Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

v0.9.0 #129

Merged
merged 181 commits into from
Sep 6, 2019
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
181 commits
Select commit Hold shift + click to select a range
68b7392
x
juniperlsimonis Jul 16, 2019
d7dce65
wip
juniperlsimonis Jul 16, 2019
1dccc95
patching some bugs in portalcast
juniperlsimonis Jul 16, 2019
ed770e7
cleaning
juniperlsimonis Jul 16, 2019
f2cd1d0
oops
juniperlsimonis Jul 16, 2019
802d769
removing models control from portalcast
juniperlsimonis Jul 17, 2019
e93a8a3
stripping it down to rebuild
juniperlsimonis Aug 5, 2019
26b1fb4
Update .travis.yml
juniperlsimonis Aug 5, 2019
31e5fc6
Update .travis.yml
juniperlsimonis Aug 5, 2019
7da98e2
starting to build out fill_dir
juniperlsimonis Aug 5, 2019
4b7f547
removing the dirtree list
juniperlsimonis Aug 5, 2019
c8d9532
removing base
juniperlsimonis Aug 6, 2019
99d779c
adding the PortalPredictions data file
juniperlsimonis Aug 6, 2019
0c64585
model filling functionality
juniperlsimonis Aug 9, 2019
10dc363
prepare_moons
juniperlsimonis Aug 10, 2019
ed1cd7d
Update test-20-download.R
juniperlsimonis Aug 10, 2019
83d9f55
Update test-65-prepare_moons.R
juniperlsimonis Aug 10, 2019
7cfc318
Update download.R
juniperlsimonis Aug 10, 2019
15ced47
Update test-65-prepare_moons.R
juniperlsimonis Aug 10, 2019
41ba8d6
travis testing
juniperlsimonis Aug 10, 2019
790c61e
Update download.R
juniperlsimonis Aug 10, 2019
f26bb98
Update test-20-download.R
juniperlsimonis Aug 10, 2019
11e3986
trying
juniperlsimonis Aug 10, 2019
dd78daa
Update test-20-download.R
juniperlsimonis Aug 10, 2019
7eaafc5
Update download.R
juniperlsimonis Aug 10, 2019
823bcc6
more trying with travis
juniperlsimonis Aug 10, 2019
30f8253
removing commented out code
juniperlsimonis Aug 10, 2019
2590d86
wrapping examples in donttest
juniperlsimonis Aug 10, 2019
1bc8075
Update test-65-prepare_moons.R
juniperlsimonis Aug 10, 2019
f836350
reducing the test redundancy
juniperlsimonis Aug 10, 2019
a817772
Update test-30-fill_dir.R
juniperlsimonis Aug 10, 2019
5ce6688
prep_rodents_table
juniperlsimonis Aug 10, 2019
132648a
Update test-70-prepare_rodents.R
juniperlsimonis Aug 10, 2019
06f6f12
bug fix
juniperlsimonis Aug 10, 2019
ab005a0
Update portalcasting.R
juniperlsimonis Aug 11, 2019
659521d
doc editing
juniperlsimonis Aug 11, 2019
2c7cfa3
adding in data_out
juniperlsimonis Aug 11, 2019
292657b
prep_rodents_list rodents_control transpose_args
juniperlsimonis Aug 11, 2019
145ddbb
documenting covariate forecasting functions
juniperlsimonis Aug 13, 2019
5567abd
massive bunch of work on covariate casting
juniperlsimonis Aug 14, 2019
85e2992
bug fixing
juniperlsimonis Aug 14, 2019
62a784c
Update test-40-cast_covariates.R
juniperlsimonis Aug 14, 2019
c924b90
dummy testing
juniperlsimonis Aug 14, 2019
559c983
prep metadata
juniperlsimonis Aug 14, 2019
462d4aa
testing and documentation
juniperlsimonis Aug 14, 2019
aa939dd
Update cast_covariates.R
juniperlsimonis Aug 14, 2019
edc2f38
Update cast_covariates.Rd
juniperlsimonis Aug 14, 2019
50d888e
Update utilities.R
juniperlsimonis Aug 14, 2019
310991f
Update cast_covariates.R
juniperlsimonis Aug 14, 2019
5d0d4e6
Update cast_covariates.R
juniperlsimonis Aug 14, 2019
5a2ef07
eh?
juniperlsimonis Aug 14, 2019
d97c2ee
Update cast_covariates.R
juniperlsimonis Aug 14, 2019
fa130a0
Update cast_covariates.R
juniperlsimonis Aug 14, 2019
b347b54
trying still
juniperlsimonis Aug 14, 2019
c22310d
Update download.R
juniperlsimonis Aug 14, 2019
ab3df23
maybe?
juniperlsimonis Aug 15, 2019
266478d
Update fill_dir.R
juniperlsimonis Aug 15, 2019
044a29f
yusss
juniperlsimonis Aug 15, 2019
e306329
documentation and testing edits for new functions
juniperlsimonis Aug 15, 2019
237f40d
paths
juniperlsimonis Aug 15, 2019
da9b1d1
generalized the tools functions
juniperlsimonis Aug 15, 2019
cb6e0f4
