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Commit2753ac3

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author
Ilja J. Kocken
committed
docs updates
1 parent5580f15 commit2753ac3

17 files changed

+211
-140
lines changed

‎CITATION.cff‎

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@@ -26,7 +26,7 @@ repository-code: 'https://github.com/japhir/snvecR'
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url:'https://japhir.github.io/snvecR/'
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repository-artifact:'https://zenodo.org/record/7865280'
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abstract:>-
29-
Easily calculate precession and obliquity from an astronomical solution (defaults to ZB18a from Zeebe and Lourens (2019)) and assumed or reconstructed values fortidal dissipation (Td) anddynamical ellipticity (Ed). This is a translation and adaptation of the 'C'-code in the supplementary material to Zeebe and Lourens (2022), with further details on the methodology described in Zeebe (2022). The name of the 'C'-routine is 'snvec', which refers to the key units of computation: spin vector s and orbit normal vector n.
29+
Easily calculate precession and obliquity from an astronomical solution (defaults to ZB18a from Zeebe and Lourens (2019)) and assumed or reconstructed values fordynamical ellipticity (Ed) andtidal dissipation (Td). This is a translation and adaptation of the 'C'-code in the supplementary material to Zeebe and Lourens (2022), with further details on the methodology described in Zeebe (2022). The name of the 'C'-routine is 'snvec', which refers to the key units of computation: spin vector s and orbit normal vector n.
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keywords:
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-orbital forcing
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-precession

‎DESCRIPTION‎

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@@ -7,7 +7,7 @@ Authors@R:
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person("Richard", "Zeebe", , "zeebe@soest.hawaii.edu", role = c("aut"),
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comment = c(ORCID = "0000-0003-0806-8387"))
99
)
10-
Description: Easily calculate precession and obliquity from an orbital solution (defaults to ZB18a from Zeebe and Lourens (2019) <doi:10.1126/science.aax0612>) and assumed or reconstructed values fortidal dissipation (Td) anddynamical ellipticity (Ed). This is a translation and adaptation of the 'C'-code in the supplementary material to Zeebe and Lourens (2022) <doi:10.1029/2021PA004349>, with further details on the methodology described in Zeebe (2022) <doi:10.3847/1538-3881/ac80f8>. The name of the 'C'-routine is 'snvec', which refers to the key units of computation: spin vector s and orbit normal vector n.
10+
Description: Easily calculate precession and obliquity from an orbital solution (defaults to ZB18a from Zeebe and Lourens (2019) <doi:10.1126/science.aax0612>) and assumed or reconstructed values fordynamical ellipticity (Ed) andtidal dissipation (Td). This is a translation and adaptation of the 'C'-code in the supplementary material to Zeebe and Lourens (2022) <doi:10.1029/2021PA004349>, with further details on the methodology described in Zeebe (2022) <doi:10.3847/1538-3881/ac80f8>. The name of the 'C'-routine is 'snvec', which refers to the key units of computation: spin vector s and orbit normal vector n.
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License: GPL (>= 3)
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Encoding: UTF-8
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Roxygen: list(markdown = TRUE)

