Canal Endémico en Rstudio

library("ggthemes")
library(ggplot2)
library(foreign)
library(sqldf) 

## Loading required package: gsubfn

## Loading required package: proto

## Loading required package: RSQLite

Dataset <- read.dbf("D:/descarga/Base Puente Piedra/Base Puente Piedra/ira_sp.DBF",T) 

## Field name: '
' changed to: 'X.'

## Field name: '' changed to: 'X'

## Field name: '' changed to: 'X.1'

## Field name: '' changed to: 'X.2'

## Field name: '' changed to: 'X.3'

## Field name: '' changed to: 'X.4'

## Field name: '' changed to: 'X.5'

## Field name: '' changed to: 'X.6'

head(Dataset) 

##    ANO SEMANA SUB_REG_NT RED MICRORED    E_SALUD UBIGEO IRA_M2 IRA_2_11
## 1 2007      1         40  16       00 150113D104 150125      0        0
## 2 2007     20         40  16       00 150113D104 150102      0        0
## 3 2007      1         40  17       00 150115A101 150125      0        0
## 4 2007      1         40  17       00 150115A101 150102      0        2
## 5 2007      1         40  11       00 150101A109 150102      0        0
## 6 2007      1         40  11       00 150101A109 150125      2        0
##   IRA_1_4A NEU_2_11 NEU_1_4A HOS_M2 HOS_2_11 HOS_1_4A NGR_M2 NGR_2_11 NGR_1_4A
## 1        3        0        0      0        0        0      0        0        0
## 2        2        0        0      0        0        0      0        0        0
## 3        2        0        0      0        0        0      0        0        0
## 4        0        0        0      0        0        0      0        0        0
## 5        1        0        0      0        0        0      0        0        0
## 6        0        0        0      0        1        0      0        1        0
##   DIH_M2 DIH_2_11 DIH_1_4A DEH_M2 DEH_2_11 DEH_1_4A SOB_2A SOB_2_4A  FECHA_ING
## 1      0        0        0      0        0        0      0        1 2007-01-08
## 2      0        0        0      0        0        0      1        1 2007-05-22
## 3      0        0        0      0        0        0      3        1 2007-01-08
## 4      0        0        0      0        0        0      6        0 2007-01-08
## 5      0        0        0      0        0        0      0        0 2007-01-08
## 6      0        0        0      0        0        0      4        0 2007-01-08
##                    CLAVE MIGRADO VERIFICA ETAPA IRA_5_9A IRA_60A NEU_5_9A
## 1 200701150113D104150125       N        P  <NA>        0       0        0
## 2 200720150113D104150102       N        P  <NA>        0       0        0
## 3 200701150115A101150125       N        P  <NA>        0       0        0
## 4 200701150115A101150102       N        P  <NA>        0       0        0
## 5 200701150101A109150102       N        P  <NA>        0       0        0
## 6 200701150101A109150125       N        P  <NA>        0       0        0
##   NEU_60A HOS_5_9A HOS_60A NGR_5_9A NGR_60A DIH_5_9A DIH_60A DEH_5_9A DEH_60A
## 1       0        0       0        0       0        0       0        0       0
## 2       0        0       0        0       0        0       0        0       0
## 3       0        0       0        0       0        0       0        0       0
## 4       0        0       0        0       0        0       0        0       0
## 5       0        0       0        0       0        0       0        0       0
## 6       0        0       0        0       0        0       0        0       0
##   SOB_5_9A SOB_60A ESTADO LOCALCOD NEU_10_19 NEU_20_59 HOS_10_19 HOS_20_59
## 1        0       0      Z     <NA>         0         0         0         0
## 2        0       0      Z     <NA>         0         0         0         0
## 3        0       0      Z     <NA>         0         0         0         0
## 4        0       0      Z     <NA>         0         0         0         0
## 5        0       0      Z     <NA>         0         0         0         0
## 6        0       0      Z     <NA>         0         0         0         0
##   DIH_10_19 DIH_20_59 DEH_10_19 DEH_20_59   X.    X  X.1  X.2  X.3  X.4  X.5
## 1         0         0         0         0 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 2         0         0         0         0 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 3         0         0         0         0 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 4         0         0         0         0 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 5         0         0         0         0 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 6         0         0         0         0 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
##    X.6
## 1 <NA>
## 2 <NA>
## 3 <NA>
## 4 <NA>
## 5 <NA>
## 6 <NA>

names(Dataset) 

