From 16d9dbb281da60a109c30948482825a8aeae1d08 Mon Sep 17 00:00:00 2001 From: "N. Brouard" Date: Tue, 18 Aug 2015 16:43:19 +0000 Subject: [PATCH] *** empty log message *** --- distributions/CMakeLists.txt | 3 + distributions/gnulinux/CMakeLists.txt | 28 ++ distributions/osx/CMakeLists.txt | 1 + distributions/osx/IMaCh-ecrandemarrage.rsrc | Bin 0 -> 336 bytes distributions/osx/IMaChInfo.plist.in | 48 +++ distributions/osx/IMaChPkgInfo.in | 1 + distributions/osx/TXT.rtf | 4 + distributions/osx/applet | Bin 0 -> 25028 bytes distributions/osx/create-dmg | 170 +++++++++ distributions/osx/createdmg.sh | 43 +++ distributions/osx/createdmg3.sh | 149 ++++++++ distributions/windows/CMakeLists.txt | 1 + html/CMakeLists.txt | 1 + html/doc/CMakeLists.txt | 1 + html/doc/biaspar-cov.htm | 33 ++ html/doc/biaspar.gp | 271 +++++++++++++ html/doc/biaspar.htm | 76 +++- html/doc/biaspar.imach | 10 +- html/doc/biaspar.log | 400 +++++++++++++------- html/doc/mypar.imach | 10 +- 20 files changed, 1085 insertions(+), 165 deletions(-) create mode 100644 distributions/CMakeLists.txt create mode 100644 distributions/gnulinux/CMakeLists.txt create mode 100644 distributions/osx/CMakeLists.txt create mode 100644 distributions/osx/IMaCh-ecrandemarrage.rsrc create mode 100644 distributions/osx/IMaChInfo.plist.in create mode 100644 distributions/osx/IMaChPkgInfo.in create mode 100644 distributions/osx/TXT.rtf create mode 100755 distributions/osx/applet create mode 100755 distributions/osx/create-dmg create mode 100644 distributions/osx/createdmg.sh create mode 100755 distributions/osx/createdmg3.sh create mode 100644 distributions/windows/CMakeLists.txt create mode 100644 html/CMakeLists.txt create mode 100644 html/doc/CMakeLists.txt diff --git a/distributions/CMakeLists.txt b/distributions/CMakeLists.txt new file mode 100644 index 0000000..cffdca6 --- /dev/null +++ b/distributions/CMakeLists.txt @@ -0,0 +1,3 @@ +ADD_SUBDIRECTORY(gnulinux) +ADD_SUBDIRECTORY(osx) +ADD_SUBDIRECTORY(windows) \ No newline at end of file diff --git a/distributions/gnulinux/CMakeLists.txt b/distributions/gnulinux/CMakeLists.txt new file mode 100644 index 0000000..00c8e4e --- /dev/null +++ b/distributions/gnulinux/CMakeLists.txt @@ -0,0 +1,28 @@ +# set(CPACK_PACKAGE_VERSION ${IMACH_VERSION}) +# set(CPACK_PACKAGE_NAME "IMaCh") +# set(CPACK_PACKAGE_RELEASE 2) +# set(CPACK_PACKAGE_CONTACT "Nicolas Brouard") +# set(CPACK_PACKAGE_VENDOR "INED") +# SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "IMaCh Interpolated Markov Chain program") +# SET(CPACK_PACKAGE_VENDOR "IMaCh, INED") +# SET(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/../../README.txt") +# SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/../../Copyright.txt") +# SET(CPACK_PACKAGE_VERSION_MAJOR "${IMACH_VERSION_MAJOR}") +# SET(CPACK_PACKAGE_VERSION_MINOR "${IMACH_VERSION_MINOR}") +# SET(CPACK_PACKAGE_VERSION_PATCH "${IMACH_VERSION_PATCH}") +# SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CMake ${CMake_VERSION_MAJOR}.${CMake_VERSION_MINOR}") +# SET(CPACK_PACKAGE_EXECUTABLES "IMaCh" "IMaCh") +# SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "IMaCh program estimates Health Expectancies from Cross-longitudinal surveys.") +# SET(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/imach-desc.txt") +# set(CPACK_PACKAGING_INSTALL_PREFIX ${CMAKE_INSTALL_PREFIX}) +# set(CPACK_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}-${CPACK_PACKAGE_RELEASE}.