--- imach/html/doc/biaspar.gp	2006/02/09 15:20:33	1.3
+++ imach/html/doc/biaspar.gp	2019/05/22 23:11:24	1.6
@@ -1,245 +1,522 @@
-
-# Imach version 0.98b, January 2006, INED-EUROREVES 
-# biaspar.gp
-set missing 'NaNq'
-cd "C:/Program Files/IMaCh/doc/" 
-
-set out "biaspar/vbiaspar11.png" 
-
-#set out "vbiaspar11.png" 
-set xlabel "Age" 
-set ylabel "Probability" 
-set ter png small
-set size 0.65,0.65
-plot [70:95] "biaspar/vplrbiaspar.txt" every :::0::0 u 1:2 "%lf %lf (%lf) %*lf (%*lf)" t"Stable prevalence" w l 0,"biaspar/vplrbiaspar.txt" every :::0::0 u 1:($2+1.96*$3) "%lf %lf (%lf) %*lf (%*lf)" t"95% CI" w l 1,"biaspar/vplrbiaspar.txt" every :::0::0 u 1:($2-1.96*$3) "%lf %lf (%lf) %*lf (%*lf)" t"" w l 1,"biaspar/prbiaspar.txt" every :::0::0 u 1:($2) t"Observed prevalence " w l 2
-set out "biaspar/vbiaspar21.png" 
-
-#set out "vbiaspar21.png" 
-set xlabel "Age" 
-set ylabel "Probability" 
-set ter png small
-set size 0.65,0.65
-plot [70:95] "biaspar/vplrbiaspar.txt" every :::0::0 u 1:2 "%lf %*lf (%*lf) %lf (%lf)" t"Stable prevalence" w l 0,"biaspar/vplrbiaspar.txt" every :::0::0 u 1:($2+1.96*$3) "%lf %*lf (%*lf) %lf (%lf)" t"95% CI" w l 1,"biaspar/vplrbiaspar.txt" every :::0::0 u 1:($2-1.96*$3) "%lf %*lf (%*lf) %lf (%lf)" t"" w l 1,"biaspar/prbiaspar.txt" every :::0::0 u 1:($6) t"Observed prevalence " w l 2
-set out "biaspar/ebiaspar1.png" 
-set ylabel "Years" 
-set ter png small
-set size 0.65,0.65
-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 0,"biaspar/trbiaspar.txt" every :::0::0 u 1:($2+$3*2) "%lf %lf (%lf) %*lf (%*lf) %*lf (%*lf)" t"" w l 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 0,"biaspar/trbiaspar.txt" every :::0::0 u 1:($2+$3*2) "%lf %*lf (%*lf) %lf (%lf) %*lf (%*lf)" t"" w l 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 0,"biaspar/trbiaspar.txt" every :::0::0 u 1:($2+$3*2) "%lf %*lf (%*lf) %*lf (%*lf) %lf (%lf)" t"" w l 0
-set out "biaspar/expbiaspar11.png" 
-set ter png small
-set size 0.65,0.65
-plot [70:95] "biaspar/erbiaspar.txt" every :::0::0 u 1:2 t "e11" w l ,"biaspar/erbiaspar.txt" every :::0::0 u 1:4 t "e12" w l
-set out "biaspar/expbiaspar21.png" 
-set ter png small
-set size 0.65,0.65
-plot [70:95] "biaspar/erbiaspar.txt" every :::0::0 u 1:6 t "e21" w l ,"biaspar/erbiaspar.txt" every :::0::0 u 1:8 t "e22" w l
-set out "biaspar/pbiaspar11.png" 
-set xlabel "Age" 
-set ylabel "Probability" 
-set ter png small
-set size 0.65,0.65
-unset log y
-plot [70:95] "biaspar/pijrbiaspar.txt" u ($1==1 ? ($3):1/0):($5/($4+$5)) t"prev(1,2)" w l,"biaspar/pijrbiaspar.txt" u ($1==1 ? ($3):1/0):($8/($7+$8)) t"prev(2,2)" w l
-
-set out "biaspar/pbiaspar21.png" 
-set xlabel "Age" 
