From: N. Brouard Date: Wed, 22 May 2019 23:12:10 +0000 (+0000) Subject: *** empty log message *** X-Git-Tag: imach-099s7~166 X-Git-Url: https://henry.ined.fr/git/?a=commitdiff_plain;h=9b572afdf74753cfce224a2f3d3eeb008d12849d;p=.git *** empty log message *** --- diff --git a/html/doc/biaspar-cov.htm b/html/doc/biaspar-cov.htm index 2968b3f..9854ff8 100644 --- a/html/doc/biaspar-cov.htm +++ b/html/doc/biaspar-cov.htm @@ -1,33 +1,33 @@ IMaCh Cov biaspar-cov.htm - Imach version 0.98q5, August 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015
$Revision$ $Date$
-Title=1st_example
Datafile=data1.txt Firstpass=1 Lastpass=4 Stepm=1 Weight=0 Model=
+ 0.99r19
$Revision$ $Date$
+Title=1st_example
Datafile=data1.txt Firstpass=1 Lastpass=4 Stepm=1 Weight=0 Model=1+age+
+Current page is file biaspar-cov.htm

Matrix of variance-covariance of pairs of step probabilities

- file biaspar-cov.htm
-Ellipsoids of confidence centered on point (pij, pkl) are estimatedand drawn. It helps understanding how is the covariance between two incidences. They are expressed in year-1 in order to be less dependent of stepm.
+Ellipsoids of confidence centered on point (pij, pkl) are estimated and drawn. It helps understanding how is the covariance between two incidences. They are expressed in year-1 in order to be less dependent of stepm.

Contour plot corresponding to x'cov-1x = 4 (where x is the column vector (pij,pkl)) are drawn. It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis.
Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix and made the appropriate rotation to look at the uncorrelated principal directions.
To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.
-
Ellipsoids of confidence cov(p13,p12) expressed in year-1 :biaspar/varpijgrbiaspar113-12.png, -
-
Correlation at age 65 (-0.338), 70 (-0.360), 75 (-0.404), 80 (-0.456), 85 (-0.418), 90 (-0.359), 95 (-0.341), -
Ellipsoids of confidence cov(p21,p12) expressed in year-1 :biaspar/varpijgrbiaspar121-12.png, -
-
Correlation at age 65 (0.333), 70 (0.332), 75 (0.326), 80 (0.304), 85 (0.276), 90 (0.289), 95 (0.302), -
Ellipsoids of confidence cov(p23,p12) expressed in year-1 :biaspar/varpijgrbiaspar123-12.png, -
-
Correlation at age 65 (0.364), 70 (0.388), 75 (0.423), 80 (0.449), 85 (0.356), 90 (0.255), 95 (0.238), -
Ellipsoids of confidence cov(p21,p13) expressed in year-1 :biaspar/varpijgrbiaspar121-13.png, -
-
Correlation at age 65 (0.047), 70 (0.037), 75 (0.024), 80 (0.024), 85 (0.078), 90 (0.100), 95 (0.097), -
Ellipsoids of confidence cov(p23,p13) expressed in year-1 :biaspar/varpijgrbiaspar123-13.png, -
-
Correlation at age 65 (-0.409), 70 (-0.453), 75 (-0.528), 80 (-0.585), 85 (-0.513), 90 (-0.434), 95 (-0.363), -
Ellipsoids of confidence cov(p23,p21) expressed in year-1 :biaspar/varpijgrbiaspar123-21.png, -
-
Correlation at age 65 (-0.015), 70 (-0.013), 75 (-0.014), 80 (-0.029), 85 (-0.061), 90 (-0.062), 95 (-0.040),
Local time at start Tue Aug 18 18:20:44 2015 -
Local time at end Tue Aug 18 18:26:33 2015 +


Ellipsoids of confidence cov(p13,p12) expressed in year-1 : biaspar/VARPIJGR_biaspar_113-12.svg, +
+
Correlation at age 70 (-0.351), 75 (-0.393), 80 (-0.446), 85 (-0.413), 90 (-0.358), 95 (-0.340), +


Ellipsoids of confidence cov(p21,p12) expressed in year-1 : biaspar/VARPIJGR_biaspar_121-12.svg, +
+
Correlation at age 70 (0.342), 75 (0.332), 80 (0.305), 85 (0.283), 90 (0.307), 95 (0.322), +


Ellipsoids of confidence cov(p23,p12) expressed in year-1 : biaspar/VARPIJGR_biaspar_123-12.svg, +
+
Correlation at age 70 (0.368), 75 (0.405), 80 (0.436), 85 (0.352), 90 (0.249), 95 (0.226), +


Ellipsoids of confidence cov(p21,p13) expressed in year-1 : biaspar/VARPIJGR_biaspar_121-13.svg, +
+
Correlation at age 70 (0.029), 75 (0.021), 80 (0.028), 85 (0.070), 90 (0.082), 95 (0.076), +


Ellipsoids of confidence cov(p23,p13) expressed in year-1 : biaspar/VARPIJGR_biaspar_123-13.svg, +
+
Correlation at age 70 (-0.461), 75 (-0.531), 80 (-0.579), 85 (-0.506), 90 (-0.442), 95 (-0.379), +


