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Commit74a6431

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author
Ilja J. Kocken
committed
update tests and README
1 parent347e294 commit74a6431

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8 files changed

+206
-27
lines changed

8 files changed

+206
-27
lines changed

‎R/get_solution.R‎

Lines changed: 11 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -105,19 +105,19 @@ get_solution <- function(astronomical_solution = "full-ZB18a", quiet = FALSE, fo
105105
}
106106

107107
if (grepl("^La\\d{2}[a-z]?",astronomical_solution)) {
108-
cli::cli_warn(c(
108+
cli::cli_inform(c(
109109
"i"="Relying on {.pkg astrochron} to get solution {.q {astronomical_solution}}",
110-
"i"="We do not cache these results.",
111-
"!"="{.pkg astrochron} converts time from -kyr to ka by default."))
110+
"i"="We do not cache these results.",
111+
"!"="{.pkg astrochron} converts time from -kyr to ka by default."))
112112
rlang::check_installed("astrochron",
113113
reason="to use `astrochron::getLaskar()`")
114114
dat<-tibble::as_tibble(
115115
astrochron::getLaskar(sol= tolower(astronomical_solution),
116116
verbose=!quiet)
117117
)
118-
cli::cli_warn(c(
119-
"i"="Output has column names {.q {colnames(dat)}}"
120-
))
118+
cli::cli_alert_info(
119+
"Output has column names {.q {colnames(dat)}}"
120+
)
121121
return(dat)
122122
}
123123

@@ -189,7 +189,7 @@ get_ZB <- function(astronomical_solution = "full-ZB18a",
189189

190190
if (!quiet) {
191191
cli::cli_alert_info(c(
192-
"!"="The astronomical solution {.q {astronomical_solution}} has not been cached."
192+
"The astronomical solution {.q {astronomical_solution}} has not been cached."
193193
))
194194
}
195195

@@ -298,8 +298,9 @@ get_ZB <- function(astronomical_solution = "full-ZB18a",
298298
raw<- prepare_solution(raw,quiet=quiet)
299299
}else {
300300
if (grepl("^ZB23\\.R",astronomical_solution)) {
301-
cli::cli_inform(c("Downloading any of the ZB23.RXX solutions will take some time.",
302-
"Zip files are about 154 MB."))
301+
cli::cli_inform(c(
302+
"i"="Downloading any of the ZB23.RXX solutions will take some time.",
303+
"i"="Zip files are about 154 MB."))
303304
sure<-utils::askYesNo("Continue downloading and caching?")
304305
if (is.na(sure)) {
305306
cli::cli_abort("Cancelled by user.",call=NULL)
@@ -326,7 +327,7 @@ get_ZB <- function(astronomical_solution = "full-ZB18a",
326327
if (grepl("^ZB17|^ZB18|^ZB20",astronomical_solution)) {
327328
raw<-dplyr::mutate(raw,time=-.data$time)
328329
if (!quiet) {
329-
cli::cli_alert_warning(
330+
cli::cli_alert_info(
330331
"Flipped time for {.q {astronomical_solution}} so that it is in negative kyr."
331332
)
332333
}