-set ylabel "Probability" 
-set ter png small
-set size 0.65,0.65
-unset log y
-plot [70:95] "biaspar/pijrbiaspar.txt" u ($1==1 ? ($3):1/0):($6/($4+$5)) t"prev(2,3)" w l,"biaspar/pijrbiaspar.txt" u ($1==1 ? ($3):1/0):($12/($10+$11)) t"prev(3,3)" w l
-p1=-12.245240 
-p2=0.092358 
-p3=-10.671890 
-p4=0.060969 
-p5=-2.645345 
-p6=-0.022325 
-p7=-4.773317 
-p8=0.007859 
-
-set out "biaspar/pebiaspar11.png" 
-
-set title "Probability"
-
-set ter png small
-set size 0.65,0.65
-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" 
-set out "biaspar/pebiaspar12.png" 
-
-set ylabel "Quasi-incidence per year"
-
-set ter png small
-set size 0.65,0.65
-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" 
-# Routine varprob
-set parametric;unset label
-set log y;set log x; set xlabel "p13 (year-1)";set ylabel "p12 (year-1)"
-set ter png small
-set size 0.65,0.65
-set out "biaspar/varpijgrbiaspar113-12.png"
-set label "65" at  1.459e-002, 2.328e-002 center
-# Age 65, p13 - p12
-plot [-pi:pi]  1.459e-002+ 2.000*( 7.081e-001* 2.074e-003*cos(t)+ 7.061e-001* 1.411e-003*sin(t)),  2.328e-002 +2.000*(-7.061e-001* 2.074e-003*cos(t)+ 7.081e-001* 1.411e-003*sin(t)) not
-# Age 70, p13 - p12
-set label "70" at  1.976e-002, 3.688e-002 center
-replot  1.976e-002+ 2.000*( 5.375e-001* 2.333e-003*cos(t)+ 8.433e-001* 1.486e-003*sin(t)),  3.688e-002 +2.000*(-8.433e-001* 2.333e-003*cos(t)+ 5.375e-001* 1.486e-003*sin(t)) not
-# Age 75, p13 - p12
-set label "75" at  2.674e-002, 5.839e-002 center
-replot  2.674e-002+ 2.000*( 4.212e-001* 2.525e-003*cos(t)+ 9.070e-001* 1.399e-003*sin(t)),  5.839e-002 +2.000*(-9.070e-001* 2.525e-003*cos(t)+ 4.212e-001* 1.399e-003*sin(t)) not
-# Age 80, p13 - p12
-set label "80" at  3.614e-002, 9.233e-002 center
-replot  3.614e-002+ 2.000*( 3.981e-001* 2.739e-003*cos(t)+ 9.173e-001* 1.383e-003*sin(t)),  9.233e-002 +2.000*(-9.173e-001* 2.739e-003*cos(t)+ 3.981e-001* 1.383e-003*sin(t)) not
-# Age 85, p13 - p12
-set label "85" at  4.875e-002, 1.457e-001 center
-replot  4.875e-002+ 2.000*( 3.975e-001* 4.130e-003*cos(t)+ 9.176e-001* 2.278e-003*sin(t)),  1.457e-001 +2.000*(-9.176e-001* 4.130e-003*cos(t)+ 3.975e-001* 2.278e-003*sin(t)) not
-# Age 90, p13 - p12
-set label "90" at  6.557e-002, 2.292e-001 center
-replot  6.557e-002+ 2.000*( 2.928e-001* 8.973e-003*cos(t)+ 9.562e-001* 4.707e-003*sin(t)),  2.292e-001 +2.000*(-9.562e-001* 8.973e-003*cos(t)+ 2.928e-001* 4.707e-003*sin(t)) not
-# Age 95, p13 - p12
-set label "95" at  8.778e-002, 3.591e-001 center
-replot  8.778e-002+ 2.000*( 2.165e-001* 1.969e-002*cos(t)+ 9.763e-001* 8.913e-003*sin(t)),  3.591e-001 +2.000*(-9.763e-001* 1.969e-002*cos(t)+ 2.165e-001* 8.913e-003*sin(t)) not