Ellipsoids of confidence cov(p23,p21) expressed in year-1 : biaspar/VARPIJGR_biaspar_123-21.svg, +
+
Correlation at age 70 (-0.033), 75 (-0.032), 80 (-0.038), 85 (-0.055), 90 (-0.060), 95 (-0.050),
Local time at start Wed May 22 22:32:36 2019 +
Local time at end Wed May 22 22:34:09 2019
\ No newline at end of file diff --git a/html/doc/biaspar.gp b/html/doc/biaspar.gp index b7d94c7..2f34b7e 100644 --- a/html/doc/biaspar.gp +++ b/html/doc/biaspar.gp @@ -1,75 +1,267 @@ -# Imach version 0.98q5, August 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015 +# IMaCh-0.99r19 # biaspar.gp set datafile missing 'NaNq' -cd "/Users/nbrouard/Documents/imach/cvs/imach/build/osx/html/doc" +cd "/Users/nbrouard/Documents/imach/cvs/imach/html/doc" -# 1st: Period (stable) prevalence with CI: 'vpl' files +#Diagram of the model -set out "biaspar/vbiaspar1_1.png" +delta=0.03;delta2=0.07;unset arrow; +yoff=(2 > 2? 0:1); -#set out "vbiaspar1_1.png" +#Peripheral arrows +set for [i=1:2] for [j=1:2] arrow i*10+j from cos(pi*((1-(2/2)*2./2)/2+(i-1)*2./2))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(2/2)*2./2)/2+(i-1)*2./2)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(2/2)*2./2)/2+(i-1)*2./2))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(2/2)*2./2)/2+(j-1)*2./2)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(2/2)*2./2)/2+(i-1)*2./2)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(2/2)*2./2)/2+(j-1)*2./2))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2) + +#Centripete arrows (turning in other direction (1-i) instead of (i-1)) +set for [i=1:2] arrow (2+1)*10+i from cos(pi*((1-(2/2)*2./2)/2+(1-i)*2./2))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(2/2)*2./2)/2+(1-i)*2./2)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(2/2)*2./2)/2+(1-i)*2./2))+(i!=j?(i-j)/abs(i-j)*delta:0) ), -0.80*(sin(pi*((1-(2/2)*2./2)/2+(1-i)*2./2)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4 + +#show arrow +unset label + +#States labels, starting from 2 (2-i) instead of (1-i), was (i-1) +set for [i=1:2] label i sprintf("State %d",i) center at cos(pi*((1-(2/2)*2./2)/2+(2-i)*2./2)), yoff+sin(pi*((1-(2/2)*2./2)/2+(2-i)*2./2)) font "helvetica, 16" tc rgbcolor "blue" + +set label 2+1 sprintf("State %d",2+1) center at 0.,0. font "helvetica, 16" tc rgbcolor "red" + +#show label +unset border;unset xtics; unset ytics; + + +set ter svg size 640, 480;set out "biaspar/D_biaspar_.svg" +unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset; + +# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products. +# + + set log y; unset log x;set xlabel "Age"; set ylabel "Likelihood (-2Log(L))"; +set ter pngcairo size 640, 480 +set out "biaspar/ILK_biaspar-dest.png"; +set log y;plot "biaspar/ILK_biaspar.txt" u 2:(-$13):6 t "All sample, transitions colored by destination" with dots lc variable; set out; + +set out "biaspar/ILK_biaspar-ori.png"; +set log y;plot "biaspar/ILK_biaspar.txt" u 2:(-$13):5 t "All sample, transitions colored by origin" with dots lc variable; set out; + + +set out "biaspar/ILK_biaspar-p1j.png";set ylabel "Probability for each individual/wave";unset log; +# plot weighted, mean weight should have point size of 0.5 + plot "biaspar/ILK_biaspar.txt" u 2:($5 == 1 && $6==1 ? $10 : 1/0):($12/4.):6 t "p11" with points pointtype 7 ps variable lc variable \ +,\ + "" u 2:($5 == 1 && $6==2 ? $10 : 1/0):($12/4.):6 t "p12" with points pointtype 7 ps variable lc variable ,\ + "" u 2:($5 == 1 && $6==3 ? $10 : 1/0):($12/4.):6 t "p13" with points pointtype 7 ps variable lc variable ; +set out; unset ylabel; + +set out "biaspar/ILK_biaspar-p2j.png";set ylabel "Probability for each individual/wave";unset log; +# plot weighted, mean weight should have point size of 0.5 + plot "biaspar/ILK_biaspar.txt" u 2:($5 == 2 && $6==1 ? $10 : 1/0):($12/4.):6 t "p21" with points pointtype 7 ps variable lc variable \ +,\ + "" u 2:($5 == 2 && $6==2 ? $10 : 1/0):($12/4.):6 t "p22" with points pointtype 7 ps variable lc variable ,\ + "" u 2:($5 == 2 && $6==3 ? $10 : 1/0):($12/4.):6 t "p23" with points pointtype 7 ps variable lc variable ; +set out; unset ylabel; + +set out;unset log + +# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =1 +# + +set out "biaspar/V_biaspar_1-1-1.svg" + +#set out "V_biaspar_1-1-1.svg" +set title "Alive state 1 ()" font "Helvetica,12" set xlabel "Age" set ylabel "Probability" -set ter png small size 320, 240 -plot [70:95] "biaspar/vplrbiaspar.txt" every :::0::0 u 1:2 "%lf %lf (%lf) %*lf (%*lf)" t"Period (stable) prevalence" w l lt 0,"biaspar/vplrbiaspar.txt" every :::0::0 u 1:($2+1.96*$3) "%lf %lf (%lf) %*lf (%*lf)" t"95% CI" w l lt 1,"biaspar/vplrbiaspar.txt" every :::0::0 u 1:($2-1.96*$3) "%lf %lf (%lf) %*lf (%*lf)" t"" w l lt 1,"biaspar/prbiaspar.txt" every :::0::0 u 1:($2) t"Observed prevalence " w l lt 2 -set out "biaspar/vbiaspar2_1.png" +set ter svg size 640, 480 +plot [70:95] "biaspar/VPL_biaspar.txt" every :::0::0 u 1:($2==1 ? $3:1/0) "%lf %lf %lf (%lf) %*lf (%*lf)" t"Forward prevalence" w l lt 0,"biaspar/VPL_biaspar.txt" every :::0::0 u 1:($2==1 ? $3+1.96*$4 : 1/0) "%lf %lf %lf (%lf) %*lf (%*lf)" t"95% CI" w l lt 1,"biaspar/VPL_biaspar.txt" every :::0::0 u 1:($2==1 ? $3-1.96*$4 : 1/0) "%lf %lf %lf (%lf) %*lf (%*lf)" t"" w l lt 1,"biaspar/P_biaspar.txt" u 1:(($2)) t 'Observed prevalence in state 1' with line lt 3 +set out ;unset title; + +# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =2 +# -#set out "vbiaspar2_1.png" +set out "biaspar/V_biaspar_2-1-1.svg" + +#set out "V_biaspar_2-1-1.svg" +set title "Alive state 2 ()" font "Helvetica,12" set xlabel "Age" set ylabel "Probability" -set ter png small size 320, 240 -plot [70:95] "biaspar/vplrbiaspar.txt" every :::0::0 u 1:2 "%lf %*lf (%*lf) %lf (%lf)" t"Period (stable) prevalence" w l lt 0,"biaspar/vplrbiaspar.txt" every :::0::0 u 1:($2+1.96*$3) "%lf %*lf (%*lf) %lf (%lf)" t"95% CI" w l lt 1,"biaspar/vplrbiaspar.txt" every :::0::0 u 1:($2-1.96*$3) "%lf %*lf (%*lf) %lf (%lf)" t"" w l lt 1,"biaspar/prbiaspar.txt" every :::0::0 u 1:($6) t"Observed prevalence " w l lt 2 -# 2nd: Total life expectancy with CI: 't' files +set ter svg size 640, 480 +plot [70:95] "biaspar/VPL_biaspar.txt" every :::0::0 u 1:($2==1 ? $3:1/0) "%lf %lf %*lf (%*lf) %lf (%lf)" t"Forward prevalence" w l lt 0,"biaspar/VPL_biaspar.txt" every :::0::0 u 1:($2==1 ? $3+1.96*$4 : 1/0) "%lf %lf %*lf (%*lf) %lf (%lf)" t"95% CI" w l lt 1,"biaspar/VPL_biaspar.txt" every :::0::0 u 1:($2==1 ? $3-1.96*$4 : 1/0) "%lf %lf %*lf (%*lf) %lf (%lf)" t"" w l lt 1,"biaspar/P_biaspar.txt" u 1:(($5)) t 'Observed prevalence in state 2' with line lt 3 +set out ;unset title; + +# 2nd: Total life expectancy with CI: 't' files +# + +set out "biaspar/E_biaspar_1-1.svg" -set out "biaspar/ebiaspar1.png" +set label "popbased 0 ()" at graph 0.98,0.5 center rotate font "Helvetica,12" set ylabel "Years" -set ter png small size 320, 240 -plot [70:95] "biaspar/trbiaspar.txt" every :::0::0 u 1:2 "%lf %lf (%lf) %*lf (%*lf) %*lf (%*lf)" t"TLE" w l ,"biaspar/trbiaspar.txt" every :::0::0 u 1:($2-$3*2) "%lf %lf (%lf) %*lf (%*lf) %*lf (%*lf)" t"" w l lt 0,"biaspar/trbiaspar.txt" every :::0::0 u 1:($2+$3*2) "%lf %lf (%lf) %*lf (%*lf) %*lf (%*lf)" t"" w l lt 0,"biaspar/trbiaspar.txt" every :::0::0 u 1:2 "%lf %*lf (%*lf) %lf (%lf) %*lf (%*lf)" t"LE in state (1)" w l ,"biaspar/trbiaspar.txt" every :::0::0 u 1:($2-$3*2) "%lf %*lf (%*lf) %lf (%lf) %*lf (%*lf)" t"" w l lt 0,"biaspar/trbiaspar.txt" every :::0::0 u 1:($2+$3*2) "%lf %*lf (%*lf) %lf (%lf) %*lf (%*lf)" t"" w l lt 0,"biaspar/trbiaspar.txt" every :::0::0 u 1:2 "%lf %*lf (%*lf) %*lf (%*lf) %lf (%lf)" t"LE in state (2)" w l ,"biaspar/trbiaspar.txt" every :::0::0 u 1:($2-$3*2) "%lf %*lf (%*lf) %*lf (%*lf) %lf (%lf)" t"" w l lt 0,"biaspar/trbiaspar.txt" every :::0::0 u 1:($2+$3*2) "%lf %*lf (%*lf) %*lf (%*lf) %lf (%lf)" t"" w l lt 0 -set out "biaspar/expbiaspar11.png" -set ter png small size 320, 240 -plot [70:95] "biaspar/erbiaspar.txt" every :::0::0 u 1:2 t "e11" w l ,"biaspar/erbiaspar.txt" every :::0::0 u 1:3 t "e12" w l ,"biaspar/erbiaspar.txt" every :::0::0 u 1:4 t "e1." w l -set out "biaspar/expbiaspar21.png" -set ter png small size 320, 240 -plot [70:95] "biaspar/erbiaspar.txt" every :::0::0 u 1:5 t "e21" w l ,"biaspar/erbiaspar.txt" every :::0::0 u 1:6 t "e22" w l ,"biaspar/erbiaspar.txt" every :::0::0 u 1:7 t "e2." w l -# -# -#CV preval stable (period): 'pij' files, cov=1 state=1 -set out "biaspar/pbiaspar1_1.png" +set ter svg size 640, 480 +plot [70:95] "biaspar/T_biaspar.txt" every :::0::0 u 1:($2==0 && $4!=0 ?$4 : 1/0) "%lf %lf %lf %lf (%lf) %*lf (%*lf) %*lf (%*lf)" t"TLE" w l lt 1, \ +"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==0 && $4!=0 ? $4-$5*2 : 1/0) "%lf %lf %lf %lf (%lf) %*lf (%*lf) %*lf (%*lf)" t"" w l lt 0,"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==0 && $4!=0 ? $4+$5*2 : 1/0) "%lf %lf %lf %lf (%lf) %*lf (%*lf) %*lf (%*lf)" t"" w l lt 0,\ +"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==0 && $4!=0 ?$4 : 1/0) "%lf %lf %lf %*lf (%*lf) %lf (%lf) %*lf (%*lf)" t"LE in state (1)" w l lt 3, \ +"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==0 && $4!=0 ? $4-$5*2 : 1/0) "%lf %lf %lf %*lf (%*lf) %lf (%lf) %*lf (%*lf)" t"" w l lt 0,"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==0 && $4!=0 ? $4+$5*2 : 1/0) "%lf %lf %lf %*lf (%*lf) %lf (%lf) %*lf (%*lf)" t"" w l lt 0,\ +"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==0 && $4!=0 ?$4 : 1/0) "%lf %lf %lf %*lf (%*lf) %*lf (%*lf) %lf (%lf)" t"LE in state (2)" w l lt 4, \ +"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==0 && $4!=0 ? $4-$5*2 : 1/0) "%lf %lf %lf %*lf (%*lf) %*lf (%*lf) %lf (%lf)" t"" w l lt 0,"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==0 && $4!=0 ? $4+$5*2 : 1/0) "%lf %lf %lf %*lf (%*lf) %*lf (%*lf) %lf (%lf)" t"" w l lt 0 +set label "popbased 1 ()" at graph 0.98,0.5 center rotate font "Helvetica,12" + +replot "biaspar/T_biaspar.txt" every :::0::0 u 1:($2==1 && $4!=0 ?$4 : 1/0) "%lf %lf %lf %lf (%lf) %*lf (%*lf) %*lf (%*lf)" t"TLE" w l lt 1, \ +"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==1 && $4!=0 ? $4-$5*2 : 1/0) "%lf %lf %lf %lf (%lf) %*lf (%*lf) %*lf (%*lf)" t"" w l lt 0,"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==1 && $4!=0 ? $4+$5*2 : 1/0) "%lf %lf %lf %lf (%lf) %*lf (%*lf) %*lf (%*lf)" t"" w l lt 0,\ +"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==1 && $4!=0 ?$4 : 1/0) "%lf %lf %lf %*lf (%*lf) %lf (%lf) %*lf (%*lf)" t"LE in state (1)" w l lt 3, \ +"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==1 && $4!=0 ? $4-$5*2 : 1/0) "%lf %lf %lf %*lf (%*lf) %lf (%lf) %*lf (%*lf)" t"" w l lt 0,"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==1 && $4!=0 ? $4+$5*2 : 1/0) "%lf %lf %lf %*lf (%*lf) %lf (%lf) %*lf (%*lf)" t"" w l lt 0,\ +"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==1 && $4!=0 ?$4 : 1/0) "%lf %lf %lf %*lf (%*lf) %*lf (%*lf) %lf (%lf)" t"LE in state (2)" w l lt 4, \ +"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==1 && $4!=0 ? $4-$5*2 : 1/0) "%lf %lf %lf %*lf (%*lf) %*lf (%*lf) %lf (%lf)" t"" w l lt 0,"biaspar/T_biaspar.txt" every :::0::0 u 1:($2==1 && $4!=0 ? $4+$5*2 : 1/0) "%lf %lf %lf %*lf (%*lf) %*lf (%*lf) %lf (%lf)" t"" w l lt 0 +set out;set out "biaspar/E_biaspar_1-1.svg"; replot; set out; unset label; + + +# 3d: Life expectancy with EXP_ files: combination=1 state=1 +# + +set out "biaspar/EXP_biaspar_1-1-1.svg" +set label "()" at graph 0.98,0.5 center rotate font "Helvetica,12" +set ter svg size 640, 480 +plot [70:95] "biaspar/E_biaspar.txt" every :::0::0 u 1:2 t "e11" w l ,"biaspar/E_biaspar.txt" every :::0::0 u 1:3 t "e12" w l ,"biaspar/E_biaspar.txt" every :::0::0 u 1:4 t "e1." w l + +# 3d: Life expectancy with EXP_ files: combination=1 state=2 +# + +set out "biaspar/EXP_biaspar_2-1-1.svg" +set label "()" at graph 0.98,0.5 center rotate font "Helvetica,12" +set ter svg size 640, 480 +plot [70:95] "biaspar/E_biaspar.txt" every :::0::0 u 1:5 t "e21" w l ,"biaspar/E_biaspar.txt" every :::0::0 u 1:6 t "e22" w l ,"biaspar/E_biaspar.txt" every :::0::0 u 1:7 t "e2." w l +unset label; + +# +# +# Survival functions in state j : 'LIJ_' files, cov=1 state=1 +# + +set out "biaspar/LIJ_biaspar_1-1-1.svg" +set label "Alive state 1 ()" at graph 0.98,0.5 center rotate font "Helvetica,12" +set xlabel "Age" +set ylabel "Probability to be alive" +set ter svg size 640, 480 +unset log y +plot [70:95] "biaspar/PIJ_biaspar.txt" u ($1==1 ? ($3):1/0):($4/($4+$5+$6)) t "l(1,1)" w l, '' u ($1==1 ? ($3):1/0):($7/($7+$8+$9)) t "l(2,1)" w l +set out; unset label; + +# +# +# Survival functions in state j : 'LIJ_' files, cov=1 state=2 +# + +set out "biaspar/LIJ_biaspar_2-1-1.svg" +set label "Alive state 2 ()" at graph 0.98,0.5 center rotate font "Helvetica,12" +set xlabel "Age" +set ylabel "Probability to be alive" +set ter svg size 640, 480 +unset log y +plot [70:95] "biaspar/PIJ_biaspar.txt" u ($1==1 ? ($3):1/0):($5/($4+$5+$6)) t "l(1,2)" w l, '' u ($1==1 ? ($3):1/0):($8/($7+$8+$9)) t "l(2,2)" w l +set out; unset label; + +# +# +# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=1 state=1 +# + +set out "biaspar/LIJT_biaspar_1-1-1.svg" +set label "Alive state 1 ()" at graph 0.98,0.5 center rotate font "Helvetica,12" +set xlabel "Age" +set ylabel "Probability to be alive" +set ter svg size 640, 480 +unset log y +plot [70:95] "biaspar/PIJ_biaspar.txt" u (($1==1 && (floor($2)%5 == 0)) ? ($3):1/0):($4) t "l(1,1)" w l, '' u (($1==1 && (floor($2)%5 == 0)) ? ($3):1/0):($5) t "l(1,2)" w l, '' u (($1==1 && (floor($2)%5 == 0)) ? ($3):1/0):($4 +$5) t"l(1,.)" w l +set out; unset label; + +# +# +# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=1 state=2 +# + +set out "biaspar/LIJT_biaspar_2-1-1.svg" +set label "Alive state 2 ()" at graph 0.98,0.5 center rotate font "Helvetica,12" +set xlabel "Age" +set ylabel "Probability to be alive" +set ter svg size 640, 480 +unset log y +plot [70:95] "biaspar/PIJ_biaspar.txt" u (($1==1 && (floor($2)%5 == 0)) ? ($3):1/0):($7) t "l(2,1)" w l, '' u (($1==1 && (floor($2)%5 == 0)) ? ($3):1/0):($8) t "l(2,2)" w l, '' u (($1==1 && (floor($2)%5 == 0)) ? ($3):1/0):($7 +$8) t"l(2,.)" w l +set out; unset label; + +# +# +#CV preval stable (forward): 'pij' files, covariatecombination#=1 state=1 +# + +set out "biaspar/P_biaspar_1-1-1.svg" +set label "Alive state 1 ()" at graph 0.98,0.5 center rotate font "Helvetica,12" set xlabel "Age" set ylabel "Probability" -set ter png small size 320, 240 +set ter svg size 640, 480 unset log y -plot [70:95] "biaspar/pijrbiaspar.txt" u ($1==1 ? ($3):1/0):($4/($4+$5)) t "prev(1,1)" w l, '' u ($1==1 ? ($3):1/0):($7/($7+$8)) t "prev(2,1)" w l +plot [70:95] "biaspar/PIJ_biaspar.txt" u ($1==1 ? ($3):1/0):($4/($4+$5)) t "prev(1,1)" w l, '' u ($1==1 ? ($3):1/0):($7/($7+$8)) t "prev(2,1)" w l +set out; unset label; # # -#CV preval stable (period): 'pij' files, cov=1 state=2 -set out "biaspar/pbiaspar2_1.png" +#CV preval stable (forward): 'pij' files, covariatecombination#=1 state=2 +# + +set out "biaspar/P_biaspar_2-1-1.svg" +set label "Alive state 2 ()" at graph 0.98,0.5 center rotate font "Helvetica,12" set xlabel "Age" set ylabel "Probability" -set ter png small size 320, 240 +set ter svg size 640, 480 +unset log y +plot [70:95] "biaspar/PIJ_biaspar.txt" u ($1==1 ? ($3):1/0):($5/($4+$5)) t "prev(1,2)" w l, '' u ($1==1 ? ($3):1/0):($8/($7+$8)) t "prev(2,2)" w l +set out; unset label; + +# +# +#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=1 state=1 +# +# hpijx=probability over h years, hp.jx is weighted by observed prev + +set out "biaspar/PROJ_biaspar_1-1-1.svg" +set label "Alive state 1 ()" at graph 0.98,0.5 center rotate font "Helvetica,12" +set xlabel "Age" +set ylabel "Prevalence" +set ter svg size 640, 480 +unset log y +plot [70:95] "biaspar/F_biaspar.txt" u 2:( $5/(1.-$11)):1 t 'pw.1' with line lc variable ,\ + '' u 2:( (($1-$2) == 1919 ) ? $5/(1.-$11) : 1/0):1 with labels center not +set out; unset label; + +# +# +#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=1 state=2 +# +# hpijx=probability over h years, hp.jx is weighted by observed prev + +set out "biaspar/PROJ_biaspar_2-1-1.svg" +set label "Alive state 2 ()" at graph 0.98,0.5 center rotate font "Helvetica,12" +set xlabel "Age" +set ylabel "Prevalence" +set ter svg size 640, 480 unset log y -plot [70:95] "biaspar/pijrbiaspar.txt" u ($1==1 ? ($3):1/0):($5/($4+$5)) t "prev(1,2)" w l, '' u ($1==1 ? ($3):1/0):($8/($7+$8)) t "prev(2,2)" w l +plot [70:95] "biaspar/F_biaspar.txt" u 2:( $8/(1.-$11)):1 t 'pw.2' with line lc variable ,\ + '' u 2:( (($1-$2) == 1919 ) ? $8/(1.-$11) : 1/0):1 with labels center not +set out; unset label; ############## -#MLE estimated parameters +#9eme MLE estimated parameters ############# # initial state 1 # current state 2 -p1=-12.202711; p2=0.091764; +p1=-12.317578; p2=0.093112; # current state 3 -p3=-10.299238; p4=0.056626; +p3=-10.163170; p4=0.054838; # initial state 2 # current state 1 -p5=-1.545619; p6=-0.035395; +p5=-1.668569; p6=-0.033906; # current state 3 -p7=-5.565963; p8=0.016951; +p7=-5.686920; p8=0.018135; ############## # ############## -#Graphics of of probabilities or incidences +#10eme Graphics of probabilities or incidences ############# # logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age # logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age @@ -84,188 +276,247 @@ p7=-5.565963; p8=0.016951; # +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)) # +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...) # -# ng=1 -# jk=1 to 2^0=1 -# jk=1 +#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year +#model= +# Type of graphic ng=1 +# k1=1 to 2^0=1 -set out "biaspar/pebiaspar1_1.png" -set title "Probability" +# Combination of dummy k1=1 which is +# + +set out "biaspar/PE_biaspar_1-1-1.svg" +set key outside +set title "()" font "Helvetica,12" + +set ter svg size 640, 480 +set ylabel "Value of the logit of the model" + +unset log y +plot [70:95] p1+p2*x w l lw 2 lt (3*1+2)%3+1 dt 1 t "logit(p12)" , p3+p4*x w l lw 2 lt (3*1+3)%3+1 dt 1 t "logit(p13)" , p5+p6*x w l lw 2 lt (3*2+1)%3+1 dt 2 t "logit(p21)" , p7+p8*x w l lw 2 lt (3*2+3)%3+1 dt 2 t "logit(p23)" + set out; unset title;set key default; +#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year +#model= +# Type of graphic ng=2 +# k1=1 to 2^0=1 + + +# Combination of dummy k1=1 which is +# + +set out "biaspar/PE_biaspar_1-2-1.svg" +set key outside +set title "()" font "Helvetica,12" + +set ter svg size 640, 480 +set ylabel "Probability" -set ter png small size 320, 240 set log y -plot [70:95] exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)) t "p12" , exp(p3+p4*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)) t "p13" , exp(p5+p6*x)/(1+exp(p5+p6*x)+exp(p7+p8*x)) t "p21" , exp(p7+p8*x)/(1+exp(p5+p6*x)+exp(p7+p8*x)) t "p23" # ng=2 -# jk=1 to 2^0=1 -# jk=1 +plot [70:95] (1.)