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environment.yml
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environment.yml
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name: infection-timing
channels:
- conda-forge
- defaults
- bioconda
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
- _r-mutex=1.0.1=anacondar_1
- argon2-cffi=21.1.0=py39h3811e60_0
- async_generator=1.10=py_0
- attrs=21.2.0=pyhd8ed1ab_0
- backcall=0.2.0=pyh9f0ad1d_0
- backports=1.0=py_2
- backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
- binutils_impl_linux-64=2.36.1=h193b22a_2
- binutils_linux-64=2.36=hf3e587d_1
- bleach=4.1.0=pyhd8ed1ab_0
- bwidget=1.9.14=ha770c72_1
- bzip2=1.0.8=h7f98852_4
- c-ares=1.17.2=h7f98852_0
- ca-certificates=2022.9.24=ha878542_0
- cairo=1.16.0=h6cf1ce9_1008
- cffi=1.14.6=py39h4bc2ebd_1
- curl=7.79.1=h494985f_1
- debugpy=1.4.1=py39he80948d_0
- decorator=5.1.0=pyhd8ed1ab_0
- defusedxml=0.7.1=pyhd8ed1ab_0
- entrypoints=0.3=pyhd8ed1ab_1003
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=hab24e00_0
- fontconfig=2.13.1=hba837de_1005
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- freetype=2.10.4=h0708190_1
- fribidi=1.0.10=h36c2ea0_0
- gcc_impl_linux-64=9.4.0=h03d3576_11
- gcc_linux-64=9.4.0=h391b98a_1
- gettext=0.19.8.1=h73d1719_1008
- gfortran_impl_linux-64=9.4.0=h0003116_11
- gfortran_linux-64=9.4.0=hf0ab688_1
- gmp=6.2.1=h58526e2_0
- graphite2=1.3.13=h58526e2_1001
- gsl=2.7=he838d99_0
- gxx_impl_linux-64=9.4.0=h03d3576_11
- gxx_linux-64=9.4.0=h0316aca_1
- harfbuzz=3.0.0=h83ec7ef_1
- icu=68.1=h58526e2_0
- importlib-metadata=4.8.1=py39hf3d152e_0
- ipykernel=6.4.1=py39hef51801_0
- ipython=7.28.0=py39hef51801_0
- ipython_genutils=0.2.0=py_1
- jbig=2.1=h7f98852_2003
- jedi=0.18.0=py39hf3d152e_2
- jinja2=3.0.2=pyhd8ed1ab_0
- jpeg=9d=h36c2ea0_0
- jsonschema=4.1.0=pyhd8ed1ab_0
- jupyter_client=7.0.6=pyhd8ed1ab_0
- jupyter_core=4.8.1=py39hf3d152e_0
- jupyterlab_pygments=0.1.2=pyh9f0ad1d_0
- kernel-headers_linux-64=2.6.32=he073ed8_14
- krb5=1.19.2=h48eae69_2
- ld_impl_linux-64=2.36.1=hea4e1c9_2
- lerc=3.0=h9c3ff4c_0
- libblas=3.9.0=12_linux64_openblas
- libcblas=3.9.0=12_linux64_openblas
- libcurl=7.79.1=h494985f_1
- libdeflate=1.8=h7f98852_0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libffi=3.4.2=h9c3ff4c_4
- libgcc-devel_linux-64=9.4.0=hd854feb_11
- libgcc-ng=12.1.0=h8d9b700_16
- libgfortran-ng=11.2.0=h69a702a_11
- libgfortran5=11.2.0=h5c6108e_11
- libglib=2.68.4=h174f98d_1
- libgomp=12.1.0=h8d9b700_16
- libiconv=1.16=h516909a_0
- liblapack=3.9.0=12_linux64_openblas
- libnghttp2=1.43.0=ha19adfc_1
- libopenblas=0.3.18=pthreads_h8fe5266_0
- libpng=1.6.37=h21135ba_2
- libsanitizer=9.4.0=h79bfe98_11
- libsodium=1.0.18=h36c2ea0_1
- libssh2=1.10.0=ha35d2d1_2
- libstdcxx-devel_linux-64=9.4.0=hd854feb_11