-set out "biaspar/varpijgrbiaspar113-12.png";replot;
-set parametric;unset label
-set log y;set log x; set xlabel "p21 (year-1)";set ylabel "p12 (year-1)"
-set ter png small
-set size 0.65,0.65
-set out "biaspar/varpijgrbiaspar121-12.png"
-set label "65" at  1.936e-001, 2.328e-002 center
-# Age 65, p21 - p12
-plot [-pi:pi]  1.936e-001+ 2.000*( 9.998e-001* 3.139e-002*cos(t)+-1.878e-002* 1.672e-003*sin(t)),  2.328e-002 +2.000*( 1.878e-002* 3.139e-002*cos(t)+ 9.998e-001* 1.672e-003*sin(t)) not
-# Age 70, p21 - p12
-set label "70" at  1.734e-001, 3.688e-002 center
-replot  1.734e-001+ 2.000*( 9.995e-001* 2.153e-002*cos(t)+-3.254e-002* 2.005e-003*sin(t)),  3.688e-002 +2.000*( 3.254e-002* 2.153e-002*cos(t)+ 9.995e-001* 2.005e-003*sin(t)) not
-# Age 75, p21 - p12
-set label "75" at  1.552e-001, 5.839e-002 center
-replot  1.552e-001+ 2.000*( 9.984e-001* 1.374e-002*cos(t)+-5.600e-002* 2.239e-003*sin(t)),  5.839e-002 +2.000*( 5.600e-002* 1.374e-002*cos(t)+ 9.984e-001* 2.239e-003*sin(t)) not
-# Age 80, p21 - p12
-set label "80" at  1.389e-001, 9.233e-002 center
-replot  1.389e-001+ 2.000*( 9.950e-001* 8.279e-003*cos(t)+-9.943e-002* 2.449e-003*sin(t)),  9.233e-002 +2.000*( 9.943e-002* 8.279e-003*cos(t)+ 9.950e-001* 2.449e-003*sin(t)) not
-# Age 85, p21 - p12
-set label "85" at  1.243e-001, 1.457e-001 center
-replot  1.243e-001+ 2.000*( 9.670e-001* 6.440e-003*cos(t)+-2.549e-001* 3.655e-003*sin(t)),  1.457e-001 +2.000*( 2.549e-001* 6.440e-003*cos(t)+ 9.670e-001* 3.655e-003*sin(t)) not
-# Age 90, p21 - p12
-set label "90" at  1.112e-001, 2.292e-001 center
-replot  1.112e-001+ 2.000*( 5.855e-001* 9.526e-003*cos(t)+-8.106e-001* 6.807e-003*sin(t)),  2.292e-001 +2.000*( 8.106e-001* 9.526e-003*cos(t)+ 5.855e-001* 6.807e-003*sin(t)) not
-# Age 95, p21 - p12
-set label "95" at  9.952e-002, 3.591e-001 center
-replot  9.952e-002+ 2.000*( 2.226e-001* 1.969e-002*cos(t)+-9.749e-001* 9.591e-003*sin(t)),  3.591e-001 +2.000*( 9.749e-001* 1.969e-002*cos(t)+ 2.226e-001* 9.591e-003*sin(t)) not
-set out "biaspar/varpijgrbiaspar121-12.png";replot;
-set parametric;unset label
-set log y;set log x; set xlabel "p23 (year-1)";set ylabel "p12 (year-1)"
-set ter png small
-set size 0.65,0.65
-set out "biaspar/varpijgrbiaspar123-12.png"
-set label "65" at  1.640e-001, 2.328e-002 center
-# Age 65, p23 - p12
-plot [-pi:pi]  1.640e-001+ 2.000*( 9.995e-001* 2.122e-002*cos(t)+-3.110e-002* 1.646e-003*sin(t)),  2.328e-002 +2.000*( 3.110e-002* 2.122e-002*cos(t)+ 9.995e-001* 1.646e-003*sin(t)) not
-# Age 70, p23 - p12
-set label "70" at  1.708e-001, 3.688e-002 center
