Stanislaus-Tuolumne Experimental Forest 'Methods of Cutting' study plots 8-11: 88+ years of tree regeneration and forest understory cover data

Metadata:

Entity_and_Attribute_Information:

Overview_Description:

Entity_and_Attribute_Overview:

Below you will find a list and description of the files included in this data publication.

Acronyms used in these files and descriptions:
cm = centimeters
DBH = diameter at breast height
in = inches
NA = not applicable


VARIABLE DESCRIPTION FILE (1)

1. \Data\_variable_descriptions.csv: Comma-separated values (CSV) file containing a list and description of variables found in all data files. (A description of these variables is also provided in the metadata below.)

Columns include:

Filename = name of data file
Variable = name of variable
Type = type of variable (numeric, character, categorical, boolean)
Units = units (if applicable)
Precision = precision (if applicable)
Description = description of variable


DATA - TABULAR DIGITAL FILES (8)

1. \Data\MOC8-11_2016_Milacre_TreeSeedling_Info.csv: CSV file containing tree and tree regeneration data collected in 2016 in each of 440 milacre quadrats such as height, diameter at breast height, and decay class.

Variables include:

Year = The year the observation was made (2016 in this case)

Plot = The plot the observation is associated with (8-11)

Quadrat = The milacre quadrat the observation was made for (1-140)

PlotQuad = A unique identifier for milacre quadrats that includes both the plot and the quadrat number ("plot_quadrat")

Species = Species code for tree seedling or sapling from USDA Plants database (https://plants.usda.gov/):
ABCO = Abies concolor
CADE17 = Calocedrus decurrens
PILA = Pinus lambertiana
PIPO = Pinus ponderosa
QUKE = Quercus kelloggii

HeightClass = A height class value of 1-7 based on height of seedling or sapling in milacre quadrat for Year:
1 = current year
2 = older but < 4 in
3 = 4-10 in
4 = 10-19.7 in
5 = 19.7-54 in
6 = sapling (< 10 cm DBH)
7 = tree (>= 10 cm DBH)
NA = data missing

dbh_in = Diameter at breast height (DBH) of sapling/tree in 2016 in inches. Not taken for every tree.

Status = Seedling/sapling/tree status live (L) or dead (D) in 2016. NA = data missing.

Decay_class = If tree is dead, decay class describes the state of tree decay
NEEDLES = most needles still on tree
PRIMARY = most small branches still on tree
SECONDARY = only large branches or no branches left on tree
BOLE = no branches left only tree bole/stem
BROKEN BOLE = tree in advanced decay and bole broken
NA = not applicable - tree is alive

Notes = Any relevant notes for observation. Numbers are tree tag numbers from overstory dataset (Knapp and Carlson 2021) included in this column where possible.


2. \Data\MOC8-11_Milacre_Cover.csv: CSV file containing quadrat-level cover data (e.g., rock, roots, slash, litter, bare, etc.) for all quadrats in 1928/1929, 1931, 2008, and 2016. Soil moisture data is also available in every other quadrat in 2016.

Variables include:

Year = The year the observation was made

Prelogging = Whether the observation was made before (TRUE) or after logging (FALSE). Necessary because pre- and post-logging observations were both made in 1929 for plots 9-11

Plot = The plot the observation is associated with (8-11)

Quadrat = The milacre quadrat the observation was made for (1-140)

PlotQuad = A unique identifier for milacre quadrats that includes both the plot and the quadrat number ("plot_quadrat")

Rock = Cover of rock in specified milacre quadrat and year (0-1)

Roots = Cover of roots in specified milacre quadrat and year. NA values indicate years where this variable was not collected (0-1)

Logs = Cover of logs or coarse woody debris in specified milacre quadrat andyear. NA values indicate years where this variable was not collected (0-1)

Trash = Cover of trash in specified milacre quadrat and year. Not well defined, but likely smaller logging debris. NA values indicate years where this variable was not collected (0-1)

Slash = Cover of downed debris of any size from logging or windthrow in specified milacre quadrat and year. NA values indicate years where this variable was not collected (0-1)

Wood = Cover of Logs, Trash, and Slash in specified milcacre quadrat in 1900's. In 2007/2008 and 2016, cover of coarse and fine woody debris (0-1)

Litter = Cover of litter in specified milacre quadrat and year (0-1)

Litter_depth_cm = Depth of litter in cm in specified milacre quadrat and year. Only available for 2016. NA values indicate years where this variable was not collected.