/(1+exp(p1+p2*x)+exp(p3+p4*x)) w l lw 2 lt (3*1+1)%3+1 dt 1 t "p11" , exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)) w l lw 2 lt (3*1+2)%3+1 dt 1 t "p12" , exp(p3+p4*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)) w l lw 2 lt (3*1+3)%3+1 dt 1 t "p13" , exp(p5+p6*x)/(1+exp(p5+p6*x)+exp(p7+p8*x)) w l lw 2 lt (3*2+1)%3+1 dt 2 t "p21" , (1.)/(1+exp(p5+p6*x)+exp(p7+p8*x)) w l lw 2 lt (3*2+2)%3+1 dt 2 t "p22" , exp(p7+p8*x)/(1+exp(p5+p6*x)+exp(p7+p8*x)) w l lw 2 lt (3*2+3)%3+1 dt 2 t "p23" + set out; unset title;set key default; +#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year +#model= +# Type of graphic ng=3 +# k1=1 to 2^0=1 + -set out "biaspar/pebiaspar1_2.png" +# Combination of dummy k1=1 which is +# + +set out "biaspar/PE_biaspar_1-3-1.svg" +set key outside +set title "()" font "Helvetica,12" +set ter svg size 640, 480 set ylabel "Quasi-incidence per year" -set ter png small size 320, 240 set log y -plot [70:95] 12.000000*exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)) t "p12" , 12.000000*exp(p3+p4*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)) t "p13" , 12.000000*exp(p5+p6*x)/(1+exp(p5+p6*x)+exp(p7+p8*x)) t "p21" , 12.000000*exp(p7+p8*x)/(1+exp(p5+p6*x)+exp(p7+p8*x)) t "p23" +plot [70:95] (1.)/(1+exp(p1+p2*x)+exp(p3+p4*x)) w l lw 2 lt (3*1+1)%3+1 dt 1 t "i11" , 12.000000*exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)) w l lw 2 lt (3*1+2)%3+1 dt 1 t "i12" , 12.000000*exp(p3+p4*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)) w l lw 2 lt (3*1+3)%3+1 dt 1 t "i13" , 12.000000*exp(p5+p6*x)/(1+exp(p5+p6*x)+exp(p7+p8*x)) w l lw 2 lt (3*2+1)%3+1 dt 2 t "i21" , (1.)/(1+exp(p5+p6*x)+exp(p7+p8*x)) w l lw 2 lt (3*2+2)%3+1 dt 2 t "i22" , 12.000000*exp(p7+p8*x)/(1+exp(p5+p6*x)+exp(p7+p8*x)) w l lw 2 lt (3*2+3)%3+1 dt 2 t "i23" + set out; unset title;set key default; + # Routine varprob +# Ellipsoids of confidence +# + set parametric;unset label set log y;set log x; set xlabel "p13 (year-1)";set ylabel "p12 (year-1)" -set ter png small size 320, 240 -set out "biaspar/varpijgrbiaspar113-12.png" -set label "65" at 1.597e-02, 2.337e-02 center -# Age 65, p13 - p12 -plot [-pi:pi] 1.597e-02+ 2.000*( 7.325e-01* 2.084e-03*cos(t)+ 6.807e-01* 1.465e-03*sin(t)), 2.337e-02 +2.000*( -6.807e-01* 2.084e-03*cos(t)+ 7.325e-01* 1.465e-03*sin(t)) not +set ter svg size 640, 480 +set out "biaspar/VARPIJGR_biaspar_113-12.svg" +set label "70" at 2.140e-02, 3.617e-02 center # Age 70, p13 - p12 -set label "70" at 2.117e-02, 3.691e-02 center -replot 2.117e-02+ 2.000*( 5.240e-01* 2.315e-03*cos(t)+ 8.517e-01* 1.521e-03*sin(t)), 3.691e-02 +2.000*( -8.517e-01* 2.315e-03*cos(t)+ 5.240e-01* 1.521e-03*sin(t)) not +plot [-pi:pi] 2.140e-02+ 2.000*( 5.514e-01* 2.264e-03*cos(t)+ 8.342e-01* 1.523e-03*sin(t)), 3.617e-02 +2.000*( -8.342e-01* 2.264e-03*cos(t)+ 5.514e-01* 1.523e-03*sin(t)) not # Age 75, p13 - p12 -set label "75" at 2.803e-02, 5.827e-02 center -replot 2.803e-02+ 2.000*( 3.929e-01* 2.501e-03*cos(t)+ 9.196e-01* 1.403e-03*sin(t)), 5.827e-02 +2.000*( -9.196e-01* 2.501e-03*cos(t)+ 3.929e-01* 1.403e-03*sin(t)) not +set label "75" at 2.808e-02, 5.747e-02 center +replot 2.808e-02+ 2.000*( 3.943e-01* 2.448e-03*cos(t)+ 9.190e-01* 1.398e-03*sin(t)), 5.747e-02 +2.000*( -9.190e-01* 2.448e-03*cos(t)+ 3.943e-01* 1.398e-03*sin(t)) not # Age 80, p13 - p12 -set label "80" at 3.707e-02, 9.186e-02 center -replot 3.707e-02+ 2.000*( 3.828e-01* 2.718e-03*cos(t)+ 9.238e-01* 1.387e-03*sin(t)), 9.186e-02 +2.000*( -9.238e-01* 2.718e-03*cos(t)+ 3.828e-01* 1.387e-03*sin(t)) not +set label "80" at 3.681e-02, 9.123e-02 center +replot 3.681e-02+ 2.000*( 3.741e-01* 2.676e-03*cos(t)+ 9.274e-01* 1.373e-03*sin(t)), 9.123e-02 +2.000*( -9.274e-01* 2.676e-03*cos(t)+ 3.741e-01* 1.373e-03*sin(t)) not # Age 85, p13 - p12 -set label "85" at 4.893e-02, 1.445e-01 center -replot 4.893e-02+ 2.000*( 4.026e-01* 4.082e-03*cos(t)+ 9.154e-01* 2.265e-03*sin(t)), 1.445e-01 +2.000*( -9.154e-01* 4.082e-03*cos(t)+ 4.026e-01* 2.265e-03*sin(t)) not +set label "85" at 4.816e-02, 1.445e-01 center +replot 4.816e-02+ 2.000*( 3.906e-01* 4.057e-03*cos(t)+ 9.206e-01* 2.238e-03*sin(t)), 1.445e-01 +2.000*( -9.206e-01* 4.057e-03*cos(t)+ 3.906e-01* 2.238e-03*sin(t)) not # Age 90, p13 - p12 -set label "90" at 6.441e-02, 2.268e-01 center -replot 6.441e-02+ 2.000*( 2.874e-01* 8.787e-03*cos(t)+ 9.578e-01* 4.578e-03*sin(t)), 2.268e-01 +2.000*( -9.578e-01* 8.787e-03*cos(t)+ 2.874e-01* 4.578e-03*sin(t)) not +set label "90" at 6.283e-02, 2.283e-01 center +replot 6.283e-02+ 2.000*( 2.754e-01* 8.795e-03*cos(t)+ 9.613e-01* 4.488e-03*sin(t)), 2.283e-01 +2.000*( -9.613e-01* 8.795e-03*cos(t)+ 2.754e-01* 4.488e-03*sin(t)) not # Age 95, p13 - p12 -set label "95" at 8.441e-02, 3.543e-01 center -replot 8.441e-02+ 2.000*( 2.019e-01* 1.921e-02*cos(t)+ 9.794e-01* 8.453e-03*sin(t)), 3.543e-01 +2.000*( -9.794e-01* 1.921e-02*cos(t)+ 2.019e-01* 8.453e-03*sin(t)) not -set out "biaspar/varpijgrbiaspar113-12.png";replot; +set label "95" at 8.159e-02, 3.590e-01 center +replot 8.159e-02+ 2.000*( 1.909e-01* 1.934e-02*cos(t)+ 9.816e-01* 8.213e-03*sin(t)), 3.590e-01 +2.000*( -9.816e-01* 1.934e-02*cos(t)+ 1.909e-01* 8.213e-03*sin(t)) not +set out; +set out "biaspar/VARPIJGR_biaspar_113-12.svg";replot;set out; +# Ellipsoids of confidence +# + set parametric;unset label set log y;set log x; set xlabel "p21 (year-1)";set ylabel "p12 (year-1)" -set ter png small size 320, 240 -set out "biaspar/varpijgrbiaspar121-12.png" -set label "65" at 2.481e-01, 2.337e-02 center -# Age 65, p21 - p12 -plot [-pi:pi] 2.481e-01+ 2.000*( 9.999e-01* 3.884e-02*cos(t)+ -1.528e-02* 1.677e-03*sin(t)), 2.337e-02 +2.000*( 1.528e-02* 3.884e-02*cos(t)+ 9.999e-01* 1.677e-03*sin(t)) not +set ter svg size 640, 480 +set out "biaspar/VARPIJGR_biaspar_121-12.svg" +set label "70" at 2.047e-01, 3.617e-02 center # Age 70, p21 - p12 -set label "70" at 2.084e-01, 3.691e-02 center -replot 2.084e-01+ 2.000*( 9.996e-01* 2.493e-02*cos(t)+ -2.848e-02* 2.005e-03*sin(t)), 3.691e-02 +2.000*( 2.848e-02* 2.493e-02*cos(t)+ 9.996e-01* 2.005e-03*sin(t)) not +plot [-pi:pi] 2.047e-01+ 2.000*( 9.996e-01* 2.493e-02*cos(t)+ -2.854e-02* 1.942e-03*sin(t)), 3.617e-02 +2.000*( 2.854e-02* 2.493e-02*cos(t)+ 9.996e-01* 1.942e-03*sin(t)) not # Age 75, p21 - p12 -set label "75" at 1.749e-01, 5.827e-02 center -replot 1.749e-01+ 2.000*( 9.986e-01* 1.487e-02*cos(t)+ -5.306e-02* 2.233e-03*sin(t)), 5.827e-02 +2.000*( 5.306e-02* 1.487e-02*cos(t)+ 9.986e-01* 2.233e-03*sin(t)) not +set label "75" at 1.730e-01, 5.747e-02 center +replot 1.730e-01+ 2.000*( 9.986e-01* 1.494e-02*cos(t)+ -5.266e-02* 2.181e-03*sin(t)), 5.747e-02 +2.000*( 5.266e-02* 1.494e-02*cos(t)+ 9.986e-01* 2.181e-03*sin(t)) not # Age 80, p21 - p12 -set label "80" at 1.467e-01, 9.186e-02 center -replot 1.467e-01+ 2.000*( 9.949e-01* 8.452e-03*cos(t)+ -1.006e-01* 2.434e-03*sin(t)), 9.186e-02 +2.000*( 1.006e-01* 8.452e-03*cos(t)+ 9.949e-01* 2.434e-03*sin(t)) not +set label "80" at 1.462e-01, 9.123e-02 center +replot 1.462e-01+ 2.000*( 9.951e-01* 8.486e-03*cos(t)+ -9.892e-02* 2.403e-03*sin(t)), 9.123e-02 +2.000*( 9.892e-02* 8.486e-03*cos(t)+ 9.951e-01* 2.403e-03*sin(t)) not # Age 85, p21 - p12 -set label "85" at 1.230e-01, 1.445e-01 center -replot 1.230e-01+ 2.000*( 9.691e-01* 6.397e-03*cos(t)+ -2.468e-01* 3.619e-03*sin(t)), 1.445e-01 +2.000*( 2.468e-01* 6.397e-03*cos(t)+ 9.691e-01* 3.619e-03*sin(t)) not +set label "85" at 1.235e-01, 1.445e-01 center +replot 1.235e-01+ 2.000*( 9.684e-01* 6.423e-03*cos(t)+ -2.493e-01* 3.599e-03*sin(t)), 1.445e-01 +2.000*( 2.493e-01* 6.423e-03*cos(t)+ 9.684e-01* 3.599e-03*sin(t)) not # Age 90, p21 - p12 -set label "90" at 1.031e-01, 2.268e-01 center -replot 1.031e-01+ 2.000*( 5.313e-01* 9.166e-03*cos(t)+ -8.472e-01* 6.591e-03*sin(t)), 2.268e-01 +2.000*( 8.472e-01* 9.166e-03*cos(t)+ 5.313e-01* 6.591e-03*sin(t)) not +set label "90" at 1.042e-01, 2.283e-01 center +replot 1.042e-01+ 2.000*( 5.573e-01* 9.289e-03*cos(t)+ -8.303e-01* 6.600e-03*sin(t)), 2.283e-01 +2.000*( 8.303e-01* 9.289e-03*cos(t)+ 5.573e-01* 6.600e-03*sin(t)) not # Age 95, p21 - p12 -set label "95" at 8.634e-02, 3.543e-01 center -replot 8.634e-02+ 2.000*( 1.792e-01* 1.914e-02*cos(t)+ -9.838e-01* 8.537e-03*sin(t)), 3.543e-01 +2.000*( 9.838e-01* 1.914e-02*cos(t)+ 1.792e-01* 8.537e-03*sin(t)) not -set out "biaspar/varpijgrbiaspar121-12.png";replot; +set label "95" at 8.796e-02, 3.590e-01 center +replot 8.796e-02+ 2.000*( 1.959e-01* 1.934e-02*cos(t)+ -9.806e-01* 8.711e-03*sin(t)), 3.590e-01 +2.000*( 9.806e-01* 1.934e-02*cos(t)+ 1.959e-01* 8.711e-03*sin(t)) not +set out; +set out "biaspar/VARPIJGR_biaspar_121-12.svg";replot;set out; +# Ellipsoids of confidence +# + set parametric;unset label set log y;set log x; set xlabel "p23 (year-1)";set ylabel "p12 (year-1)" -set ter png small size 320, 240 -set out "biaspar/varpijgrbiaspar123-12.png" -set label "65" at 1.338e-01, 2.337e-02 center -# Age 65, p23 - p12 -plot [-pi:pi] 1.338e-01+ 2.000*( 9.993e-01* 1.768e-02*cos(t)+ -3.696e-02* 1.655e-03*sin(t)), 2.337e-02 +2.000*( 3.696e-02* 1.768e-02*cos(t)+ 9.993e-01* 1.655e-03*sin(t)) not +set ter svg size 640, 480 +set out "biaspar/VARPIJGR_biaspar_123-12.svg" +set label "70" at 1.406e-01, 3.617e-02 center # Age 70, p23 - p12 -set label "70" at 1.460e-01, 3.691e-02 center -replot 1.460e-01+ 2.000*( 9.985e-01* 1.541e-02*cos(t)+ -5.441e-02* 1.957e-03*sin(t)), 3.691e-02 +2.000*( 5.441e-02* 1.541e-02*cos(t)+ 9.985e-01* 1.957e-03*sin(t)) not +plot [-pi:pi] 1.406e-01+ 2.000*( 9.987e-01* 1.493e-02*cos(t)+ -5.178e-02* 1.920e-03*sin(t)), 3.617e-02 +2.000*( 5.178e-02* 1.493e-02*cos(t)+ 9.987e-01* 1.920e-03*sin(t)) not # Age 75, p23 - p12 -set label "75" at 1.591e-01, 5.827e-02 center -replot 1.591e-01+ 2.000*( 9.967e-01* 1.275e-02*cos(t)+ -8.076e-02* 2.137e-03*sin(t)), 5.827e-02 +2.000*( 8.076e-02* 1.275e-02*cos(t)+ 9.967e-01* 2.137e-03*sin(t)) not +set label "75" at 1.542e-01, 5.747e-02 center +replot 1.542e-01+ 2.000*( 9.970e-01* 1.241e-02*cos(t)+ -7.775e-02* 2.112e-03*sin(t)), 5.747e-02 +2.000*( 7.775e-02* 1.241e-02*cos(t)+ 9.970e-01* 2.112e-03*sin(t)) not # Age 80, p23 - p12 -set label "80" at 1.734e-01, 9.186e-02 center -replot 1.734e-01+ 2.000*( 9.924e-01* 9.884e-03*cos(t)+ -1.231e-01* 2.277e-03*sin(t)), 9.186e-02 +2.000*( 1.231e-01* 9.884e-03*cos(t)+ 9.924e-01* 2.277e-03*sin(t)) not +set label "80" at 1.690e-01, 9.123e-02 center +replot 1.690e-01+ 2.000*( 9.927e-01* 9.663e-03*cos(t)+ -1.210e-01* 2.265e-03*sin(t)), 9.123e-02 +2.000*( 1.210e-01* 9.663e-03*cos(t)+ 9.927e-01* 2.265e-03*sin(t)) not # Age 85, p23 - p12 -set label "85" at 1.889e-01, 1.445e-01 center -replot 1.889e-01+ 2.000*( 9.741e-01* 7.696e-03*cos(t)+ -2.260e-01* 3.522e-03*sin(t)), 1.445e-01 +2.000*( 2.260e-01* 7.696e-03*cos(t)+ 9.741e-01* 3.522e-03*sin(t)) not +set label "85" at 1.851e-01, 1.445e-01 center +replot 1.851e-01+ 2.000*( 9.733e-01* 7.552e-03*cos(t)+ -2.295e-01* 3.515e-03*sin(t)), 1.445e-01 +2.000*( 2.295e-01* 7.552e-03*cos(t)+ 9.733e-01* 3.515e-03*sin(t)) not # Age 90, p23 - p12 -set label "90" at 2.057e-01, 2.268e-01 center -replot 2.057e-01+ 2.000*( 6.276e-01* 9.309e-03*cos(t)+ -7.786e-01* 7.132e-03*sin(t)), 2.268e-01 +2.000*( 7.786e-01* 9.309e-03*cos(t)+ 6.276e-01* 7.132e-03*sin(t)) not +set label "90" at 2.028e-01, 2.283e-01 center +replot 2.028e-01+ 2.000*( 6.011e-01* 9.259e-03*cos(t)+ -7.992e-01* 7.110e-03*sin(t)), 2.283e-01 +2.000*( 7.992e-01* 9.259e-03*cos(t)+ 6.011e-01* 7.110e-03*sin(t)) not # Age 95, p23 - p12 -set label "95" at 2.238e-01, 3.543e-01 center -replot 2.238e-01+ 2.000*( 2.443e-01* 1.925e-02*cos(t)+ -9.697e-01* 1.172e-02*sin(t)), 3.543e-01 +2.000*( 9.697e-01* 1.925e-02*cos(t)+ 2.443e-01* 1.172e-02*sin(t)) not -set out "biaspar/varpijgrbiaspar123-12.png";replot; +set label "95" at 2.219e-01, 3.590e-01 center +replot 2.219e-01+ 2.000*( 2.273e-01* 1.937e-02*cos(t)+ -9.738e-01* 1.173e-02*sin(t)), 3.590e-01 +2.000*( 9.738e-01* 1.937e-02*cos(t)+ 2.273e-01* 1.173e-02*sin(t)) not +set out; +set out "biaspar/VARPIJGR_biaspar_123-12.svg";replot;set out; +# Ellipsoids of confidence +# + set parametric;unset label set log y;set log x; set xlabel "p21 (year-1)";set ylabel "p13 (year-1)" -set ter png small size 320, 240 -set out "biaspar/varpijgrbiaspar121-13.png" -set label "65" at 2.481e-01, 1.597e-02 center -# Age 65, p21 - p13 -plot [-pi:pi] 2.481e-01+ 2.000*( 