dilp: Generate DiLP results
In dilp: Reconstruct Paleoclimate and Paleoecology with Leaf Physiognomy
View source: R/dilp_functions.R
dilp R Documentation
Generate DiLP results
Description
dilp() processes raw leaf physiognomic data, checks for common
errors/outliers, and returns the processed data, keys to finding potential
errors or outliers, and paleoclimate reconstructions.
Usage
dilp(specimen_data, params = "PeppeGlobal", subsite_cols = NULL)
Arguments
specimen_data
A data frame containing specimen level leaf physiognomic
data. See Lowe et al. 2024 for more information on how to collect this data.
A good reference for how to put together the data: McAbeeExample
Required columns:
site
specimen_number
morphotype
margin
feret
blade_area
raw_blade_perimeter
internal_raw_blade_perimeter
length_of_cut_perimeter
no_of_primary_teeth
no_of_subsidiary_teeth
Recommended columns:
petiole_width
petiole_area
blade_perimeter
minimum_feret
raw_blade_area
internal_raw_blade_area
params
Either a string referring to one of two preloaded parameter sets
of a list of custom parameters (same format as the list below).
Preloaded parameter sets are "PeppeGlobal" and "PeppeNH" which are calibrated based on
global and northern hemisphere data respectively. Allen et al. (2020) illustrates a situation
in which the northern hemisphere parameters may be preferable. The "PeppeNH" parameters
only estimate MAT. Use "PeppeGlobal" for all MAP estimates. Defaults to "PeppeGlobal" as follows (Peppe et al. 2011):
MAT.MLR.M = 0.21,
MAT.MLR.FDR = 42.296,
MAT.MLR.TC.IP = -2.609,
MAT.MLR.constant = -16.004,
MAT.MLR.error = 4,
MAT.SLR.M = 0.204,
MAT.SLR.constant = 4.6,
MAT.SLR.error = 4.9,
MAP.MLR.LA = 0.298,
MAP.MLR.TC.IP = 0.279,
MAP.MLR.PR = -2.717,
MAP.MLR.constant = 3.033,
MAP.MLR.SE = 0.6,
MAP.SLR.LA = 0.283,
MAP.SLR.constant = 2.92,
MAP.SLR.SE = 0.61
subsite_cols
A vector or list of columns present in specimen_data to calculate
paleoclimate estimates for. A completely optional parameter - allows different groupings of
specimens to be tested, or comparisons of paleoclimate estimates at different levels of grouping.
Adds additional estimates to $results.
Value
A list of tables that includes all pertinent DiLP
information:
processed_leaf_data: the full set of cleaned and newly calculated leaf
physiognomic data that is necessary for DiLP analysis. See dilp_processing()
for more information.
processed_morphotype_data: morphospecies-site pair means for all leaf
physiognomic data.
processed_site_data: site means for all leaf physiognomic data.
errors: lists any specimens that may be causing common errors in DiLP
calculations. See dilp_errors() for more information.
outliers: flags outliers in variables used for DiLP analysis that may
represent incorrect data. See dilp_outliers() for more information.
results: climate reconstructions of MAT and MAP using single and multi-linear
regressions.
References
Allen, S. E., Lowe, A. J., Peppe, D. J., & Meyer, H. W. (2020). Paleoclimate and paleoecology of the latest Eocene Florissant flora of central Colorado, USA. Palaeogeography, Palaeoclimatology, Palaeoecology, 551, 109678.
Peppe, D.J., Royer, D.L., Cariglino, B., Oliver, S.Y., Newman, S., Leight, E., Enikolopov, G., Fernandez-Burgos, M., Herrera, F., Adams, J.M., Correa, E., Currano, E.D., Erickson, J.M., Hinojosa, L.F., Hoganson, J.W., Iglesias, A., Jaramillo, C.A., Johnson, K.R., Jordan, G.J., Kraft, N.J.B., Lovelock, E.C., Lusk, C.H., Niinemets, Ü., Peñuelas, J., Rapson, G., Wing, S.L. and Wright, I.J. (2011), Sensitivity of leaf size and shape to climate: global patterns and paleoclimatic applications. New Phytologist, 190: 724-739. https://doi.org/10.1111/j.1469-8137.2010.03615.x
Lowe. A.J., Flynn, A.G., Butrim, M.J., Baumgartner, A., Peppe, D.J., and Royer, D.L. (2024), Reconstructing terrestrial paleoclimate and paleoecology with fossil leaves using Digital Leaf Physiognomy and leaf mass per area. JoVE.
