From: N. Brouard Date: Fri, 19 Jul 2024 12:01:40 +0000 (+0000) Subject: *** empty log message *** X-Git-Tag: imach-099s7~4 X-Git-Url: https://henry.ined.fr/git/?a=commitdiff_plain;h=e9790ab123d443b7d3939ec070e77b3832e9ed5d;p=.git *** empty log message *** --- diff --git a/html/doc/biaspar-cov.htm b/html/doc/biaspar-cov.htm deleted file mode 100644 index 19a332a..0000000 --- a/html/doc/biaspar-cov.htm +++ /dev/null @@ -1,33 +0,0 @@ - -IMaCh Cov biaspar-cov.htm - 0.99r24
$Revision$ $Date$
-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

- -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/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 Thu May 20 15:42:13 2021 -
Local time at end Thu May 20 15:43:12 2021 -
- \ No newline at end of file diff --git a/html/doc/biaspar.gp b/html/doc/biaspar.gp deleted file mode 100644 index ba9f46e..0000000 --- a/html/doc/biaspar.gp +++ /dev/null @@ -1,522 +0,0 @@ - -# IMaCh-0.99r24 -# biaspar.gp -set datafile missing 'NaNq' -cd "/Users/nbrouard/Documents/imach/cvs/imach/html/doc" - -#Diagram of the model - -delta=0.03;delta2=0.07;unset arrow; -yoff=(2 > 2? 0:1); - -#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 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 "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 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 label "popbased 0 ()" at graph 0.98,0.5 center rotate font "Helvetica,12" -set ylabel "Years" -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 svg size 640, 480 -unset log y -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 (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 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/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; - -############## -#9eme MLE estimated parameters -############# -# initial state 1 -# current state 2 -p1=-12.317578; p2=0.093112; -# current state 3 -p3=-10.163170; p4=0.054838; -# initial state 2 -# current state 1 -p5=-1.668569; p6=-0.033906; -# current state 3 -p7=-5.686920; p8=0.018135; -############## -# - -############## -#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 -# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age -# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age -# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age) -# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...) -# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age) -# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...) -# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/ -# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age) -# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)) -# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...) -# -#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 - - -# 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 log y -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 - - -# 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 log y -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 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 -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 2.808e-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 3.681e-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 4.816e-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 6.283e-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 8.159e-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 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 -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 1.730e-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 1.462e-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 1.235e-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 1.042e-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 8.796e-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 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 -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 1.542e-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 1.690e-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 1.851e-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 2.028e-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 2.219e-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 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 -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 1.730e-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 1.462e-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 1.235e-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 1.042e-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 8.796e-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 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 -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 1.542e-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 1.690e-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 1.851e-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 2.028e-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 2.219e-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 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 -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 1.542e-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 1.690e-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 1.851e-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 2.028e-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 2.219e-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 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--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 deleted file mode 100644 index 620dc06..0000000 --- a/html/doc/biaspar.htm +++ /dev/null @@ -1,107 +0,0 @@ - - - -IMaCh biaspar.htm - 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-0.99r24
$Revision$ $Date$
-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=24.06
- -
File of contributions to the likelihood computed with optimized parameters mle = 1. You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: biaspar/ILK_biaspar.txt
- -
Equation of the model: model=1+age+
-
- Probability p1j by origin 1 and destination j. Dot's sizes are related to corresponding weight: biaspar/ILK_biaspar-p1j.png

- Probability p2j by origin 2 and destination j. Dot's sizes are related to corresponding weight: biaspar/ILK_biaspar-p2j.png

- The function drawn is -2Log(L) in Log scale: by state of origin biaspar/ILK_biaspar-ori.png

- and by state of destination biaspar/ILK_biaspar-dest.png