1.000e+00* 3.883e-02*cos(t)+ -2.210e-03* 1.821e-03*sin(t)), 1.597e-02 +2.000*( 2.210e-03* 3.883e-02*cos(t)+ 1.000e+00* 1.821e-03*sin(t)) not +set ter svg size 640, 480 +set out "biaspar/VARPIJGR_biaspar_121-13.svg" +set label "70" at 2.047e-01, 2.140e-02 center # Age 70, p21 - p13 -set label "70" at 2.084e-01, 2.117e-02 center -replot 2.084e-01+ 2.000*( 1.000e+00* 2.492e-02*cos(t)+ -2.683e-03* 1.773e-03*sin(t)), 2.117e-02 +2.000*( 2.683e-03* 2.492e-02*cos(t)+ 1.000e+00* 1.773e-03*sin(t)) not +plot [-pi:pi] 2.047e-01+ 2.000*( 1.000e+00* 2.492e-02*cos(t)+ -2.081e-03* 1.781e-03*sin(t)), 2.140e-02 +2.000*( 2.081e-03* 2.492e-02*cos(t)+ 1.000e+00* 1.781e-03*sin(t)) not # Age 75, p21 - p13 -set label "75" at 1.749e-01, 2.803e-02 center -replot 1.749e-01+ 2.000*( 1.000e+00* 1.485e-02*cos(t)+ -2.605e-03* 1.622e-03*sin(t)), 2.803e-02 +2.000*( 2.605e-03* 1.485e-02*cos(t)+ 1.000e+00* 1.622e-03*sin(t)) not +set label "75" at 1.730e-01, 2.808e-02 center +replot 1.730e-01+ 2.000*( 1.000e+00* 1.492e-02*cos(t)+ -2.295e-03* 1.606e-03*sin(t)), 2.808e-02 +2.000*( 2.295e-03* 1.492e-02*cos(t)+ 1.000e+00* 1.606e-03*sin(t)) not # Age 80, p21 - p13 -set label "80" at 1.467e-01, 3.707e-02 center -replot 1.467e-01+ 2.000*( 1.000e+00* 8.412e-03*cos(t)+ -4.929e-03* 1.650e-03*sin(t)), 3.707e-02 +2.000*( 4.929e-03* 8.412e-03*cos(t)+ 1.000e+00* 1.650e-03*sin(t)) not +set label "80" at 1.462e-01, 3.681e-02 center +replot 1.462e-01+ 2.000*( 1.000e+00* 8.448e-03*cos(t)+ -5.527e-03* 1.619e-03*sin(t)), 3.681e-02 +2.000*( 5.527e-03* 8.448e-03*cos(t)+ 1.000e+00* 1.619e-03*sin(t)) not # Age 85, p21 - p13 -set label "85" at 1.230e-01, 4.893e-02 center -replot 1.230e-01+ 2.000*( 9.992e-01* 6.267e-03*cos(t)+ -3.981e-02* 2.636e-03*sin(t)), 4.893e-02 +2.000*( 3.981e-02* 6.267e-03*cos(t)+ 9.992e-01* 2.636e-03*sin(t)) not +set label "85" at 1.235e-01, 4.816e-02 center +replot 1.235e-01+ 2.000*( 9.994e-01* 6.288e-03*cos(t)+ -3.508e-02* 2.591e-03*sin(t)), 4.816e-02 +2.000*( 3.508e-02* 6.288e-03*cos(t)+ 9.994e-01* 2.591e-03*sin(t)) not # Age 90, p21 - p13 -set label "90" at 1.031e-01, 6.441e-02 center -replot 1.031e-01+ 2.000*( 9.921e-01* 7.441e-03*cos(t)+ -1.255e-01* 5.013e-03*sin(t)), 6.441e-02 +2.000*( 1.255e-01* 7.441e-03*cos(t)+ 9.921e-01* 5.013e-03*sin(t)) not +set label "90" at 1.042e-01, 6.283e-02 center +replot 1.042e-01+ 2.000*( 9.956e-01* 7.558e-03*cos(t)+ -9.337e-02* 4.919e-03*sin(t)), 6.283e-02 +2.000*( 9.337e-02* 7.558e-03*cos(t)+ 9.956e-01* 4.919e-03*sin(t)) not # Age 95, p21 - p13 -set label "95" at 8.634e-02, 8.441e-02 center -replot 8.634e-02+ 2.000*( 6.785e-01* 9.541e-03*cos(t)+ -7.346e-01* 8.651e-03*sin(t)), 8.441e-02 +2.000*( 7.346e-01* 9.541e-03*cos(t)+ 6.785e-01* 8.651e-03*sin(t)) not -set out "biaspar/varpijgrbiaspar121-13.png";replot; +set label "95" at 8.796e-02, 8.159e-02 center +replot 8.796e-02+ 2.000*( 8.858e-01* 9.520e-03*cos(t)+ -4.641e-01* 8.679e-03*sin(t)), 8.159e-02 +2.000*( 4.641e-01* 9.520e-03*cos(t)+ 8.858e-01* 8.679e-03*sin(t)) not +set out; +set out "biaspar/VARPIJGR_biaspar_121-13.svg";replot;set out; +# Ellipsoids of confidence +# + set parametric;unset label set log y;set log x; set xlabel "p23 (year-1)";set ylabel "p13 (year-1)" -set ter png small size 320, 240 -set out "biaspar/varpijgrbiaspar123-13.png" -set label "65" at 1.338e-01, 1.597e-02 center -# Age 65, p23 - p13 -plot [-pi:pi] 1.338e-01+ 2.000*( 9.991e-01* 1.769e-02*cos(t)+ 4.256e-02* 1.662e-03*sin(t)), 1.597e-02 +2.000*( -4.256e-02* 1.769e-02*cos(t)+ 9.991e-01* 1.662e-03*sin(t)) not +set ter svg size 640, 480 +set out "biaspar/VARPIJGR_biaspar_123-13.svg" +set label "70" at 1.406e-01, 2.140e-02 center # Age 70, p23 - p13 -set label "70" at 1.460e-01, 2.117e-02 center -replot 1.460e-01+ 2.000*( 9.986e-01* 1.541e-02*cos(t)+ 5.267e-02* 1.580e-03*sin(t)), 2.117e-02 +2.000*( -5.267e-02* 1.541e-02*cos(t)+ 9.986e-01* 1.580e-03*sin(t)) not +plot [-pi:pi] 1.406e-01+ 2.000*( 9.985e-01* 1.494e-02*cos(t)+ 5.556e-02* 1.579e-03*sin(t)), 2.140e-02 +2.000*( -5.556e-02* 1.494e-02*cos(t)+ 9.985e-01* 1.579e-03*sin(t)) not # Age 75, p23 - p13 -set label "75" at 1.591e-01, 2.803e-02 center -replot 1.591e-01+ 2.000*( 9.977e-01* 1.273e-02*cos(t)+ 6.800e-02* 1.375e-03*sin(t)), 2.803e-02 +2.000*( -6.800e-02* 1.273e-02*cos(t)+ 9.977e-01* 1.375e-03*sin(t)) not +set label "75" at 1.542e-01, 2.808e-02 center +replot 1.542e-01+ 2.000*( 9.976e-01* 1.240e-02*cos(t)+ 6.965e-02* 1.358e-03*sin(t)), 2.808e-02 +2.000*( -6.965e-02* 1.240e-02*cos(t)+ 9.976e-01* 1.358e-03*sin(t)) not # Age 80, p23 - p13 -set label "80" at 1.734e-01, 3.707e-02 center -replot 1.734e-01+ 2.000*( 9.950e-01* 9.861e-03*cos(t)+ 9.978e-02* 1.332e-03*sin(t)), 3.707e-02 +2.000*( -9.978e-02* 9.861e-03*cos(t)+ 9.950e-01* 1.332e-03*sin(t)) not +set label "80" at 1.690e-01, 3.681e-02 center +replot 1.690e-01+ 2.000*( 9.951e-01* 9.643e-03*cos(t)+ 9.913e-02* 1.314e-03*sin(t)), 3.681e-02 +2.000*( -9.913e-02* 9.643e-03*cos(t)+ 9.951e-01* 1.314e-03*sin(t)) not # Age 85, p23 - p13 -set label "85" at 1.889e-01, 4.893e-02 center -replot 1.889e-01+ 2.000*( 9.810e-01* 7.672e-03*cos(t)+ 1.938e-01* 2.231e-03*sin(t)), 4.893e-02 +2.000*( -1.938e-01* 7.672e-03*cos(t)+ 9.810e-01* 2.231e-03*sin(t)) not +set label "85" at 1.851e-01, 4.816e-02 center +replot 1.851e-01+ 2.000*( 9.815e-01* 7.522e-03*cos(t)+ 1.914e-01* 2.205e-03*sin(t)), 4.816e-02 +2.000*( -1.914e-01* 7.522e-03*cos(t)+ 9.815e-01* 2.205e-03*sin(t)) not # Age 90, p23 - p13 -set label "90" at 2.057e-01, 6.441e-02 center -replot 2.057e-01+ 2.000*( 9.336e-01* 8.471e-03*cos(t)+ 3.582e-01* 4.337e-03*sin(t)), 6.441e-02 +2.000*( -3.582e-01* 8.471e-03*cos(t)+ 9.336e-01* 4.337e-03*sin(t)) not +set label "90" at 2.028e-01, 6.283e-02 center +replot 2.028e-01+ 2.000*( 9.340e-01* 8.361e-03*cos(t)+ 3.573e-01* 4.223e-03*sin(t)), 6.283e-02 +2.000*( -3.573e-01* 8.361e-03*cos(t)+ 9.340e-01* 4.223e-03*sin(t)) not # Age 95, p23 - p13 -set label "95" at 2.238e-01, 8.441e-02 center -replot 2.238e-01+ 2.000*( 9.049e-01* 1.305e-02*cos(t)+ 4.257e-01* 8.023e-03*sin(t)), 8.441e-02 +2.000*( -4.257e-01* 1.305e-02*cos(t)+ 9.049e-01* 8.023e-03*sin(t)) not -set out "biaspar/varpijgrbiaspar123-13.png";replot; +set label "95" at 2.219e-01, 8.159e-02 center +replot 2.219e-01+ 2.000*( 9.094e-01* 1.298e-02*cos(t)+ 