PecanProject/pecan-v1.7.2.zip
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PecanProject-pecan-e423ac0
.dockerignore
378 Bytes
.gitattributes
296 Bytes
.github
ISSUE_TEMPLATE
Bug_report.md
738 Bytes
Doc_changes.md
897 Bytes
Feature_request.md
627 Bytes
ISSUE_TEMPLATE.md
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PULL_REQUEST_TEMPLATE.md
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workflows
book.yml
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ci.yml
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depends.yml
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docker.yml
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stale.yml
655 Bytes
styler-actions.yml
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.gitignore
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.prettierignore
165 Bytes
.zenodo.json
6.4 kB
CHANGELOG.md
44.7 kB
CONTRIBUTING.md
5.9 kB
DEBUGING.md
1.8 kB
DEV-INTRO.md
17.6 kB
LICENSE
1.7 kB
Makefile
6.1 kB
Makefile.depends
5.3 kB
README.md
9.6 kB
apps
api
Dockerfile
1.3 kB
R
auth.R
2.5 kB
available-models.R
1.4 kB
entrypoint.R
2.5 kB
formats.R
2.7 kB
general.R
987 Bytes
get.file.R
1.5 kB
inputs.R
5.6 kB
models.R
2.2 kB
pfts.R
2.4 kB
runs.R
10.4 kB
sites.R
1.6 kB
submit.workflow.R
9.9 kB
workflows.R
6.8 kB
README.md
709 Bytes
pecanapi-spec.yml
35.1 kB
test_pecanapi.sh
187 Bytes
tests
alltests.R
48 Bytes
test.auth.R
640 Bytes
test.formats.R
1.1 kB
test.inputs.R
1.6 kB
test.models.R
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test.pfts.R
982 Bytes
test.ping.R
182 Bytes
test.runs.R
2.6 kB
test.sites.R
936 Bytes
test.status.R
188 Bytes
test.workflows.R
2.9 kB
test_workflows
api.sipnet.json
551 Bytes
api.sipnet.xml
703 Bytes
testthat.R
18 Bytes
base
all
DESCRIPTION
1.9 kB
LICENSE
1.6 kB
NAMESPACE
46 Bytes
data
pecan.packages.csv
341 Bytes
inst
CITATION
654 Bytes
tests
Rcheck_reference.log
2.7 kB
testthat
test.workflow.R
1.1 kB
testthat.R
593 Bytes
db
.Rbuildignore
40 Bytes
.gitignore
37 Bytes
DESCRIPTION
3.0 kB
LICENSE
1.6 kB
NAMESPACE
1.5 kB
NEWS.md
361 Bytes
R
PEcAn.DB-package.R
341 Bytes
assign.treatments.R
2.5 kB
check.lists.R
1.4 kB
clone_pft.R
3.5 kB
covariate.functions.R
5.7 kB
db_merge_into.R
1.2 kB
dbfiles.R
33.5 kB
derive.trait.R
2.5 kB
derive.traits.R
3.1 kB
fetch.stats2se.R
1.3 kB
get.trait.data.R
3.4 kB
get.trait.data.pft.R
14.8 kB
get_postgres_envvars.R
2.7 kB
input.name.check.R
150 Bytes
insert.format.vars.R
7.1 kB
insert_table.R
3.3 kB
met_inputs.R
1.5 kB
query.data.R
2.8 kB
query.dplyr.R
9.7 kB
query.file.path.R
1.1 kB
query.format.vars.R
8.4 kB
query.pft.R
4.3 kB
query.prior.R
8.3 kB
query.site.R
582 Bytes
query.trait.data.R
7.4 kB
query.traits.R
2.6 kB
query.yields.R
2.4 kB
query_pfts.R
1.5 kB
search_references.R
2.4 kB
symmetric_setdiff.R
2.7 kB
take.samples.R
1.5 kB
try2sqlite.R
3.8 kB
utils_db.R
16.6 kB
inst
PFT_builder
PFT_builder.R
1.7 kB
bety_mstmip_lookup.csv
2.1 kB
import-ForestGEO
ForestGEO_spp_website.csv
1.1 MB
import_species_list.R
5.1 kB
import-try
.gitignore
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01_try_sqlite.R
413 Bytes
02_citations.R
2.2 kB
91.global.subset.R
1.7 kB
92.data.specific.subset.R
3.1 kB
93.create.try.sites.R
5.0 kB
94.match.species.R
4.2 kB
95.citations.R
1.6 kB
96.load.data.R
2.7 kB
README.md
4.1 kB
bety_connect.R
113 Bytes
common.R
420 Bytes
config.R
345 Bytes
helpers.species.R
3.0 kB
misc
add.self.sql
188 Bytes
man
PEcAn.DB-package.Rd
1.6 kB
append.covariate.Rd
936 Bytes
arrhenius.scaling.traits.Rd
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assign.treatments.Rd
1.0 kB
bety2pecan.Rd
441 Bytes
betyConnect.Rd
368 Bytes
check.lists.Rd
521 Bytes
clone_pft.Rd
1.3 kB
db.close.Rd
538 Bytes
db.exists.Rd
564 Bytes
db.getShowQueries.Rd
