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‎workflows/working_example/config/config.yaml‎

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input_namespace: null
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output_namespace: out
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params:
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path: "data.csv"
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out: "out.csv"

‎workflows/working_example/epiestim_estimate_r.input.schema.yaml‎

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fields:
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- name: dates
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type: date
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- name: I
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type: integer

‎workflows/working_example/epiestim_estimate_r.output.schema.yaml‎

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fields:
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- name: t_start
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type: integer
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- name: t_end
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type: integer
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- name: Mean(R)
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type: number
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- name: Std(R)
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type: number
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- name: Quantile.0.025(R)
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type: number
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- name: Quantile.0.05(R)
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type: number
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- name: Quantile.0.25(R)
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type: number
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- name: Median(R)
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type: number
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- name: Quantile.0.75(R)
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type: number
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- name: Quantile.0.95(R)
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type: number
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- name: Quantile.0.975(R)
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type: number

‎workflows/working_example/epiestim_incidence.csv‎

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"dates","I"
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2009-04-27,1
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2009-04-28,1
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2009-04-29,0
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2009-04-30,2
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2009-05-01,5
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2009-05-04,3
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2009-05-22,0
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2009-05-23,0
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2009-05-24,0
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2009-05-25,2
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2009-05-26,0
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2009-05-27,2
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2009-05-28,0

‎workflows/working_example/epinow2_reported_cases.csv‎

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"date","confirm"
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2020-02-22,14
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2020-02-23,62
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2020-02-24,53
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‎workflows/working_example/out.csv‎

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dates,I
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2020-02-22,14
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2020-02-25,97
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‎workflows/working_example/output.csv‎

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"t_start","t_end","Mean(R)","Std(R)","Quantile.0.025(R)","Quantile.0.05(R)","Quantile.0.25(R)","Median(R)","Quantile.0.75(R)","Quantile.0.95(R)","Quantile.0.975(R)"
2+
2,8,2.24150921524098,0.0759070801626508,2.09518352956806,2.11813155565786,2.18985435170575,2.2406524274645,2.29223009644538,2.3678094697857,2.39270388467396
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3,9,1.86352323714699,0.0575095756447964,1.75249683361836,1.76994808771344,1.82441790328051,1.8629316758682,1.90198370850029,1.95911626348778,1.97791139421853
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7,13,1.63490775656697,0.0315222431202462,1.57370294831855,1.58340610035917,1.61353734222148,1.63470517023047,1.656057327984,1.68710045370823,1.69726384087048
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8,14,1.58884954264117,0.0280477427028148,1.53434742665519,1.54299830610413,1.56984274398435,1.58868450470634,1.60767643028723,1.63526373882758,1.64428955192381
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9,15,1.52405862535008,0.0248910921682078,1.47565915588075,1.48334883631668,1.50719679414159,1.52392311947894,1.54077273885901,1.56523063732639,1.57322816092841
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10,16,1.61594180562792,0.0234317536989426,1.57033906789541,1.57759412872001,1.60007620124791,1.61582855067491,1.6316839483211,1.65467580544493,1.66218816022022
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32,38,0.991588935459849,0.00505019578917344,0.981715117626536,0.983296750939276,0.988177973077257,0.991580361867374,0.994990551542201,0.999910365253406,1.00151147629711
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33,39,0.974079421936965,0.00500926262404248,0.964285869412895,0.965854589295851,0.970696061537542,0.974070835137933,0.977453421639442,0.98233354489986,0.983921772516425
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35,41,0.95458141914833,0.00501793100186796,0.944771462587645,0.946342680410886,0.951192100632754,0.954572626606802,0.957961152681888,0.962850150013369,0.964441342980922
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36,42,0.932933167042165,0.0050079590128277,0.923143234420733,0.924711118925198,0.929550483487021,0.932924206196403,0.936306082142668,0.941185781387369,0.942774023393514
37+
37,43,0.916499524969295,0.0050201256502425,0.906686329902359,0.908257815474985,0.913108524151223,0.916490359073751,0.919880533802821,0.924772500134765,0.926364809045963
38+
38,44,0.912200412819561,0.00508657546850865,0.902257799861916,0.903849896811598,0.908764435896179,0.9121909583174,0.915626083140976,0.920583178961274,0.922196754913211
39+
39,45,0.917663607057938,0.00519025890019086,0.907518719502348,0.909143112651982,0.914157517403484,0.91765382179597,0.921159029540668,0.926217479848431,0.927864103428911
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40,46,0.935231938152645,0.00532820012582989,0.924817639064073,0.926485120468016,0.931632627722277,0.93522181957107,0.93882021805093,0.944013271204229,0.945703740283365
41+
41,47,0.930270139492449,0.00538936237392633,0.919736786720691,0.921423213066601,0.92662941928466,0.930259732060673,0.933899514285246,0.939152566578758,0.940862636816754
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42,48,0.924608464638303,0.0054436786882541,0.91396943902503,0.915672667844807,0.920930959232306,0.924597781349855,0.928274323911,0.933580703063719,0.935308202473368
43+
43,49,0.936570682516146,0.00555899277582318,0.925706542048387,0.927445749765927,0.932815228061003,0.936559684116437,0.940314147327087,0.945733131770482,0.947497325955804
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44,50,0.940694329278112,0.00564688843216319,0.92965877251528,0.931425335566758,0.936879427085563,0.940683030077837,0.944496913916101,0.950001865550805,0.951794098436273
45+
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46+
46,52,0.969557089024138,0.0058555991677663,0.958113857914338,0.95994563267617,0.965601148288287,0.96954530083484,0.973500179145804,0.9792087559179,0.981067311411968
47+
47,53,0.966191759551539,0.00588332521779059,0.954694622892835,0.956534960343083,0.96221703485506,0.966179818016048,0.970153466467314,0.97588929238321,0.977756758941144
48+
48,54,0.975873708001942,0.00594967525296217,0.964246953548765,0.966108028608617,0.971854149659711,0.97586161676604,0.979880085371158,0.985680631659713,0.987569175920649
49+
49,55,0.943812621090132,0.00588345088498595,0.932316045971148,0.93415610104905,0.939837658299122,0.943800395882913,0.947774256863016,0.953510842383917,0.955378671020763
50+
50,56,0.944050351016111,0.0059333178537992,0.932456621874306,0.934312157846479,0.940041642441267,0.944037920825175,0.948045509114923,0.953830944656001,0.955714719873998
51+
51,57,0.948502480341031,0.00601596608240287,0.936747585353223,0.938628836860723,0.944437869948741,0.948489761428016,0.952553225514042,0.958419509148068,0.960329655827235
52+
52,58,0.921418613257084,0.0059909473766279,0.909713509468589,0.911586576372965,0.917370734564399,0.921405629162038,0.925452337649314,0.931294940027545,0.933197504548943
53+
53,59,0.90439072399206,0.00601458709498585,0.892640281256497,0.894520401081982,0.900326711852313,0.904377390830426,0.908440201305438,0.914306527485671,0.916216937944726
54+
54,60,0.900300929926303,0.00610981109143928,0.888365240940949,0.890274812850502,0.896172426056688,0.90028710873665,0.904414366958158,0.910374192292452,0.912315163548433