implementing the character separator situation
juniperlsimonis Aug 15, 2019
ed93698
setup functions
juniperlsimonis Aug 15, 2019
5225f78
lots of work on portalcast
juniperlsimonis Aug 16, 2019
6a39eed
bug fixing tests
juniperlsimonis Aug 16, 2019
22ab6cb
extract_min_lag and some other minor edits
juniperlsimonis Aug 16, 2019
1d5d8b5
bug fix attempt
juniperlsimonis Aug 17, 2019
199658d
catch for when no covariate models so no lag
juniperlsimonis Aug 17, 2019
9612a99
portalcast helpers
juniperlsimonis Aug 17, 2019
726c09f
models_to_cast
juniperlsimonis Aug 17, 2019
4fa6cd5
prefab model functions
juniperlsimonis Aug 17, 2019
952a72d
combining cast output
juniperlsimonis Aug 17, 2019
6be4146
portalcast
juniperlsimonis Aug 17, 2019
17763ab
documentation and testing
juniperlsimonis Aug 18, 2019
e62d68d
some figure functions
juniperlsimonis Aug 18, 2019
62ef25a
res of the figure functions
juniperlsimonis Aug 18, 2019
9f1b20d
arg checking in progress
juniperlsimonis Aug 19, 2019
1efc8d5
bug fixing and doc editing
juniperlsimonis Aug 19, 2019
d57febf
documenting check_args
juniperlsimonis Aug 19, 2019
6f62820
select_most_ab_spp function
juniperlsimonis Aug 19, 2019
0a5b4cc
Update process_casts.R
juniperlsimonis Aug 19, 2019
54d199f
adding the time hack to the travis yaml as the checks take longer now
juniperlsimonis Aug 20, 2019
91defe2
Update .travis.yml
juniperlsimonis Aug 20, 2019
e9fa670
bunch of work on the flow of arg checking and pass and calling
juniperlsimonis Aug 21, 2019
f314ac9
removed pass and call
juniperlsimonis Aug 21, 2019
800c236
tests and documentation
juniperlsimonis Aug 21, 2019
80db245
part
juniperlsimonis Aug 21, 2019
04ab148
additional testing ad docs
juniperlsimonis Aug 21, 2019
59577f1
typo fixes
juniperlsimonis Aug 21, 2019
30ee669
doc eds
juniperlsimonis Aug 21, 2019
ed39c2b
test edges
juniperlsimonis Aug 21, 2019
b52f478
test changes
juniperlsimonis Aug 21, 2019
5c81fb8
Update test-85-process_casts.R
juniperlsimonis Aug 21, 2019
00190a0
blargs
juniperlsimonis Aug 21, 2019
316aa33
Update test-90-utilities.R
juniperlsimonis Aug 21, 2019
d96eb4d
increasing test coverage
juniperlsimonis Aug 22, 2019
038f210
testing updates
juniperlsimonis Aug 22, 2019
a72148a
edit one test eep
juniperlsimonis Aug 22, 2019
299c2fc
Update .gitignore
juniperlsimonis Aug 22, 2019
c5b84d5
Update .travis.yml
juniperlsimonis Aug 22, 2019
25aa35c
Update test-15-prefab_models.R
juniperlsimonis Aug 22, 2019
ee21990
Update test-19-clear_out.R
juniperlsimonis Aug 22, 2019
51e03a4
Update .travis.yml
juniperlsimonis Aug 22, 2019
b15e6f2
updating examples in docs
juniperlsimonis Aug 22, 2019
ff97741
Update NEWS.md
juniperlsimonis Aug 23, 2019
a2eb646
documentation editing
juniperlsimonis Aug 23, 2019
afe79a4
adding the old vignette files in
juniperlsimonis Aug 23, 2019
4f72241
tidying some documentation
juniperlsimonis Aug 23, 2019
b941c7b
vignette work
juniperlsimonis Aug 23, 2019
eb8f21c
tracking down example failures
juniperlsimonis Aug 23, 2019
2df2b87
fix default on cast_window
juniperlsimonis Aug 23, 2019
26db0a8
edit examp
juniperlsimonis Aug 23, 2019
40a1d70
skipping ensemble building testing
juniperlsimonis Aug 23, 2019
1438abd
Update portalcast.Rd
juniperlsimonis Aug 23, 2019
9b0ca5c
in progress works through to plot cast ts
juniperlsimonis Aug 27, 2019
ab3d794
big push on tidying and pull through of directory config
juniperlsimonis Aug 28, 2019
14a4548
testing and edge case catching
juniperlsimonis Aug 28, 2019
d42f6d6
doc editing
juniperlsimonis Aug 28, 2019
943df7d
check passing
juniperlsimonis Aug 28, 2019
f63da30
Update test-18-utilities.R
juniperlsimonis Aug 28, 2019
4a581a4
Update test-18-utilities.R
juniperlsimonis Aug 28, 2019
df27ecd
Update test-18-utilities.R
juniperlsimonis Aug 28, 2019
375ea20
Update test-18-utilities.R
juniperlsimonis Aug 28, 2019
6ebeaf1
Update .travis.yml
juniperlsimonis Aug 28, 2019
24c5c13
Update .travis.yml