‎R/data.R‎

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@@ -1,51 +1,50 @@
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# document the astronomical solutions
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# we cache them locally, so I document them with @name and return type NULL.
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#' Full Astronomical Solution ZB18a for the past 100 Myr
4+
#' Full Astronomical Solution ZB18a
55
#'
6-
#' The HNBody output of Zeebe & Lourens (2019) after some pre-processing using
6+
#' The full ZB18a solution spans the past 100 Myr.
7+
#' It contains the HNBody output of Zeebe & Lourens (2019) after some pre-processing using
78
#' [prepare_solution()]. The wikipedia page on [Orbital
89
#' elements](https://en.wikipedia.org/wiki/Orbital_elements) describes what the
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#' components relate to in order to uniquely specify an orbital plane. The
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#' function asks to download the files to the user's cache directory so that
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#' they can be accessed more quickly in the future.
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#' components relate to in order to uniquely specify an orbital plane.
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#'
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#' @format ## `get_solution("full-ZB18a")`
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#' A data frame with 250,001 rows and 20 columns:
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#' \describe{
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#' \item{t}{Time \eqn{t} (days).}
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#' \item{t}{Time \eqn{t}{t} (days).}
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#' \item{time}{Time in thousands of years (kyr).}
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#' \item{aa}{Semimajor axis \eqn{a} in astronomical units (au).}
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#' \item{ee}{Eccentricity \eqn{e} (unitless).}
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#' \item{inc}{Inclination \eqn{I} (degrees).}
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#' \item{lph}{Longitude of perihelion \eqn{\varpi} (degrees).}
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#' \item{lan}{Longitude of the ascending node \eqn{\Omega} (degrees).}
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#' \item{arp}{Argument of perihelion \eqn{\omega} (degrees).}
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#' \item{mna}{Mean anomaly \eqn{M} (degrees).}
17+
#' \item{aa}{Semimajor axis \eqn{a}{a} in astronomical units (au).}
18+
#' \item{ee}{Eccentricity \eqn{e}{e} (unitless).}
19+
#' \item{inc}{Inclination \eqn{I}{I} (degrees).}
20+
#' \item{lph}{Longitude of perihelion \eqn{\varpi}{varpi} (degrees).}
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#' \item{lan}{Longitude of the ascending node \eqn{\Omega}{Omega} (degrees).}
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#' \item{arp}{Argument of perihelion \eqn{\omega}{omega} (degrees).}
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#' \item{mna}{Mean anomaly \eqn{M}{M} (degrees).}
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#'
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#' The following columns were computed from the above input with [prepare_solution()]:
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#'
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#' \item{lphu}{Unwrapped longitude of perihelion \eqn{\varpi} (degrees without
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#' jumps).}
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#' \item{lphu}{Unwrapped longitude of perihelion \eqn{\varpi}{varpi} (degrees
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#'withoutjumps).}
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#'
31-
#' \item{lanu}{Unwrapped longitude of the ascending node \eqn{\Omega}
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#' \item{lanu}{Unwrapped longitude of the ascending node \eqn{\Omega}{Omega}
3231
#' (degrees without jumps).}
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#'
34-
#' \item{hh}{Variable: \eqn{e\sin(\varpi)}{ee *sin(lph / R2D)}.}
33+
#' \item{hh}{Variable: \eqn{e\sin(\varpi)}{esin(lph)}.}
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#'
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#' \item{kk}{Variable: \eqn{e\cos(\varpi)}{ee *cos(lph / R2D)}.}
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#' \item{kk}{Variable: \eqn{e\cos(\varpi)}{ecos(lph)}.}
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#'
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#' \item{pp}{Variable: \eqn{2\sin(0.5I)\sin(\Omega)}{2*sin(0.5* inc / R2D) *
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#' sin(lan / R2D)}.}
37+
#' \item{pp}{Variable: \eqn{2\sin(0.5I)\sin(\Omega)}{2 sin(0.5I)
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#' sin(Omega)}.}
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#'
