tree_phylm: Phylogenetic uncertainty - Phylogenetic Linear Regression
In sensiPhy: Sensitivity Analysis for Comparative Methods
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
Description
Performs Phylogenetic linear regression evaluating
uncertainty in trees topology.
Usage
1
tree_phylm(formula, data, phy, n.tree = 2, model = "lambda", track = TRUE, ...)
Arguments
formula
The model formula
data
Data frame containing species traits with species as row names.
phy
A phylogeny (class 'multiPhylo', see ?ape).
n.tree
Number of times to repeat the analysis with n different trees picked
randomly in the multiPhylo file.
If NULL, n.tree = 2
model
The phylogenetic model to use (see Details). Default is lambda.
track
Print a report tracking function progress (default = TRUE)
...
Further arguments to be passed to phylolm
Details
This function fits a phylogenetic linear regression model using phylolm
to n trees, randomly picked in a multiPhylo file.
All phylogenetic models from phylolm can be used, i.e. BM,
OUfixedRoot, OUrandomRoot, lambda, kappa,
delta, EB and trend. See ?phylolm for details.
Currently, this function can only implement simple linear models (i.e. trait~
predictor). In the future we will implement more complex models.
Output can be visualised using sensi_plot.
Value
The function tree_phylm returns a list with the following
components:
formula: The formula
data: Original full dataset
sensi.estimates: Coefficients, aic and the optimised
value of the phylogenetic parameter (e.g. lambda) for each regression with a
different phylogenetic tree.
N.obs: Size of the dataset after matching it with tree tips and removing NA's.
stats: Main statistics for model parameters.CI_low and CI_high are the lower
and upper limits of the 95
all.stats: Complete statistics for model parameters. sd_intra is the standard deviation
due to intraspecific variation. CI_low and CI_high are the lower and upper limits
of the 95
Author(s)
Caterina Penone & Pablo Ariel Martinez
References
Paterno, G. B., Penone, C. Werner, G. D. A.
sensiPhy:
An r-package for sensitivity analysis in phylogenetic
comparative methods. Methods in Ecology and Evolution
2018, 9(6):1461-1467
Donoghue, M.J. & Ackerly, D.D. (1996). Phylogenetic Uncertainties and
Sensitivity Analyses in Comparative Biology. Philosophical Transactions:
Biological Sciences, pp. 1241-1249.
Ho, L. S. T. and Ane, C. 2014. "A linear-time algorithm for
Gaussian and non-Gaussian trait evolution models". Systematic Biology 63(3):397-408.
See Also
phylolm, sensi_plot, tree_phyglm
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
# Load data:
data(alien)
# This analysis needs a multiphylo file:
class(alien$phy)
alien$phy
# run PGLS accounting for phylogenetic uncertain:
tree <- tree_phylm(log(gestaLen) ~ log(adultMass), phy = alien$phy,
data = alien$data, n.tree = 30)
# To check summary results:
summary(tree)
# Visual diagnostics
sensi_plot(tree)
# You can specify which graph to print:
sensi_plot(tree, graphs = 3)
Example output
Loading required package: ape
Loading required package: phylolm
Loading required package: ggplot2
[1] "multiPhylo"
101 phylogenetic trees
Used dataset has 84 species that match data and phylogeny
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Warning messages:
1: In match_dataphy(formula, data, phy, ...) :
NA's in response or predictor, rows with NA's were removed
2: In match_dataphy(formula, data, phy, ...) :
Some phylo tips do not match species in data (this can be due to NA removal) species were dropped from phylogeny or data
mean CI_low CI_high
intercept 2.330 2.318 2.343
se.intercept 0.341 0.340 0.342
pval.intercept 0.000 0.000 0.000
estimate 0.152 0.150 0.153
se.estimate 0.022 0.021 0.022
pval.estimate 0.000 0.000 0.000
sensiPhy documentation built on April 14, 2020, 7:15 p.m.
