Generates simulated daily incidence data for specified respiratory viruses over a defined number of days. Each virus is modeled using a Gaussian-like curve, parameterized by peak day, amplitude, and scale.
Arguments
- days
Integer. Number of days to simulate (default is 365).
- peaks
Named numeric vector. Peak day for each virus (e.g.,
c("flua"=90,"rsv"=110,"sars_cov2"=160)).- amplitudes
Named numeric vector. Amplitude for each virus's peak (e.g.,
c("flua"=50,"rsv"=40,"sars_cov2"=20)).- scales
Named numeric vector. Scale controlling spread of the peak for each virus (e.g.,
c("flua"=-0.004,"rsv"=-0.005,"sars_cov2"=-0.001)).- time_offset
Integer. Number of days to offset start of the simulation. useful if want to test data with larger values in the middle of a respiratory season.
- noise_sd
numeric or named numeric. Gaussian noise applied to each virus signal. can either be a single value or named for each virus e.g.,
c("flu_a"=2,"rsv"=5,"sars_cov2"=7)- start_date
string
Examples
simulate_data()
#> date flu_a rsv sars_cov2
#> 1 2024-01-07 0 6 0
#> 2 2024-01-08 0 0 1
#> 3 2024-01-09 1 6 0
#> 4 2024-01-10 0 0 2
#> 5 2024-01-11 9 6 0
#> 6 2024-01-12 0 2 2
#> 7 2024-01-13 0 0 0
#> 8 2024-01-14 0 4 4
#> 9 2024-01-15 0 0 1
#> 10 2024-01-16 0 3 3
#> 11 2024-01-17 0 0 2
#> 12 2024-01-18 0 7 3
#> 13 2024-01-19 0 0 9
#> 14 2024-01-20 0 0 0
#> 15 2024-01-21 0 5 0
#> 16 2024-01-22 1 8 0
#> 17 2024-01-23 0 0 2
#> 18 2024-01-24 4 4 0
#> 19 2024-01-25 7 0 0
#> 20 2024-01-26 2 0 0
#> 21 2024-01-27 0 1 2
#> 22 2024-01-28 0 2 0
#> 23 2024-01-29 1 0 0
#> 24 2024-01-30 0 0 0
#> 25 2024-01-31 0 2 0
#> 26 2024-02-01 0 0 3
#> 27 2024-02-02 5 6 10
#> 28 2024-02-03 0 2 0
#> 29 2024-02-04 0 2 0
#> 30 2024-02-05 0 0 0
#> 31 2024-02-06 0 0 9
#> 32 2024-02-07 0 4 5
#> 33 2024-02-08 1 8 3
#> 34 2024-02-09 1 0 0
#> 35 2024-02-10 0 0 1
#> 36 2024-02-11 0 1 0
#> 37 2024-02-12 0 3 1
#> 38 2024-02-13 9 0 0
#> 39 2024-02-14 8 0 0
#> 40 2024-02-15 0 0 0
#> 41 2024-02-16 0 0 0
#> 42 2024-02-17 0 2 0
#> 43 2024-02-18 0 0 3
#> 44 2024-02-19 0 0 0
#> 45 2024-02-20 6 0 4
#> 46 2024-02-21 0 2 2
#> 47 2024-02-22 0 0 0
#> 48 2024-02-23 0 1 0
#> 49 2024-02-24 0 5 10
#> 50 2024-02-25 4 0 10
#> 51 2024-02-26 0 0 2
#> 52 2024-02-27 0 0 6
#> 53 2024-02-28 0 1 0
#> 54 2024-02-29 0 1 5
#> 55 2024-03-01 3 0 0
#> 56 2024-03-02 8 8 3
#> 57 2024-03-03 0 5 3
#> 58 2024-03-04 0 0 0
#> 59 2024-03-05 3 1 0
