17b1c3a4f6107bb37c9bc5d430975a6c *DESCRIPTION
b234ee4d69f5fce4486a80fdaf4a4263 *LICENSE
20c1ae443f7f925c4d6913a6547e8d2a *NAMESPACE
cc1a0f1bfc3698af747506a2f66d8cb2 *R/Class-Host.R
3c46e50504c0f49ff3898c7e4ba073bc *R/Class-ViralPop.R
4f10280d0b9b14fddbae03e2bcb814b1 *R/Methods-Host.R
ffc2a8d46963fa580a8581ede13a948d *R/Methods-ViralPop.R
22935407eadadea2965ef5176d5dcf5b *R/Methods-time.R
5cac700152f9138e9b2df858f7115a10 *R/SMITIDstruct.R
b89719d047d8f6b2cf294bbfe295a04b *R/demo.R
02603ec6962120c7f55a61011686ba7c *R/diversity.R
832652da02595cfb7b5b32502403280a *R/index.R
95c443354b9ae7f85b848655b341e62c *inst/extdata/data-simul/104_4.fasta
b438613cf3440a75cc524697d7801838 *inst/extdata/data-simul/104_5.fasta
548c9e3bbb01de97b1530c2c6de17ce1 *inst/extdata/data-simul/104_6.fasta
81d5c05737ce2ed6b925ea8baeb5393a *inst/extdata/data-simul/105_9.fasta
2cf65d6385411a6744717eea2fbdf766 *inst/extdata/data-simul/106_15.fasta
feea2cf10e4bbaccbf7eb9cdab80cb13 *inst/extdata/data-simul/108_10.fasta
d755b1e4764c2d8a426f9e0c135bc5f3 *inst/extdata/data-simul/108_9.fasta
98b2be427f1dc3ef7128fc22880754f5 *inst/extdata/data-simul/109_7.fasta
6a06150a26b033c54917cc5655a95a13 *inst/extdata/data-simul/109_8.fasta
7f780f17cefdbd92881263c35f1cb873 *inst/extdata/data-simul/111_7.fasta
08c00ef360298d86b7229c6d8cc13f2d *inst/extdata/data-simul/111_8.fasta
f5e56e8601064ddb9677b2cfa7a3c2bb *inst/extdata/data-simul/112_12.fasta
bec6011a4679869d5ef3a5896e20dc2d *inst/extdata/data-simul/112_15.fasta
5f2b0e1047f9604459635910e8e2eff2 *inst/extdata/data-simul/113_2.fasta
19a02dc071037a58112ef3eccfbd9c90 *inst/extdata/data-simul/113_3.fasta
8b8014da4f7e6152ed495c47eac26138 *inst/extdata/data-simul/113_4.fasta
1070e7fd3232a573fdc0abb210f8a8a5 *inst/extdata/data-simul/115_2.fasta
8c5baafeeb5ca0d464bebc2853e7d0e4 *inst/extdata/data-simul/115_3.fasta
c9c47bbe38c0092fafd805d963a05951 *inst/extdata/data-simul/115_4.fasta
0942aa5fbf3e3779193333e4433f7222 *inst/extdata/data-simul/116_5.fasta
ac9eeaf974e598a64595dd0b318a0bca *inst/extdata/data-simul/116_6.fasta
309bb44e93106165d0e8f74a72bb53bb *inst/extdata/data-simul/hosts_coords.txt
7f74ac2dba42a01a5e5b27f298570326 *inst/extdata/data-simul/obs.txt
cf6788612b80630533045f7d292ec2ef *inst/extdata/data-simul/tree.txt
8a5e429a9198f5f7bde597dc03ad0c23 *man/Host.Rd
ae4c8849641caef1d1baad762904cd87 *man/SMITIDstruct-package.Rd
a21b882c2959ad68ef7f4694ec0b2ab7 *man/ViralPop-class.Rd
323ed1e023926f8e7e0de93a82182f5c *man/addHost.Rd
f7f3591ac30d7b24bcbb866952b56ae7 *man/addIndex.Rd
76899d8b71e5ca06062188dbb8318b48 *man/addViralObs.Rd
5a242d70427c2bf76a77945947d97d91 *man/addcode.Rd
657e96b7384c3198b2cb12a67737e0db *man/alleleCount.Rd
c4505883259788a5fb2fb3a12e61f1f4 *man/concatViralPop.Rd
da63db7d772f4e178c3f602eb5c346f0 *man/createAViralPop.Rd
7c19d951d64117a0f4600943a78a8dae *man/createHost.Rd
0412268ef0ae54e56a6dd056dcf65c8a *man/createIndex.Rd
ca1a8c33d757fc8de97613c54c8a7057 *man/demo.SMITIDstruct.run.Rd
3edf76778c269d58232b7c654a063b99 *man/diversity.pDistance.Rd
33ea88fdde5aba4e343c4beddaa7c03c *man/diversity.sfs.Rd
bfcb5c37bf3ad4ab40d7e08d7e832aca *man/getCov.Rd
34221858c7eb67b6831b6c7b6a70d6d1 *man/getDate.Rd
22c4176df99553d9821f436a75688fc6 *man/getDiversity.pDistance.Rd
0196a9ec99bff240ff78f1ea9ecc18d0 *man/getDiversity.sfs.Rd
7b4aa092b82dec5adc18d41d1ef0eeed *man/getInfosByHostAndTime.Rd
eeda2f9be4c890abe3bebf11c8b5efc1 *man/getStates.Rd
19fcdb04c29e77f20534b1066d2b9ad6 *man/getTimeLine.Rd
5121f86eed1f089e2386b0c38c533ba6 *man/getTimestamp.Rd
c9a71c7dfb9b2304ca213f3dbce3bd42 *man/getTransmissionTree.Rd
3fd5f99c755f40822a6bf1074db6dfbd *man/is.StringDate.Rd
5e79464938bc0a06938af7696a971d54 *man/is.juliendate.Rd
bf5c372032c651f183fce657e3043af4 *man/is.timestamp.Rd
2552599b0c5a5e8fa847897a69f67913 *man/isInCode.Rd
c1c5cf3a8ec1bae7e033baa0d3d410aa *man/loadCoords.Rd
dc004585c1d72709d12e54fad4bb18e3 *man/loadCovs.Rd
8e5693416ac4ded731e6606dc6eadfdd *man/loadHost.Rd
5feccdc946980aab391e69e635bef510 *man/loadStates.Rd
b08f4cf0bd93125c810a8e3e86f69397 *man/loadTree.Rd
65f63ad06ce7d31fd568b84b40f9651c *man/loadTreeDF.Rd
4fe3202215a4a73503f552aed940f008 *man/loadViralObs.Rd
4dcb937a0d4954a934a78644c3716358 *man/loadViralPop.Rd
b5e788d2ed07d36cc3d5749f284b5cfb *man/loadViralPopSet.Rd
f247b11c0f3d77397506ac8858ddde72 *man/mergeCode.Rd
3dbcb3915f92fa16bf6b4db7c01a6651 *man/plotDiversity.pDistance.Rd
db2da999fa489935dc7f6ead19d765dc *man/plotDiversity.sfs.Rd
4bb4441fcd6004d5d84d8b273b9d148a *man/setStates.Rd
9d3b8c3f36c6ba9debfd509acbe59233 *man/simulateStates.Rd
88848932e8473f9682648611146fe5f6 *tests/testthat.R
d31d8e681f9e9d4ef30442fc7db7f18b *tests/testthat/test-time.R