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Description Usage Arguments Details Value Author(s) References See Also Examples
Description
Performs Phylogenetic linear regression evaluating uncertainty in trees topology.
Usage
1 | tree_phylm(formula, data, phy, n.tree = 2, model = "lambda", track = TRUE, ...)
|
Arguments
formula |
The model formula |
data |
Data frame containing species traits with species as row names. |
phy |
A phylogeny (class 'multiPhylo', see ? |
n.tree |
Number of times to repeat the analysis with n different trees picked
randomly in the multiPhylo file.
If NULL, |
model |
The phylogenetic model to use (see Details). Default is |
track |
Print a report tracking function progress (default = TRUE) |
... |
Further arguments to be passed to |
Details
This function fits a phylogenetic linear regression model using phylolm
to n trees, randomly picked in a multiPhylo file.
All phylogenetic models from phylolm can be used, i.e. BM,
OUfixedRoot, OUrandomRoot, lambda, kappa,
delta, EB and trend. See ?phylolm for details.
Currently, this function can only implement simple linear models (i.e. trait~ predictor). In the future we will implement more complex models.
Output can be visualised using sensi_plot.
Value
The function tree_phylm returns a list with the following
components:
formula: The formula
data: Original full dataset
sensi.estimates: Coefficients, aic and the optimised
value of the phylogenetic parameter (e.g. lambda) for each regression with a
different phylogenetic tree.
N.obs: Size of the dataset after matching it with tree tips and removing NA's.
stats: Main statistics for model parameters.CI_low and CI_high are the lower
and upper limits of the 95
all.stats: Complete statistics for model parameters. sd_intra is the standard deviation
due to intraspecific variation. CI_low and CI_high are the lower and upper limits
of the 95
Author(s)
Caterina Penone & Pablo Ariel Martinez
References
Paterno, G. B., Penone, C. Werner, G. D. A. sensiPhy: An r-package for sensitivity analysis in phylogenetic comparative methods. Methods in Ecology and Evolution 2018, 9(6):1461-1467
Donoghue, M.J. & Ackerly, D.D. (1996). Phylogenetic Uncertainties and Sensitivity Analyses in Comparative Biology. Philosophical Transactions: Biological Sciences, pp. 1241-1249.
Ho, L. S. T. and Ane, C. 2014. "A linear-time algorithm for Gaussian and non-Gaussian trait evolution models". Systematic Biology 63(3):397-408.
See Also
phylolm, sensi_plot, tree_phyglm
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | # Load data:
data(alien)
# This analysis needs a multiphylo file:
class(alien$phy)
alien$phy
# run PGLS accounting for phylogenetic uncertain:
tree <- tree_phylm(log(gestaLen) ~ log(adultMass), phy = alien$phy,
data = alien$data, n.tree = 30)
# To check summary results:
summary(tree)
# Visual diagnostics
sensi_plot(tree)
# You can specify which graph to print:
sensi_plot(tree, graphs = 3)
|
Example output
Loading required package: ape
Loading required package: phylolm
Loading required package: ggplot2
[1] "multiPhylo"
101 phylogenetic trees
Used dataset has 84 species that match data and phylogeny
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|============================================================= | 87%
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|=============================================================== | 90%
|
|================================================================= | 93%
|
|==================================================================== | 97%
|
|======================================================================| 100%
Warning messages:
1: In match_dataphy(formula, data, phy, ...) :
NA's in response or predictor, rows with NA's were removed
2: In match_dataphy(formula, data, phy, ...) :
Some phylo tips do not match species in data (this can be due to NA removal) species were dropped from phylogeny or data
mean CI_low CI_high
intercept 2.330 2.318 2.343
se.intercept 0.341 0.340 0.342
pval.intercept 0.000 0.000 0.000
estimate 0.152 0.150 0.153
se.estimate 0.022 0.021 0.022
pval.estimate 0.000 0.000 0.000
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