#> 60 2024-03-06 3 0 0
#> 61 2024-03-07 3 0 0
#> 62 2024-03-08 0 0 6
#> 63 2024-03-09 4 3 0
#> 64 2024-03-10 13 0 0
#> 65 2024-03-11 4 7 2
#> 66 2024-03-12 6 2 1
#> 67 2024-03-13 12 0 0
#> 68 2024-03-14 0 0 4
#> 69 2024-03-15 6 0 1
#> 70 2024-03-16 6 0 0
#> 71 2024-03-17 13 2 4
#> 72 2024-03-18 18 0 0
#> 73 2024-03-19 12 8 0
#> 74 2024-03-20 18 0 0
#> 75 2024-03-21 13 1 0
#> 76 2024-03-22 17 0 0
#> 77 2024-03-23 26 0 4
#> 78 2024-03-24 28 1 0
#> 79 2024-03-25 28 0 0
#> 80 2024-03-26 31 1 0
#> 81 2024-03-27 34 4 3
#> 82 2024-03-28 28 0 0
#> 83 2024-03-29 40 3 7
#> 84 2024-03-30 54 0 0
#> 85 2024-03-31 40 1 0
#> 86 2024-04-01 44 5 0
#> 87 2024-04-02 41 8 1
#> 88 2024-04-03 48 2 0
#> 89 2024-04-04 38 1 0
#> 90 2024-04-05 50 3 0
#> 91 2024-04-06 54 7 0
#> 92 2024-04-07 50 6 4
#> 93 2024-04-08 45 14 0
#> 94 2024-04-09 42 4 5
#> 95 2024-04-10 44 12 2
#> 96 2024-04-11 41 12 0
#> 97 2024-04-12 47 7 0
#> 98 2024-04-13 42 17 0
#> 99 2024-04-14 26 19 2
#> 100 2024-04-15 33 22 3
#> 101 2024-04-16 34 16 2
#> 102 2024-04-17 33 28 0
#> 103 2024-04-18 29 31 0
#> 104 2024-04-19 23 33 2
#> 105 2024-04-20 27 23 1
#> 106 2024-04-21 20 36 0
#> 107 2024-04-22 13 39 0
#> 108 2024-04-23 19 46 0
#> 109 2024-04-24 10 28 0
#> 110 2024-04-25 6 36 3
#> 111 2024-04-26 15 33 0
#> 112 2024-04-27 12 37 4
#> 113 2024-04-28 6 34 9
#> 114 2024-04-29 3 44 5
#> 115 2024-04-30 7 40 0
#> 116 2024-05-01 5 39 6
#> 117 2024-05-02 0 31 3
#> 118 2024-05-03 2 24 5
#> 119 2024-05-04 6 24 2
#> 120 2024-05-05 6 26 9
#> 121 2024-05-06 0 32 7
#> 122 2024-05-07 0 15 5
#> 123 2024-05-08 7 20 8
#> 124 2024-05-09 0 25 1
#> 125 2024-05-10 0 12 7
#> 126 2024-05-11 4 7 7
#> 127 2024-05-12 0 14 11
#> 128 2024-05-13 4 23 11
#> 129 2024-05-14 2 2 14
#> 130 2024-05-15 0 6 8
#> 131 2024-05-16 0 12 10
#> 132 2024-05-17 0 0 8
#> 133 2024-05-18 0 9 15
#> 134 2024-05-19 0 12 4
#> 135 2024-05-20 0 8 5
#> 136 2024-05-21 1 0 0
#> 137 2024-05-22 1 3 14
#> 138 2024-05-23 3 0 10
#> 139 2024-05-24 0 0 4
#> 140 2024-05-25 1 1 11
#> 141 2024-05-26 4 8 1
#> 142 2024-05-27 0 0 8
#> 143 2024-05-28 2 0 16
#> 144 2024-05-29 0 0 19
#> 145 2024-05-30 0 6 14
#> 146 2024-05-31 0 0 14
#> 147 2024-06-01 0 0 10
#> 148 2024-06-02 0 2 16
#> 149 2024-06-03 9 5 24
#> 150 2024-06-04 4 8 17
#> 151 2024-06-05 5 3 16
#> 152 2024-06-06 6 1 20
#> 153 2024-06-07 2 0 11
#> 154 2024-06-08 0 0 11
#> 155 2024-06-09 2 0 18
#> 156 2024-06-10 4 1 15