- libstdcxx-ng=11.2.0=he4da1e4_11
- libtiff=4.3.0=h6f004c6_2
- libuuid=2.32.1=h7f98852_1000
- libv8=8.9.83=ha720a15_0
- libwebp-base=1.2.1=h7f98852_0
- libxcb=1.13=h7f98852_1003
- libxml2=2.9.12=h72842e0_0
- libzlib=1.2.11=h36c2ea0_1013
- lz4-c=1.9.3=h9c3ff4c_1
- make=4.3=hd18ef5c_1
- markupsafe=2.0.1=py39h3811e60_0
- matplotlib-inline=0.1.3=pyhd8ed1ab_0
- mistune=0.8.4=py39h3811e60_1004
- nbclient=0.5.4=pyhd8ed1ab_0
- nbconvert=6.2.0=py39hf3d152e_0
- nbformat=5.1.3=pyhd8ed1ab_0
- ncurses=6.2=h58526e2_4
- nest-asyncio=1.5.1=pyhd8ed1ab_0
- notebook=6.4.4=pyha770c72_0
- openssl=3.0.7=h166bdaf_0
- packaging=21.0=pyhd8ed1ab_0
- pandoc=2.14.2=h7f98852_0
- pandocfilters=1.5.0=pyhd8ed1ab_0
- pango=1.48.10=h54213e6_2
- parso=0.8.2=pyhd8ed1ab_0
- pcre=8.45=h9c3ff4c_0
- pcre2=10.37=h032f7d1_0
- pexpect=4.8.0=pyh9f0ad1d_2
- pickleshare=0.7.5=py_1003
- pip=21.3=pyhd8ed1ab_0
- pixman=0.40.0=h36c2ea0_0
- prometheus_client=0.11.0=pyhd8ed1ab_0
- prompt-toolkit=3.0.20=pyha770c72_0
- pthread-stubs=0.4=h36c2ea0_1001
- ptyprocess=0.7.0=pyhd3deb0d_0
- pycparser=2.20=pyh9f0ad1d_2
- pygments=2.10.0=pyhd8ed1ab_0
- pyparsing=2.4.7=pyh9f0ad1d_0
- pyrsistent=0.17.3=py39h3811e60_2
- python=3.9.7=hf930737_3_cpython
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python_abi=3.9=2_cp39
- pyzmq=22.3.0=py39h37b5a0c_0
- r-abind=1.4_5=r41hc72bb7e_1003
- r-askpass=1.1=r41hcfec24a_2
- r-assertthat=0.2.1=r41hc72bb7e_2
- r-backports=1.2.1=r41hcfec24a_0
- r-base=4.1.1=hb93adac_1
- r-base64enc=0.1_3=r41hcfec24a_1004
- r-bayesplot=1.9.0=r41hc72bb7e_0
- r-bit=4.0.4=r41hcfec24a_0
- r-bit64=4.0.5=r41hcfec24a_0
- r-blob=1.2.2=r41hc72bb7e_0
- r-boot=1.3_28=r41hc72bb7e_0
- r-brio=1.1.2=r41hcfec24a_0
- r-broom=0.7.9=r41hc72bb7e_0
- r-bslib=0.3.1=r41hc72bb7e_0
- r-cachem=1.0.6=r41hcfec24a_0
- r-callr=3.7.0=r41hc72bb7e_0
- r-caret=6.0_90=r41hcfec24a_0
- r-cellranger=1.1.0=r41hc72bb7e_1003
- r-checkmate=2.0.0=r41hcfec24a_1
- r-class=7.3_19=r41hcfec24a_0
- r-cli=3.0.1=r41h03ef668_1
- r-clipr=0.7.1=r41hc72bb7e_0
- r-cluster=2.1.2=r41h859d828_0
- r-codetools=0.2_18=r41hc72bb7e_0
- r-colorspace=2.0_2=r41hcfec24a_0
- r-colourpicker=1.1.1=r41hc72bb7e_0
- r-commonmark=1.7=r41hcfec24a_1002
- r-cpp11=0.4.0=r41hc72bb7e_0
- r-crayon=1.4.1=r41hc72bb7e_0
- r-crosstalk=1.2.0=r41hc72bb7e_0
- r-crul=1.1.0=r41h785f33e_0
- r-curl=4.3.2=r41hcfec24a_0
- r-data.table=1.14.2=r41hcfec24a_0
- r-dbi=1.1.1=r41hc72bb7e_0
- r-dbplyr=2.1.1=r41hc72bb7e_0
- r-desc=1.4.0=r41hc72bb7e_0
- r-diffobj=0.3.5=r41hcfec24a_0
- r-digest=0.6.28=r41h03ef668_0
- r-distributional=0.3.1=r41hc72bb7e_0
- r-dplyr=1.0.7=r41h03ef668_0
- r-dt=0.25=r41hc72bb7e_0
- r-dtplyr=1.1.0=r41hc72bb7e_0
- r-dygraphs=1.1.1.6=r41hc72bb7e_1003
- r-e1071=1.7_9=r41h03ef668_0
- r-ellipsis=0.3.2=r41hcfec24a_0
- r-essentials=4.1=r41hd8ed1ab_2002
