| Type: | Package |
| Title: | Derive Leaf Angle Distribution (LAD) from Measured Leaf Inclination Angles |
| Version: | 0.1.0 |
| Maintainer: | Francesco Chianucci <fchianucci@gmail.com> |
| Description: | Calculate mean statistics and leaf angle distribution type from measured leaf inclination angles. LAD distribution is fitted using a two-parameters (mu, nu) Beta distribution and compared with six theoretical LAD distributions. Additional information is provided in Chianucci and Cesaretti (2022) <doi:10.1101/2022.10.28.513998>. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.2.2 |
| Imports: | cowplot, dplyr, ggplot2, magrittr, purrr, rlang, stats, tidyr, tidyselect, utils |
| Depends: | R (≥ 2.10) |
| NeedsCompilation: | no |
| Packaged: | 2023-06-10 16:58:48 UTC; francescochianucci |
| Author: | Francesco Chianucci
 [aut, cre],
Lorenzo Cesaretti [aut] |
| Repository: | CRAN |
| Date/Publication: | 2023-06-11 11:30:04 UTC |
LAD: Derive Leaf Angle Distribution (LAD) from Measured Leaf Inclination Angles
Description
Calculate mean statistics and leaf angle distribution type from measured leaf inclination angles. LAD distribution is fitted using a two-parameters (mu, nu) Beta distribution and compared with six theoretical LAD distributions. Additional information is provided in Chianucci and Cesaretti (2022) doi:10.1101/2022.10.28.513998.
Author(s)
Maintainer: Francesco Chianucci fchianucci@gmail.com (ORCID)
Authors:
Lorenzo Cesaretti lorenzo.cesaretti@crea.gov.it
Pipe operator
Description
See magrittr::%>% for details.
Usage
lhs %>% rhs
Arguments
lhs |
A value or the magrittr placeholder. |
rhs |
A function call using the magrittr semantics. |
Value
The result of calling rhs(lhs).
Chianucci dataset
Description
The dataset provide measured leaf inclination angles from 138 temperate and boreal woody species.
Usage
Chianucci
Format
Chianucci
A data frame with 23,882 rows and 9 columns:
- N
row ID record
- ICP_Code
ICP species code, when available
- Family, Genus, Species
Family, Genus, Species taxonomy information
- Author_citation
Species author name
- Canopy_sector
The portion of the canopy where the leaves have been measured
- Angle_degree
Measured leaf inclination angles (degree)
- Date
Date of sampling (dd-mm-yy)
...
Source
Calculate summary statistics from measured leaf inclination angles
Description
The function derives summary statistics from measured leaf inclination angles:.
Mean (MTA), standard deviation (SD) and frequency (NR) observations.
The two (mu, nu) Beta parameters derived from the formula provided by Goel and Strebel (1984) doi:10.2134/agronj1984.00021962007600050021x.
The distribution type, comparing the distribution against the six theoretical LAD distributions provided by de Wit (1965).
Arguments
data |
Dataframe. The dataframe containing leaf inclination angle measurements. |
angles |
Numeric. The column containing leaf inclination angle measurements (in degrees). |
type |
Character. If set to "summary", it gives summary distributions. If set to "extended", it calculates LAD probability density (pdf) and G-function (G) for view or inclination angles (theta). Default set to "summary". |
... |
The column(s) indicating the grouping variables to be considered for calculating summary statistics. |
Value
A dataframe with the grouping variable(s), and:
summary statistics (MTA, SD, N, mu, nu, distribution) in case of type="summary";
LAD (pdf) and G-function (G) in case of type="extended".
Examples
head(Chianucci)
calcLAD(Chianucci,Angle_degree,type='summary',Genus,Species)
calcLAD(Chianucci,Angle_degree,type='extended',Genus,Species)
Fit Leaf Angle Distribution (LAD) from two-parameters (mu, nu) Beta distribution
Description
The function derives both the Leaf Angle Distribution (LAD) and the G-function from two-parameters (mu, nu) Beta distribution.
The LAD function is fitted through a Beta distribution as recommended by Goel and Strebel (1984).
The G-function is derived from LAD using the formula provided by Ross (1981) and reported as Equations 2-3 by Chianucci et al. (2018).
The fitted LAD is also compared with six theoretical LAD distributions provided by de Wit (1965).
The distribution type is then classified using a leaf inclination index Ross (1975) and reported as Equation 8 by Chianucci et al. (2018).
Arguments
mu |
Numeric. The mu parameter of the Beta distribution. |
nu |
Numeric. The nu parameter of the Beta distribution. |
plot |
Logical. If set to TRUE, it plots the measured and theoretical LAD and G distributions. Default set to FALSE. |
Value
A list of two elements:
dataset: a dataframe with three columns indicating the measured LAD (pdf), the G-function (G), for view or inclination angle (theta).
distribution: a vector containing the matched distribution type.
Examples
fitLAD(0.9,0.9) # uniform LAD distribution
fitLAD(2.8,1.18)# planophile LAD distribution
fitLAD(1.1,1.7, plot=TRUE)# spherical LAD distribution