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Starting to work on warnings fixing dependencies and global vars (sti…
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…ll some stuff to deal)
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@mhesselbarth
mhesselbarth committed Mar 14, 2023
1 parent c4e4b53 commit a7fe5b7
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63 changes: 32 additions & 31 deletions .Rbuildignore
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@@ -1,31 +1,32 @@
^\.travis\.yml$
^.*\.Rproj$
^\.Rproj\.user$
man-roxygen/*
\.github/*
vignettes/_output.yaml
src/stan_files/.*\.o$
src/stan_files/.*\.cc$
src/stan_files/.*\.hpp$
src/stan_files/.*\.exe$
tests/testthat/stan_files/.*\.o$
tests/testthat/stan_files/.*\.cc$
tests/testthat/stan_files/.*\.hpp$
^\cleanup*
configure.ac
^inst/doc/[A-Za-z0-9\-_]+[.]svg$
^inst/doc/[A-Za-z0-9\-_]+[.]txt$
^inst/doc/[A-Za-z0-9\-_]+[.]csv
^inst/doc/\.install_extras$
^_pkgdown\.yml$
^docs$
^\.github$
^pkgdown$
LICENSE.md
README.Rmd
^CITATION\.cff$
^vignettes/articles$
CONTRIBUTING.md
^cran-comments\.md$
^revdep$
^codecov\.yml$
^\.travis\.yml$
^.*\.Rproj$
^\.Rproj\.user$
man-roxygen/*
\.github/*
vignettes/_output.yaml
src/stan_files/.*\.o$
src/stan_files/.*\.cc$
src/stan_files/.*\.hpp$
src/stan_files/.*\.exe$
tests/testthat/stan_files/.*\.o$
tests/testthat/stan_files/.*\.cc$
tests/testthat/stan_files/.*\.hpp$
^\cleanup*
configure.ac
^inst/doc/[A-Za-z0-9\-_]+[.]svg$
^inst/doc/[A-Za-z0-9\-_]+[.]txt$
^inst/doc/[A-Za-z0-9\-_]+[.]csv
^inst/doc/\.install_extras$
^_pkgdown\.yml$
^docs$
^\.github$
^pkgdown$
LICENSE.md
README.Rmd
^CITATION\.cff$
^vignettes/articles$
CONTRIBUTING.md
^cran-comments\.md$
^revdep$
^codecov\.yml$
.covrignore
284 changes: 147 additions & 137 deletions DESCRIPTION
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@@ -1,137 +1,147 @@
Package: ibis.iSDM
Type: Package
Title: Modelling Framework for Integrated Biodiversity Distribution Scenarios
Version: 0.0.2
Authors@R:
c(person(given = "Martin",
family = "Jung",
role = c("aut", "cre", "cph"),
email = "jung@iiasa.ac.at",
comment = c(ORCID = "0000-0002-7569-1390")),
person(given = "Maximilian H.K.",
family = "Hesselbarth",
role = c("ctb"),
email = "hesselbarth@iiasa.ac.at",
comment = c(ORCID = "0000-0003-1125-9918"))
)
Maintainer: Martin Jung <jung@iiasa.ac.at>
Description: Integrated framework of modelling the distribution of species and ecosystems in a suitability framing. This package allows the estimation of integrated species distribution models (iSDM) based on several sources of evidence and provided presence-only and presence-absence datasets. It makes heavy use of point-process models for estimating habitat suitability and allows to include spatial latent effects and priors in the estimation. To do so 'ibis.iSDM' supports a number of engines for Bayesian and more non-parametric machine learning estimation. Further, the 'ibis.iSDM' is specifically customized to support spatial-temporal projections of habitat suitability into the future.