- r-evaluate=0.14=r41hc72bb7e_2
- r-fansi=0.4.2=r41hcfec24a_0
- r-farver=2.1.0=r41h03ef668_0
- r-fastmap=1.1.0=r41h03ef668_0
- r-fastmatrix=0.4_124=r41hb361e29_0
- r-fontawesome=0.2.2=r41hc72bb7e_0
- r-forcats=0.5.1=r41hc72bb7e_0
- r-foreach=1.5.1=r41hc72bb7e_0
- r-foreign=0.8_81=r41hcfec24a_0
- r-formatr=1.11=r41hc72bb7e_0
- r-fs=1.5.0=r41h03ef668_0
- r-future=1.22.1=r41hc72bb7e_0
- r-future.apply=1.8.1=r41hc72bb7e_0
- r-gargle=1.2.0=r41hc72bb7e_0
- r-generics=0.1.0=r41hc72bb7e_0
- r-ggh4x=0.2.3=r41hc72bb7e_0
- r-ggplot2=3.3.5=r41hc72bb7e_0
- r-ggridges=0.5.4=r41hc72bb7e_0
- r-gistr=0.9.0=r41hc72bb7e_0
- r-glmnet=4.1_2=r41h859d828_0
- r-globals=0.14.0=r41hc72bb7e_0
- r-glue=1.4.2=r41hcfec24a_0
- r-googledrive=2.0.0=r41hc72bb7e_0
- r-googlesheets4=1.0.0=r41h785f33e_0
- r-gower=0.2.2=r41hcfec24a_0
- r-gridextra=2.3=r41hc72bb7e_1003
- r-gtable=0.3.0=r41hc72bb7e_3
- r-gtools=3.9.3=r41h06615bd_0
- r-haven=2.4.3=r41h2713e49_0
- r-hexbin=1.28.2=r41h859d828_0
- r-highr=0.9=r41hc72bb7e_0
- r-hms=1.1.1=r41hc72bb7e_0
- r-htmltools=0.5.2=r41h03ef668_0
- r-htmlwidgets=1.5.4=r41hc72bb7e_0
- r-httpcode=0.3.0=r41ha770c72_1
- r-httpuv=1.6.3=r41h03ef668_0
- r-httr=1.4.2=r41hc72bb7e_0
- r-ids=1.0.1=r41hc72bb7e_1
- r-igraph=1.3.0=r41hf10d5bd_0
- r-inline=0.3.19=r41hc72bb7e_0
- r-ipred=0.9_12=r41hcfec24a_0
- r-irdisplay=1.0=r41hd8ed1ab_0
- r-irkernel=1.2=r41hc72bb7e_0
- r-isoband=0.2.5=r41h03ef668_0
- r-iterators=1.0.13=r41hc72bb7e_0
- r-jquerylib=0.1.4=r41hc72bb7e_0
- r-jsonlite=1.7.2=r41hcfec24a_0
- r-kernsmooth=2.23_20=r41h742201e_0
- r-knitr=1.35=r41hc72bb7e_0
- r-l1pack=0.41=r41h8da6f51_0
- r-labeling=0.4.2=r41hc72bb7e_0
- r-later=1.2.0=r41h03ef668_0
- r-lattice=0.20_45=r41hcfec24a_0
- r-lava=1.6.10=r41hc72bb7e_0
- r-lazyeval=0.2.2=r41hcfec24a_2
- r-lifecycle=1.0.1=r41hc72bb7e_0
- r-listenv=0.8.0=r41hc72bb7e_1
- r-lme4=1.1_29=r41h7525677_0
- r-lobstr=1.1.1=r41h03ef668_1
- r-loo=2.4.1=r41hc72bb7e_0
- r-lubridate=1.8.0=r41h03ef668_0
- r-magrittr=2.0.1=r41hcfec24a_1
- r-maps=3.4.0=r41hcfec24a_0
- r-markdown=1.1=r41hcfec24a_1
- r-mass=7.3_54=r41hcfec24a_0
- r-matrix=1.3_4=r41he454529_0
- r-matrixstats=0.61.0=r41hcfec24a_0
- r-mgcv=1.8_38=r41he454529_0
- r-mime=0.12=r41hcfec24a_0
- r-miniui=0.1.1.1=r41hc72bb7e_1002
- r-minqa=1.2.4=r41h5ee154c_1006
- r-modelmetrics=1.2.2.2=r41h03ef668_1
- r-modelr=0.1.8=r41hc72bb7e_0
- r-munsell=0.5.0=r41hc72bb7e_1003
- r-nlme=3.1_153=r41h859d828_0
- r-nloptr=1.2.2.3=r41h5ee154c_0
- r-nnet=7.3_16=r41hcfec24a_0
- r-numderiv=2016.8_1.1=r41hc72bb7e_3
- r-openssl=1.4.5=r41he82ab30_1
- r-packrat=0.8.1=r41hc72bb7e_0
- r-parallelly=1.28.1=r41hc72bb7e_0
- r-pbdzmq=0.3_5=r41h42bf92c_1
- r-pillar=1.6.3=r41hc72bb7e_0
- r-pkgbuild=1.2.0=r41hc72bb7e_0
- r-pkgconfig=2.0.3=r41hc72bb7e_1
- r-pkgload=1.2.3=r41h03ef668_0