345 Bytes
db.open.Rd
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db.print.connections.Rd
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db.query.Rd
3.2 kB
db.showQueries.Rd
428 Bytes
dbHostInfo.Rd
307 Bytes
db_merge_into.Rd
1.2 kB
dbfile.check.Rd
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dbfile.file.Rd
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dbfile.input.check.Rd
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dbfile.input.insert.Rd
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dbfile.insert.Rd
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dbfile.move.Rd
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dbfile.posterior.check.Rd
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dbfile.posterior.insert.Rd
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default_hostname.Rd
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derive.trait.Rd
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derive.traits.Rd
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dplyr.count.Rd
296 Bytes
fancy_scientific.Rd
372 Bytes
fetch.stats2se.Rd
701 Bytes
filter_sunleaf_traits.Rd
447 Bytes
get.id.Rd
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get.trait.data.Rd
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get.trait.data.pft.Rd
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get_postgres_envvars.Rd
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get_run_ids.Rd
396 Bytes
get_users.Rd
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get_var_names.Rd
569 Bytes
get_workflow_ids.Rd
403 Bytes
insert.format.vars.Rd
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insert_table.Rd
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load_data_single_run.Rd
442 Bytes
match_colnames.Rd
468 Bytes
match_dbcols.Rd
800 Bytes
met_inputs.Rd
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ncdays2date.Rd
265 Bytes
query.covariates.Rd
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query.data.Rd
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query.file.path.Rd
490 Bytes
query.format.vars.Rd
662 Bytes
query.pft_cultivars.Rd
964 Bytes
query.pft_species.Rd
725 Bytes
query.priors.Rd
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query.site.Rd
351 Bytes
query.trait.data.Rd
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query.traits.Rd
1.1 kB
query.yields.Rd
940 Bytes
query_pfts.Rd
667 Bytes
query_priors.Rd
2.3 kB
reexports.Rd
405 Bytes
runs.Rd
375 Bytes
search_reference_single.Rd
617 Bytes
search_references.Rd
776 Bytes
symmetric_setdiff.Rd
1.2 kB
take.samples.Rd
754 Bytes
try2sqlite.Rd
1.1 kB
var_names_all.Rd
473 Bytes
workflow.Rd
365 Bytes
workflows.Rd
391 Bytes
tests
Rcheck_reference.log
5.3 kB
testthat
helper-db-setup.R
1.8 kB
test-get.trait.data.pft.R
3.2 kB
test-query.pft.R
2.2 kB
test-query.traits.R
3.3 kB
test.contents_sanity.R
4.0 kB
test.db.utils.R
1.1 kB
test.derive.traits.R
3.2 kB
test.insert.R
1.5 kB
test.query.base.R
811 Bytes
test.query_pfts.R
893 Bytes
test.symmetric-setdiff.R
1.3 kB
testthat.R
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vignettes
betydb_access.Rmd
2.0 kB
create_sites.geometry.Rmd
2.4 kB
logger
.Rbuildignore
17 Bytes
DESCRIPTION
1.4 kB
LICENSE
1.7 kB
NAMESPACE
426 Bytes
NEWS.md
322 Bytes
R
logger.R
9.1 kB
logifnot.R
2.2 kB
print2string.R
1.0 kB
cran-comments.md
563 Bytes
man
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445 Bytes
logger.error.Rd
459 Bytes
logger.getLevel.Rd
429 Bytes
logger.info.Rd
465 Bytes
logger.message.Rd
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logger.setLevel.Rd
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logger.setOutputFile.Rd
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logger.setQuitOnSevere.Rd
