Model sapwood data and compute the highest posterior density interval
Source:R/sw_model.R
sw_model.RdThis function fits a distribution to a data set of observed sapwood numbers and computes the highest posterior density interval (hdi) for a given credibility mass.
Usage
sw_model(
sw_data = "Hollstein_1980",
densfun = "lognormal",
cred_mass = 0.954,
source = NA,
plot = FALSE
)Arguments
- sw_data
The name of the sapwood data set to use for modelling. It should be one of the data sets listed in
sw_data_overview(), or the name of adata.framewith sapwood data in columnsn_sapwoodandcount.- densfun
Name of the density function to fit to the sapwood data set. Should be one of:
lognormal (the default value),
normal,
weibull,
gammma.
- cred_mass
A
scalarin the range of[0, 1]specifying the mass within the credible interval (default = .954).- source
A character string with info on the data source. This info is incorporated in the titel of the plot when a sapwood data set is provided from a user-defined
data.frame.- plot
A
logical. IfTRUEa plot of the fitted density function is returned. WhenFALSE, a list with numeric output of the modelling process is returned.
Value
The return value depends on the plot parameter.
if
plotis TRUE, a ggplot-style graph is returned.if
plotis FALSE, alistwith the numeric output of the modelling process is returned.
Examples
sw_model(sw_data = "Sohar_2012_ELL_c",
densfun = "lognormal",
cred_mass = .095,
plot = FALSE)
#> $sapwood_data
#> [1] "Sohar_2012_ELL_c"
#>
#> $n
#> [1] 562
#>
#> $range
#> min mean max
#> 2.00 14.05 27.00
#>
#> $density_function
#> [1] "lognormal"
#>
#> $fit_parameters
#> meanlog sdlog
#> 2.426831039 0.259874475
#> (0.010962143) (0.007751406)
#>
#> $sapwood_model
#> n_sapwood p model_fit count
#> 1 1 1.775685e-19 9.979348e-17 NA
#> 2 2 1.663010e-10 9.346118e-08 1
#> 3 3 1.088009e-06 6.114613e-04 NA
#> 4 4 1.267019e-04 7.120648e-02 NA
#> 5 5 2.182256e-03 1.226428e+00 2
#> 6 6 1.291805e-02 7.259944e+00 12
#> 7 7 3.957205e-02 2.223949e+01 18
#> 8 8 7.852913e-02 4.413337e+01 35
#> 9 9 1.154500e-01 6.488290e+01 60
#> 10 10 1.369339e-01 7.695686e+01 63
#> 11 11 1.386953e-01 7.794674e+01 79
#> 12 12 1.247730e-01 7.012242e+01 94
#> 13 13 1.025333e-01 5.762373e+01 60
#> 14 14 7.855963e-02 4.415051e+01 60
#> 15 15 5.698656e-02 3.202645e+01 30
#> 16 16 3.959475e-02 2.225225e+01 24
#> 17 17 2.658857e-02 1.494277e+01 5
#> 18 18 1.737775e-02 9.766296e+00 7