##  [1] "ANO"        "SEMANA"     "SUB_REG_NT" "RED"        "MICRORED"  
##  [6] "E_SALUD"    "UBIGEO"     "IRA_M2"     "IRA_2_11"   "IRA_1_4A"  
## [11] "NEU_2_11"   "NEU_1_4A"   "HOS_M2"     "HOS_2_11"   "HOS_1_4A"  
## [16] "NGR_M2"     "NGR_2_11"   "NGR_1_4A"   "DIH_M2"     "DIH_2_11"  
## [21] "DIH_1_4A"   "DEH_M2"     "DEH_2_11"   "DEH_1_4A"   "SOB_2A"    
## [26] "SOB_2_4A"   "FECHA_ING"  "CLAVE"      "MIGRADO"    "VERIFICA"  
## [31] "ETAPA"      "IRA_5_9A"   "IRA_60A"    "NEU_5_9A"   "NEU_60A"   
## [36] "HOS_5_9A"   "HOS_60A"    "NGR_5_9A"   "NGR_60A"    "DIH_5_9A"  
## [41] "DIH_60A"    "DEH_5_9A"   "DEH_60A"    "SOB_5_9A"   "SOB_60A"   
## [46] "ESTADO"     "LOCALCOD"   "NEU_10_19"  "NEU_20_59"  "HOS_10_19" 
## [51] "HOS_20_59"  "DIH_10_19"  "DIH_20_59"  "DEH_10_19"  "DEH_20_59" 
## [56] "X."         "X"          "X.1"        "X.2"        "X.3"       
## [61] "X.4"        "X.5"        "X.6"

contar=sqldf("select ano,semana,sum(ira_m2+ira_2_11+ira_1_4a+neu_2_11+neu_1_4a+sob_2a+sob_2_4a) as suma from Dataset where ano > 2001 group by ANO,semana ") 
pob=read.table("D:/descarga/Base Puente Piedra/Base Puente Piedra/pob.txt",T) 
head(contar) 

##    ANO SEMANA suma
## 1 2002      1  257
## 2 2002      2  258
## 3 2002      3  262
## 4 2002      4  218
## 5 2002      5  302
## 6 2002      6  501

caso=sqldf("select semana, suma as tasa from contar where ano=2014")
(pob)

##    year  Poblacion
## 1  2001 295897.000
## 2  2002    296.877
## 3  2003    297.258
## 4  2004    320.383
## 5  2005    318.864
## 6  2006    301.872
## 7  2007    303.819
## 8  2008    303.673
## 9  2009    303.026
## 10 2010    335.123
## 11 2011    303.222
## 12 2012    362.483
## 13 2013    362.023

Bloque 1

bloq=sqldf("select c.*, p.poblacion pob from contar c join pob p on p.year=c.ano")
head(bloq)

##    ANO SEMANA suma     pob
## 1 2002      1  257 296.877
## 2 2002      2  258 296.877
## 3 2002      3  262 296.877
## 4 2002      4  218 296.877
## 5 2002      5  302 296.877
## 6 2002      6  501 296.877