‎README.Rmd‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,8 @@ knitr::opts_chunk$set(
1111
fig.path = "man/figures/README-",
1212
out.width = "100%"
1313
)
14-
options(snvecR.cachedir = withr::local_tempdir(pattern = "snvecR"))
14+
pth <- withr::local_tempdir(pattern = "snvecR")
15+
withr::local_options(list(snvecR.cachedir = pth))
1516
```
1617

1718
#snvecR

‎README.md‎

Lines changed: 21 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -62,7 +62,7 @@ sol <- get_solution("full-ZB18a")
6262
#> ℹ The astronomical solution "full-ZB18a" has not been cached.
6363
#> ℹ Reading 'full-ZB18a.dat' from website <http://www.soest.hawaii.edu/oceanography/faculty/zeebe_files/Astro/PrecTilt/OS/ZB18a/ems-plan3.dat>.
6464
#> ℹ Calculating helper columns.
65-
#> ℹ The cache directory is '/tmp/RtmpR5G9yC/snvecR43dce2ecdb925'.
65+
#> ℹ The cache directory is '/tmp/Rtmpya43uW/snvecR1942b47b14132e'.
6666
#> ℹ Saved astronomical solution with helper columns 'full-ZB18a.rds' to cache.
6767
#> ℹ Future calls to `get_solution("full-ZB18a")` will read from the cache.
6868
#> ! If you want to read from scratch, specify `force = TRUE`.
@@ -71,30 +71,32 @@ ZB18a <- get_solution("ZB18a-300")
7171
#> ℹ The astronomical solution "ZB18a-300" has not been cached.
7272
#> ℹ Reading 'ZB18a-300.dat' from website <http://www.soest.hawaii.edu/oceanography/faculty/zeebe_files/Astro/300Myr/ZB18a.dat>.
7373
#> ! Flipped time for "ZB18a-300" so that it is in negative kyr.
74-
#> ℹ The cache directory is '/tmp/RtmpR5G9yC/snvecR43dce2ecdb925'.
74+
#> ℹ The cache directory is '/tmp/Rtmpya43uW/snvecR1942b47b14132e'.
7575
#> ℹ Saved astronomical solution with helper columns 'ZB18a-300.rds' to cache.
7676
#> ℹ Future calls to `get_solution("ZB18a-300")` will read from the cache.
7777
#> ! If you want to read from scratch, specify `force = TRUE`.
7878
ZB20a<- get_solution("ZB20a")
7979
#> ℹ The astronomical solution "ZB20a" has not been cached.
8080
#> ℹ Reading 'ZB20a.dat' from website <http://www.soest.hawaii.edu/oceanography/faculty/zeebe_files/Astro/300Myr/ZB20a.dat>.
8181
#> ! Flipped time for "ZB20a" so that it is in negative kyr.
82-
#> ℹ The cache directory is '/tmp/RtmpR5G9yC/snvecR43dce2ecdb925'.
82+
#> ℹ The cache directory is '/tmp/Rtmpya43uW/snvecR1942b47b14132e'.
8383
#> ℹ Saved astronomical solution with helper columns 'ZB20a.rds' to cache.
8484
#> ℹ Future calls to `get_solution("ZB20a")` will read from the cache.
8585
#> ! If you want to read from scratch, specify `force = TRUE`.
8686
# a pre-computed precession-tilt solution (PT)
8787
ZB18a_1_1<- get_solution("PT-ZB18a(1,1)")
8888
#> ℹ The astronomical solution "PT-ZB18a(1.0000,1.0000)" has not been cached.
8989
#> ℹ Reading 'PT-ZB18a(1.0000,1.0000).dat' from website <http://www.soest.hawaii.edu/oceanography/faculty/zeebe_files/Astro/PrecTilt/ZB18a/asc/PT.De1.0000Td1.0000.dat>.
90-
#> ℹ The cache directory is '/tmp/RtmpR5G9yC/snvecR43dce2ecdb925'.
90+
#> ℹ The cache directory is '/tmp/Rtmpya43uW/snvecR1942b47b14132e'.
9191
#> ℹ Saved astronomical solution with helper columns 'PT-ZB18a(1.0000,1.0000).rds'
9292
#> to cache.
9393
#> ℹ Future calls to `get_solution("PT-ZB18a(1.0000,1.0000)")` will read from the
9494
#> cache.
9595
#> ! If you want to read from scratch, specify `force = TRUE`.
9696
```
9797