4.159e-01* 7.733e-03*sin(t)), 8.159e-02 +2.000*( -4.159e-01* 1.298e-02*cos(t)+ 9.094e-01* 7.733e-03*sin(t)) not +set out; +set out "biaspar/VARPIJGR_biaspar_123-13.svg";replot;set out; +# Ellipsoids of confidence +# + set parametric;unset label set log y;set log x; set xlabel "p23 (year-1)";set ylabel "p21 (year-1)" -set ter png small size 320, 240 -set out "biaspar/varpijgrbiaspar123-21.png" -set label "65" at 1.338e-01, 2.481e-01 center -# Age 65, p23 - p21 -plot [-pi:pi] 1.338e-01+ 2.000*( 8.647e-03* 3.884e-02*cos(t)+ 1.000e+00* 1.767e-02*sin(t)), 2.481e-01 +2.000*( -1.000e+00* 3.884e-02*cos(t)+ 8.647e-03* 1.767e-02*sin(t)) not +set ter svg size 640, 480 +set out "biaspar/VARPIJGR_biaspar_123-21.svg" +set label "70" at 1.406e-01, 2.047e-01 center # Age 70, p23 - p21 -set label "70" at 1.460e-01, 2.084e-01 center -replot 1.460e-01+ 2.000*( 1.255e-02* 2.493e-02*cos(t)+ 9.999e-01* 1.539e-02*sin(t)), 2.084e-01 +2.000*( -9.999e-01* 2.493e-02*cos(t)+ 1.255e-02* 1.539e-02*sin(t)) not +plot [-pi:pi] 1.406e-01+ 2.000*( 3.099e-02* 2.492e-02*cos(t)+ 9.995e-01* 1.490e-02*sin(t)), 2.047e-01 +2.000*( -9.995e-01* 2.492e-02*cos(t)+ 3.099e-02* 1.490e-02*sin(t)) not # Age 75, p23 - p21 -set label "75" at 1.591e-01, 1.749e-01 center -replot 1.591e-01+ 2.000*( 4.580e-02* 1.486e-02*cos(t)+ 9.990e-01* 1.270e-02*sin(t)), 1.749e-01 +2.000*( -9.990e-01* 1.486e-02*cos(t)+ 4.580e-02* 1.270e-02*sin(t)) not +set label "75" at 1.542e-01, 1.730e-01 center +replot 1.542e-01+ 2.000*( 8.468e-02* 1.494e-02*cos(t)+ 9.964e-01* 1.235e-02*sin(t)), 1.730e-01 +2.000*( -9.964e-01* 1.494e-02*cos(t)+ 8.468e-02* 1.235e-02*sin(t)) not # Age 80, p23 - p21 -set label "80" at 1.734e-01, 1.467e-01 center -replot 1.734e-01+ 2.000*( 9.957e-01* 9.824e-03*cos(t)+ 9.255e-02* 8.399e-03*sin(t)), 1.467e-01 +2.000*( -9.255e-02* 9.824e-03*cos(t)+ 9.957e-01* 8.399e-03*sin(t)) not +set label "80" at 1.690e-01, 1.462e-01 center +replot 1.690e-01+ 2.000*( 9.896e-01* 9.619e-03*cos(t)+ 1.436e-01* 8.421e-03*sin(t)), 1.462e-01 +2.000*( -1.436e-01* 9.619e-03*cos(t)+ 9.896e-01* 8.421e-03*sin(t)) not # Age 85, p23 - p21 -set label "85" at 1.889e-01, 1.230e-01 center -replot 1.889e-01+ 2.000*( 9.875e-01* 7.569e-03*cos(t)+ 1.578e-01* 6.226e-03*sin(t)), 1.230e-01 +2.000*( -1.578e-01* 7.569e-03*cos(t)+ 9.875e-01* 6.226e-03*sin(t)) not +set label "85" at 1.851e-01, 1.235e-01 center +replot 1.851e-01+ 2.000*( 9.870e-01* 7.423e-03*cos(t)+ 1.606e-01* 6.252e-03*sin(t)), 1.235e-01 +2.000*( -1.606e-01* 7.423e-03*cos(t)+ 9.870e-01* 6.252e-03*sin(t)) not # Age 90, p23 - p21 -set label "90" at 2.057e-01, 1.031e-01 center -replot 2.057e-01+ 2.000*( 9.508e-01* 8.134e-03*cos(t)+ 3.099e-01* 7.328e-03*sin(t)), 1.031e-01 +2.000*( -3.099e-01* 8.134e-03*cos(t)+ 9.508e-01* 7.328e-03*sin(t)) not +set label "90" at 2.028e-01, 1.042e-01 center +replot 2.028e-01+ 2.000*( 9.136e-01* 8.053e-03*cos(t)+ 4.065e-01* 7.432e-03*sin(t)), 1.042e-01 +2.000*( -4.065e-01* 8.053e-03*cos(t)+ 9.136e-01* 7.432e-03*sin(t)) not # Age 95, p23 - p21 -set label "95" at 2.238e-01, 8.634e-02 center -replot 2.238e-01+ 2.000*( 9.979e-01* 1.231e-02*cos(t)+ 6.495e-02* 9.056e-03*sin(t)), 8.634e-02 +2.000*( -6.495e-02* 1.231e-02*cos(t)+ 9.979e-01* 9.056e-03*sin(t)) not -set out "biaspar/varpijgrbiaspar123-21.png";replot; +set label "95" at 2.219e-01, 8.796e-02 center +replot 2.219e-01+ 2.000*( 9.960e-01* 1.226e-02*cos(t)+ 8.959e-02* 9.318e-03*sin(t)), 8.796e-02 +2.000*( -8.959e-02* 1.226e-02*cos(t)+ 9.960e-01* 9.318e-03*sin(t)) not +set out; +set out "biaspar/VARPIJGR_biaspar_123-21.svg";replot;set out; +# Routine varevsij +unset title + +unset parametric;unset label; set ter svg size 640, 480 + set log y; unset log x;set xlabel "Age"; set ylabel "Force of mortality (year-1)"; +set out "biaspar/VARMUPTJGR--STABLBASED_biaspar1.svg"; + plot "biaspar/PRMORPREV-1-STABLBASED_biaspar.txt" u 1:($3) not w l lt 1 + replot "biaspar/PRMORPREV-1-STABLBASED_biaspar.txt" u 1:(($3+1.96*$4)) t "95% interval" w l lt 2 + replot "biaspar/PRMORPREV-1-STABLBASED_biaspar.txt" u 1:(($3-1.96*$4)) not w l lt 2 +set out; +set out "biaspar/VARMUPTJGR--STABLBASED_biaspar1.svg";replot;set out; + # Routine varevsij -unset parametric;unset label; set ter png small size 320, 240 +unset title + +unset parametric;unset label; set ter svg size 640, 480 set log y; unset log x;set xlabel "Age"; set ylabel "Force of mortality (year-1)"; - plot "biaspar/prmorprev1-stablbased-rbiaspar.txt" u 1:($3) not w l lt 1 - replot "biaspar/prmorprev1-stablbased-rbiaspar.txt" u 1:(($3+1.96*$4)) t "95% interval" w l lt 2 - replot "biaspar/prmorprev1-stablbased-rbiaspar.txt" u 1:(($3-1.96*$4)) not w l lt 2 -set out "biaspar/varmuptjgr-stablbased-biaspar1.png";replot; +set out "biaspar/VARMUPTJGR--POPULBASED-NOMOBIL_biaspar1.svg"; + plot "biaspar/PRMORPREV-1-POPULBASED-NOMOBIL_biaspar.txt" u 1:($3) not w l lt 1 + replot "biaspar/PRMORPREV-1-POPULBASED-NOMOBIL_biaspar.txt" u 1:(($3+1.96*$4)) t "95% interval" w l lt 2 + replot "biaspar/PRMORPREV-1-POPULBASED-NOMOBIL_biaspar.txt" u 1:(($3-1.96*$4)) not w l lt 2 +set out; +set out "biaspar/VARMUPTJGR--POPULBASED-NOMOBIL_biaspar1.svg";replot;set out; diff --git a/html/doc/biaspar.htm b/html/doc/biaspar.htm index a7b053f..6921d63 100644 --- a/html/doc/biaspar.htm +++ b/html/doc/biaspar.htm @@ -1,58 +1,107 @@ + + IMaCh biaspar.htm - Imach version 0.98q5, August 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015
$Revision$ $Date$

-Title=1st_example
Datafile=data1.txt Firstpass=1 Lastpass=4 Stepm=1 Weight=0 Model=
+ IMaCh for Interpolated Markov Chain
+Sponsored by Copyright (C) 2002-2015 INED-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (Grant-in-Aid for Scientific Research 25293121) - Intel Software 2015-2018
+IMaCh-0.99r19
$Revision$ $Date$
+Title=1st_example
Datafile=data1.txt Firstpass=1 Lastpass=4 Stepm=1 Weight=0 Model=1+age+
+

Parameter line 2

+

Diagram of states biaspar/D_biaspar_.svg

+ +

Some descriptive statistics


Total number of observations=8270
Youngest age at first (selected) pass 70.00, oldest age 104.17
-Interval (in months) between two waves: Min=1 Max=74 Mean=24.04
+Interval (in months) between two waves: Min=1 Max=74 Mean=24.06
-
File of contributions to the likelihood: biaspar/ilkrbiaspar.txt
-