datos=xtabs(bloq$suma~bloq$ANO+bloq$SEMANA)
datos

##         bloq$SEMANA
## bloq$ANO   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17
##     2002 257 258 262 218 302 501 307 348 427 354 370 466 297 327 482 648 508
##     2003 459 569 488 533 531 393 515 612 680 618 657 570  41 608 656 556 646
##     2004 573  66 468 486 461 588 491 480 427 382 382 352 317 378 325 255 228
##     2005 499 442 349 306 356 417 395 320 197 120 203 330 407 468 600 593 542
##     2006 491 460 440 314 371 404 417 563 312 508 515 621 546 674 542 752 810
##     2007 324 433 411 399 382 355 428 450 406 265 387 443 553 454 590 606 730
##     2008 421 353 294 291 277 449 466 522 508 556 605 528 478 622 588 678 675
##     2009 534 630 491 438 449 500 452 457 454 520 498 557 651 590 676 511 610
##     2010 454 369 344 280 336 294 328 330 365 389 431 581 469 636 608 495 501
##     2011 401 410 327 299 323 267 319 301 335 335 359 415 484 456 591 545 478
##     2012 448 434 363 343 369 274 337 321 353 319 303 403 452 402 506 480 496
##     2013 495 506 421 497 507 354 526 468 514 569 617 709 567 767 638 634 777
##         bloq$SEMANA
## bloq$ANO  18  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34
##     2002 462 631 846 739 775 637 731 806 593 752 778 677 726 631 712 624 573
##     2003  46 624 658 791 614 670 630 630 727 595 622 613 655 558 601 640 641
##     2004 464 496 530 432 575 498 513 514 520 473 439 436 355 455 407 434 446
##     2005 440 559 715 518 543 530 526 442 440 532 614 511 419 447 609 451 477
##     2006 720 848 944 967 667 809 579 705 528 692 576 642 451 569 619 546 549
##     2007 579 568 607 578 541 610 543 599 500 544 568 623 403 418 506 502 538
##     2008 529 581 466 610 605 596 630 547 673 555 754 586 422 591 581 399 481
##     2009 651 641 505 530 566 487 470 534 657 558 597 470 465 428 389 431 482
##     2010 538 482 443 504 423 487 437 340 516 451 495 476 380 554 471 449 381
##     2011 510 519 569 479 479 434 453 484 434 430 438 455 334 429 396 436 359
##     2012 426 490 527 525 628 482 560 466 526 519 456 551 456 501 420 406 457
##     2013 721 637 705 627 551 690 573 771 408 468 667   0   0   0   0   0   0
##         bloq$SEMANA
## bloq$ANO  35  36  37  38  39  40  41  42  43  44  45  46  47  48  49  50  51
##     2002 549 833 695 711 824 672 631 747 746 560 560 822 759 576 565 586 569
##     2003 338 784 734 756 786 711 728 718 734 717 919 929 335 263 298  25  48
##     2004 475 495 393 525 485 420 534 504 608 497 537 515 350 490 485 520 345
##     2005 434 489 507 482 452 393 576 551 422 456 610 516 444 573 592 576 390
##     2006 491 550 522 486 544 434 513 497 465 448 557 493 520 506 456 577 451
##     2007 252 503 507 629 573 619 461 714 670 465 762 665 585 675 583 594  94
##     2008 498 640 641 482 578 532 523 657 526 628 530 642 492 621 483 536 538
##     2009 407 427 446 477 388 419 479 536 500 489 467 515 394 345 448 466 406
##     2010 396 395 387 391 409 438 419 456 362 452 431 395 452 488 386 417 372
##     2011 435 526 461 519 468 481 459 456 313 519 489 445 393 496 425 435 401
##     2012 382 514 461 249 119 145 204 147 415 396 497 528 569 365 412 492 344
##     2013   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
##         bloq$SEMANA
## bloq$ANO  52  53
##     2002 496   0
##     2003 434 689
##     2004 571   0
##     2005 440   0
##     2006 517   0
##     2007 561   0
##     2008 453 406
##     2009 383   0
##     2010 420   0
##     2011 512   0
##     2012 399   0
##     2013   0   0

Bloque 2: Cálculo de tasas y suma 1

bloq$tasa=round((bloq$suma/bloq$pob * 100000 + 1),2)
head(bloq)

##    ANO SEMANA suma     pob      tasa
## 1 2002      1  257 296.877  86568.84
## 2 2002      2  258 296.877  86905.68
## 3 2002      3  262 296.877  88253.04
## 4 2002      4  218 296.877  73432.08
## 5 2002      5  302 296.877 101726.63
## 6 2002      6  501 296.877 168757.76

