covid19.tex

% +++
% clean_files = ["%B.aux", "%B.log", "data.csv"]
% clobber_files = ["%B.pdf", "%B.png", "%B-2.png"]
% sequence = ["tex2img"]
%
% [programs.tex2img]
% command = "tex2img"
% opts = [
%   '--latex "lualatex -shell-escape"',
%   "--no-transparent",
%   "--keep-page-size",
% ]
% args = ["%T", "%B.png"]
%
% [programs.latex]
% command = "lualatex"
% opts = ["-shell-escape"]
% +++
\documentclass[12pt,border=4mm]{standalone}

% dependecies
\usepackage{luacode}
\usepackage{download}
\usepackage{pgfplots}

% data file
\def\DataFile{./data.csv}

% download data: always fetch a new one
\begin{luacode}
do
  data_file = '\DataFile'
  if lfs.isfile(data_file) then
    local ok = os.remove(data_file)
    if not ok then
      io.stderr:write('Warning: failed to delete an existing data.')
    end
  end
end
\end{luacode}

\download[\DataFile]{%
  https://stopcovid19.metro.tokyo.lg.jp/data/130001_tokyo_covid19_patients.csv}

% the main logic
\begin{luacode*}
function string.split(str, delim)
  if str:find(delim) == nil then return {str} end

  local res = {}
  local pat = '(.-)' .. delim .. '()'
  local last

  for part, pos in string.gmatch(str, pat) do
    table.insert(res, part)
    last = pos
  end
  table.insert(res, string.sub(str, last))

  return res
end

function table.map(tab, f)
  for k, v in ipairs(tab) do
    tab[k] = f(v)
  end
end

function main()
  -- load the data
  local f = io.open(data_file, 'r')

  local first_date_sig, last_date_sig = 1232, 0
  local nof_patients = {}

  for l in f:lines() do
    local field_date = string.split(l, ',')[5]
    local date = string.split(field_date, '-')
    if #date == 3 then
      local tmp = string.format('%02d/%02d', date[2], date[3])
      if nof_patients[tmp] == nil then
        local tmp_sig = tonumber(date[2]) * 100 + tonumber(date[3])
        if tmp_sig < first_date_sig then first_date_sig = tmp_sig end
        if tmp_sig > last_date_sig then last_date_sig = tmp_sig end
        nof_patients[tmp] = 1
      else
        nof_patients[tmp] = nof_patients[tmp] + 1
      end
    end
  end
  f:close()

  -- make the date list
  local date_list = {}
  do
    first_date_day = first_date_sig % 100
    first_date_month = (first_date_sig - first_date_day) / 100
    last_date_day = last_date_sig % 100
    last_date_month = (last_date_sig - last_date_day) / 100
    local days_of_month = {31, 29, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31}

    local function add_date(m, d)
      table.insert(date_list, string.format('%02d/%02d', m, d))
    end

    local nof_days
    for m=first_date_month,last_date_month do
      nof_days = days_of_month[m]
      if m == first_date_month then
        for d=first_date_day,nof_days do
          add_date(m, d)
        end
      elseif m == last_date_month then
        for d=1,last_date_day do
          add_date(m, d)
        end
      else
        for d=1,nof_days do
          add_date(m, d)
        end
      end
    end
  end

  -- build the data
  local data = {}
  for i, date in ipairs(date_list) do
    local num = nof_patients[date]
    if num ~= nil then
      data[i] = {date, num}
    else
      data[i] = {date, nil}
    end
  end

  return data
end

function print_period(data)
  tex.sprint(string.format('%s--%s', data[1][1], data[#data][1]))
end

function print_coords(data)
  for _, tp in ipairs(data) do
    tex.sprint(tp[1] .. ',')
  end
end

function print_accumulation(data)
  local acc = 0
  for _, tp in ipairs(data) do
    if type(tp[2]) == 'number' then
      acc = acc + tp[2]
      tex.sprint(string.format('(%s, %d)', tp[1], acc))
    end
  end
end

function print_double_in(x, start, data)
  tex.sprint(string.format('(%s, %d)', start, 1))

  local nof_days = 0
  for i, tp in ipairs(data) do
    if tp[1] == start then
      nof_days = #data - i
      break
    end
  end

  tex.sprint(string.format('(%s, %f)', data[#data][1],
                                       2 ^ (nof_days / x)))
end

function print_trajectory(data)
  local total = 0
  local new = 0

  for i, tp in ipairs(data) do
    if i - 8 > 0 then
      local d = data[i - 8][2] or 0
      new = new - d
    end

    if type(tp[2]) == 'number' then
      total = total + tp[2]
      new = new + tp[2]
      tex.sprint(string.format('(%d, %d)', total, new))
    end
  end
end

data = main()
\end{luacode*}

% setup standalone and pgfplots
\standaloneenv{tikzpicture}
\pgfplotsset{compat=1.16}

%<*> \DoubleIn {<x>} {<start date>}
\newcommand{\DoubleIn}[3][]{
  \addplot+ [no markers, #1] coordinates {
    \directlua{print_double_in(#2, '#3', data)}
  };
  \addlegendentry{Double in #2 days};
}

%<*> \TodaysPatients {<date>} {<number of patients>}
\newcommand{\TodaysPatients}[2]{%
  \bgroup\escapechar=-1\relax
  \directlua{data[\string\#data + 1] = {'#1', #2}}%
  \egroup}

\begin{document}

\begin{tikzpicture}
\begin{semilogyaxis}[
  title={%
    Number of COVID-19 patients \& deaths in Tokyo
    (\directlua{print_period(data)})%
  },
  xlabel={Date},
  ylabel={\#Patients},
  enlarge x limits=0,
  height=100mm,
  ymin=1,
  xticklabel style={rotate=90},
  symbolic x coords/.expand once={%
    \directlua{print_coords(data)}
  },
  grid=both,
  major grid style={black!50},
  legend pos=north west,
  axis lines*=left]
\addplot coordinates {
  \directlua{print_accumulation(data)}
};
\addlegendentry{Patients};
\end{semilogyaxis}
\end{tikzpicture}

\begin{tikzpicture}
\begin{loglogaxis}[
  title={%
    Trajectory of COVID-19 confirmed cases in Tokyo
    (\directlua{print_period(data)})%
  },
  xlabel={Total confirmed cases},
  ylabel={New confirmed cases (in a week)},
  enlarge x limits=0,
  height=100mm,
  ymin=1,
  grid=both,
  major grid style={black!50},
  axis lines*=left]
\addplot+ [no markers] coordinates {
  \directlua{print_trajectory(data)}
};
\end{loglogaxis}
\end{tikzpicture}

\end{document}

How to build:

$ lualatex -shell-escape covid19.tex

Latest auto-generated figures (thanks @yy-u):

The source repository of these files is:

• https://github.com/y-yu/covid19.tex