#> 19 19 1.111591e-02 6.247143e+00 5
#> 20 20 6.989977e-03 3.928367e+00 2
#> 21 21 4.336480e-03 2.437101e+00 2
#> 22 22 2.661888e-03 1.495981e+00 1
#> 23 23 1.620552e-03 9.107503e-01 1
#> 24 24 9.804003e-04 5.509850e-01 NA
#> 25 25 5.903513e-04 3.317774e-01 NA
#> 26 26 3.542948e-04 1.991137e-01 NA
#> 27 27 2.121533e-04 1.192302e-01 1
#> 28 28 1.268731e-04 7.130269e-02 NA
#> 29 29 7.583378e-05 4.261858e-02 NA
#> 30 30 4.533286e-05 2.547707e-02 NA
#> 31 31 2.711814e-05 1.524039e-02 NA
#> 32 32 1.624066e-05 9.127252e-03 NA
#> 33 33 9.741231e-06 5.474572e-03 NA
#> 34 34 5.853724e-06 3.289793e-03 NA
#> 35 35 3.525157e-06 1.981138e-03 NA
#> 36 36 2.127906e-06 1.195883e-03 NA
#> 37 37 1.287769e-06 7.237261e-04 NA
#> 38 38 7.814555e-07 4.391780e-04 NA
#> 39 39 4.755642e-07 2.672671e-04 NA
#> 40 40 2.902683e-07 1.631308e-04 NA
#> 41 41 1.777110e-07 9.987356e-05 NA
#> 42 42 1.091399e-07 6.133662e-05 NA
#> 43 43 6.724062e-08 3.778923e-05 NA
#> 44 44 4.156016e-08 2.335681e-05 NA
#> 45 45 2.577115e-08 1.448339e-05 NA
#> 46 46 1.603285e-08 9.010462e-06 NA
#> 47 47 1.000723e-08 5.624062e-06 NA
#> 48 48 6.266796e-09 3.521939e-06 NA
#> 49 49 3.937367e-09 2.212800e-06 NA
#> 50 50 2.481946e-09 1.394854e-06 NA
#> 51 51 1.569641e-09 8.821384e-07 NA
#> 52 52 9.959186e-10 5.597063e-07 NA
#> 53 53 6.339499e-10 3.562799e-07 NA
#> 54 54 4.048413e-10 2.275208e-07 NA
#> 55 55 2.593601e-10 1.457604e-07 NA
#> 56 56 1.666860e-10 9.367752e-08 NA
#> 57 57 1.074634e-10 6.039446e-08 NA
#> 58 58 6.949855e-11 3.905818e-08 NA
#> 59 59 4.508489e-11 2.533771e-08 NA
#> 60 60 2.933683e-11 1.648730e-08 NA
#> 61 61 1.914733e-11 1.076080e-08 NA
#> 62 62 1.253436e-11 7.044310e-09 NA
#> 63 63 8.229636e-12 4.625056e-09 NA
#> 64 64 5.419124e-12 3.045548e-09 NA
#> 65 65 3.578763e-12 2.011265e-09 NA
#> 66 66 2.370158e-12 1.332029e-09 NA
#> 67 67 1.574155e-12 8.846752e-10 NA
#> 68 68 1.048404e-12 5.892033e-10 NA
#> 69 69 7.001748e-13 3.934983e-10 NA
#> 70 70 4.688844e-13 2.635130e-10 NA
#> 71 71 3.148415e-13 1.769409e-10 NA
#> 72 72 2.119682e-13 1.191261e-10 NA
#> 73 73 1.430827e-13 8.041250e-11 NA
#> 74 74 9.683394e-14 5.442067e-11 NA
#> 75 75 6.570182e-14 3.692442e-11 NA
#> 76 76 4.469127e-14 2.511649e-11 NA
#> 77 77 3.047541e-14 1.712718e-11 NA
#> 78 78 2.083263e-14 1.170794e-11 NA
#> 79 79 1.427556e-14 8.022863e-12 NA
#> 80 80 9.805796e-15 5.510858e-12 NA
#> 81 81 6.751500e-15 3.794343e-12 NA
#> 82 82 4.659425e-15 2.618597e-12 NA
#> 83 83 3.223043e-15 1.811350e-12 NA