datos=xtabs(bloq$tasa~bloq$ANO+bloq$SEMANA)
datos

##         bloq$SEMANA
## bloq$ANO         1         2         3         4         5         6         7
##     2002  86568.84  86905.68  88253.04  73432.08 101726.63 168757.76 103410.83
##     2003 154412.32 191417.21 164168.15 179306.52 178633.70 132209.38 173251.17
##     2004 178849.44  20601.34 146076.17 151694.44 143891.28 183531.34 153255.07
##     2005 156494.05 138618.09 109452.05  95966.68 111647.34 130777.76 123878.26
##     2006 162652.72 152383.47 145758.14 104018.60 122900.77 133832.56 138139.02
##     2007 106643.44 142520.07 135278.91 131329.19 125733.76 116846.89 140874.35
##     2008 138636.97 116244.46  96815.67  95827.76  91217.54 147857.41 153455.54
##     2009 176223.50 207903.95 162033.30 144543.05 148173.10 165003.34 149163.12
##     2010 135473.65 110109.83 102649.88  83552.41 100262.69  87729.98  97875.51
##     2011 132247.34 135215.46 107842.78  98608.62 106523.61  88055.30 105204.45
##     2012 123593.00 119730.75 100143.63  94626.13 101798.88  75590.75  92970.88
##     2013 136732.64 139771.13 116291.95 137285.10 140047.35  97784.84 145295.64
##         bloq$SEMANA
## bloq$ANO         8         9        10        11        12        13        14
##     2002 117221.26 143831.61 119242.30 124631.74 156968.36 100042.43 110147.63
##     2003 205882.76 228758.51 207901.21 221021.12 191753.62  13793.73 204537.13
##     2004 149821.68 133278.98 119233.29 119233.29 109869.50  98945.08 117984.79
##     2005 100357.26  61782.83  37634.60  63664.51 103493.40 127641.62 146772.04
##     2006 186503.89 103356.06 168284.25 170603.11 205717.33 180872.36 223274.44
##     2007 148115.50 133633.20  87223.98 127379.47 145811.50 182017.27 149432.08
##     2008 171896.43 167286.20 183092.68 199228.46 173872.24 157407.16 204826.59
##     2009 150813.14 149823.13 171603.44 164343.33 183813.61 214834.05 194703.76
##     2010  98472.31 108916.23 116077.78 128610.50 173370.18 139949.62 189782.07
##     2011  99268.20 110481.11 110481.11 118396.10 136864.42 159620.03 150385.87
##     2012  88556.88  97384.88  88005.13  83591.13 111178.63 124696.50 110902.75
##     2013 129274.55 141980.93 157173.33 170432.16 195844.91 156620.88 211865.99
##         bloq$SEMANA
## bloq$ANO        15        16        17        18        19        20        21
##     2002 162357.80 218273.21 171115.64 155621.00 212546.94 284967.50 248925.64
##     2003 220684.72 187043.91 217320.63  15475.77 209919.66 221357.53 266099.81
##     2004 101442.09  79593.24  71165.82 144827.66 154815.71 165428.00 134839.62
##     2005 188169.00 185973.70 169979.42 137990.86 175310.85 224234.53 162452.70
##     2006 179547.30 249113.21 268326.65 238512.69 280914.76 312716.32 320335.45
##     2007 194195.57 199461.86 240275.64 190574.99 186954.42 199791.01 190245.85
##     2008 193630.33 223267.47 222279.57 174201.54 191325.22 153455.54 200874.97
##     2009 223084.17 168633.39 201303.86 214834.05 211534.00 166653.37 174903.48
##     2010 181426.92 147707.96 149498.35 160539.07 143828.79 132191.27 150393.54
##     2011 194907.70 179737.30 157641.28 168194.60 171162.72 187652.29 157971.07
##     2012 139593.75 132421.00 136835.00 117523.75 135179.75 145387.13 144835.38
##     2013 176232.90 175127.99 214628.25 199159.62 175956.67 194740.01 173194.42
##         bloq$SEMANA
## bloq$ANO        22        23        24        25        26        27        28
##     2002 261051.87 214567.98 246230.92 271493.91 199747.02 253304.56 262062.39
##     2003 206555.58 225394.43 211938.11 211938.11 244569.69 200163.82 209246.84
##     2004 179473.69 155439.96 160121.86 160433.98 162306.74 147636.80 137024.50
##     2005 170293.04 166216.06 164961.61 138618.09 137990.86 166843.29 192559.58
##     2006 220955.58 267995.38 191804.15 233543.69 174909.57 229237.23 190810.35
##     2007 178067.55 200778.44 178725.83 197157.86 164572.67 179054.98 186954.42
##     2008 199228.46 196264.74 207461.00 180128.97 221620.97 182763.38 248294.39
##     2009 186783.65 160713.28 155103.20 176223.50 216814.08 184143.61 197013.80
##     2010 126223.31 145320.78 130400.88 101456.29 153974.32 134578.45 147707.96
##     2011 157971.07 