#> 157 2024-06-11 1 6 24
#> 158 2024-06-12 3 8 22
#> 159 2024-06-13 2 1 17
#> 160 2024-06-14 0 1 17
#> 161 2024-06-15 0 0 26
#> 162 2024-06-16 0 6 22
#> 163 2024-06-17 0 7 11
#> 164 2024-06-18 9 0 28
#> 165 2024-06-19 0 0 16
#> 166 2024-06-20 2 7 20
#> 167 2024-06-21 4 2 20
#> 168 2024-06-22 5 3 22
#> 169 2024-06-23 5 4 13
#> 170 2024-06-24 2 12 21
#> 171 2024-06-25 1 0 10
#> 172 2024-06-26 0 0 21
#> 173 2024-06-27 0 0 15
#> 174 2024-06-28 3 5 9
#> 175 2024-06-29 2 0 10
#> 176 2024-06-30 0 0 20
#> 177 2024-07-01 0 0 18
#> 178 2024-07-02 0 0 15
#> 179 2024-07-03 1 6 13
#> 180 2024-07-04 7 0 17
#> 181 2024-07-05 7 2 10
#> 182 2024-07-06 0 10 12
#> 183 2024-07-07 13 13 6
#> 184 2024-07-08 0 0 9
#> 185 2024-07-09 8 2 10
#> 186 2024-07-10 0 0 4
#> 187 2024-07-11 2 0 7
#> 188 2024-07-12 0 0 12
#> 189 2024-07-13 1 3 1
#> 190 2024-07-14 0 0 10
#> 191 2024-07-15 4 0 8
#> 192 2024-07-16 0 0 8
#> 193 2024-07-17 4 4 12
#> 194 2024-07-18 3 7 0
#> 195 2024-07-19 2 0 8
#> 196 2024-07-20 3 1 3
#> 197 2024-07-21 0 0 3
#> 198 2024-07-22 3 0 6
#> 199 2024-07-23 0 0 0
#> 200 2024-07-24 0 3 0
#> 201 2024-07-25 3 0 7
#> 202 2024-07-26 0 6 3
#> 203 2024-07-27 0 1 0
#> 204 2024-07-28 1 0 5
#> 205 2024-07-29 4 0 6
#> 206 2024-07-30 0 0 11
#> 207 2024-07-31 2 0 3
#> 208 2024-08-01 0 0 3
#> 209 2024-08-02 0 0 0
#> 210 2024-08-03 1 0 0
#> 211 2024-08-04 2 0 3
#> 212 2024-08-05 1 0 8
#> 213 2024-08-06 0 0 0
#> 214 2024-08-07 0 1 4
#> 215 2024-08-08 4 8 0
#> 216 2024-08-09 0 0 0
#> 217 2024-08-10 0 3 0
#> 218 2024-08-11 0 0 0
#> 219 2024-08-12 1 3 0
#> 220 2024-08-13 0 2 2
#> 221 2024-08-14 0 0 3
#> 222 2024-08-15 0 0 2
#> 223 2024-08-16 0 0 0
#> 224 2024-08-17 0 13 0
#> 225 2024-08-18 4 0 2
#> 226 2024-08-19 11 0 0
#> 227 2024-08-20 4 2 0
#> 228 2024-08-21 0 1 5
#> 229 2024-08-22 0 1 0
#> 230 2024-08-23 0 6 0
#> 231 2024-08-24 2 0 2
#> 232 2024-08-25 0 0 0
#> 233 2024-08-26 0 0 4
#> 234 2024-08-27 1 0 0
#> 235 2024-08-28 1 4 0
#> 236 2024-08-29 0 0 0
#> 237 2024-08-30 0 0 0
#> 238 2024-08-31 0 0 4
#> 239 2024-09-01 0 4 0
#> 240 2024-09-02 3 2 3
#> 241 2024-09-03 0 0 4
#> 242 2024-09-04 5 0 0
#> 243 2024-09-05 0 0 0
#> 244 2024-09-06 1 8 0
#> 245 2024-09-07 5 0 2
#> 246 2024-09-08 0 4 0
#> 247 2024-09-09 0 4 0
#> 248 2024-09-10 0 0 4
#> 249 2024-09-11 2 4 0
#> 250 2024-09-12 0 10 0
#> 251 2024-09-13 1 1 0
#> 252 2024-09-14 3 3 0
#> 253 2024-09-15 10 0 1
#> 254 2024-09-16 0 0 0
