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'emlEditor'
        |     |        \___attribute 'app' = 'ezEML'
        |     |        \___attribute 'release' = '2022.09.28'
        |     |___text '\n    '
        |___text '\n  '

Copyright 2024 Environmental Data Initiative. This material is based upon work supported by the National Science Foundation under grants #2223103 and #2223104. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Please contact us with questions, comments, or for technical assistance regarding this web site or the Environmental Data Initiative. Please read our privacy policy to know what information we collect about you and to understand your privacy rights.

EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

Data Package Metadata View Summary

California Blue Oak reproduction and recruitment, Sierra Foothills, 2005-2010

Data Entities

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Data Package Usage Rights

Keywords

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Parent Project Information:

Maintenance

Additional Metadata

Additional Metadata

Recently Added

Recently Updated

Data Package Metadata View Summary

California Blue Oak reproduction and recruitment, Sierra Foothills, 2005-2010

+/- Data Entities

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

+/- Data Package Usage Rights

+/- Keywords

+/- Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

+/- People and Organizations

+/- Temporal, Geographic and Taxonomic Coverage

+/- Project

Parent Project Information:

+/- Maintenance

+/- Additional Metadata

+/- Additional Metadata

Data Entities

Data Package Usage Rights

Keywords

Methods and Protocols

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Maintenance

Additional Metadata

Additional Metadata