143130.46 149396.49 159620.03 143130.46 141811.29 144449.62
##     2012 173250.50 132972.75 154491.00 128558.75 145111.25 143180.13 125800.00
##     2013 152201.27 190596.63 158278.24 212970.89 112701.02 129274.55 184243.44
##         bloq$SEMANA
## bloq$ANO        29        30        31        32        33        34        35
##     2002 228041.57 244546.72 212546.94 239830.96 210189.06 193010.23 184926.07
##     2003 206219.17 220348.31 187716.72 202182.27 215302.19 215638.59 113706.94
##     2004 136088.12 110805.88 142018.52 127036.45 135463.87 139209.38 148261.05
##     2005 160257.41 131404.98 140186.16 190991.52 141440.61 149594.56 136109.18
##     2006 212673.92 149402.07 188491.49 205054.80 180872.36 181866.16 162652.72
##     2007 205057.30 132645.77 137582.92 166547.53 165230.96 177080.12  82945.12
##     2008 192971.73 138966.27 194618.24 191325.22 131392.33 158395.06 163993.19
##     2009 155103.20 153453.18 141243.01 128372.82 142233.02 159063.26 134312.91
##     2010 142038.40 113392.20 165313.44 140546.41 133981.66 113690.60 118166.57
##     2011 150056.08 110151.32 141481.50 130598.38 143790.04 118396.10 143460.25
##     2012 152008.13 125800.00 138214.38 115868.50 112006.25 126075.88 105385.25
##     2013      0.00      0.00      0.00      0.00      0.00      0.00      0.00
##         bloq$SEMANA
## bloq$ANO        36        37        38        39        40        41        42
##     2002 280588.58 234104.69 239494.12 277557.02 226357.37 212546.94 251620.36
##     2003 263744.95 246924.55 254325.53 264417.77 239187.16 244906.10 241542.02
##     2004 154503.58 122666.68 163867.37 151382.32 131094.10 166676.51 157312.72
##     2005 153357.92 159002.96 151162.62 141754.22 123251.04 180642.28 172801.94
##     2006 182197.43 172921.97 160996.39 180209.83 143770.54 169940.58 164640.32
##     2007 165560.10 166876.67 207032.16 188600.13 203740.73 151736.08 235009.34
##     2008 210754.01 211083.32 158724.36 190337.32 175189.44 172225.73 216352.14
##     2009 140913.00 147183.09 157413.24 128042.82 138272.96 158073.24 176883.51
##     2010 117868.17 115480.99 116674.58 122045.74 130699.28 125029.72 136070.44
##     2011 173471.26 152034.82 171162.72 154343.36 158630.65 151375.24 150385.87
##     2012 141800.75 127179.38  68693.88  32830.13  40002.88  56279.50  40554.63
##     2013      0.00      0.00      0.00      0.00      0.00      0.00      0.00
##         bloq$SEMANA
## bloq$ANO        43        44        45        46        47        48        49
##     2002 251283.52 188631.31 188631.31 276883.35 255662.44 194020.75 190315.51
##     2003 246924.55 241205.61 309160.05 312524.13 112697.71  88476.33 100250.61
##     2004 189773.87 155127.83 167612.89 160746.11 109245.25 152942.95 151382.32
##     2005 132345.82 143008.68 191305.13 161825.48 139245.32 179701.44 185660.09
##     2006 154039.80 148408.27 184516.29 163315.25 172259.44 167621.71 151058.40
##     2007 220527.04 153052.65 250808.22 218881.32 192549.85 222172.75 191891.57
##     2008 173213.63 206802.39 174530.84 211412.62 162017.38 204497.28 159053.67
##     2009 165003.34 161373.29 154113.19 169953.41 130022.85 113852.62 147843.10
##     2010 108021.04 134876.85 128610.50 117868.17 134876.85 145619.18 115182.59
##     2011 103225.70 171162.72 161268.98 146758.16 129609.01 163577.52 140162.33
##     2012 114489.13 109247.50 137110.88 145663.00 156973.88 100695.38 113661.50
##     2013      0.00      0.00      0.00      0.00      0.00      0.00      0.00
##         bloq$SEMANA
## bloq$ANO        50        51        52        53
##     2002 197389.14 191662.87 167073.56      0.00
##     2003   8411.20  16148.59 146002.12 231786.18
##     2004 162306.74 107684.62 178225.19      0.00
##     2005 180642.28 122310.20 137990.86      0.00
##     2006 191141.62 149402.07 171265.64      0.00
##     2007 195512.14  30940.47 184650.41      0.00
##     2008 176506.65 177165.25 149174.62 133697.44
##     2009 153783.18 133982.90 126392.79      0.00
##     2010 124432.92 111005.02 125328.12      0.00
##     2011 143460.25 132247.34 168854.18      0.00
##     2012 135731.50  94902.00 110075.13      0.00
##     2013      0.00      0.00      0.00      0.00

