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Markdown vignette #11

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2d2d143
ignore mac .ds_store
dsjohnson Sep 13, 2019
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changed vignette to rmarkdown
dsjohnson Sep 16, 2019
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3 changes: 2 additions & 1 deletion .gitignore
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Expand Up @@ -6,4 +6,5 @@ mcmcTesting.R
*.o
*.so
marked.Rcheck
*.tar.gz
*.tar.gz
.DS_Store
2 changes: 2 additions & 0 deletions marked/.Rbuildignore
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^doc$
^Meta$
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doc
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87 changes: 44 additions & 43 deletions marked/DESCRIPTION
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Package: marked
Version: 1.2.2
Date: 2018-09-12
Title: Mark-Recapture Analysis for Survival and Abundance Estimation
Author: Jeff Laake <jefflaake@gmail.com>, Devin Johnson
<devin.johnson@noaa.gov>, Paul Conn <paul.conn@noaa.gov>, example for simHMM
from Jay Rotella
Maintainer: Jeff Laake <jefflaake@gmail.com>
Description: Functions for fitting various models to capture-recapture data
including mixed-effects Cormack-Jolly-Seber(CJS) and multistate models and
the multi-variate state model structure for survival
estimation and POPAN structured Jolly-Seber models for abundance estimation.
There are also Hidden Markov model (HMM) implementations of CJS and multistate
models with and without state uncertainty and a simulation capability for HMM
models.
Depends:
R (>= 3.2.0),
lme4,
methods,
parallel
Imports:
graphics,
stats,
utils,
R2admb,
truncnorm,
coda,
Matrix,
numDeriv,
expm,
Rcpp (>= 0.9.13),
TMB,
optimx (>= 2013.8.6),
data.table
Suggests:
ggplot2
LinkingTo: Rcpp
SystemRequirements: ADMB version 11 <http://admb-project.org/> for
use.admb=TRUE; see readme.txt
LazyLoad: yes
License: GPL (>=2)
RoxygenNote: 6.1.1
Encoding: UTF-8
Package: marked
Version: 1.2.2
Date: 2018-09-12
Title: Mark-Recapture Analysis for Survival and Abundance Estimation\
Author: Jeff Laake <jefflaake@gmail.com>, Devin Johnson
<devin.johnson@noaa.gov>, Paul Conn <paul.conn@noaa.gov>, example for simHMM
from Jay Rotella
Maintainer: Jeff Laake <jefflaake@gmail.com>
Description: Functions for fitting various models to capture-recapture data
including mixed-effects Cormack-Jolly-Seber(CJS) and multistate models and
the multi-variate state model structure for survival
estimation and POPAN structured Jolly-Seber models for abundance estimation.
There are also Hidden Markov model (HMM) implementations of CJS and multistate
models with and without state uncertainty and a simulation capability for HMM
models.
Depends:
R (>= 3.2.0),
lme4,
methods,
parallel
Imports:
graphics,
stats,
utils,
R2admb,
truncnorm,
coda,
Matrix,
numDeriv,
expm,
Rcpp (>= 0.9.13),
TMB,
optimx (>= 2013.8.6),
data.table
Suggests:
ggplot2
LinkingTo: Rcpp
SystemRequirements: ADMB version 11 <http://admb-project.org/> for
use.admb=TRUE; see readme.txt
LazyLoad: yes
VignetteBuilder: knitr
License: GPL (>=2)
RoxygenNote: 6.1.1
Encoding: UTF-8
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