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#' \item{qq}{Variable: \eqn{2\sin(0.5I)\cos(\Omega)}{2*sin(0.5*inc / R2D) *
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#' cos(lan / R2D)}.}
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#' \item{qq}{Variable: \eqn{2\sin(0.5I)\cos(\Omega)}{2 sin(0.5 inc) *
41+
#' cos(Omega)}.}
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#'
44-
#' \item{cc}{Helper: \eqn{\cos(I)}{cos(inc / R2D)}.}
43+
#' \item{cc}{Helper: \eqn{\cos(I)}{cos(I)}.}
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#'
46-
#' \item{dd}{Helper: \eqn{\cos(I)/2}{cos(inc /R2D / 2)}.}
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#' \item{dd}{Helper: \eqn{\cos(I)/2}{cos(I) /2}.}
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#'
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#' \item{nnx, nny, nnz}{The \eqn{x}, \eqn{y}, and \eqn{z}-components of the
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#' \item{nnx, nny, nnz}{The \eqn{x}{x}, \eqn{y}{y}, and \eqn{z}{z}-components of the
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#' Eart's orbit unit normal vector \eqn{\vec{n}}{n}, normal to Earth's
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#' instantaneous orbital plane.}
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# HCI = heliocentric inertial
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#' @aliases full-ZB18a
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NULL
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79-
#' Astronomical Solutions ZB17 for the past 100 Myr
78+
#' Astronomical Solutions ZB17
79+
#'
80+
#' The ZB17x eccentricity solutions span the past 100 Myr.
81+
#' Available solutions include `"ZB17a"`, `"ZB17b"`, `"ZB17c"`, `"ZB17d"`,
82+
#' `"ZB17e"`, `"ZB17f"`, `"ZB17h"`, `"ZB17i"`, `"ZB17j"`, `"ZB17k"`, and
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#' `"ZB17p"`.
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#'
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#' @format ## `get_solution("ZB17x")`
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#' A data frame with 62,501 rows and 3 columns:
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#' \describe{
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#' \item{time}{Time in thousands of years (kyr).}
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#' \item{ecc}{Eccentricity \eqn{e} (unitless).}
86-
#' \item{inc}{Inclination \eqn{I} (degrees).}
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#' \item{ecc}{Eccentricity \eqn{e}{e} (unitless).}
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#' \item{inc}{Inclination \eqn{I}{I} (degrees).}
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#' }
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#' @inherit full_ZB18a source
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#' @references
@@ -94,14 +98,17 @@ NULL
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#' @aliases ZB17a ZB17b ZB17c ZB17d ZB17e ZB17f ZB17h ZB17i ZB17j ZB17k ZB17p
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NULL
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97-
#' Astronomical Solution ZB18a for the Past 100 Myr
101+
#' Astronomical Solution ZB18a
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#'
103+
#' The ZB18a_100 eccentricity solution spans the past 100 Myr. See [ZB18a_300]
104+
#' for the past 300 Myr.
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#'
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#' @format ## `get_solution("ZB18a-100")`
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#' A data frame with 62,501 rows and 3 columns:
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#' \describe{
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#' \item{time}{Time in thousands of years (kyr).}
103-
#' \item{ecc}{Eccentricity \eqn{e} (unitless).}
104-
#' \item{inc}{Inclination \eqn{I} (degrees).}
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#' \item{ecc}{Eccentricity \eqn{e}{e} (unitless).}
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#' \item{inc}{Inclination \eqn{I}{I} (degrees).}
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#' }
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#' @inherit full_ZB18a source
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#' @references
@@ -112,19 +119,21 @@ NULL
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#' @aliases "ZB18a-100"
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NULL
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115-
#' Astronomical Solution ZB18a for the Past 300 Myr
122+
#' Astronomical Solution ZB18a
123+
#'
124+
#' The ZB18a_300 eccentricity solution spans the past 300 Myr. See [ZB18a_100]
125+
#' for the past 100 Myr.
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#'
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#' @format ## `get_solution("ZB18a-300")`
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#' A data frame with 187,501 rows and 3 columns:
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#' \describe{
120-
#' \item{time}{Time in thousands of years (kyr).}
121-