-replot  1.708e-001+ 2.000*( 9.988e-001* 1.755e-002*cos(t)+-4.814e-002* 1.950e-003*sin(t)),  3.688e-002 +2.000*( 4.814e-002* 1.755e-002*cos(t)+ 9.988e-001* 1.950e-003*sin(t)) not
-# Age 75, p23 - p12
-set label "75" at  1.778e-001, 5.839e-002 center
-replot  1.778e-001+ 2.000*( 9.972e-001* 1.375e-002*cos(t)+-7.534e-002* 2.131e-003*sin(t)),  5.839e-002 +2.000*( 7.534e-002* 1.375e-002*cos(t)+ 9.972e-001* 2.131e-003*sin(t)) not
-# Age 80, p23 - p12
-set label "80" at  1.851e-001, 9.233e-002 center
-replot  1.851e-001+ 2.000*( 9.926e-001* 1.011e-002*cos(t)+-1.215e-001* 2.277e-003*sin(t)),  9.233e-002 +2.000*( 1.215e-001* 1.011e-002*cos(t)+ 9.926e-001* 2.277e-003*sin(t)) not
-# Age 85, p23 - p12
-set label "85" at  1.926e-001, 1.457e-001 center
-replot  1.926e-001+ 2.000*( 9.723e-001* 7.665e-003*cos(t)+-2.338e-001* 3.559e-003*sin(t)),  1.457e-001 +2.000*( 2.338e-001* 7.665e-003*cos(t)+ 9.723e-001* 3.559e-003*sin(t)) not
-# Age 90, p23 - p12
-set label "90" at  2.004e-001, 2.292e-001 center
-replot  2.004e-001+ 2.000*( 6.216e-001* 9.497e-003*cos(t)+-7.833e-001* 7.226e-003*sin(t)),  2.292e-001 +2.000*( 7.833e-001* 9.497e-003*cos(t)+ 6.216e-001* 7.226e-003*sin(t)) not
-# Age 95, p23 - p12
-set label "95" at  2.085e-001, 3.591e-001 center
-replot  2.085e-001+ 2.000*( 2.331e-001* 1.967e-002*cos(t)+-9.725e-001* 1.154e-002*sin(t)),  3.591e-001 +2.000*( 9.725e-001* 1.967e-002*cos(t)+ 2.331e-001* 1.154e-002*sin(t)) not
-set out "biaspar/varpijgrbiaspar123-12.png";replot;
-set parametric;unset label
-set log y;set log x; set xlabel "p21 (year-1)";set ylabel "p13 (year-1)"
-set ter png small
-set size 0.65,0.65
-set out "biaspar/varpijgrbiaspar121-13.png"
-set label "65" at  1.936e-001, 1.459e-002 center
-# Age 65, p21 - p13
-plot [-pi:pi]  1.936e-001+ 2.000*( 1.000e+000* 3.138e-002*cos(t)+-2.829e-003* 1.772e-003*sin(t)),  1.459e-002 +2.000*( 2.829e-003* 3.138e-002*cos(t)+ 1.000e+000* 1.772e-003*sin(t)) not
-# Age 70, p21 - p13
-set label "70" at  1.734e-001, 1.976e-002 center
-replot  1.734e-001+ 2.000*( 1.000e+000* 2.152e-002*cos(t)+-3.296e-003* 1.771e-003*sin(t)),  1.976e-002 +2.000*( 3.296e-003* 2.152e-002*cos(t)+ 1.000e+000* 1.771e-003*sin(t)) not
-# Age 75, p21 - p13
-set label "75" at  1.552e-001, 2.674e-002 center
-replot  1.552e-001+ 2.000*( 1.000e+000* 1.372e-002*cos(t)+-3.023e-003* 1.655e-003*sin(t)),  2.674e-002 +2.000*( 3.023e-003* 1.372e-002*cos(t)+ 1.000e+000* 1.655e-003*sin(t)) not
-# Age 80, p21 - p13
-set label "80" at  1.389e-001, 3.614e-002 center
-replot  1.389e-001+ 2.000*( 1.000e+000* 8.242e-003*cos(t)+-4.787e-003* 1.672e-003*sin(t)),  3.614e-002 +2.000*( 4.787e-003* 8.242e-003*cos(t)+ 1.000e+000* 1.672e-003*sin(t)) not
-# Age 85, p21 - p13
-set label "85" at  1.243e-001, 4.875e-002 center