Bloque 3: Transformación logarítmica de las tasas

bloq$lntasa=round(log(bloq$tasa),2) 
head(bloq) 

##    ANO SEMANA suma     pob      tasa lntasa
## 1 2002      1  257 296.877  86568.84  11.37
## 2 2002      2  258 296.877  86905.68  11.37
## 3 2002      3  262 296.877  88253.04  11.39
## 4 2002      4  218 296.877  73432.08  11.20
## 5 2002      5  302 296.877 101726.63  11.53
## 6 2002      6  501 296.877 168757.76  12.04

datos=xtabs(bloq$lntasa~bloq$ANO+bloq$SEMANA) 
datos 

##         bloq$SEMANA
## bloq$ANO     1     2     3     4     5     6     7     8     9    10    11
##     2002 11.37 11.37 11.39 11.20 11.53 12.04 11.55 11.67 11.88 11.69 11.73
##     2003 11.95 12.16 12.01 12.10 12.09 11.79 12.06 12.24 12.34 12.24 12.31
##     2004 12.09  9.93 11.89 11.93 11.88 12.12 11.94 11.92 11.80 11.69 11.69
##     2005 11.96 11.84 11.60 11.47 11.62 11.78 11.73 11.52 11.03 10.54 11.06
##     2006 12.00 11.93 11.89 11.55 11.72 11.80 11.84 12.14 11.55 12.03 12.05
##     2007 11.58 11.87 11.82 11.79 11.74 11.67 11.86 11.91 11.80 11.38 11.75
##     2008 11.84 11.66 11.48 11.47 11.42 11.90 11.94 12.05 12.03 12.12 12.20
##     2009 12.08 12.24 12.00 11.88 11.91 12.01 11.91 11.92 11.92 12.05 12.01
##     2010 11.82 11.61 11.54 11.33 11.52 11.38 11.49 11.50 11.60 11.66 11.76
##     2011 11.79 11.81 11.59 11.50 11.58 11.39 11.56 11.51 11.61 11.61 11.68
##     2012 11.72 11.69 11.51 11.46 11.53 11.23 11.44 11.39 11.49 11.39 11.33
##     2013 11.83 11.85 11.66 11.83 11.85 11.49 11.89 11.77 11.86 11.97 12.05
##         bloq$SEMANA
## bloq$ANO    12    13    14    15    16    17    18    19    20    21    22
##     2002 11.96 11.51 11.61 12.00 12.29 12.05 11.96 12.27 12.56 12.42 12.47
##     2003 12.16  9.53 12.23 12.30 12.14 12.29  9.65 12.25 12.31 12.49 12.24
##     2004 11.61 11.50 11.68 11.53 11.28 11.17 11.88 11.95 12.02 11.81 12.10
##     2005 11.55 11.76 11.90 12.15 12.13 12.04 11.83 12.07 12.32 12.00 12.05
##     2006 12.23 12.11 12.32 12.10 12.43 12.50 12.38 12.55 12.65 12.68 12.31
##     2007 11.89 12.11 11.91 12.18 12.20 12.39 12.16 12.14 12.21 12.16 12.09
##     2008 12.07 11.97 12.23 12.17 12.32 12.31 12.07 12.16 11.94 12.21 12.20
##     2009 12.12 12.28 12.18 12.32 12.04 12.21 12.28 12.26 12.02 12.07 12.14
##     2010 12.06 11.85 12.15 12.11 11.90 11.92 11.99 11.88 11.79 11.92 11.75
##     2011 11.83 11.98 11.92 12.18 12.10 11.97 12.03 12.05 12.14 11.97 11.97
##     2012 11.62 11.73 11.62 11.85 11.79 11.83 11.67 11.81 11.89 11.88 12.06
##     2013 12.19 11.96 12.26 12.08 12.07 12.28 12.20 12.08 12.18 12.06 11.93
##         bloq$SEMANA
## bloq$ANO    23    24    25    26    27    28    29    30    31    32    33
##     2002 12.28 12.41 12.51 12.20 12.44 12.48 12.34 12.41 12.27 12.39 12.26
##     2003 12.33 