SkidTrail = Cover of bare or disturbed ground from skidding logs and equiptment in specified milacre quadrat and year. Not available for 2007/2008, and 2016, though available in the pre-logging period. Maps show cover notes such as "soil broken by turning cat". NA values indicate years where this variable was not collected. (0-1)

Bare = Cover of bare ground not associated with skidding logs in specified milacre quadrat and year (0-1)

Burn = Cover of area burned - from slash piles post-logging - in specified milacre quadrat and year. NA values indicate years where this variable was not collected (0-1)

Soil_moisture = Percent soil moisture taken with 15 cm probe in specified milacre quadrat and year. Only available for every other quadra in 2016. NA values indicate years or quadrats where this variable was not collected (0-100)

Stem = Cover of bole of mature trees (> 10 cm diameter at breast height) in specified milacre quadrat and year. Only taken 2007/2008, NA values indicate years or quadrats where this variable was not collected (0-1)


3. \Data\MOC8-11_Milacre_Seedling_Growth.csv: CSV file containing individual-level measurements for seedlings and saplings between 1928/1929 and 1942 including height, diameter at breast height, and status (live or dead).

Variables include:

Plot = The plot the observation is associated with (8-11)

Quadrat = The milacre quadrat the observation was made for (1-140)

PlotQuad = A unique identifier for milacre quadrats that includes both the plot and the quadrat number ("plot_quadrat")

Species = Species code for tree seedling or sapling from USDA Plants database (https://plants.usda.gov/):
ABCO = Abies concolor
CADE17 = Calocedrus decurrens
PILA = Pinus lambertiana
PIPO = Pinus ponderosa

tree_number = Number given to to identify individual seedling, unique within milacre quadrat but repeated among milacre quadrats

establishment_year = Year of seedling/sapling establishment. Where NA likely that seedling/sapling was more than two years old at time of first sampling and year of seedling establishment was not estimated.

status_prelogging = Seedling/sapling status live (L) or dead (D) before logging. This status is NA for most of plot 8 because this plot is missing pre-logging data for individual seedlings, but if the individual does not have an establishment year and is alive post-logging in 1929 it is likely that the individual was alive pre-logging and survived through logging disturbance ("advance regeneration").

height_ft_prelogging = Height of seedling/sapling prelogging in feet. NA where not measured for established seedlings and where row represents a seedling that has yet to establish (i.e. establishes in later year).

status_1929 = Seedling/sapling status live (L) or dead (D) in 1929 postlogging (pre-logging was also in 1929 for plots 9-11. pre-logging status for plots 9-11 can be found in status_prelogging). NA where not measured for established seedlings and where row represents a seedling that has yet to establish (i.e. establishes in later year).

height_ft_1929 = Height of seedling/sapling in 1929 post-logging in feet. NA where not measured for established seedlings and where row represents a seedling that has yet to establish (i.e. establishes in later year).

status_[YEAR] = Seedling/sapling status live (L) or dead (D) in [YEAR] (where YEAR = 1930-1938, 1942, 1947). NA where not measured for established seedlings and where row represents a seedling that has yet to establish (i.e. establishes in later year).

height_ft_[YEAR] = Height of seedling/sapling in [YEAR] in feet (where YEAR = 1930-1938, 1942, 1947). NA where not measured for established seedlings and where row represents a seedling that has yet to establish (i.e. establishes in later year).

dbh_in_[YEAR] = Diameter at breast height (DBH) of seedling/sapling in [YEAR] in inches (where YEAR = 1931-1938, 1942, 1947). NA where not measured for established seedlings and where row represents a seedling that has yet to establish (i.e. establishes in later year).


4. \Data\MOC8-11_Milacre_Shrubs.csv: CSV file containing quadrat-level shrub cover measurements for 1928/29, 1931, and 2008/2016.

Variables include:

Year = The year the observation was made

Prelogging = Whether the observation was made before (TRUE) or after logging (FALSE). Necessary because pre- and post-logging observations were both made in 1929 for plots 9-11

Plot = The plot the observation is associated with (8-11)

Quadrat = The milacre quadrat the observation was made for (1-140)

PlotQuad = A unique identifier for milacre quadrats that includes both the plot and the quadrat number ("plot_quadrat")

SpCode_original = Codes used for shrubs by early 1900's foresters. This column does not adhere to present day "tidy data" standards and sometimes includes multiple species codes indicating a mixture of species. (See \Data\MOC8-11_Shrub_Species_archive.csv for a crosswalk between old codes, new codes, and scientific names.)

SpCode_usda_plants = The USDA Plants database (https://plants.usda.gov/) species code for the species in question; "UNK" is used for an unknown species; "MIXED SPECIES" is used for a species mixture when more than one historical code is used in the same observation. (See \Data\MOC8-11_Shrub_Species_archive.csv for scientific names.)

Cover = Cover of shrub in specified milacre quadrat and time period (0-1)


5. \Data\MOC8-11_Milacre_TreeSeedlingCount.csv: CSV file containing quadrat-level regeneration counts by species for 1928/1929 - 1948 and 2008/2016.