‎workflows/working_example/workflow/Snakefile‎

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# Load configuration from config.yaml
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configfile: "config/config.yaml"
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# Rule to run the R script with the path parameter
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rule run_r_script:
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input:
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script = "epiestim_estimate_r.R"
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params:
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path = config["path"]
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out = config["out"]
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shell:
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"""
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Rscript {input.script} --path={params.path} > {params.out}
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"""

‎workflows/working_example/workflow/epiestim_estimate_r.R‎

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# Example of using the EpiEstim package to estimate the effective reproduction number R parametrically
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if (!require(EpiEstim)) { install.packages('EpiEstim') }
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if (!require(ggplot2)) { install.packages('ggplot2') }
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if (!require(incidence)) { install.packages('incidence') }
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# get command line args
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args <- commandArgs(trailingOnly = TRUE)
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# print args
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# print(args)
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# check if the file argument is provided
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if (length(args) == 0) {
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stop("No file argument provided. Usage: Rscript using_epiestim.R <file>")
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}
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# read the file path
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file_path <- args[1]
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# function to do the analysis
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parametric_estimation_of_R <- function(file_path) {
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# notify the user
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print(cat("Carrying out analysis using file '", file_path, "'..."))
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data <- read.csv(file_path, colClasses=c("Date", "numeric"))
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res_parametric_si <- estimate_R(
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data,
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method="parametric_si",
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config = make_config(list(
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mean_si = 2.6,
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std_si = 1.5))
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)
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# png("output_plot.png")
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quartz() # macOS
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# x11() # linux
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# windows() # windows
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# plot(res_parametric_si, legend = FALSE)
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# Sys.sleep(10) # goes together with quartz/x11/windows
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# dev.off() # goes together with png(...)
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write.csv(res_parametric_si$R, "output.csv", row.names=FALSE)
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}
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# load the file
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if (file.exists(file_path)) {
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parametric_estimation_of_R(file_path)
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} else {
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stop("File does not exist.")
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}

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