- r-plyr=1.8.6=r41h03ef668_1
- r-posterior=1.3.1=r41hc72bb7e_0
- r-praise=1.0.0=r41hc72bb7e_1004
- r-prettyunits=1.1.1=r41hc72bb7e_1
- r-proc=1.18.0=r41h03ef668_0
- r-processx=3.5.2=r41hcfec24a_0
- r-prodlim=2019.11.13=r41h03ef668_1
- r-progress=1.2.2=r41hc72bb7e_2
- r-progressr=0.9.0=r41hc72bb7e_0
- r-promises=1.2.0.1=r41h03ef668_0
- r-proxy=0.4_26=r41hcfec24a_0
- r-pryr=0.1.5=r41h03ef668_0
- r-ps=1.6.0=r41hcfec24a_0
- r-purrr=0.3.4=r41hcfec24a_1
- r-quantmod=0.4.18=r41hc72bb7e_0
- r-r6=2.5.1=r41hc72bb7e_0
- r-randomforest=4.6_14=r41h859d828_1004
- r-rappdirs=0.3.3=r41hcfec24a_0
- r-rbokeh=0.5.2=r41hc72bb7e_0
- r-rcolorbrewer=1.1_2=r41h785f33e_1003
- r-rcpp=1.0.7=r41h03ef668_0
- r-rcppeigen=0.3.3.9.1=r41h306847c_0
- r-rcppparallel=5.1.4=r41h03ef668_0
- r-readr=2.0.2=r41h03ef668_0
- r-readxl=1.3.1=r41h2713e49_4
- r-recipes=0.1.17=r41hc72bb7e_0
- r-recommended=4.1=r41hd8ed1ab_1004
- r-rematch=1.0.1=r41hc72bb7e_1003
- r-rematch2=2.1.2=r41hc72bb7e_1
- r-repr=1.1.3=r41h785f33e_0
- r-reprex=2.0.1=r41hc72bb7e_0
- r-reshape2=1.4.4=r41h03ef668_1
- r-rlang=0.4.11=r41hcfec24a_0
- r-rmarkdown=2.11=r41hc72bb7e_0
- r-rpart=4.1_15=r41hcfec24a_2
- r-rprojroot=2.0.2=r41hc72bb7e_0
- r-rsconnect=0.8.27=r41hc72bb7e_0
- r-rstan=2.21.2=r41h03ef668_2
- r-rstanarm=2.21.3=r41h7525677_0
- r-rstantools=2.2.0=r41h7525677_0
- r-rstudioapi=0.13=r41hc72bb7e_0
- r-rvest=1.0.2=r41hc72bb7e_0
- r-sass=0.4.0=r41h03ef668_0
- r-scales=1.1.1=r41hc72bb7e_0
- r-selectr=0.4_2=r41hc72bb7e_1
- r-shape=1.4.6=r41ha770c72_0
- r-shiny=1.7.1=r41h785f33e_0
- r-shinyjs=2.1.0=r41hc72bb7e_0
- r-shinystan=2.6.0=r41hc72bb7e_0
- r-shinythemes=1.2.0=r41hc72bb7e_0
- r-sourcetools=0.1.7=r41h9c3ff4c_1002
- r-spatial=7.3_14=r41hcfec24a_0
- r-squarem=2021.1=r41hc72bb7e_0
- r-stanheaders=2.21.0_7=r41h5ee154c_0
- r-statmod=1.4.37=r41hc3ea6d6_0
- r-stringi=1.7.5=r41hcabe038_0
- r-stringr=1.4.0=r41hc72bb7e_2
- r-survival=3.2_13=r41hcfec24a_0
- r-sys=3.4=r41hcfec24a_0
- r-tensora=0.36.2=r41hcfec24a_0
- r-testthat=3.1.0=r41h03ef668_0
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- send2trash=1.8.0=pyhd8ed1ab_0
- setuptools=58.2.0=py39hf3d152e_0
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- tktable=2.10=hb7b940f_3
- tornado=6.1=py39h3811e60_1
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- tzdata=2021d=he74cb21_0
- wcwidth=0.2.5=pyh9f0ad1d_2
- webencodings=0.5.1=py_1
- wheel=0.37.0=pyhd8ed1ab_1
- xorg-kbproto=1.0.7=h7f98852_1002
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- xorg-libsm=1.2.3=hd9c2040_1000
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- xorg-xproto=7.0.31=h7f98852_1007
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- zipp=3.6.0=pyhd8ed1ab_0
- zlib=1.2.11=h36c2ea0_1013
- zstd=1.5.0=ha95c52a_0
prefix: /home/mrussel2/miniconda3/envs/infection-timing