#> 255 2024-09-17 0 5 6
#> 256 2024-09-18 0 8 2
#> 257 2024-09-19 0 11 9
#> 258 2024-09-20 0 0 0
#> 259 2024-09-21 4 0 9
#> 260 2024-09-22 0 0 0
#> 261 2024-09-23 0 0 0
#> 262 2024-09-24 0 5 0
#> 263 2024-09-25 0 1 3
#> 264 2024-09-26 3 0 1
#> 265 2024-09-27 4 0 0
#> 266 2024-09-28 2 1 0
#> 267 2024-09-29 0 3 6
#> 268 2024-09-30 0 0 0
#> 269 2024-10-01 1 0 6
#> 270 2024-10-02 4 2 4
#> 271 2024-10-03 7 0 5
#> 272 2024-10-04 0 0 0
#> 273 2024-10-05 2 0 0
#> 274 2024-10-06 0 4 0
#> 275 2024-10-07 0 5 0
#> 276 2024-10-08 0 3 3
#> 277 2024-10-09 0 0 0
#> 278 2024-10-10 3 0 0
#> 279 2024-10-11 0 0 0
#> 280 2024-10-12 4 2 0
#> 281 2024-10-13 7 8 3
#> 282 2024-10-14 4 0 0
#> 283 2024-10-15 5 8 0
#> 284 2024-10-16 0 5 1
#> 285 2024-10-17 0 0 9
#> 286 2024-10-18 0 10 1
#> 287 2024-10-19 6 0 0
#> 288 2024-10-20 0 0 0
#> 289 2024-10-21 0 0 5
#> 290 2024-10-22 1 0 0
#> 291 2024-10-23 1 10 0
#> 292 2024-10-24 6 0 8
#> 293 2024-10-25 10 0 3
#> 294 2024-10-26 0 0 0
#> 295 2024-10-27 0 0 0
#> 296 2024-10-28 0 6 5
#> 297 2024-10-29 0 0 0
#> 298 2024-10-30 0 1 0
#> 299 2024-10-31 0 0 7
#> 300 2024-11-01 0 0 0
#> 301 2024-11-02 0 6 1
#> 302 2024-11-03 0 2 0
#> 303 2024-11-04 4 0 6
#> 304 2024-11-05 0 0 0
#> 305 2024-11-06 15 3 0
#> 306 2024-11-07 0 3 0
#> 307 2024-11-08 0 0 0
#> 308 2024-11-09 0 6 3
#> 309 2024-11-10 0 0 0
#> 310 2024-11-11 0 3 9
#> 311 2024-11-12 5 1 8
#> 312 2024-11-13 0 0 0
#> 313 2024-11-14 0 5 0
#> 314 2024-11-15 0 0 0
#> 315 2024-11-16 13 0 0
#> 316 2024-11-17 0 2 0
#> 317 2024-11-18 0 0 1
#> 318 2024-11-19 1 0 0
#> 319 2024-11-20 4 8 3
#> 320 2024-11-21 0 4 5
#> 321 2024-11-22 0 0 0
#> 322 2024-11-23 0 0 0
#> 323 2024-11-24 0 0 0
#> 324 2024-11-25 10 0 0
#> 325 2024-11-26 0 0 0
#> 326 2024-11-27 2 1 0
#> 327 2024-11-28 0 0 0
#> 328 2024-11-29 10 6 0
#> 329 2024-11-30 6 0 6
#> 330 2024-12-01 3 0 0
#> 331 2024-12-02 0 0 3
#> 332 2024-12-03 0 0 0
#> 333 2024-12-04 0 0 5
#> 334 2024-12-05 0 6 0
#> 335 2024-12-06 6 1 5
#> 336 2024-12-07 12 0 0
#> 337 2024-12-08 0 2 3
#> 338 2024-12-09 0 4 8
#> 339 2024-12-10 6 0 0
#> 340 2024-12-11 0 0 0
#> 341 2024-12-12 0 0 5
#> 342 2024-12-13 5 0 3
#> 343 2024-12-14 8 0 6
#> 344 2024-12-15 1 4 0
#> 345 2024-12-16 0 0 0
#> 346 2024-12-17 5 0 6
#> 347 2024-12-18 0 0 3
#> 348 2024-12-19 0 0 7
#> 349 2024-12-20 1 5 0
#> 350 2024-12-21 0 0 0
#> 351 2024-12-22 0 7 2
#> 352 2024-12-23 2 2 0
#> 353 2024-12-24 0 0 3
