AvianFluH7N7_2003: Avian influenza (H7N7) epidemic
In phybreak: Analysis of Outbreaks with Sequence Data
Description
Usage
Format
References
Description
DNA sequences (base order randomized) of NA, HA, and PB2 genes of samples taken from farms during the Dutch avian
influenza (H7N7) epidemic in 2003. The dataset contains 241 farms, of which 231 were sampled and sequenced
(for the other 10, identified by the prefix UNK, only the detection day + 2 days is given, as in Klinkenberg
et al (2017)). The labels of the sequences refer to the labels in GISAID (www.gisaid.org), where the
sequences in correct base order can be found.
Usage
1
Format
A list with four elements:
- sequences_HA
the HA gene
- sequences_NA
the NA gene
- sequences_PB2
the PB2 gene
- sampledays
the days at which the samples were taken (or the detection day + 2 days, for the 10
unsampled farms)
References
Bataille et al. (2011) Evolutionary
analysis of inter-farm transmission dynamics in a highly pathogenic avian influenza epidemic.
PLoS Pathog, 7(6): e1002094.
Klinkenberg et al. (2017) Simultaneous
inference of phylogenetic and transmission trees in infectious disease outbreaks.
PLoS Comput Biol, 13(5): e1005495.
phybreak documentation built on May 2, 2019, 3:36 p.m.
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Description Usage Format References
Description
DNA sequences (base order randomized) of NA, HA, and PB2 genes of samples taken from farms during the Dutch avian influenza (H7N7) epidemic in 2003. The dataset contains 241 farms, of which 231 were sampled and sequenced (for the other 10, identified by the prefix UNK, only the detection day + 2 days is given, as in Klinkenberg et al (2017)). The labels of the sequences refer to the labels in GISAID (www.gisaid.org), where the sequences in correct base order can be found.
Usage
1 |
Format
A list with four elements:
- sequences_HA
the HA gene
- sequences_NA
the NA gene
- sequences_PB2
the PB2 gene
- sampledays
the days at which the samples were taken (or the detection day + 2 days, for the 10 unsampled farms)
References
Bataille et al. (2011) Evolutionary analysis of inter-farm transmission dynamics in a highly pathogenic avian influenza epidemic. PLoS Pathog, 7(6): e1002094.
Klinkenberg et al. (2017) Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Comput Biol, 13(5): e1005495.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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