-replot  1.243e-001+ 2.000*( 9.991e-001* 6.301e-003*cos(t)+-4.129e-002* 2.647e-003*sin(t)),  4.875e-002 +2.000*( 4.129e-002* 6.301e-003*cos(t)+ 9.991e-001* 2.647e-003*sin(t)) not
-# Age 90, p21 - p13
-set label "90" at  1.112e-001, 6.557e-002 center
-replot  1.112e-001+ 2.000*( 9.920e-001* 7.882e-003*cos(t)+-1.263e-001* 5.157e-003*sin(t)),  6.557e-002 +2.000*( 1.263e-001* 7.882e-003*cos(t)+ 9.920e-001* 5.157e-003*sin(t)) not
-# Age 95, p21 - p13
-set label "95" at  9.952e-002, 8.778e-002 center
-replot  9.952e-002+ 2.000*( 8.713e-001* 1.061e-002*cos(t)+-4.908e-001* 9.377e-003*sin(t)),  8.778e-002 +2.000*( 4.908e-001* 1.061e-002*cos(t)+ 8.713e-001* 9.377e-003*sin(t)) not
-set out "biaspar/varpijgrbiaspar121-13.png";replot;
-set parametric;unset label
-set log y;set log x; set xlabel "p23 (year-1)";set ylabel "p13 (year-1)"
-set ter png small
-set size 0.65,0.65
-set out "biaspar/varpijgrbiaspar123-13.png"
-set label "65" at  1.640e-001, 1.459e-002 center
-# Age 65, p23 - p13
-plot [-pi:pi]  1.640e-001+ 2.000*( 9.992e-001* 2.122e-002*cos(t)+ 3.961e-002* 1.564e-003*sin(t)),  1.459e-002 +2.000*(-3.961e-002* 2.122e-002*cos(t)+ 9.992e-001* 1.564e-003*sin(t)) not
-# Age 70, p23 - p13
-set label "70" at  1.708e-001, 1.976e-002 center
-replot  1.708e-001+ 2.000*( 9.987e-001* 1.755e-002*cos(t)+ 5.131e-002* 1.529e-003*sin(t)),  1.976e-002 +2.000*(-5.131e-002* 1.755e-002*cos(t)+ 9.987e-001* 1.529e-003*sin(t)) not
-# Age 75, p23 - p13
-set label "75" at  1.778e-001, 2.674e-002 center
-replot  1.778e-001+ 2.000*( 9.977e-001* 1.374e-002*cos(t)+ 6.811e-002* 1.369e-003*sin(t)),  2.674e-002 +2.000*(-6.811e-002* 1.374e-002*cos(t)+ 9.977e-001* 1.369e-003*sin(t)) not
-# Age 80, p23 - p13
-set label "80" at  1.851e-001, 3.614e-002 center
-replot  1.851e-001+ 2.000*( 9.950e-001* 1.009e-002*cos(t)+ 1.004e-001* 1.338e-003*sin(t)),  3.614e-002 +2.000*(-1.004e-001* 1.009e-002*cos(t)+ 9.950e-001* 1.338e-003*sin(t)) not
-# Age 85, p23 - p13
-set label "85" at  1.926e-001, 4.875e-002 center
-replot  1.926e-001+ 2.000*( 9.803e-001* 7.637e-003*cos(t)+ 1.977e-001* 2.231e-003*sin(t)),  4.875e-002 +2.000*(-1.977e-001* 7.637e-003*cos(t)+ 9.803e-001* 2.231e-003*sin(t)) not
-# Age 90, p23 - p13
-set label "90" at  2.004e-001, 6.557e-002 center
-replot  2.004e-001+ 2.000*( 9.247e-001* 8.660e-003*cos(t)+ 3.806e-001* 4.366e-003*sin(t)),  6.557e-002 +2.000*(-3.806e-001* 8.660e-003*cos(t)+ 9.247e-001* 4.366e-003*sin(t)) not
-# Age 95, p23 - p13
-set label "95" at  2.085e-001, 8.778e-002 center
-replot  2.085e-001+ 2.000*( 8.590e-001* 1.328e-002*cos(t)+ 5.121e-001* 8.035e-003*sin(t)),  8.778e-002 +2.000*(-5.121e-001* 1.328e-002*cos(t)+ 8.590e-001* 8.035e-003*sin(t)) not
