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Type 'q()' to quit R. > library('diseasemapping') > data('kentucky') > kentucky = terra::unwrap(kentucky) > > head(larynx) County Cases sex age 1 Hickman 2 M NA 2 Caldwell 3 M NA 3 Anderson 3 M NA 4 Marion 3 M NA 5 Wayne 4 M NA 6 Lincoln 3 M NA > 10^5*larynxRates[paste(c("M","F"), 50, sep="_")] M_50 F_50 9.9 2.3 > > kentucky1 = getSMR(terra::values(kentucky), larynxRates) > kentucky1[1:4,c(1,2,grep("expected", names(kentucky1),ignore.case=TRUE))] County M.0 expected logExpected 1 Adair 594 0.916000 -0.08773891 2 Allen 667 0.973271 -0.02709272 3 Anderson 747 0.924600 -0.07839407 4 Ballard 237 0.448540 -0.80175742 > > kentucky1 = getSMR(kentucky, larynxRates) > kentucky1[1:4,c(1,2,grep("expected", names(kentucky1),ignore.case=TRUE))] class : SpatVector geometry : polygons dimensions : 4, 6 (geometries, attributes) extent : -89.18153, -84.79649, 36.62915, 38.1288 (xmin, xmax, ymin, ymax) coord. ref. : +proj=longlat +datum=WGS84 +no_defs names : County M.0 expected expected_surfaceArea type : values : Adair 594 0.916 8.573e-10 Allen 667 0.9733 1.073e-09 Anderson 747 0.9246 1.743e-09 logExpected_surfaceArea logExpected -20.88 -0.08774 -20.65 -0.02709 -20.17 -0.07839 > > if(require('mapmisc', quietly=TRUE)) { + # kmap = openmap(kentucky) + col = colourScale( + kentucky1$expected, + style='fixed', + breaks=c(0:5,max(kentucky1$expected)), + dec=0,opacity=c(0.6,1) + ) + + plot(kentucky1, col=col$plot) + legendBreaks('topleft', col) + } > > junk = getSMR(kentucky, larynxRates, regionCode='junk') > > > kentucky2 = getSMR(terra::values(kentucky), larynxRates, + larynx, + regionCode="County") > kentucky2[1:4,c(1,2,grep("expected|observed", names(kentucky2),ignore.case=TRUE))] County M.0 expected logExpected observed 1 Adair 594 0.916000 -0.08773891 4 2 Allen 667 0.973271 -0.02709272 0 3 Anderson 747 0.924600 -0.07839407 3 4 Ballard 237 0.448540 -0.80175742 0 > > > kentucky2 = getSMR(kentucky, + larynxRates, + casedata=larynx, + regionCode="County") > terra::values(kentucky2)[1:4,c(1,2,grep("expected|observed", names(kentucky2),ignore.case=TRUE))] County M.0 expected expected_surfaceArea logExpected_surfaceArea 1 Adair 594 0.916000 8.572729e-10 -20.87726 2 Allen 667 0.973271 1.072726e-09 -20.65306 3 Anderson 747 0.924600 1.743098e-09 -20.16760 4 Ballard 237 0.448540 6.327389e-10 -21.18096 logExpected observed 1 -0.08773891 4 2 -0.02709272 0 3 -0.07839407 3 4 -0.80175742 0 > > if(require('mapmisc', quietly=TRUE)) { + + + col = colourScale( + kentucky2$observed, + col='RdYlBu', + style='quantile', + breaks=12, dec=0,opacity=c(0.6,1), + rev=TRUE + ) + + plot(kentucky1, col=col$plot) + legendBreaks('topleft', col) + + + col = colourScale( + kentucky2$expected, + style='fixed', + col=col$col, + breaks=col$breaks,opacity=c(0.6,1) + ) + + plot(kentucky2, col=col$plot) + legendBreaks('topleft', col) + + } > > > kentucky3 = getSMR(terra::values(kentucky), + model=list(larynxRates, larynxRates*2) + ) > kentucky3[1:4,c(1,2,grep("expected|observed", names(kentucky3),ignore.case=TRUE))] County M.0 expected_1 logExpected_1 expected_2 logExpected_2 1 Adair 594 0.916000 -0.08773891 1.832000 0.6054083 2 Allen 667 0.973271 -0.02709272 1.946542 0.6660545 3 Anderson 747 0.924600 -0.07839407 1.849200 0.6147531 4 Ballard 237 0.448540 -0.80175742 0.897080 -0.1086102 > > kentucky3 = getSMR(kentucky, + model=list('1990'=larynxRates, '1991'=larynxRates*2) + ) > terra::values(kentucky3)[1:4,c(1,2,grep("expected|observed", names(kentucky3),ignore.case=TRUE))] County M.0 expected_1990 expected_surfaceArea_1990 1 Adair 594 0.916000 8.572729e-10 2 Allen 667 0.973271 1.072726e-09 3 Anderson 747 0.924600 1.743098e-09 4 Ballard 237 0.448540 6.327389e-10 logExpected_surfaceArea_1990 logExpected_1990 expected_1991 1 -20.87726 -0.08773891 1.832000 2 -20.65306 -0.02709272 1.946542 3 -20.16760 -0.07839407 1.849200 4 -21.18096 -0.80175742 0.897080 expected_surfaceArea_1991 logExpected_surfaceArea_1991 logExpected_1991 1 1.714546e-09 -20.18412 0.6054083 2 2.145451e-09 -19.95992 0.6660545 3 3.486196e-09 -19.47445 0.6147531 4 1.265478e-09 -20.48782 -0.1086102 > > modelList = list() > for (D in 3:12) { + modelList[[ + as.character(D) + ]] = larynxRates*D/5 + } > > > kentucky4 = getSMR( + popdata=list( + '5'=kentucky, '10'=kentucky + ), + model=modelList + ) > terra::values(kentucky4[[1]])[1:4,c(1,2,grep("expected|observed", + names(kentucky4[[1]]),ignore.case=TRUE)) + ] County M.0 expected_3 expected_surfaceArea_3 logExpected_surfaceArea_3 1 Adair 594 0.5496000 5.143638e-10 -21.38809 2 Allen 667 0.5839626 6.436354e-10 -21.16389 3 Anderson 747 0.5547600 1.045859e-09 -20.67843 4 Ballard 237 0.2691240 3.796434e-10 -21.69179 logExpected_3 expected_4 expected_surfaceArea_4 logExpected_surfaceArea_4 1 -0.5985645 0.7328000 6.858184e-10 -21.10041 2 -0.5379183 0.7786168 8.581805e-10 -20.87621 3 -0.5892197 0.7396800 1.394478e-09 -20.39075 4 -1.3125830 0.3588320 5.061912e-10 -21.40411 logExpected_4 expected_5 expected_surfaceArea_5 logExpected_surfaceArea_5 1 -0.3108825 0.916000 8.572729e-10 -20.87726 2 -0.2502363 0.973271 1.072726e-09 -20.65306 3 -0.3015376 0.924600 1.743098e-09 -20.16760 4 -1.0249010 0.448540 6.327389e-10 -21.18096 logExpected_5 expected_6 expected_surfaceArea_6 logExpected_surfaceArea_6 1 -0.08773891 1.099200 1.028728e-09 -20.69494 2 -0.02709272 1.167925 1.287271e-09 -20.47074 3 -0.07839407 1.109520 2.091718e-09 -19.98528 4 -0.80175742 0.538248 7.592867e-10 -20.99864 logExpected_6 expected_7 expected_surfaceArea_7 logExpected_surfaceArea_7 1 0.09458264 1.282400 1.200182e-09 -20.54079 2 0.15522884 1.362579 1.501816e-09 -20.31659 3 0.10392749 1.294440 2.440337e-09 -19.83113 4 -0.61943586 0.627956 8.858345e-10 -20.84449 logExpected_7 expected_8 expected_surfaceArea_8 logExpected_surfaceArea_8 1 0.2487333 1.465600 1.371637e-09 -20.40726 2 0.3093795 1.557234 1.716361e-09 -20.18306 3 0.2580782 1.479360 2.788957e-09 -19.69760 4 -0.4652852 0.717664 1.012382e-09 -20.71096 logExpected_8 expected_9 expected_surfaceArea_9 logExpected_surfaceArea_9 1 0.3822647 1.648800 1.543091e-09 -20.28948 2 0.4429109 1.751888 1.930906e-09 -20.06528 3 0.3916096 1.664280 3.137576e-09 -19.57982 4 -0.3317538 0.807372 1.138930e-09 -20.59318 logExpected_9 expected_10 expected_surfaceArea_10 logExpected_surfaceArea_10 1 0.5000478 1.832000 1.714546e-09 -20.18412 2 0.5606939 1.946542 2.145451e-09 -19.95992 3 0.5093926 1.849200 3.486196e-09 -19.47445 4 -0.2139708 0.897080 1.265478e-09 -20.48782 logExpected_10 expected_11 expected_surfaceArea_11 logExpected_surfaceArea_11 1 0.6054083 2.015200 1.886000e-09 -20.08881 2 0.6660545 2.141196 2.359996e-09 -19.86461 3 0.6147531 2.034120 3.834816e-09 -19.37914 4 -0.1086102 0.986788 1.392026e-09 -20.39251 logExpected_11 expected_12 expected_surfaceArea_12 logExpected_surfaceArea_12 1 0.70071845 2.198400 2.057455e-09 -20.00180 2 0.76136464 2.335850 