Update Contents to V1.0.1

[ysaito8015]

• [x] at the end of updating, check bookdown build

./data

• data/africa_countries.geo.json
  • it is duplicated of ./data/gis/africa_countries.geo.json and it didn't use in ./new_pages/interactive_plot.Rmd
• data/case_linelists/linelist_cleaned.xlsx
  • updated
• data/country_demographics.csv
  • it is duplicated of ./data/standardization/country_demographics.csv
• data/covid_example_data/
  • added by this commit
• data/covid_incidence.csv
  • it is duplicated of ./data/gis/covid_incidence.csv and it didn't use in ./new_pages/interactive_plot.Rmd
• data/covid_incidence_map.R
  • it is duplicated of ./data/gis/covid_incidence_map.R
• data/district_count_data.xlsx
  • new but didn't use
• data/facility_count_data.rds
  • used in...
    • ./new_pages/data_used.Rmd
    • ./new_pages/ggplot_basics.Rmd
    • ./new_pages/ggplot_basics_old.Rmd
    • ./new_pages/ggplot_tips.Rmd
    • ./new_pages/heatmaps.Rmd
    • ./new_pages/interactive_plots.Rmd
    • ./new_pages/pivoting.Rmd
    • ./new_pages/shiny_basics.Rmd
• data/fluH7N9_China_2013.csv
  • it is duplicated of ./data/case_linelists/fluH7N9_China_2013.csv
• data/linelist_cleaned.rds
  • it is duplicated of ./data/case_linelists/linelist_cleaned.rds
• data/linelist_raw.xlsx
  • the same as before
• data/make_evd_dataset-DESKTOP-JIEUMMI.R
  • ?
• data/make_evd_dataset.R
  • updated

./images/

• images/Applied_Epi_logo.png
  • Added
• images/R_data_structures.png
  • Updated
• images/data_cleaning.png
  • Added
• images/donate_button_long.png
  • Added
• images/donate_buttondefault.png
  • Added
• images/markdown/1_yaml.PNG
  • Added, but didn't use

index.md

• [x] index.Rmd

./new_pages/

• [x] new_pages/basics.Rmd
• [x] new_pages/cleaning.Rmd
• [x] new_pages/combination_analysis.Rmd
• [x] new_pages/dates.Rmd
• [x] new_pages/editorial_style.Rmd
• [x] new_pages/epicurves.Rmd
• [x] new_pages/ggplot_tips.Rmd
• [x] new_pages/gis.Rmd
• [x] new_pages/heatmaps.Rmd
• [x] new_pages/interactive_plots.Rmd
• [x] new_pages/iteration.Rmd
• [x] new_pages/phylogenetic_trees.Rmd
• [x] new_pages/pivoting.Rmd
• [x] new_pages/survey_analysis.Rmd
• [x] new_pages/time_series.Rmd
• [x] new_pages/transmission_chains.Rmd