-set out "biaspar/varpijgrbiaspar123-13.png";replot;
-set parametric;unset label
-set log y;set log x; set xlabel "p23 (year-1)";set ylabel "p21 (year-1)"
-set ter png small
-set size 0.65,0.65
-set out "biaspar/varpijgrbiaspar123-21.png"
-set label "65" at  1.640e-001, 1.936e-001 center
-# Age 65, p23 - p21
-plot [-pi:pi]  1.640e-001+ 2.000*( 5.483e-002* 3.141e-002*cos(t)+ 9.985e-001* 2.117e-002*sin(t)),  1.936e-001 +2.000*(-9.985e-001* 3.141e-002*cos(t)+ 5.483e-002* 2.117e-002*sin(t)) not
-# Age 70, p23 - p21
-set label "70" at  1.708e-001, 1.734e-001 center
-replot  1.708e-001+ 2.000*( 9.437e-002* 2.155e-002*cos(t)+ 9.955e-001* 1.749e-002*sin(t)),  1.734e-001 +2.000*(-9.955e-001* 2.155e-002*cos(t)+ 9.437e-002* 1.749e-002*sin(t)) not
-# Age 75, p23 - p21
-set label "75" at  1.778e-001, 1.552e-001 center
-replot  1.778e-001+ 2.000*( 7.002e-001* 1.395e-002*cos(t)+ 7.140e-001* 1.347e-002*sin(t)),  1.552e-001 +2.000*(-7.140e-001* 1.395e-002*cos(t)+ 7.002e-001* 1.347e-002*sin(t)) not
-# Age 80, p23 - p21
-set label "80" at  1.851e-001, 1.389e-001 center
-replot  1.851e-001+ 2.000*( 9.962e-001* 1.005e-002*cos(t)+ 8.694e-002* 8.227e-003*sin(t)),  1.389e-001 +2.000*(-8.694e-002* 1.005e-002*cos(t)+ 9.962e-001* 8.227e-003*sin(t)) not
-# Age 85, p23 - p21
-set label "85" at  1.926e-001, 1.243e-001 center
-replot  1.926e-001+ 2.000*( 9.869e-001* 7.529e-003*cos(t)+ 1.612e-001* 6.261e-003*sin(t)),  1.243e-001 +2.000*(-1.612e-001* 7.529e-003*cos(t)+ 9.869e-001* 6.261e-003*sin(t)) not
-# Age 90, p23 - p21
-set label "90" at  2.004e-001, 1.112e-001 center
-replot  2.004e-001+ 2.000*( 8.505e-001* 8.378e-003*cos(t)+ 5.260e-001* 7.632e-003*sin(t)),  1.112e-001 +2.000*(-5.260e-001* 8.378e-003*cos(t)+ 8.505e-001* 7.632e-003*sin(t)) not
-# Age 95, p23 - p21
-set label "95" at  2.085e-001, 9.952e-002 center
-replot  2.085e-001+ 2.000*( 9.743e-001* 1.222e-002*cos(t)+ 2.251e-001* 1.022e-002*sin(t)),  9.952e-002 +2.000*(-2.251e-001* 1.222e-002*cos(t)+ 9.743e-001* 1.022e-002*sin(t)) not
-set out "biaspar/varpijgrbiaspar123-21.png";replot;
-# Routine varevsij
-set noparametric;set nolabel; set ter png small;set size 0.65, 0.65
- set log y; set nolog x;set xlabel "Age"; set ylabel "Force of mortality (year-1)";
- plot "biaspar/prmorprev1-stablbased-rbiaspar.txt"  u 1:($3) not w l 1 
- replot "biaspar/prmorprev1-stablbased-rbiaspar.txt"  u 1:(($3+1.96*$4)) t "95% interval" w l 2 
- replot "biaspar/prmorprev1-stablbased-rbiaspar.txt"  u 1:(($3-1.96*$4)) not w l 2 
-set out "biaspar/varmuptjgr-stablbased-biaspar1.png";replot;
+
+# IMaCh-0.99r19
+# 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;