#' \item{ecc}{Eccentricity \eqn{e} (unitless).}
122-
#'\item{inc}{Inclination\eqn{I} (degrees).}
130+
#'\item{time}{Time in thousands of years (kyr).}
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#'\item{ecc}{Eccentricity \eqn{e}{e} (unitless).} \item{inc}{Inclination
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#'\eqn{I}{I} (degrees).}
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#' }
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#' @inherit full_ZB18a source
125-
#' @references
126-
#' Zeebe, R. E., & Lourens, L. J. (2019). Solar System chaos and the
127-
#' Paleocene–Eocene boundary age constrained by geology and astronomy.
135+
#' @references Zeebe, R. E., & Lourens, L. J. (2019). Solar System chaos and
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#' the Paleocene–Eocene boundary age constrained by geology and astronomy.
128137
#' _Science_, 365(6456), 926–929. \doi{10.1126/science.aax0612}.'
129138
#'
130139
#' Zeebe, R. E. and Lourens, L. J. (2022). Geologically constrained
@@ -134,14 +143,17 @@ NULL
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#' @aliases ZB18a "ZB18a-300"
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NULL
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137-
#' Astronomical Solutions ZB20 for the past 300 Myr
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#' Astronomical Solutions ZB20
147+
#'
148+
#' The ZB20x eccentricity solutions span the past 300 Myr. Available solutions
149+
#' include `"ZB20a"`, `"ZB20b"`, `"ZB20c"`, and `"ZB20d"`.
138150
#'
139151
#' @format ## `get_solution("ZB20x")`
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#' A data frame with 187,501 rows and 3 columns:
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#' \describe{
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#' \item{time}{Time in thousands of years (kyr).}
143-
#' \item{ee}{Eccentricity \eqn{e} (unitless).}
144-
#' \item{inc}{Inclination \eqn{I} (degrees).}
155+
#' \item{ee}{Eccentricity \eqn{e}{e} (unitless).}
156+
#' \item{inc}{Inclination \eqn{I}{I} (degrees).}
145157
#' }
146158
#' @inherit full_ZB18a source
147159
#' @references
@@ -152,15 +164,21 @@ NULL
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#' @aliases ZB20a ZB20b ZB20c ZB20d
153165
NULL
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155-
#' Astronomical Solutions PT-ZB18a(x.xxxx,y.yyyy) for the past 100 Myr
167+
#' Astronomical Solutions PT-ZB18a(E<sub>d</sub>,T<sub>d</sub>)
156168
#'
157-
#' @format ## `get_solution("PT-ZB18a(1,1)")`
169+
#' The pre-computed precession-tilt solutions
170+
#' PT-ZB18a(E<sub>d</sub>,T<sub>d</sub>) span the past 100 Myr. Available
171+
#' solutions include all combinations of dynamical ellipticity values between
172+
#' 0.9950 and 1.0050 in increments of 0.0010 and tidal dissipation values
173+
#' between 0.000 and 1.2000 in increments of 0.1.
174+
#'
175+
#' @format ## `get_solution("PT-ZB18a(1.000,1.000)")`
158176
#' A data frame with 249,480 rows and 4 columns:
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#' \describe{
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#' \item{time}{Time in thousands of years (kyr).}
161-
#' \item{epl}{Obliqity \eqn{\epsilon} (radians).}
162-
#' \item{phi}{Axial Precession \eqn{phi} (radians).}
163-
#' \item{cp}{Climatic Precession \eqn{e sin(\bar{\omega})} (unitless).}
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#' \item{epl}{Obliqity \eqn{\epsilon}{epsilon} (radians).}
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#' \item{phi}{Axial Precession \eqn{\phi}{phi} (radians).}
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#' \item{cp}{Climatic Precession \eqn{e\sin(\bar{\omega})}{e sin(baromega)} (unitless).}
164182
#' }
165183
#' @inherit full_ZB18a source
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#' @references
@@ -171,16 +189,19 @@ NULL
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#' @aliases PT-ZB18a "PT-ZB18a(1,1)" "PT-ZB18a(1,0)"
172190
NULL
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#' Astronomical Solutions ZB23.RXX for the past 3.6 Gyr
192+
#' Astronomical Solutions ZB23.Rxx
193+
#'
194+
#' The ZB23.Rxx eccentricity solutions spand the past 3.6 Gyr. Available solutions include
195+
#' `"ZB23.R01"` to `"ZB23.R60"` and `"ZB23.R62"` to `"ZB23.R64"`.
175196
#'
176197
#' @format ## `get_solution("ZB23.Rxx")`
177198
#' A data frame with 8,750,001 rows and 5 columns:
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#' \describe{
179200
#' \item{time}{Time in thousands of years (kyr).}
180-
#' \item{ecc}{Eccentricity \eqn{e} (unitless).}
181-
#' \item{inc}{Inclination \eqn{I} (radians).}
182-
#' \item{obliquity}{Obliqity \eqn{\epsilon} (radians).}
183-
#' \item{cp}{Climatic Precession \eqn{e sin(\bar{\omega})} (unitless).}
201+
#' \item{ecc}{Eccentricity \eqn{e}{e} (unitless).}
202+
#' \item{inc}{Inclination \eqn{I}{I} (radians).}
203+
#' \item{obliquity}{Obliqity \eqn{\epsilon}{epsilon} (radians).}
204+
#' \item{cp}{Climatic Precession \eqn{e\sin(\bar{\omega})}{e sin(baromega)} (unitless).}
184205
#' }
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#' @inherit full_ZB18a source
186207
#' @references