Language: en-GB
License: CC BY 4.0
Encoding: UTF-8
Imports:
assertthat (>= 0.2.0),
geodist,
ggplot2,
magrittr,
methods,
ncdf4,
parallel,
foreach,
future (>= 1.23.0),
doFuture (>= 0.12.2),
proto (>= 1.0.0),
raster (>= 3.4-5),
Rcpp (>= 0.12.0),
RcppParallel (>= 5.0.1),
rgeos (>= 0.5-5),
rgdal (>= 1.5-32),
sf (>= 0.9),
stars (>= 0.5),
testthat (>= 3.0.0),
tibble (>= 2.0.0),
uuid,
posterior
Depends:
R(>= 4.0.0)
Suggests:
deldir,
mboost,
dbarts (>= 0.9-22),
modEvA,
xgboost,
progress,
ellipsis,
doParallel,
rstan (>= 2.21.0),
rstantools (>= 2.1.1),
BoomSpikeSlab (>= 1.2.4),
rmarkdown,
knitr,
covr
URL: https://iiasa.github.io/ibis.iSDM/
BugReports: https://github.com/iiasa/ibis.iSDM/issues
RoxygenNote: 7.2.3
Config/testthat/edition: 3
Collate:
'utils.R'
'bdproto.R'
'waiver.R'
'bdproto-biodiversitydataset.R'
'bdproto-biodiversitydistribution.R'
'add_biodiversity.R'
'bdproto-biodiversityscenario.R'
'add_constraint.R'
'add_constraint_MigClim.R'
'add_control_bias.R'
'add_latent.R'
'bdproto-log.R'
'add_log.R'
'add_offset.R'
'bdproto-predictors.R'
'add_predictors.R'
'identifier.R'
'bdproto-distributionmodel.R'
'bdproto-priorlist.R'
'bdproto-prior.R'
'add_priors.R'
'bdproto-engine.R'
'bdproto-settings.R'
'utils-spatial.R'
'data.R'
'distribution.R'
'effects.R'
'engine_bart.R'
'engine_breg.R'
'engine_gdb.R'
'engine_glmnet.R'
'utils-inla.R'
'engine_inla.R'
'engine_inlabru.R'
'engine_stan.R'
'engine_xgboost.R'
'ensemble.R'
'misc.R'
'partial.R'
'plot.R'
'print.R'
'prior_bart.R'
'prior_breg.R'
'prior_gdb.R'
'prior_glmnet.R'
'prior_inla.R'
'prior_stan.R'
'prior_xgb.R'
'priors.R'
'project.R'
'pseudoabsence.R'
'scenario.R'
'similarity.R'
'summary.R'
'threshold.R'
'train.R'
'utils-bart.R'
'utils-breg.R'
'utils-gdb.R'
'utils-glmnet.R'
'utils-predictors.R'
'utils-scenario.R'
'utils-stan.R'
'utils-xgboost.R'
'validate.R'
'write_output.R'
'zzz.R'
Roxygen: list(markdown = TRUE)
Biarch: true
SystemRequirements: GNU make
VignetteBuilder: knitr
Package: ibis.iSDM
Type: Package
Title: Modelling Framework for Integrated Biodiversity Distribution Scenarios
Version: 0.0.2
Authors@R:
c(person(given = "Martin",
family = "Jung",
role = c("aut", "cre", "cph"),
email = "jung@iiasa.ac.at",
comment = c(ORCID = "0000-0002-7569-1390")),
person(given = "Maximilian H.K.",
family = "Hesselbarth",
role = c("ctb"),
email = "hesselbarth@iiasa.ac.at",
comment = c(ORCID = "0000-0003-1125-9918"))
)
Maintainer: Martin Jung <jung@iiasa.ac.at>
Description: Integrated framework of modelling the distribution of species and ecosystems in a suitability framing. This package allows the estimation of integrated species distribution models (iSDM) based on several sources of evidence and provided presence-only and presence-absence datasets. It makes heavy use of point-process models for estimating habitat suitability and allows to include spatial latent effects and priors in the estimation. To do so 'ibis.iSDM' supports a number of engines for Bayesian and more non-parametric machine learning estimation. Further, the 'ibis.iSDM' is specifically customized to support spatial-temporal projections of habitat suitability into the future.