98+
<!-- we put this in a separate block so building the README is a little faster-->
99+
98100
```r
99101
# the 3.5 Gyr solutions, e.g. number 5
100102
ZB23.R05<- get_solution("ZB23.R05")
@@ -111,7 +113,9 @@ ZB23.R05 <- get_solution("ZB23.R05")
111113

112114
##Calculating Precession and Obliquity
113115

114-
Here’s the main function that does the work in action:
116+
Here’s the`snvec()` function that calculates climatic precession and
117+
obliquity from an orbital solution input and values for tidal
118+
dissipation (T<sub>d</sub>) and dynamical ellipticity (E<sub>d</sub>).
115119

116120
```r
117121
solution<- snvec(tend=-1000,# final timestep in kyr
@@ -120,7 +124,7 @@ solution <- snvec(tend = -1000, # final timestep in kyr
120124
astronomical_solution="full-ZB18a",# see ?full_ZB18a for details
121125
tres=-0.4# timestep resolution in kyr (so this is 400 years)
122126
)
123-
#> This is snvecR VERSION: 3.10.0.9000 2025-03-04
127+
#> This is snvecR VERSION: 3.10.0.9000 2025-03-05
124128
#> Richard E. Zeebe
125129
#> Ilja J. Kocken
126130
#>
@@ -136,15 +140,15 @@ solution <- snvec(tend = -1000, # final timestep in kyr
136140
#> • `atol` = 1e-05
137141
#> • `rtol` = 0
138142
#> • `solver` = "vode"
139-
#> ℹ started at "2025-03-04 16:12:43.23286"
143+
#> ℹ started at "2025-03-0512:04:56.589572"
140144
#> Final values:
141145
#> • s[1][2][3]: 0.404184487124565, -0.0537555129057148, and 0.913036138471423
142146
#> • s-error = |s|-1: -5.51290422495798e-05
143147
#> Final values:
144148
#> • obliquity: 0.413060472710089 rad
145149
#> • precession: -0.562357122261026 rad
146-
#> ℹ stopped at "2025-03-04 16:12:43.956671"
147-
#> ℹ total duration: 0.72
150+
#> ℹ stopped at "2025-03-0512:04:57.417171"
151+
#> ℹ total duration: 0.83
148152
```
149153

150154
To quickly save out the results for further study to CSV[^1]:
@@ -182,6 +186,14 @@ solution |>
182186

183187
<imgsrc="man/figures/README-plot-1.png"width="100%" />
184188

189+
#Contributing
190+
191+
Contributions are more than welcome! If something doesn’t work the way
192+
you expect and you don’t know how to fix it,[write an
193+
issue](https://github.com/japhir/snvecR/issues). If you do know how to
194+
fix it, feel free to[create a pull
195+
request](https://github.com/japhir/snvecR/pulls)!
196+
185197
#References
186198

187199
Zeebe, R. E., & Lourens, L. J. (2019). Solar System chaos and the

‎tests/testthat/_snaps/get_solution.md‎

Lines changed: 69 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@
1414
#get_solution() can load eccentricity solutions
1515

1616
Code
17-
head(get_solution(astronomical_solution = "ZB20b", quiet = TRUE, force = TRUE))
17+
head(get_solution(astronomical_solution = "ZB17a", quiet = TRUE, force = TRUE))
1818
Output
1919
# A tibble: 6 x 3
2020
time ecc inc
@@ -26,6 +26,71 @@
2626
5 -6.4 0.0188 6.84
2727
6 -8 0.0192 6.70
2828

29+
---
30+
31+
Code
32+
head(get_solution(astronomical_solution = "ZB18a-100", quiet = TRUE, force = TRUE))
33+
Output
34+
# A tibble: 6 x 3
35+
time ecc inc
36+
<dbl> <dbl> <dbl>
37+
1 0 0.0167 7.15
38+
2 -1.6 0.0173 7.11
39+
3 -3.2 0.0179 7.04
40+
4 -4.8 0.0184 6.95
41+
5 -6.4 0.0188 6.84
42+
6 -8 0.0192 6.70
43+
44+
---
45+
46+
Code
47+
head(get_solution(astronomical_solution = "ZB18a-300", quiet = TRUE, force = TRUE))
48+
Output
49+
# A tibble: 6 x 3
50+
time ecc inc
51+
<dbl> <dbl> <dbl>
52+
1 0 0.0167 7.15
53+
2 -1.6 0.0173 7.11
54+
3 -3.2 0.0179 7.04
55+
4 -4.8 0.0184 6.95
56+
5 -6.4 0.0188 6.84
57+
6 -8 0.0192 6.70
58+
59+
---
60+
61+
Code
62+
head(get_solution(astronomical_solution = "ZB20a", quiet = TRUE, force = TRUE))