12.26 12.26 12.41 12.21 12.25 12.24 12.30 12.14 12.22 12.28
##     2004 11.95 11.98 11.99 12.00 11.90 11.83 11.82 11.62 11.86 11.75 11.82
##     2005 12.02 12.01 11.84 11.83 12.02 12.17 11.98 11.79 11.85 12.16 11.86
##     2006 12.50 12.16 12.36 12.07 12.34 12.16 12.27 11.91 12.15 12.23 12.11
##     2007 12.21 12.09 12.19 12.01 12.10 12.14 12.23 11.80 11.83 12.02 12.02
##     2008 12.19 12.24 12.10 12.31 12.12 12.42 12.17 11.84 12.18 12.16 11.79
##     2009 11.99 11.95 12.08 12.29 12.12 12.19 11.95 11.94 11.86 11.76 11.87
##     2010 11.89 11.78 11.53 11.94 11.81 11.90 11.86 11.64 12.02 11.85 11.81
##     2011 11.87 11.91 11.98 11.87 11.86 11.88 11.92 11.61 11.86 11.78 11.88
##     2012 11.80 11.95 11.76 11.89 11.87 11.74 11.93 11.74 11.84 11.66 11.63
##     2013 12.16 11.97 12.27 11.63 11.77 12.12  0.00  0.00  0.00  0.00  0.00
##         bloq$SEMANA
## bloq$ANO    34    35    36    37    38    39    40    41    42    43    44
##     2002 12.17 12.13 12.54 12.36 12.39 12.53 12.33 12.27 12.44 12.43 12.15
##     2003 12.28 11.64 12.48 12.42 12.45 12.49 12.39 12.41 12.39 12.42 12.39
##     2004 11.84 11.91 11.95 11.72 12.01 11.93 11.78 12.02 11.97 12.15 11.95
##     2005 11.92 11.82 11.94 11.98 11.93 11.86 11.72 12.10 12.06 11.79 11.87
##     2006 12.11 12.00 12.11 12.06 11.99 12.10 11.88 12.04 12.01 11.94 11.91
##     2007 12.08 11.33 12.02 12.03 12.24 12.15 12.22 11.93 12.37 12.30 11.94
##     2008 11.97 12.01 12.26 12.26 11.97 12.16 12.07 12.06 12.28 12.06 12.24
##     2009 11.98 11.81 11.86 11.90 11.97 11.76 11.84 11.97 12.08 12.01 11.99
##     2010 11.64 11.68 11.68 11.66 11.67 11.71 11.78 11.74 11.82 11.59 11.81
##     2011 11.68 11.87 12.06 11.93 12.05 11.95 11.97 11.93 11.92 11.54 12.05
##     2012 11.74 11.57 11.86 11.75 11.14 10.40 10.60 10.94 10.61 11.65 11.60
##     2013  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00
##         bloq$SEMANA
## bloq$ANO    45    46    47    48    49    50    51    52    53
##     2002 12.15 12.53 12.45 12.18 12.16 12.19 12.16 12.03  0.00
##     2003 12.64 12.65 11.63 11.39 11.52  9.04  9.69 11.89 12.35
##     2004 12.03 11.99 11.60 11.94 11.93 12.00 11.59 12.09  0.00
##     2005 12.16 11.99 11.84 12.10 12.13 12.10 11.71 11.83  0.00
##     2006 12.13 12.00 12.06 12.03 11.93 12.16 11.91 12.05  0.00
##     2007 12.43 12.30 12.17 12.31 12.16 12.18 10.34 12.13  0.00
##     2008 12.07 12.26 12.00 12.23 11.98 12.08 12.08 11.91 11.80
##     2009 11.95 12.04 11.78 11.64 11.90 11.94 11.81 11.75  0.00
##     2010 11.76 11.68 11.81 11.89 11.65 11.73 11.62 11.74  0.00
##     2011 11.99 11.90 11.77 12.01 11.85 11.87 11.79 12.04  0.00
##     2012 11.83 11.89 11.96 11.52 11.64 11.82 11.46 11.61  0.00
##     2013  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00