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logger.setUseConsole.Rd
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logger.setWidth.Rd
510 Bytes
logger.severe.Rd
924 Bytes
logger.warn.Rd
452 Bytes
print2string.Rd
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severeifnot.Rd
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tests
testthat
test.logger.R
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qaqc
DESCRIPTION
1.2 kB
LICENSE
1.6 kB
NAMESPACE
203 Bytes
R
cull_database_entries.R
3.1 kB
find_formats_without_inputs.R
2.4 kB
find_inputs_without_formats.R
2.0 kB
get_table_column_names.R
1.4 kB
taylor.plot.R
1.4 kB
write_out_table.R
1.3 kB
README.Rmd
2.1 kB
inst
extdata
data.csv
409 Bytes
ebifarm
ed2in-template-pavi
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fast
misi.xml
519 Bytes
pavi.xml
1.9 kB
post
pavi.xml
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prior
pavi.xml
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extdata.R
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testdata1.csv
477 Bytes
man
cull_database_entries.Rd
1.2 kB
find_formats_without_inputs.Rd
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find_inputs_without_formats.Rd
1.1 kB
get_table_column_names.Rd
840 Bytes
new.taylor.Rd
453 Bytes
write_out_table.Rd
854 Bytes
tests
Rcheck_reference.log
3.8 kB
testthat
_snaps
taylorplot
taylor-diagram.svg
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test-taylorplot.R
889 Bytes
testthat.R
594 Bytes
vignettes
Pre-release-database-cleanup.Rmd
3.4 kB
function_relationships.Rmd
1.3 kB
module_output.Rmd
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remote
.Rbuildignore
28 Bytes
DESCRIPTION
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LICENSE
1.6 kB
NAMESPACE
572 Bytes
R
check_model_run.R
628 Bytes
check_qsub_status.R
1.2 kB
fqdn.R
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is.localhost.R
622 Bytes
kill.tunnel.R
691 Bytes
open.tunnel.R
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qsub_get_jobid.R
725 Bytes
rabbitmq.R
8.1 kB
remote.copy.from.R
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remote.copy.to.R
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remote.copy.update.R
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remote.execute.R.R
3.0 kB
remote.execute.cmd.R
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setup_modellauncher.R
1.0 kB
stamp.R
847 Bytes
start.model.runs.R
10.3 kB
start_qsub.R
2.1 kB
start_rabbitmq.R
426 Bytes
start_serial.R
549 Bytes
test_remote.R
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man
check_model_run.Rd
565 Bytes
fqdn.Rd
544 Bytes
is.localhost.Rd
534 Bytes
kill.tunnel.Rd
276 Bytes
open_tunnel.Rd
937 Bytes
qsub_get_jobid.Rd
603 Bytes
qsub_run_finished.Rd
499 Bytes
rabbitmq_create_queue.Rd
951 Bytes
rabbitmq_get_message.Rd
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rabbitmq_parse_uri.Rd
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rabbitmq_post_message.Rd
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rabbitmq_send_message.Rd
805 Bytes
remote.copy.from.Rd
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remote.copy.to.Rd
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remote.copy.update.Rd
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remote.execute.R.Rd
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remote.execute.cmd.Rd
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setup_modellauncher.Rd
718 Bytes
stamp_started.Rd
409 Bytes
start.model.runs.Rd
709 Bytes
start_qsub.Rd
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start_rabbitmq.Rd
424 Bytes
start_serial.Rd
832 Bytes
test_remote.Rd
870 Bytes
tests
Rcheck_reference.log
5.3 kB
testthat