63+
Output
64+
# A tibble: 6 x 3
65+
time ecc inc
66+
<dbl> <dbl> <dbl>
67+
1 0 0.0167 7.15
68+
2 -1.6 0.0173 7.11
69+
3 -3.2 0.0179 7.04
70+
4 -4.8 0.0184 6.95
71+
5 -6.4 0.0188 6.84
72+
6 -8 0.0192 6.70
73+
74+
---
75+
76+
Code
77+
head(get_solution(astronomical_solution = "La10d", quiet = TRUE, force = TRUE))
78+
Message
79+
i Relying on astrochron to get solution "La10d"
80+
i We do not cache these results.
81+
! astrochron converts time from -kyr to ka by default.
82+
i Output has column names "Time_ka" and "ecc_LA10d"
83+
Output
84+
# A tibble: 6 x 2
85+
Time_ka ecc_LA10d
86+
<dbl> <dbl>
87+
1 0 0.0167
88+
2 1 0.0172
89+
3 2 0.0175
90+
4 3 0.0178
91+
5 4 0.0182
92+
6 5 0.0185
93+
2994
#get_solution() can load full solutions
3095

3196
Code
@@ -108,10 +173,10 @@
108173
Message
109174
i The astronomical solution "ZB23.R01" has not been cached.
110175
i Reading 'ZB23.R01.dat' from website <http://www.soest.hawaii.edu/oceanography/faculty/zeebe_files/Astro/3.5Gyr/ZB23-N64-eiop/ZB23.R01.eiop.dat.zip>.
111-
Downloading any of the ZB23.RXX solutions will take some time.
112-
Zip files are about 154 MB.
176+
iDownloading any of the ZB23.RXX solutions will take some time.
177+
iZip files are about 154 MB.
113178
Output
114-
Continue downloading and caching {.q {astronomical_solution}}? (Yes/no/cancel)
179+
Continue downloading and caching? (Yes/no/cancel)
115180
Message
116181
i The cache directory is 'transformed-for-CI'.
117182
i Saved astronomical solution with helper columns 'ZB23.R01.rds' to cache.

‎tests/testthat/_snaps/snvec.md‎

Lines changed: 62 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
11
#snvec() works
22

33
Code
4-
print(dplyr::select(snvec(tend = -49, ed = 1, td = 0, tres = -1,quiet =TRUE, output ="all"),
5-
tidyselect::all_of(c("time", "sx", "sy", "sz", "epl", "phi", "lpx", "cp"))), n = 50)
4+
print(dplyr::select(snvec(tend = -49, ed = 1, td = 0, tres = -1,os_ref_frame ="HCI", quiet =TRUE,
5+
output = "all"),tidyselect::all_of(c("time", "sx", "sy", "sz", "epl", "phi", "lpx", "cp"))), n = 50)
66
Output
77
# A tibble: 50 x 8
88
time sx sy sz epl phi lpx cp
@@ -58,3 +58,63 @@
5858
49 -48 0.376 -0.171 0.911 0.426 -0.867 1.30 0.0137
5959
50 -49 0.424 -0.0836 0.902 0.426 -0.631 1.07 0.0126
6060

61+
---
62+
63+
Code
64+
print(dplyr::select(snvec(tend = -49, ed = 1, td = 0, tres = -1, quiet = TRUE, os_ref_frame = "J2000",
65+
output = "all"), tidyselect::all_of(c("time", "sx", "sy", "sz", "epl", "phi", "lpx", "cp"))), n = 50)
66+
Output
67+
# A tibble: 50 x 8
68+
time sx sy sz epl phi lpx cp
69+
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
70+
1 0 0 0.509 0.861 0.409 0 0.477 0.00767
71+
2 -1 -0.0962 0.497 0.862 0.409 0.239 0.183 0.00312
72+
3 -2 -0.187 0.464 0.866 0.409 0.478 -0.112 -0.00195
73+
4 -3 -0.267 0.410 0.872 0.409 0.717 -0.405 -0.00703
74+
5 -4 -0.332 0.338 0.881 0.408 0.957 -0.697 -0.0117
75+
6 -5 -0.378 0.254 0.890 0.406 1.20 -0.994 -0.0155
76+
7 -6 -0.402 0.161 0.901 0.405 1.44 -1.29 -0.0180
77+
8 -7 -0.404 0.0659 0.913 0.403 1.68 -1.58 -0.0190
78+
9 -8 -0.382 -0.0267 0.924 0.401 1.92 -1.87 -0.0183
79+
10 -9 -0.339 -0.111 0.934 0.399 2.16 -2.17 -0.0160
80+
11 -10 -0.277 -0.182 0.943 0.396 2.41 -2.46 -0.0122
81+
12 -11 -0.200 -0.236 0.951 0.393 2.65 -2.76 -0.00735
82+
13 -12 -0.112 -0.269 0.957 0.391 2.90 -3.05 -0.00175
83+
14 -13 -0.0198 -0.280 0.960 0.388 -3.14 2.93 0.00404
84+
15 -14 0.0722 -0.268 0.961 0.386 -2.89 2.64 0.00948
85+
16 -15 0.158 -0.234 0.959 0.383 -2.64 2.34 0.0141
86+
17 -16 0.232 -0.179 0.956 0.381 -2.38 2.04 0.0174
87+