Bloque 4: Cálculo de medias. DE e IC 95%

esta=sqldf("select semana, avg(lntasa) as lnmedia, StDev(lntasa) as lnsd, count(*) as n from bloq  where ano < 2013 and semana < 53  group by semana")
esta=sqldf("select e.*,c.tasa from esta e left join caso c on e.semana=c.semana")
head(esta)

##   SEMANA  lnmedia      lnsd  n tasa
## 1      1 11.83636 0.2185988 11   NA
## 2      2 11.64636 0.6194073 11   NA
## 3      3 11.70182 0.2238222 11   NA
## 4      4 11.60727 0.2777802 11   NA
## 5      5 11.68545 0.2043704 11   NA
## 6      6 11.73727 0.2928512 11   NA

Definir el nivel significancia.

alfa=0.05
esta$lnICinf=esta$lnmedia-qt(1-alfa/2,esta$n[1])*esta$lnsd/sqrt(esta$n[1])
esta$lnICsup=esta$lnmedia+qt(1-alfa/2,esta$n[1])*esta$lnsd/sqrt(esta$n[1])

Bloque 5: Transformación a unidades originales, menos 1 y cálculo de casos

esta$medialn=exp(esta$lnmedia)-1
esta$IClninf=exp(esta$lnICinf)-1
esta$IClnsup=exp(esta$lnICsup)-1
esta$media=esta$medialn*pob$Poblacion[13]/100000
esta$icinf=esta$IClninf*pob$Poblacion[13]/100000
esta$icsup=esta$IClnsup*pob$Poblacion[13]/100000

Bloque 6: Cálculo de las diferencias

esta$zex=esta$icinf
esta$zse=esta$media-esta$zex
esta$zal=esta$icsup-esta$media

Graficando mi canal endemico

ggplot(esta,aes(SEMANA,colour="gold"))+geom_area(aes(,icsup),color="sky blue",position = 'stack',fill = I("sky blue"))+
  geom_area(aes(,media),color="gold",position = 'stack',fill = I("gold"))+
  geom_area(aes(,zex),color="green",position = 'stack',fill = I("green"))+
  geom_bar(aes(,tasa),color="black",position = 'stack',fill = I("blue"),stat = "identity")+
  theme(
    panel.grid.major = element_line(colour = "red"),
    panel.grid.minor = element_blank(),
    panel.background = element_rect(fill = "red")
  )+
  ggtitle("CANAL ENDEMICO DISA V LC-SE 14")+ 
  xlab("Semanas Epidemiológicas")+ ylab("Episodios")

## Warning: Removed 52 rows containing missing values (position_stack).

head(esta)

##   SEMANA  lnmedia      lnsd  n tasa  lnICinf  lnICsup  medialn   IClninf
## 1      1 11.83636 0.2185988 11   NA 11.69130 11.98143 138186.1 119525.89
## 2      2 11.64636 0.6194073 11   NA 11.23531 12.05742 114274.1  75757.91
## 3      3 11.70182 0.2238222 11   NA 11.55328 11.85035 120790.1 104117.49
## 4      4 11.60727 0.2777802 11   NA 11.42293 11.79161 109893.1  91392.69
## 5      5 11.68545 0.2043704 11   NA 11.54983 11.82108 118829.6 103758.38
## 6      6 11.73727 0.2928512 11   NA 11.54293 11.93162 125149.6 103044.95
##    IClnsup    media    icinf    icsup      zex       zse       zal
## 1 159759.4 500.2654 432.7112 578.3659 432.7112  67.55415  78.10051
## 2 172372.0 413.6984 274.2610 624.0263 274.2610 139.43734 210.32788
## 3 140132.6 437.2881 376.9293 507.3122 376.9293  60.35881  70.02415
## 4 132138.5 397.8384 330.8626 478.3719 330.8626  66.97585  80.53349
## 5 136090.0 430.1906 375.6292 492.6772 375.6292  54.56142  62.48658
## 6 151995.9 453.0702 373.0464 550.2600 373.0464  80.02377  97.18984