test.check_qsub.R
506 Bytes
test.localhost.R
696 Bytes
test.remote.R
549 Bytes
test.remote.execute.R.R
314 Bytes
testthat.R
69 Bytes
settings
.Rbuildignore
28 Bytes
DESCRIPTION
647 Bytes
LICENSE
1.7 kB
NAMESPACE
1.4 kB
R
MultiSettings.R
5.5 kB
SafeList.R
2.3 kB
Settings.R
1.3 kB
addSecrets.R
2.4 kB
check.all.settings.R
42.3 kB
clean.settings.R
2.3 kB
createMultisiteMultiSettings.r
6.1 kB
fix.deprecated.settings.R
2.8 kB
get_args.R
977 Bytes
listToXml.R
1.4 kB
loadPath_sitePFT.R
1.1 kB
papply.R
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pft_site_linker.R
2.7 kB
prepare.settings.R
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read.settings.R
3.6 kB
site_pft_link_settings.R
1.9 kB
update.settings.R
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write.settings.R
710 Bytes
examples
examples.MultiSite.MultiSettings.r
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examples.papply.R
817 Bytes
man
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MultiSettings.Rd
690 Bytes
SafeList.Rd
1.1 kB
Settings.Rd
663 Bytes
addSecrets.Rd
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cash-.SafeList.Rd
541 Bytes
check.bety.version.Rd
324 Bytes
check.database.Rd
328 Bytes
check.database.settings.Rd
323 Bytes
check.ensemble.settings.Rd
323 Bytes
check.inputs.Rd
332 Bytes
check.model.settings.Rd
322 Bytes
check.run.settings.Rd
312 Bytes
check.settings.Rd
657 Bytes
check.workflow.settings.Rd
337 Bytes
clean.settings.Rd
777 Bytes
createMultiSiteSettings.Rd
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createSitegroupMultiSettings.Rd
6.1 kB
fix.deprecated.settings.Rd
434 Bytes
getRunSettings.Rd
589 Bytes
get_args.Rd
413 Bytes
listToXml.default.Rd
519 Bytes
loadPath.sitePFT.Rd
680 Bytes
papply.Rd
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prepare.settings.Rd
618 Bytes
read.settings.Rd
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setDates.Rd
772 Bytes
setOutDir.Rd
838 Bytes
site.pft.link.settings.Rd
524 Bytes
site.pft.linkage.Rd
1.3 kB
update.settings.Rd
475 Bytes
write.settings.Rd
542 Bytes
tests
Rcheck_reference.log
4.8 kB
testthat
helper-get.test.settings.R
812 Bytes
test.MultiSettings.class.R
10.1 kB
test.Safelist.class.R
1.7 kB
test.Settings.class.R
1.3 kB
test.deprecated.settings.R
2.2 kB
test.papply.R
3.0 kB
test.read.settings.R
10.5 kB
testinput.pecan2.bu.edu.xml
757 Bytes
testinput.xml
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testsettings.xml
228 Bytes
testthat.R
692 Bytes
utils
.Rbuildignore
37 Bytes
DESCRIPTION
1.7 kB
LICENSE
1.6 kB
NAMESPACE
1.3 kB
R
cf2date.R
2.7 kB
clear.scratch.R
1.5 kB
convert.input.R
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datasets.R
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days_in_year.R
744 Bytes
distn.stats.R
2.2 kB
download.url.R
1.3 kB
full.path.R
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get.ensemble.inputs.R
846 Bytes
help.R
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listToArgString.R
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load_local.R
550 Bytes
mail.R
1.6 kB
match_file.R
1.5 kB
mcmc.list2init.R
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n_leap_day.R
871 Bytes
need_packages.R
883 Bytes
r2bugs.distributions.R
5.1 kB
read.output.R
11.9 kB
read_web_config.R
2.0 kB
regrid.R
3.0 kB
remove.config.R
847 Bytes
seconds_in_year.R
652 Bytes
status.R
3.9 kB
timezone_hour.R
528 Bytes
to_nc.R
2.5 kB
transformstats.R
2.9 kB
units_are_equivalent.R
444 Bytes
utils.R
29.2 kB
write.config.utils.R
3.5 kB
data
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91 Bytes
standard_vars.csv
17.5 kB
trait.dictionary.csv
5.5 kB
inst
LBNL_remote_test.R
2.0 kB
clear.scratch.sh
952 Bytes
test-data
CRUNCEP.2000.nc
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man
