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.
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:
McAbeeExampleRequired 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_datato 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
#> # A tibble: 192 × 40
#> site specimen_number morphotype measurer_comments margin petiole_width
#> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 McAbee H1 BU-712-1006 M1 NA 0 0.165
#> 2 McAbee H1 BU-712-1022A M1 NA 0 0.047
#> 3 McAbee H1 BU-712-1065B M1 NA 0 NA
#> 4 McAbee H1 BU-712-1083 M1 NA 0 0.075
#> 5 McAbee H1 BU-712-1122 M1 NA 0 0.074
#> 6 McAbee H1 BU-712-1133 M1 NA 0 0.051
#> 7 McAbee H1 BU-712-1210 M1 NA 0 0.138
#> 8 McAbee H1 BU-712-1214A M1 NA 0 0.142
#> 9 McAbee H1 BU-712-1216 M1 NA 0 0.05
#> 10 McAbee H1 M-2015-1-104 M1 NA 0 0.121
#> # ℹ 182 more rows
#> # ℹ 34 more variables: petiole_area <dbl>, blade_area <dbl>,
#> # blade_perimeter <lgl>, feret <dbl>, minimum_feret <lgl>,
#> # raw_blade_area <dbl>, raw_blade_perimeter <dbl>,
#> # internal_raw_blade_area <dbl>, internal_raw_blade_perimeter <dbl>,
#> # length_of_cut_perimeter <dbl>, no_of_primary_teeth <dbl>,
#> # no_of_subsidiary_teeth <dbl>, leaf_area <dbl>, feret_diameter <dbl>, …
dilp_results$processed_morphotype_data
#> # A tibble: 61 × 38
#> site morphotype margin petiole_width petiole_area blade_area blade_perimeter
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 McAb… M1 0 0.0962 0.0223 6.14 NaN
#> 2 McAb… M3 0 NaN NaN NaN NaN
#> 3 McAb… M5 0 0.114 0.029 9.83 NaN
#> 4 McAb… M8 0 0.0765 0.0407 8.79 NaN
#> 5 McAb… M11 1 NaN NaN NaN NaN
#> 6 McAb… M12 1 0.038 0.01 1.33 NaN
#> 7 McAb… M13 0 0.069 0.047 7.80 NaN
#> 8 McAb… M15 0 NaN NaN NaN NaN
#> 9 McAb… M16 0 NaN NaN NaN NaN
#> 10 McAb… M18 0 0.11 0.101 14.8 NaN
#> # ℹ 51 more rows
#> # ℹ 31 more variables: feret <dbl>, minimum_feret <dbl>, raw_blade_area <dbl>,
#> # raw_blade_perimeter <dbl>, internal_raw_blade_area <dbl>,
#> # internal_raw_blade_perimeter <dbl>, length_of_cut_perimeter <dbl>,
#> # no_of_primary_teeth <dbl>, no_of_subsidiary_teeth <dbl>, leaf_area <dbl>,
#> # feret_diameter <dbl>, fdr <dbl>, raw_blade_perimeter_corrected <dbl>,
#> # internal_raw_blade_perimeter_corrected <dbl>, total_tooth_count <dbl>, …
dilp_results$processed_site_data
#> # A tibble: 2 × 37
#> site margin petiole_width petiole_area blade_area blade_perimeter feret
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 McAbee H1 32.3 0.0710 0.0709 11.6 NaN 5.19
#> 2 McAbee H2 23.3 0.0766 0.0894 16.4 NaN 5.92
#> # ℹ 30 more variables: minimum_feret <dbl>, raw_blade_area <dbl>,
#> # raw_blade_perimeter <dbl>, internal_raw_blade_area <dbl>,
#> # internal_raw_blade_perimeter <dbl>, length_of_cut_perimeter <dbl>,
#> # no_of_primary_teeth <dbl>, no_of_subsidiary_teeth <dbl>, leaf_area <dbl>,
#> # feret_diameter <dbl>, fdr <dbl>, raw_blade_perimeter_corrected <dbl>,
#> # internal_raw_blade_perimeter_corrected <dbl>, total_tooth_count <dbl>,
#> # tc_ip <dbl>, perimeter_ratio <dbl>, ln_leaf_area <dbl>, ln_pr <dbl>, …
dilp_results$errors
#> Check Specimen1
#> 1 Entire tooth count not NA none
#> 2 Entire tooth count : IP not NA none
#> 3 Entire perimeter ratio not NA none
#> 4 FDR not between 0-1 none
#> 5 External perimeter not larger than internal perimeter none
#> 6 Feret is not larger than minimum Feret none
#> 7 Perimeter ratio not greater than 1 none
dilp_results$outliers
#> Variable Outlier1 Outlier2 Outlier3 Outlier4
#> 1 fdr <NA> <NA> <NA> <NA>
#> 2 tc_ip BU-712-1117 BU-712-1169A BU-712-1176A <NA>
#> 3 leaf_area BU-712-2173A BU-712-2105A BU-712-2124 <NA>
#> 4 perimeter_ratio M-2015-1-1 BU-712-1073A BU-712-1165 M-2015-1-62
dilp_results$results
#> site margin fdr tc_ip ln_leaf_area ln_tc_ip ln_pr
#> 1 McAbee H1 32.25806 0.6965086 2.562487 6.792833 0.6070757 0.2047427
#> 2 McAbee H2 23.33333 0.7012671 2.651242 7.037892 0.6218561 0.1504205
#> MAT.MLR MAT.MLR.error MAT.SLR MAT.SLR.error MAP.MLR MAP.MLR.error.plus
#> 1 13.54419 4 11.18065 4.8 106.7353 87.74914
#> 2 11.63970 4 9.36000 4.8 133.6330 109.86219
#> MAP.MLR.error.minus MAP.SLR MAP.SLR.error.plus MAP.SLR.error.minus
#> 1 48.15775 126.7697 106.5412 57.88926
#> 2 60.29365 135.8734 114.1923 62.04646