Language: en-GB
License: CC BY 4.0
Encoding: UTF-8
Imports:
assertthat (>= 0.2.0),
cmdstanr,
doFuture (>= 0.12.2),
foreach,
future (>= 1.23.0),
geodist,
ggplot2,
glmnet,
glmnetUtils,
graphics,
INLA,
inlabru,
magrittr,
methods,
ncdf4,
parallel,
posterior,
proto (>= 1.0.0),
raster (>= 3.4-5),
rgeos (>= 0.5-5),
sf (>= 0.9),
stars (>= 0.5),
stats,
tibble (>= 2.0.0),
uuid,
utils
Depends:
R(>= 4.0.0)
Suggests:
abind,
BoomSpikeSlab (>= 1.2.4),
covr,
dbarts (>= 0.9-22),
deldir,
doParallel,
ellipsis,
igraph,
knitr,
mboost,
modEvA,
ncmeta,
progress,
rmarkdown,
rstan (>= 2.21.0),
rstantools (>= 2.1.1),
testthat,
xgboost
URL: https://iiasa.github.io/ibis.iSDM/
BugReports: https://github.com/iiasa/ibis.iSDM/issues
RoxygenNote: 7.2.3
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
Biarch: true
SystemRequirements: GNU make
VignetteBuilder: knitr
Collate:
'utils.R'
'bdproto.R'
'waiver.R'
'bdproto-biodiversitydataset.R'
'bdproto-biodiversitydistribution.R'
'add_biodiversity.R'
'bdproto-biodiversityscenario.R'
'add_constraint.R'
'add_constraint_MigClim.R'
'add_control_bias.R'
'add_latent.R'
'bdproto-log.R'
'add_log.R'
'add_offset.R'
'bdproto-predictors.R'
'add_predictors.R'
'identifier.R'
'bdproto-distributionmodel.R'
'bdproto-priorlist.R'
'bdproto-prior.R'
'add_priors.R'
'bdproto-engine.R'
'bdproto-settings.R'
'utils-spatial.R'
'data.R'
'distribution.R'
'effects.R'
'engine_bart.R'
'engine_breg.R'
'engine_gdb.R'
'engine_glmnet.R'
'utils-inla.R'
'engine_inla.R'
'engine_inlabru.R'
'engine_stan.R'
'engine_xgboost.R'
'ensemble.R'
'ibis.iSDM-package.R'
'misc.R'
'partial.R'
'plot.R'
'print.R'
'prior_bart.R'
'prior_breg.R'
'prior_gdb.R'
'prior_glmnet.R'
'prior_inla.R'
'prior_stan.R'
'prior_xgb.R'
'priors.R'
'project.R'
'pseudoabsence.R'
'scenario.R'
'similarity.R'
'summary.R'
'threshold.R'
'train.R'
'utils-bart.R'
'utils-breg.R'
'utils-gdb.R'
'utils-glmnet.R'
'utils-pipe.R'
'utils-predictors.R'
'utils-scenario.R'
'utils-stan.R'
'utils-xgboost.R'
'validate.R'
'write_output.R'
'zzz.R'
1 change: 0 additions & 1 deletion NAMESPACE
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Expand Up @@ -196,7 +196,6 @@ import(raster)
import(sf)
importFrom(foreach,"%do%")
importFrom(foreach,"%dopar%")
importFrom(magrittr,"%>%")
importFrom(methods,is)
importFrom(raster,as.data.frame)
importFrom(raster,init)
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2 comments on commit a7fe5b7

@Martin-Jung
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Could you summarize what you did here? Seems like everything is breaking now :D
Also I would like to avoid adding modelling frameworks (e.g. INLA) as imports (which is not even on CRAN).

@mhesselbarth
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The idea was/is the move many of the frameworks to suggests later, but for now I just tried to fix the code dependecies warnings. There were and still are couple of functions in the code without a proper dependencies (or suggests). Thus, RCMD throws warnings which are not allowed when submitting to cran

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