#> 84 84 2.234544e-15 1.255814e-12 NA
#> 85 85 1.552703e-15 8.726191e-13 NA
#> 86 86 1.081315e-15 6.076989e-13 NA
#> 87 87 7.546889e-16 4.241351e-13 NA
#> 88 88 5.278664e-16 2.966609e-13 NA
#> 89 89 3.700057e-16 2.079432e-13 NA
#> 90 90 2.599021e-16 1.460650e-13 NA
#> 91 91 1.829434e-16 1.028142e-13 NA
#> 92 92 1.290380e-16 7.251938e-14 NA
#> 93 93 9.120153e-17 5.125526e-14 NA
#> 94 94 6.458904e-17 3.629904e-14 NA
#> 95 95 4.583290e-17 2.575809e-14 NA
#> 96 96 3.258719e-17 1.831400e-14 NA
#> 97 97 2.321440e-17 1.304649e-14 NA
#> 98 98 1.656909e-17 9.311829e-15 NA
#> 99 99 1.184842e-17 6.658814e-15 NA
#> 100 100 8.488547e-18 4.770564e-15 NA
#>
#> $hdi_model
#> lower upper p
#> 1 11 11 0.1386953
#>
sw_model("Hollstein_1980")
#> $sapwood_data
#> [1] "Hollstein_1980"
#>
#> $n
#> [1] 490
#>
#> $range
#> min mean max
#> 6.00 25.05 67.00
#>
#> $density_function
#> [1] "lognormal"
#>
#> $fit_parameters
#> meanlog sdlog
#> 2.81357890 0.41620736
#> (0.01880233) (0.01329526)
#>
#> $sapwood_model
#> n_sapwood p model_fit count
#> 1 1 1.143856e-10 5.604897e-08 NA
#> 2 2 1.107667e-06 5.427569e-04 NA
#> 3 3 6.572161e-05 3.220359e-02 NA
#> 4 4 6.697648e-04 3.281848e-01 NA
#> 5 5 2.917879e-03 1.429761e+00 NA
#> 6 6 7.845478e-03 3.844284e+00 4
#> 7 7 1.558774e-02 7.637994e+00 9
#> 8 8 2.528777e-02 1.239101e+01 18
#> 9 9 3.557549e-02 1.743199e+01 21
#> 10 10 4.511128e-02 2.210453e+01 21
#> 11 11 5.291838e-02 2.593001e+01 21
#> 12 12 5.847980e-02 2.865510e+01 27
#> 13 13 6.168335e-02 3.022484e+01 27
#> 14 14 6.270361e-02 3.072477e+01 37
#> 15 15 6.187987e-02 3.032113e+01 25
#> 16 16 5.961755e-02 2.921260e+01 21
#> 17 17 5.632071e-02 2.759715e+01 24
#> 18 18 5.235228e-02 2.565261e+01 29
#> 19 19 4.801543e-02 2.352756e+01 23
#> 20 20 4.354902e-02 2.133902e+01 18
#> 21 21 3.913128e-02 1.917433e+01 19
#> 22 22 3.488778e-02 1.709501e+01 26
#> 23 23 3.090081e-02 1.514139e+01 17
#> 24 24 2.721872e-02 1.333717e+01 19
#> 25 25 2.386428e-02 1.169350e+01 14
#> 26 26 2.084176e-02 1.021246e+01 9
#> 27 27 1.814260e-02 8.889875e+00 11
#> 28 28 1.574987e-02 7.717438e+00 8
#> 29 29 1.364165e-02 6.684408e+00 6
#> 30 30 1.179345e-02 5.778789e+00 3
#> 31 31 1.017998e-02 4.988188e+00 3
#> 32 32 8.776330e-03 4.300402e+00 3
#> 33 33 7.558758e-03 3.703792e+00 5
#> 34 34 6.505127e-03 3.187512e+00 NA
#> 35 35 5.595166e-03 2.741631e+00 4
#> 36 36 4.810558e-03 2.357174e+00 5
#> 37 37 4.134922e-03 2.026112e+00 4