juniperlsimonis Aug 28, 2019
058a02f
bug fix
juniperlsimonis Aug 28, 2019
486dbcb
Update test-14-portalcast.R
juniperlsimonis Aug 28, 2019
8d8e938
Update test-14-portalcast.R
juniperlsimonis Aug 28, 2019
0d826ae
bug fix
juniperlsimonis Aug 28, 2019
d49db51
vignette work
juniperlsimonis Aug 28, 2019
b6715f3
updating args docs
juniperlsimonis Aug 28, 2019
d78bae2
tidying up documentation
juniperlsimonis Aug 28, 2019
3d1a2b1
test fixing
juniperlsimonis Aug 29, 2019
e483ac1
simple adding model interface!
juniperlsimonis Aug 29, 2019
3e379ac
eep
juniperlsimonis Aug 29, 2019
d13864d
Update test-09-prepare_models.R
juniperlsimonis Aug 29, 2019
daf2e92
website yaml model error softening
juniperlsimonis Aug 29, 2019
df462fa
figures
juniperlsimonis Sep 2, 2019
2af5f5d
tests
juniperlsimonis Sep 2, 2019
ada9924
working on edges and testing
juniperlsimonis Sep 2, 2019
ab206cb
test fixes edges
juniperlsimonis Sep 2, 2019
780cfa1
Update notes.R
juniperlsimonis Sep 2, 2019
11c6f45
Update test-19-figures.R
juniperlsimonis Sep 2, 2019
146260b
tests
juniperlsimonis Sep 2, 2019
bb87e73
Update test-11-prepare_rodents.R
juniperlsimonis Sep 2, 2019
64c0bb3
Update test-11-prepare_rodents.R
juniperlsimonis Sep 2, 2019
036d940
coverages
juniperlsimonis Sep 2, 2019
0b3c72c
Update test-11-prepare_rodents.R
juniperlsimonis Sep 2, 2019
71fb303
Update process_casts.R
juniperlsimonis Sep 3, 2019
346ed83
condensing arguments
juniperlsimonis Sep 3, 2019
9510dc8
swap name
juniperlsimonis Sep 3, 2019
5781a85
bug fix
juniperlsimonis Sep 3, 2019
fce3a58
retidying names
juniperlsimonis Sep 3, 2019
a78499c
tidying
juniperlsimonis Sep 3, 2019
40a483d
in prog
juniperlsimonis Sep 3, 2019
61d19b4
bit of tidying
juniperlsimonis Sep 3, 2019
45dcfbb
verbose in models
juniperlsimonis Sep 3, 2019
203eebe
oops bug fixing
juniperlsimonis Sep 3, 2019
65fc435
better logo
juniperlsimonis Sep 3, 2019
d8b72e6
doc fixing
juniperlsimonis Sep 3, 2019
ddc0ee1
adding control_files to prefab models
juniperlsimonis Sep 3, 2019
3805a09
Update test-17-data_input_output.R
juniperlsimonis Sep 4, 2019
313c4b3
document editing
juniperlsimonis Sep 4, 2019
fe43b77
doc edits
juniperlsimonis Sep 4, 2019
ac0774f
Update _pkgdown.yml
juniperlsimonis Sep 4, 2019
01309d3
doc edits
juniperlsimonis Sep 4, 2019
c8f702f
figure formatting
juniperlsimonis Sep 4, 2019
64eb6c7
vignettes and docs
juniperlsimonis Sep 4, 2019
9645f35
vignettes
juniperlsimonis Sep 4, 2019
42322af
doc editing
juniperlsimonis Sep 4, 2019
fa6c69c
vignette working
juniperlsimonis Sep 4, 2019
80b855f
tightening control list naming
juniperlsimonis Sep 4, 2019
4bd6bdb
oops
juniperlsimonis Sep 4, 2019
d792360
Update test-11-prepare_rodents.R
juniperlsimonis Sep 4, 2019
dc6ff44
vignettes
juniperlsimonis Sep 4, 2019
10c21a2
spell checking
juniperlsimonis Sep 4, 2019
50f052b
vignette updates
juniperlsimonis Sep 4, 2019
153d8d8
Update NEWS.md
juniperlsimonis Sep 4, 2019
e57b99c
Update test-13-figures.R
juniperlsimonis Sep 5, 2019
ea3b9f1
documentation editing
juniperlsimonis Sep 5, 2019
8e68492
Update NEWS.md
juniperlsimonis Sep 6, 2019
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 2 additions & 5 deletions .Rbuildignore
Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,10 @@
^.*\.Rproj$
^\.Rproj\.user$
^\.travis\.yml$
^models$
^package_outline.txt$
^in_dev.R$
^CONTRIBUTING\.md$
^CODE_OF_CONDUCT\.md$
^_pkgdown\.yml$
^LICENSE\.md$
^cran-comments\.md$
^\.zenodo\.json$
^inst/WORDLIST$
^inst/WORDLIST$
^notes.R$
3 changes: 3 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -5,3 +5,6 @@ doc
.RData
docs/*
inst/doc
tests/testthat/testing/*
tests/testthat/prod/*
tests/testthat/sand/*
50 changes: 23 additions & 27 deletions .travis.yml
Original file line number Diff line number Diff line change
@@ -1,37 +1,33 @@
language: r
cache: packages
sudo: false
sudo: required
warnings_are_errors: false
r:
- release
- devel