Variables include:

Plot = The plot the observation is associated with (8-11)

Quadrat = The milacre quadrat the observation was made for (1-140)

PlotQuad = A unique identifier for milacre quadrats that includes both the plot and the quadrat number ("plot_quadrat")

Year = The year the observation was made

HeightClass =
A height class value of 1-7 based on height of seedling or sapling in milacre quadrat for Year:
1 = current year
2 = older but < 4 in
3 = 4-10 in
4 = 10-19.7 in
5 = 19.7-54 in
6 = sapling (< 10 cm DBH)
7 = tree (>= 10 cm DBH)
NA indicates no height class available. For example, no height class data is available in the pre-logging period for plot 8.

Prelogging = Whether the observation was made before (TRUE) or after logging (FALSE). Necessary because pre- and post-logging observations were both made in 1929 for plots 9-11

Species = Species code for tree seedling or sapling from USDA Plants database (https://plants.usda.gov/):
ABCO = Abies concolor
CADE17 = Calocedrus decurrens
PILA = Pinus lambertiana
PIPO = Pinus ponderosa
QUKE = Quercus kelloggii

Count = Number of seedlings or saplings of a particular height class and species in milacre quadrat for Year


6. \Data\MOC8-11_MilacreCoordinates.csv: CSV file containing coordinate locations for all quadrats within plots.

Variables include:

Plot = The plot the observation is associated with (8-11)

Quadrat = The milacre quadrat the observation was made for (1-140)

PlotQuad = A unique identifier for milacre quadrats that includes both the plot and the quadrat number ("plot_quadrat")

x = Milacre quadrat coordinate easting. Projected coordinate system: NAD83 Zone 10. Geographic coordinate system: NAD83

y = Milacre quadrat coordinate northing. Projected coordinate system: NAD83 Zone 10. Geographic coordinate system: NAD83


7. \Data\MOC8-11_Shrub_Species.csv: CSV file containing a crosswalk between historical and contemporary shrub species codes.

Variables include:

SpCode_original = Codes used for shrubs by early 1900's foresters. This column does not adhere to present day "tidy data" standards and sometimes includes multiple species codes indicating a mixture of species.

SpCode_usda_plants = The usda plants database species code for the species in question; "UNK" is used for an unknown species; "MIXED SPECIES" is used for a species mixture when more than one historical code is used in the same observation.

Genus = Species genus name

species = Species specific epithet

Type = Species type, whether shrub, subshrub, or tree

Notes = Notes to help understand relationship between species codes and uncertainty based on historical dataset


8. \Data\MOC9-11_Milacre_Herbaceous.csv: CSV file containing quadrat-level counts of the number of stems of herbaceous plants by species for plots 9-11 only for years 1929, 1930, 1931, and 2008.

Variables include:

Year = The year the observation was made

Prelogging = Whether the observation was made before (TRUE) or after logging (FALSE). Neccessary because pre- and post-logging observations were both made in 1929 for plots 9-11

Plot = The plot the observation is associated with (9-11)

Quadrat = The milacre quadrat the observation was made for (1-100)

SpCode_original = Codes used for shrubs by early 1900's foresters. This column does not adhere to present day "tidy data" standards and sometimes includes multiple species codes indicating a mixture of species. See \Data\MOC8-11_Shrub_Species.csv for a crosswalk between old codes, new codes, and scientific names.

SpCode_usda_plants = The USDA Plants database species code for the species in question; "UNK" is used for an unknown species.

Stems = The number of stems of an herbaceous plant present in the plot


SUPPLEMENTAL FILES - ORIGINAL DATA SHEETS (8)

1. \Supplements\orig_data_sheets\MOC08_1928-1931_cover_regenCount.pdf: Portable Document Format (PDF) file containing original data sheets for quadrat-level regeneration counts for plot 8, 1928-1931.

2. \Supplements\orig_data_sheets\MOC08_1930-1932_herbaceous.pdf: PDF file containing original data sheets for quadrat-level number of stems of herbaceous species for plot 8, 1930-1932.

3. \Supplements\orig_data_sheets\MOC09_1929-1931_cover_regenCount.pdf: PDF file containing original data sheets for quadrat-level regeneration counts for plot 9, 1929-1931.

4. \Supplements\orig_data_sheets\MOC09_1929-1931_herbaceous.pdf: PDF file containing original data sheets for quadrat-level number of stems of herbaceous species for plot 9, 1929-1931.

5. \Supplements\orig_data_sheets\MOC10_1929-1931_cover_regenCount.pdf: PDF file containing original data sheets for quadrat-level regeneration counts for plot 10, 1929-1931.