‎R/get_solution.R‎

Lines changed: 29 additions & 9 deletions
Original file line numberDiff line numberDiff line change
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#' Get an Astronomical Solution
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#'
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#' Download supported astronomical solutions from the web and store it in the
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#' user's cache directory. The next use of the function will load the data from
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#' the cache rather than downloading it again. This also provides a wrapper for
6-
#' [astrochron::getLaskar()] if one of their supported solutions is specified,
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#' but converts the output to a [tibble][tibble::tibble-package]. Note that we
8-
#' do not cache these solutions locally, however.
3+
#' `get_solution()` downloads an astronomical solution and stores it in the user's cache
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#' directory. The next time the function is called, it will load the data from
5+
#' the cache rather than downloading it again.
6+
#'
7+
#' @details
8+
#'
9+
#' All astronomical solutions by Zeebe can be found on
10+
#' <http://www.soest.hawaii.edu/oceanography/faculty/zeebe_files/Astro.html>.
11+
#' Supported solutions include:
12+
#'
13+
#' - [full-ZB18a]
14+
#' - [ZB17]
15+
#' - [ZB18a_100] and [ZB18a_300]
16+
#' - [ZB20]
17+
#' - [ZB23]
18+
#' - [PT-ZB18a]
19+
#'
20+
#' See their respective documentation pages for details and citations.
21+
#'
22+
#' This also provides a wrapper for [astrochron::getLaskar()] if one of
23+
#' `"La04"`, `"La10a"`, `"La10b"`, `"La10c"`, `"La10d"`, or `"La11"` is
24+
#' specified, but converts the output to a [tibble][tibble::tibble-package].
25+
#' Note that we do not cache these solutions locally, however.
26+
#'
27+
#' It is possible to change the location of the cache directory with
28+
#' `options(snvecR.cachedir = "/path/to/cache")`.
929
#'
1030
# astronomical_solution, quiet, and force are documented in get_ZB
1131
#' @inheritParams get_ZB
1232
#' @inherit get_ZB references
13-
#' @seealso [full_ZB18a], [ZB17], [ZB18a_100], [ZB18a_300] [ZB20], [PT_ZB18a], [ZB23]
33+
#' @seealso [prepare_solution], [full_ZB18a], [ZB17], [ZB18a_100], [ZB18a_300] [ZB20], [ZB23], [PT_ZB18a]
1434
#' @returns A [tibble][tibble::tibble-package] with the astronomical solution
1535
#' (and some preprocessed new columns).
1636
#' @examples
17-
#' \donttest{
1837
#' \dontshow{
1938
#' # set the cachedir to a temporary directory
2039
#' pth <- withr::local_tempdir(pattern = "snvecR")
2140
#' withr::local_options(snvecR.cachedir = pth)
2241
#' }
42+
#' \donttest{
2343
#' get_solution("full-ZB18a") # input for snvec
2444
#' get_solution("ZB18a-300") # eccentricity
2545
#' get_solution("ZB20a")
@@ -153,7 +173,7 @@ get_solution <- function(astronomical_solution = "full-ZB18a", quiet = FALSE, fo
153173
# #'
154174
#' @param astronomical_solution Character vector with the name of the desired
155175
#' solution. Defaults to `"full-ZB18a"`.
156-
# TODO:add something like "for list of valid solutions, mistype it on purpose."
176+
# TODO:document that you can also pass a dataframe directly?
157177
#' @param quiet Be quiet?
158178
#'
159179
#' * If `TRUE`, hide info messages.

‎R/prepare_solution.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
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#' Prepare Astronomical Solution
22
#'
3-
#'Calculates helper columns from an astronomical solution input.
3+
#'`prepare_solution()` calculates helper columns from an astronomical solution input.
44
#'
55
#' @export
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#' @param data A data frame with the following columns:

‎README.Rmd‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -29,8 +29,8 @@ withr::local_options(list(snvecR.cachedir = pth))
2929

3030
Easily calculate precession and obliquity from an astronomical solution (AS,
3131
defaults to ZB18a from Zeebe and Lourens (2019)) and assumed or reconstructed
32-
values fortidal dissipation (T<sub>d</sub>) anddynamical ellipticity
33-
(E<sub>d</sub>). This is a translation and adaptation of the C-code in the
32+
values fordynamical ellipticity (E<sub>d</sub>) andtidal dissipation
33+
(T<sub>d</sub>). This is a translation and adaptation of the C-code in the
3434
supplementary material to Zeebe and Lourens (2022), with further details on the
3535
methodology described in Zeebe (2022). The name of the C-routine is snvec,
3636
which refers to the key units of computation: spin vector s and orbit normal

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