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Generate DiLP results

Source: R/dilp_functions.R
dilp.Rd

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. J. Vis. Exp. (212), e66838, doi:10.3791/66838 (2024).

Examples

dilp_results <- dilp(McAbeeExample)
#> Warning: Outliers found. Please evaluate $outliers for possible wrong measurements
dilp_results$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$errors
#>                                                   Check specimen_number
#> 1                             Entire tooth count not NA No errors found
#> 2                        Entire tooth count : IP not NA No errors found
#> 3                         Entire perimeter ratio not NA No errors found
#> 4                                   FDR not between 0-1 No errors found
#> 5 External perimeter not larger than internal perimeter No errors found
#> 6                Feret is not larger than minimum Feret No errors found
#> 7                    Perimeter ratio not greater than 1 No errors found
dilp_results$outliers
#>         site specimen_number morphotype         outlier         within
#> 1  McAbee H1     BU-712-1117         M8           tc_ip entire dataset
#> 2  McAbee H1    BU-712-1169A         M8           tc_ip entire dataset
#> 3  McAbee H1    BU-712-1176A         M8           tc_ip entire dataset
#> 4  McAbee H2    BU-712-2173A        M18       leaf_area entire dataset
#> 5  McAbee H2    BU-712-2105A        M47       leaf_area entire dataset
#> 6  McAbee H2     BU-712-2124        M94       leaf_area entire dataset
#> 7  McAbee H1      M-2015-1-1        M24 perimeter_ratio entire dataset
#> 8  McAbee H1    BU-712-1073A        M28 perimeter_ratio entire dataset
#> 9  McAbee H1     BU-712-1165        M28 perimeter_ratio entire dataset
#> 10 McAbee H1     M-2015-1-62        M28 perimeter_ratio entire dataset
#> 11 McAbee H1    BU-712-1182A         M5           tc_ip     morphotype
#> 12 McAbee H1      M-2015-1-3         M5           tc_ip     morphotype
#> 13 McAbee H1    BU-712-1182A         M5 perimeter_ratio     morphotype
#> 14 McAbee H1    M-2015-1-122         M5 perimeter_ratio     morphotype
#> 15 McAbee H1      M-2015-1-3         M5 perimeter_ratio     morphotype
#> 16 McAbee H1     M-2015-1-40         M5 perimeter_ratio     morphotype
#> 17 McAbee H1     BU-712-1117         M8           tc_ip     morphotype
#> 18 McAbee H1    BU-712-1169A         M8           tc_ip     morphotype
#> 19 McAbee H1    BU-712-1176A         M8           tc_ip     morphotype
#> 20 McAbee H1     M-2015-1-69         M8 perimeter_ratio     morphotype
#> 21 McAbee H1      M-2015-1-7        M19           tc_ip     morphotype
#> 22 McAbee H2     M-2015-2-15        M19           tc_ip     morphotype
#> 23 McAbee H2     M-2015-2-84        M19           tc_ip     morphotype
#> 24 McAbee H2     BU-712-2197        M19 perimeter_ratio     morphotype
#> 25 McAbee H1      M-2015-1-1        M24 perimeter_ratio     morphotype
#> 26 McAbee H1     M-2015-1-17        M28 perimeter_ratio     morphotype
#> 27 McAbee H1     M-2015-1-62        M28 perimeter_ratio     morphotype
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