Examples
dilp_results <- dilp(McAbeeExample)
dilp_results$processed_leaf_data
dilp_results$processed_morphotype_data
dilp_results$processed_site_data
dilp_results$errors
dilp_results$outliers
dilp_results$results
dilp documentation built on May 29, 2024, 8:54 a.m.
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View source: R/dilp_functions.R
| dilp | R Documentation |
Generate DiLP results
Description
dilp() processes raw leaf physiognomic data, checks for common
errors/outliers, and returns the processed data, keys to finding potential
errors or outliers, and paleoclimate reconstructions.
Usage
dilp(specimen_data, params = "PeppeGlobal", subsite_cols = NULL)
Arguments
specimen_data |
A data frame containing specimen level leaf physiognomic
data. See Lowe et al. 2024 for more information on how to collect this data.
A good reference for how to put together the data: Required columns:
Recommended columns:
|
params |
Either a string referring to one of two preloaded parameter sets of a list of custom parameters (same format as the list below). Preloaded parameter sets are "PeppeGlobal" and "PeppeNH" which are calibrated based on global and northern hemisphere data respectively. Allen et al. (2020) illustrates a situation in which the northern hemisphere parameters may be preferable. The "PeppeNH" parameters only estimate MAT. Use "PeppeGlobal" for all MAP estimates. Defaults to "PeppeGlobal" as follows (Peppe et al. 2011):
|
subsite_cols |
A vector or list of columns present in |
Value
A list of tables that includes all pertinent DiLP information:
processed_leaf_data: the full set of cleaned and newly calculated leaf physiognomic data that is necessary for DiLP analysis. See
dilp_processing()for more information.processed_morphotype_data: morphospecies-site pair means for all leaf physiognomic data.
processed_site_data: site means for all leaf physiognomic data.
errors: lists any specimens that may be causing common errors in DiLP calculations. See
dilp_errors()for more information.outliers: flags outliers in variables used for DiLP analysis that may represent incorrect data. See
dilp_outliers()for more information.results: climate reconstructions of MAT and MAP using single and multi-linear regressions.
References
Allen, S. E., Lowe, A. J., Peppe, D. J., & Meyer, H. W. (2020). Paleoclimate and paleoecology of the latest Eocene Florissant flora of central Colorado, USA. Palaeogeography, Palaeoclimatology, Palaeoecology, 551, 109678.
Peppe, D.J., Royer, D.L., Cariglino, B., Oliver, S.Y., Newman, S., Leight, E., Enikolopov, G., Fernandez-Burgos, M., Herrera, F., Adams, J.M., Correa, E., Currano, E.D., Erickson, J.M., Hinojosa, L.F., Hoganson, J.W., Iglesias, A., Jaramillo, C.A., Johnson, K.R., Jordan, G.J., Kraft, N.J.B., Lovelock, E.C., Lusk, C.H., Niinemets, Ü., Peñuelas, J., Rapson, G., Wing, S.L. and Wright, I.J. (2011), Sensitivity of leaf size and shape to climate: global patterns and paleoclimatic applications. New Phytologist, 190: 724-739. https://doi.org/10.1111/j.1469-8137.2010.03615.x
Lowe. A.J., Flynn, A.G., Butrim, M.J., Baumgartner, A., Peppe, D.J., and Royer, D.L. (2024), Reconstructing terrestrial paleoclimate and paleoecology with fossil leaves using Digital Leaf Physiognomy and leaf mass per area. JoVE.
Examples
dilp_results <- dilp(McAbeeExample)
dilp_results$processed_leaf_data
dilp_results$processed_morphotype_data
dilp_results$processed_site_data
dilp_results$errors
dilp_results$outliers
dilp_results$results
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