6. \Supplements\orig_data_sheets\MOC10_1929-1931_herbaceous.pdf: PDF file containing original data sheets for quadrat-level number of stems of herbaceous species for plot 10, 1929-1931.

7. \Supplements\orig_data_sheets\MOC11_1929-1931_cover_regenCount.pdf: PDF file containing original data sheets for quadrat-level regeneration counts for plot 11, 1929-1931.

8. \Supplements\orig_data_sheets\MOC11_1929-1931_herbaceous.pdf: PDF file containing original data sheets for quadrat-level number of stems of herbaceous species for plot 11, 1929-1931.


SUPPLEMENTAL FILES - MAPS (9)

1. \Supplements\MOC08_1928_milacreQuadrat_maps_lowDetail.pdf: PDF file containing quadrat-level maps of plot 8 in 1928 before logging.

2. \Supplements\MOC08_milacreQuadrat_maps_1-70.pdf: PDF file containing quadrat-level maps of plot 8 quadrats 1-70, 1929-1947.

3. \Supplements\MOC08_milacreQuadrat_maps_71-140.pdf: PDF file containing quadrat-level maps of plot 8 quadrats 71-140, 1929-1947.

4. \Supplements\MOC09_milacreQuadrat_maps_initial.pdf: PDF file containing quadrat-level maps of plot 9, 1929-various.

5. \Supplements\MOC09_milacreQuadrat_maps_later.pdf: PDF file containing quadrat-level maps of plot 9 for years after those provided in MOC09_milacreQuadrat_maps_inital.pdf.

6. \Supplements\MOC10_milacreQuadrat_maps_initial.pdf: PDF file containing quadrat-level maps of plot 10, 1929-various.

7. \Supplements\MOC10_milacreQuadrat_maps_later.pdf: PDF file containing quadrat-level maps of plot 10 for years after those provided in MOC10_milacreQuadrat_maps_inital.pdf.

8. \Supplements\MOC11_milacreQuadrat_maps_initial.pdf: PDF file containing quadrat-level maps of plot 11, 1929-various.

9. \Supplements\MOC11_milacreQuadrat_maps_later.pdf: PDF file containing quadrat-level maps of plot 11 for years after those provided in MOC11_milacreQuadrat_maps_inital.pdf.

Entity_and_Attribute_Detail_Citation:

Brodie, Emily G.; Knapp, Eric E.; Latimer, Andrew M.; Safford, Hugh D.; Vossmer, Marissa A.; Bisbing, Sarah M. [In review]. The century-long shadow of fire exclusion: historical data reveal early and lasting effects of fire regime change on contemporary forest composition. Forest Ecology and Management.

Dunning, Duncan. 1926. Instructions for the establishment and measurement of methods of cutting sample plots, District 5. U.S. Department of Agriculture, Forest Service.

Hasel, A. A.; Wohletz, E.; Tallmon, W. B. 1934. Methods of cutting: California Forest and Range Experiment Station Stanislaus Branch - plots 9, 10, 11. Progress Report. Stanislaus Branch: U.S. Department of Agriculture, Forest Service, California Forest and Range Experiment Station. 10 pages. https://www.fs.usda.gov/research/treesearch/60121

Knapp, Eric E.; Skinner, Carl N.; North, Malcolm P.; Estes, Becky L. 2013. Long-term overstory and understory change following logging and fire exclusion in a Sierra Nevada mixed-conifer forest. Forest Ecology and Management. 310: 903–914. https://doi.org/10.1016/j.foreco.2013.09.041 and https://www.fs.usda.gov/research/treesearch/45212

Knapp, Eric E.; Carlson, Robert L. 2021. Stanislaus-Tuolumne Experimental Forest ‘Methods of Cutting’ study plots 8-11: 88+ years of forest composition. Fort Collins, CO: Forest Service Research Data Archive. https://doi.org/10.2737/RDS-2021-0061

USDA, NRCS. 2022. The PLANTS Database (http://plants.usda.gov). National Plant Data Team, Greensboro, NC 27401-4901 USA.

Metadata_Reference_Information:

Metadata_Date: 20230330

Metadata_Contact:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: USDA Forest Service, Pacific Southwest Research Station

Contact_Person: Emily G. Brodie

Contact_Position: Postdoctoral scholar

Contact_Address:

Address_Type: mailing and physical

Address: 3644 Avtech Parkway

City: Redding

State_or_Province: CA

Postal_Code: 96002-9241

Country: USA

Contact_Voice_Telephone: 425-233-2317

Contact_Electronic_Mail_Address: emily.brodie@usda.gov

Metadata_Standard_Name: FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata

Metadata_Standard_Version: FGDC-STD-001.1-1999