#> 38 38 3.553733e-03 1.741329e+00 1
#> 39 39 3.054196e-03 1.496556e+00 3
#> 40 40 2.625106e-03 1.286302e+00 NA
#> 41 41 2.256692e-03 1.105779e+00 1
#> 42 42 1.940470e-03 9.508301e-01 1
#> 43 43 1.669088e-03 8.178532e-01 NA
#> 44 44 1.436201e-03 7.037387e-01 NA
#> 45 45 1.236339e-03 6.058060e-01 NA
#> 46 46 1.064793e-03 5.217487e-01 2
#> 47 47 9.175209e-04 4.495852e-01 NA
#> 48 48 7.910512e-04 3.876151e-01 NA
#> 49 49 6.824083e-04 3.343801e-01 NA
#> 50 50 5.890423e-04 2.886307e-01 NA
#> 51 51 5.087694e-04 2.492970e-01 NA
#> 52 52 4.397201e-04 2.154628e-01 NA
#> 53 53 3.802943e-04 1.863442e-01 NA
#> 54 54 3.291226e-04 1.612701e-01 NA
#> 55 55 2.850331e-04 1.396662e-01 NA
#> 56 56 2.470227e-04 1.210411e-01 NA
#> 57 57 2.142330e-04 1.049741e-01 NA
#> 58 58 1.859287e-04 9.110504e-02 NA
#> 59 59 1.614803e-04 7.912533e-02 NA
#> 60 60 1.403484e-04 6.877070e-02 NA
#> 61 61 1.220707e-04 5.981464e-02 NA
#> 62 62 1.062509e-04 5.206292e-02 NA
#> 63 63 9.254883e-05 4.534893e-02 NA
#> 64 64 8.067277e-05 3.952966e-02 NA
#> 65 65 7.037208e-05 3.448232e-02 NA
#> 66 66 6.143144e-05 3.010140e-02 NA
#> 67 67 5.366574e-05 2.629621e-02 1
#> 68 68 4.691575e-05 2.298872e-02 NA
#> 69 69 4.104443e-05 2.011177e-02 NA
#> 70 70 3.593374e-05 1.760753e-02 NA
#> 71 71 3.148196e-05 1.542616e-02 NA
#> 72 72 2.760137e-05 1.352467e-02 NA
#> 73 73 2.421627e-05 1.186597e-02 NA
#> 74 74 2.126129e-05 1.041803e-02 NA
#> 75 75 1.867996e-05 9.153180e-03 NA
#> 76 76 1.642343e-05 8.047483e-03 NA
#> 77 77 1.444946e-05 7.080237e-03 NA
#> 78 78 1.272146e-05 6.233514e-03 NA
#> 79 79 1.120772e-05 5.491782e-03 NA
#> 80 80 9.880763e-06 4.841574e-03 NA
#> 81 81 8.716743e-06 4.271204e-03 NA
#> 82 82 7.694957e-06 3.770529e-03 NA
#> 83 83 6.797416e-06 3.330734e-03 NA
#> 84 84 6.008483e-06 2.944157e-03 NA
#> 85 85 5.314552e-06 2.604130e-03 NA
#> 86 86 4.703779e-06 2.304852e-03 NA
#> 87 87 4.165844e-06 2.041264e-03 NA
#> 88 88 3.691753e-06 1.808959e-03 NA
#> 89 89 3.273657e-06 1.604092e-03 NA
#> 90 90 2.904707e-06 1.423306e-03 NA
#> 91 91 2.578917e-06 1.263669e-03 NA
#> 92 92 2.291057e-06 1.122618e-03 NA
#> 93 93 2.036553e-06 9.979109e-04 NA
#> 94 94 1.811399e-06 8.875853e-04 NA
#> 95 95 1.612087e-06 7.899228e-04 NA
#> 96 96 1.435545e-06 7.034171e-04 NA
#> 97 97 1.279077e-06 6.267475e-04 NA
#> 98 98 1.140316e-06 5.587548e-04 NA
#> 99 99 1.017186e-06 4.984211e-04 NA
#> 100 100 9.078620e-07 4.448524e-04 NA
#>
#> $hdi_model
#> lower upper p
#> 1 6 34 0.9561202
#>