PEcAn.Rd
2.2 kB
arrhenius.scaling.Rd
669 Bytes
as.sequence.Rd
571 Bytes
bibtexify.Rd
474 Bytes
bugs.rdist.Rd
736 Bytes
capitalize.Rd
292 Bytes
cf2datetime.Rd
758 Bytes
clear.scratch.Rd
548 Bytes
convert.expr.Rd
323 Bytes
convert.input.Rd
5.8 kB
datetime2cf.Rd
713 Bytes
datetime2doy.Rd
939 Bytes
days_in_year.Rd
692 Bytes
distn.stats.Rd
648 Bytes
distn.table.stats.Rd
569 Bytes
download.file.Rd
896 Bytes
download.url.Rd
1.0 kB
full.path.Rd
574 Bytes
get.ensemble.inputs.Rd
447 Bytes
get.parameter.stat.Rd
577 Bytes
get.quantiles.Rd
428 Bytes
get.run.id.Rd
1.1 kB
get.sa.sample.list.Rd
477 Bytes
get.sa.samples.Rd
899 Bytes
get.stats.mcmc.Rd
528 Bytes
grid2netcdf.Rd
499 Bytes
left.pad.zeros.Rd
480 Bytes
listToArgString.Rd
468 Bytes
load.modelpkg.Rd
390 Bytes
load_local.Rd
755 Bytes
match_file.Rd
831 Bytes
mcmc.list2init.Rd
397 Bytes
met2model.exists.Rd
374 Bytes
misc.are.convertible.Rd
462 Bytes
misc.convert.Rd
514 Bytes
mstmipvar.Rd
734 Bytes
n_leap_day.Rd
372 Bytes
need_packages.Rd
776 Bytes
newxtable.Rd
737 Bytes
paste.stats.Rd
612 Bytes
pdf.stats.Rd
517 Bytes
r2bugs.distributions.Rd
1.1 kB
read.output.Rd
2.9 kB
read_web_config.Rd
992 Bytes
regrid.Rd
360 Bytes
retry.func.Rd
1.2 kB
rsync.Rd
503 Bytes
seconds_in_year.Rd
718 Bytes
sendmail.Rd
652 Bytes
ssh.Rd
364 Bytes
standard_vars.Rd
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status.Rd
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summarize.result.Rd
449 Bytes
tabnum.Rd
428 Bytes
temp.settings.Rd
610 Bytes
timezone_hour.Rd
433 Bytes
to_ncdim.Rd
554 Bytes
to_ncvar.Rd
571 Bytes
trait.lookup.Rd
923 Bytes
transformstats.Rd
887 Bytes
tryl.Rd
460 Bytes
units_are_equivalent.Rd
587 Bytes
vecpaste.Rd
366 Bytes
zero.bounded.density.Rd
1.2 kB
zero.truncate.Rd
336 Bytes
scripts
metutils.R
24.9 kB
time.constants.R
1.7 kB
tests
Rcheck_reference.log
3.9 kB
testthat
data
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4.5 kB
post.distns.RData
616 Bytes
prior.distns.RData
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helper.R
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test-read.output.R
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test-status.R
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test.distn.stats.R
1.0 kB
test.read_web_config.R
1.1 kB
test.trait.dictionary.R
889 Bytes
test.utils.R
4.2 kB
testthat.R
595 Bytes
visualization
DESCRIPTION
1.5 kB
LICENSE
1.7 kB
NAMESPACE
177 Bytes
R
add_icon.R
1.2 kB
ciEnvelope.R
1.1 kB
map.output.R
1.0 kB
plot_netcdf.R
6.0 kB
plots.R
12.1 kB
visually.weighted.watercolor.plots.R
11.0 kB
data
counties.RData
75.5 kB
yielddf.RData
119.9 kB
inst
extdata
miscanthusyield.csv
451.3 kB
favicon.png
5.2 kB
man
add_icon.Rd
376 Bytes
ciEnvelope.Rd
584 Bytes
dhist.Rd
1.9 kB
iqr.Rd
421 Bytes
map.output.Rd
403 Bytes
plot_data.Rd
805 Bytes
plot_netcdf.Rd
1.1 kB
theme_border.Rd
1.3 kB
vwReg.Rd
3.2 kB
tests
Rcheck_reference.log
4.0 kB
testthat
test.viz.R
535 Bytes
testthat.R
611 Bytes
vignettes
usmap.Rmd
3.3 kB
workflow
DESCRIPTION
1.3 kB
LICENSE
1.6 kB
NAMESPACE
272 Bytes
R
create_execute_test_xml.R
6.9 kB
do_conversions.R
4.0 kB
run.write.configs.R
6.8 kB
runModule.get.trait.data.R
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runModule.run.write.configs.R
1.6 kB
inst
batch_run.R
7.2 kB
default_tests.csv
406 Bytes
permutation_tests.R
4.7 kB
man
create_execute_test_xml.Rd
2.3 kB
do_conversions.Rd
512 Bytes
model_specific_tags.Rd
408 Bytes
run.write.configs.Rd
1.6 kB
runModule.get.trait.data.Rd
436 Bytes
runModule.run.write.configs.Rd
611 Bytes
tests
Rcheck_reference.log
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testthat
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sensitivity
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