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bacteria_graph_1

Ilya 1/30/2019

install and load required packages

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1. Get bacteria-caused dx in GIDEON

2. Match dx to pathogen spp. names

3. Match spp. names (from GIDEON zdx and GMPD) to traits (in GMPD & other)

4. Compile master list of bacteria spp & traits

5. Feature construction with bacterial traits

6. Data visualization: summary “state of knowledge” on bacteria causing disease in mammals or humans

7. Use traits to predict transmissibility and human disease outcomes

  1. Data visualization: summary “state of knowledge” on bacteria causing disease in mammals or humans

Processing data

load bacteria_pathogenic_mammals.Rdata and make graph of bacteria order vs. host order

source("R_graph_pathogen_order_host_order1.R")
plot

make graph of histogram of number of hosts per bacteria, across zoonotic categories (human only, zoonotic, wild only)

source("R_bacteria_host_species_hist_graph1.R")
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## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

plot
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.