#> 354 2024-12-25 10 0 5
#> 355 2024-12-26 0 2 0
#> 356 2024-12-27 0 3 0
#> 357 2024-12-28 0 0 0
#> 358 2024-12-29 0 8 0
#> 359 2024-12-30 0 1 0
#> 360 2024-12-31 0 0 0
#> 361 2025-01-01 0 11 7
#> 362 2025-01-02 0 5 0
#> 363 2025-01-03 5 1 7
#> 364 2025-01-04 2 0 5
#> 365 2025-01-05 10 0 4
#> 366 2025-01-06 1 4 0
simulate_data(days = 100, peaks = c(flu_a = 30), amplitudes = c(flu_a = 60),
scales = c(flu_a = -0.01), noise_sd = c(flu_a = 5))
#> date flu_a
#> 1 2024-01-07 0
#> 2 2024-01-08 0
#> 3 2024-01-09 0
#> 4 2024-01-10 0
#> 5 2024-01-11 4
#> 6 2024-01-12 4
#> 7 2024-01-13 0
#> 8 2024-01-14 0
#> 9 2024-01-15 0
#> 10 2024-01-16 0
#> 11 2024-01-17 2
#> 12 2024-01-18 6
#> 13 2024-01-19 0
#> 14 2024-01-20 11
#> 15 2024-01-21 7
#> 16 2024-01-22 3
#> 17 2024-01-23 12
#> 18 2024-01-24 12
#> 19 2024-01-25 18
#> 20 2024-01-26 24
#> 21 2024-01-27 17
#> 22 2024-01-28 22
#> 23 2024-01-29 37
#> 24 2024-01-30 29
#> 25 2024-01-31 34
#> 26 2024-02-01 38
#> 27 2024-02-02 48
#> 28 2024-02-03 52
#> 29 2024-02-04 55
#> 30 2024-02-05 51
#> 31 2024-02-06 64
#> 32 2024-02-07 58
#> 33 2024-02-08 55
#> 34 2024-02-09 56
#> 35 2024-02-10 50
#> 36 2024-02-11 44
#> 37 2024-02-12 34
#> 38 2024-02-13 36
#> 39 2024-02-14 36
#> 40 2024-02-15 28
#> 41 2024-02-16 21
#> 42 2024-02-17 25
#> 43 2024-02-18 19
#> 44 2024-02-19 10
#> 45 2024-02-20 9
#> 46 2024-02-21 0
#> 47 2024-02-22 1
#> 48 2024-02-23 0
#> 49 2024-02-24 4
#> 50 2024-02-25 0
#> 51 2024-02-26 0
#> 52 2024-02-27 0
#> 53 2024-02-28 0
#> 54 2024-02-29 0
#> 55 2024-03-01 0
#> 56 2024-03-02 2
#> 57 2024-03-03 0
#> 58 2024-03-04 6
#> 59 2024-03-05 0
#> 60 2024-03-06 9
#> 61 2024-03-07 1
#> 62 2024-03-08 0
#> 63 2024-03-09 0
#> 64 2024-03-10 0
#> 65 2024-03-11 0
#> 66 2024-03-12 7
#> 67 2024-03-13 2
#> 68 2024-03-14 0
#> 69 2024-03-15 2
#> 70 2024-03-16 0
#> 71 2024-03-17 1
#> 72 2024-03-18 0
#> 73 2024-03-19 0
#> 74 2024-03-20 8
#> 75 2024-03-21 0
#> 76 2024-03-22 8
#> 77 2024-03-23 0
#> 78 2024-03-24 3
#> 79 2024-03-25 3
#> 80 2024-03-26 7
#> 81 2024-03-27 0
#> 82 2024-03-28 0
#> 83 2024-03-29 15
#> 84 2024-03-30 8
#> 85 2024-03-31 5
#> 86 2024-04-01 0
#> 87 2024-04-02 1
#> 88 2024-04-03 0
#> 89 2024-04-04 3
#> 90 2024-04-05 0
#> 91 2024-04-06 5
#> 92 2024-04-07 0
#> 93 2024-04-08 0
#> 94 2024-04-09 4
#> 95 2024-04-10 0
#> 96 2024-04-11 0
#> 97 2024-04-12 0
#> 98 2024-04-13 0
#> 99 2024-04-14 0
#> 100 2024-04-15 0
#> 101 2024-04-16 1