before_install:
- sudo apt-get update -qq
- sudo apt-get install texlive-latex-base

r_packages:
- covr
- covr

script:
- |
R CMD build .
travis_wait 20 R CMD check portalcasting*tar.gz

addons:
apt:
packages:
- libgsl0-dbg
- libgsl0-dev
- libgsl0ldbl
update: true

after_success:
- R CMD INSTALL .
- Rscript -e 'pkgdown::build_site()'
- travis_wait 20 Rscript -e 'library(covr); codecov()'
travis_wait 40 R CMD check portalcasting*tar.gz

deploy:
provider: pages
skip-cleanup: true
github-token: $GITHUB_PAT
keep-history: true
local-dir: docs
on:
branch: master
matrix:
include:
- r: devel
- r: release
after_success:
- R CMD INSTALL .
- Rscript -e 'pkgdown::build_site(examples = FALSE)'
- travis_wait 40 Rscript -e 'library(covr); codecov()'
deploy:
provider: pages
skip-cleanup: true
github-token: $GITHUB_PAT
keep-history: true
local-dir: docs
on:
branch: master
12 changes: 5 additions & 7 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: portalcasting
Title: Functions Used in Predicting Portal Rodent Dynamics
Version: 0.8.1
Version: 0.9.0
Authors@R: c(
person(c("Juniper", "L."), "Simonis",
email = "[email protected]", role = c("aut", "cre"),
Expand All @@ -20,25 +20,23 @@ Authors@R: c(
Description: Create a directory, populate it with data, build
models, forecast rodent populations, and visualize the results.
This package provides the functionality underlying the
Portal Predictions Project: <https://github.com/weecology/portalpredictions>.
Portal Predictions Project <https://github.com/weecology/portalpredictions>
as well as support for exploring and developing new models in sandbox environments.
URL: https://weecology.github.io/portalcasting, https://github.com/weecology/portalcasting
BugReports: https://github.com/weecology/portalcasting/issues
Depends: R (>= 3.2.3)
License: MIT + file LICENSE
LazyData: true
Imports:
curl,
DesignLibrary,
digest,
dplyr,
forecast,
httr,
lubridate,
magrittr,
portalr,
purrr,
RCurl,
readr,
rlang,
tidyselect,
tscount,
viridis,
yaml
Expand Down
Loading