2.574542e-09 -19.77759 3 0.71006329 2.219040 4.183435e-09 -19.29213 4 -0.01330005 1.076496 1.518573e-09 -20.30549 logExpected_12 1 0.78772982 2 0.84837602 3 0.79707467 4 0.07371132 > terra::values(kentucky4[[2]])[1:4,c(1,2,grep("expected|observed", + names(kentucky4[[2]]),ignore.case=TRUE)) + ] County M.0 expected_3 expected_surfaceArea_3 logExpected_surfaceArea_3 1 Adair 594 0.5496000 5.143638e-10 -21.38809 2 Allen 667 0.5839626 6.436354e-10 -21.16389 3 Anderson 747 0.5547600 1.045859e-09 -20.67843 4 Ballard 237 0.2691240 3.796434e-10 -21.69179 logExpected_3 expected_4 expected_surfaceArea_4 logExpected_surfaceArea_4 1 -0.5985645 0.7328000 6.858184e-10 -21.10041 2 -0.5379183 0.7786168 8.581805e-10 -20.87621 3 -0.5892197 0.7396800 1.394478e-09 -20.39075 4 -1.3125830 0.3588320 5.061912e-10 -21.40411 logExpected_4 expected_5 expected_surfaceArea_5 logExpected_surfaceArea_5 1 -0.3108825 0.916000 8.572729e-10 -20.87726 2 -0.2502363 0.973271 1.072726e-09 -20.65306 3 -0.3015376 0.924600 1.743098e-09 -20.16760 4 -1.0249010 0.448540 6.327389e-10 -21.18096 logExpected_5 expected_6 expected_surfaceArea_6 logExpected_surfaceArea_6 1 -0.08773891 1.099200 1.028728e-09 -20.69494 2 -0.02709272 1.167925 1.287271e-09 -20.47074 3 -0.07839407 1.109520 2.091718e-09 -19.98528 4 -0.80175742 0.538248 7.592867e-10 -20.99864 logExpected_6 expected_7 expected_surfaceArea_7 logExpected_surfaceArea_7 1 0.09458264 1.282400 1.200182e-09 -20.54079 2 0.15522884 1.362579 1.501816e-09 -20.31659 3 0.10392749 1.294440 2.440337e-09 -19.83113 4 -0.61943586 0.627956 8.858345e-10 -20.84449 logExpected_7 expected_8 expected_surfaceArea_8 logExpected_surfaceArea_8 1 0.2487333 1.465600 1.371637e-09 -20.40726 2 0.3093795 1.557234 1.716361e-09 -20.18306 3 0.2580782 1.479360 2.788957e-09 -19.69760 4 -0.4652852 0.717664 1.012382e-09 -20.71096 logExpected_8 expected_9 expected_surfaceArea_9 logExpected_surfaceArea_9 1 0.3822647 1.648800 1.543091e-09 -20.28948 2 0.4429109 1.751888 1.930906e-09 -20.06528 3 0.3916096 1.664280 3.137576e-09 -19.57982 4 -0.3317538 0.807372 1.138930e-09 -20.59318 logExpected_9 expected_10 expected_surfaceArea_10 logExpected_surfaceArea_10 1 0.5000478 1.832000 1.714546e-09 -20.18412 2 0.5606939 1.946542 2.145451e-09 -19.95992 3 0.5093926 1.849200 3.486196e-09 -19.47445 4 -0.2139708 0.897080 1.265478e-09 -20.48782 logExpected_10 expected_11 expected_surfaceArea_11 logExpected_surfaceArea_11 1 0.6054083 2.015200 1.886000e-09 -20.08881 2 0.6660545 2.141196 2.359996e-09 -19.86461 3 0.6147531 2.034120 3.834816e-09 -19.37914 4 -0.1086102 0.986788 1.392026e-09 -20.39251 logExpected_11 expected_12 expected_surfaceArea_12 logExpected_surfaceArea_12 1 0.70071845 2.198400 2.057455e-09 -20.00180 2 0.76136464 2.335850 2.574542e-09 -19.77759 3 0.71006329 2.219040 4.183435e-09 -19.29213 4 -0.01330005 1.076496 1.518573e-09 -20.30549 logExpected_12 1 0.78772982 2 0.84837602 3 0.79707467 4 0.07371132 > > if(require('mapmisc', quietly=TRUE)) { + + + col = colourScale( + kentucky4[[1]]$expected_6, + col='RdYlBu', + style='quantile', + breaks=15, dec=0,opacity=c(0.6,1), + rev=TRUE + ) + + plot(kentucky4[[1]], col=col$plot) + legendBreaks('topleft', col) + + + col = colourScale( + kentucky4[[2]]$expected_11, + col='RdYlBu', + style='quantile', + breaks=15, dec=0,opacity=c(0.6,1), + rev=TRUE + ) + + plot(kentucky4[[2]], col=col$plot) + legendBreaks('topleft', col) + + } > > proc.time() user system elapsed 6.43 0.39 6.84