18 -17 0.290 -0.109 0.951 0.380 -2.13 1.75 0.0192
88+
19 -18 0.329 -0.0263 0.944 0.378 -1.88 1.45 0.0192
89+
20 -19 0.345 0.0629 0.936 0.377 -1.62 1.15 0.0175
90+
21 -20 0.338 0.153 0.928 0.377 -1.37 0.860 0.0144
91+
22 -21 0.309 0.239 0.921 0.377 -1.11 0.565 0.0101
92+
23 -22 0.259 0.315 0.913 0.378 -0.858 0.272 0.00500
93+
24 -23 0.191 0.375 0.907 0.379 -0.604 -0.0193 -0.000354
94+
25 -24 0.110 0.417 0.902 0.381 -0.350 -0.307 -0.00547
95+
26 -25 0.0202 0.437 0.899 0.383 -0.0976 -0.594 -0.00999
96+
27 -26 -0.0720 0.435 0.898 0.385 0.154 -0.878 -0.0135
97+
28 -27 -0.161 0.409 0.898 0.388 0.404 -1.16 -0.0158
98+
29 -28 -0.242 0.362 0.900 0.391 0.653 -1.43 -0.0168
99+
30 -29 -0.309 0.297 0.904 0.394 0.900 -1.70 -0.0165
100+
31 -30 -0.358 0.216 0.908 0.397 1.15 -1.97 -0.0151
101+
32 -31 -0.386 0.126 0.914 0.400 1.39 -2.24 -0.0126
102+
33 -32 -0.392 0.0304 0.920 0.403 1.63 -2.50 -0.00944
103+
34 -33 -0.374 -0.0639 0.925 0.405 1.87 -2.75 -0.00584
104+
35 -34 -0.335 -0.152 0.930 0.408 2.11 -3.01 -0.00202
105+
36 -35 -0.275 -0.228 0.934 0.410 2.35 -3.26 0.00172
106+
37 -36 -0.199 -0.288 0.937 0.412 2.59 -3.50 0.00519
107+
38 -37 -0.110 -0.329 0.938 0.413 2.83 -3.74 0.00818
108+
39 -38 -0.0141 -0.348 0.937 0.414 3.07 -3.99 0.0107
109+
40 -39 0.0838 -0.344 0.935 0.415 -2.98 2.06 0.0124
110+
41 -40 0.178 -0.317 0.932 0.415 -2.74 1.82 0.0135
111+
42 -41 0.263 -0.269 0.927 0.414 -2.51 1.59 0.0138
112+
43 -42 0.335 -0.202 0.920 0.414 -2.27 1.36 0.0134
113+
44 -43 0.388 -0.121 0.914 0.412 -2.03 1.12 0.0123
114+
45 -44 0.421 -0.0294 0.907 0.411 -1.80 0.895 0.0107
115+
46 -45 0.431 0.0669 0.900 0.409 -1.56 0.658 0.00842
116+
47 -46 0.418 0.163 0.894 0.406 -1.32 0.426 0.00572
117+
48 -47 0.382 0.252 0.889 0.404 -1.07 0.188 0.00262
118+
49 -48 0.327 0.330 0.886 0.401 -0.832 -0.0503 -0.000713
119+
50 -49 0.255 0.392 0.884 0.398 -0.589 -0.291 -0.00414
120+

‎tests/testthat/test-get_solution.R‎

Lines changed: 13 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,6 +4,7 @@ test_that("get_solution() bad inputs throw errors", {
44
expect_error(get_solution(astronomical_solution="hoi"))
55
expect_error(get_solution(astronomical_solution="full-La11"))
66
expect_error(get_solution(astronomical_solution=data.frame(x=1,y=5)))# this runs via prepare_solution
7+
expect_error(get_solution(astronomical_solution="ZB18a"))
78
})
89

910
test_that("get_solution() can return a dataframe", {
@@ -26,9 +27,20 @@ test_that("get_solution() can load eccentricity solutions", {
2627
pth<-withr::local_tempdir(pattern="snvecR")
2728
withr::local_options(list(snvecR.cachedir=pth,width=150))
2829

29-
expect_snapshot(head(get_solution(astronomical_solution="ZB20b",
30+
expect_snapshot(head(get_solution(astronomical_solution="ZB17a",
3031
quiet=TRUE,force=TRUE)))
3132

33+
expect_snapshot(head(get_solution(astronomical_solution="ZB18a-100",
34+
quiet=TRUE,force=TRUE)))
35+
36+
expect_snapshot(head(get_solution(astronomical_solution="ZB18a-300",
37+
quiet=TRUE,force=TRUE)))
38+
39+
expect_snapshot(head(get_solution(astronomical_solution="ZB20a",
40+
quiet=TRUE,force=TRUE)))
41+
42+
expect_snapshot(head(get_solution(astronomical_solution="La10d",
43+
quiet=TRUE,force=TRUE)))
3244
})
3345

3446
test_that("get_solution() can load full solutions", {

‎tests/testthat/test-globals.R‎

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test_that("cachedir() works", {
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expect_type(snvecR:::cachedir(),"character")
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})

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