${CMAKE_SYSTEM_PROCESSOR}") + +set(CPACK_GENERATOR "RPM") +SET(CPACK_RPM_PACKAGE_LICENSE "GPL") +SET(CPACK_RPM_PACKAGE_GROUP "Applications/Sciences") +set(CPACK_RPM_PACKAGE_REQUIRES "gnuplot >= 4.2, cmake >= 2.8") +set(CPACK_RPM_CHANGELOG_FILE "${CMAKE_CURRENT_SOURCE_DIR}/specchangelog") + +INCLUDE(InstallRequiredSystemLibraries) + +INCLUDE(CPack) diff --git a/distributions/osx/CMakeLists.txt b/distributions/osx/CMakeLists.txt new file mode 100644 index 0000000..1279c4a --- /dev/null +++ b/distributions/osx/CMakeLists.txt @@ -0,0 +1 @@ +# ADD_SUBDIRECTORY(osx) diff --git a/distributions/osx/IMaCh-ecrandemarrage.rsrc 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DMG file." + echo "Usage: $(basename $0) options... image.dmg source_folder" + echo "All contents of source_folder will be copied into the disk image." + echo "Options:" + echo " --volname name" + echo " set volume name (displayed in the Finder sidebar and window title)" + echo " --background pic.png" + echo " set folder background image (provide png, gif, jpg)" + echo " --window-pos x y" + echo " set position the folder window" + echo " --window-size width height" + echo " set size of the folder window" + echo " --icon-size icon_size" + echo " set window icons size (up to 128)" + echo " --icon file_name x y" + echo " set position of the file's icon" + echo " --custom-icon file_name custom_icon_or_sample_file x y" + echo " set position and custom icon" + echo " --version show tool version number" + echo " -h, --help display this help" + exit 0 +} + +WINX=10 +WINY=60 +WINW=600 +WINH=400 +ICON_SIZE=128 + +while test "${1:0:1}" = "-"; do + case $1 in + --volname) + VOLUME_NAME="$2" + shift; shift;; + --background) + BACKGROUND_FILE="$2" + BACKGROUND_FILE_NAME="$(basename $BACKGROUND_FILE)" + BACKGROUND_CLAUSE="set background picture of opts to file \".background:$BACKGROUND_FILE_NAME\"" + shift; shift;; + --icon-size) + ICON_SIZE="$2" + shift; shift;; + --window-pos) + WINX=$2; WINY=$3 + shift; shift; shift;; + --window-size) + WINW=$2; WINH=$3 + shift; shift; shift;; + --icon) + POSITION_CLAUSE="${POSITION_CLAUSE}set position of item \"$2\" to {$3, $4} +" + shift; shift; shift; shift;; + --custom-icon) + shift; shift; shift; shift; shift;; + -h | --help) + usage;; + --version) + version; exit 0;; + --pure-version) + pure_version; exit 0;; + -*) + echo "Unknown option $1. Run with --help for help." + exit 1;; + esac +done + +test -z "$2" && { + echo "Not enough arguments. Invoke with --help for help." + exit 1 +} + +DMG_PATH="$1" +DMG_DIRNAME="$(dirname "$DMG_PATH")" +DMG_DIR="$(cd $DMG_DIRNAME > /dev/null; pwd)" +DMG_NAME="$(basename "$DMG_PATH")" +DMG_TEMP_NAME="$DMG_DIR/rw.${DMG_NAME}" +SRC_FOLDER="$(cd "$2" > /dev/null; pwd)" +test -z "$VOLUME_NAME" && VOLUME_NAME="$(basename "$DMG_PATH" .dmg)" + +AUX_PATH="$(cd "$(dirname $0)"; pwd)/support" + +test -d "$AUX_PATH" || { + echo "Cannot find support directory: $AUX_PATH" + exit 1 +} + +# Create the image +echo "Creating disk image..." +test -f "${DMG_TEMP_NAME}" && rm -f "${DMG_TEMP_NAME}" +hdiutil create -srcfolder "$SRC_FOLDER" -volname "${VOLUME_NAME}" -fs HFS+ -fsargs "-c c=64,a=16,e=16" -format UDRW -size 300m "${DMG_TEMP_NAME}" + +# mount it +echo "Mounting disk image..." +MOUNT_DIR="/Volumes/${VOLUME_NAME}" +echo "Mount directory: $MOUNT_DIR" +DEV_NAME=$(hdiutil attach -readwrite -noverify -noautoopen "${DMG_TEMP_NAME}" | egrep '^/dev/' | sed 1q | awk '{print $1}') +echo "Device name: $DEV_NAME" + +#cp RightDS_Store "/Volumes/${VOLUME_NAME}/.DS_Store" + +if ! test -z "$BACKGROUND_FILE"; then + echo "Copying background file..." + test -d "$MOUNT_DIR/.background" || mkdir "$MOUNT_DIR/.background" + cp "$BACKGROUND_FILE" "$MOUNT_DIR/.background/$BACKGROUND_FILE_NAME" +fi + +# run applescript +APPLESCRIPT=$(mktemp -t createdmg.XXXXXXX) +echo APPLESCRIPT1=$APPLESCRIPT +cat "$AUX_PATH/template.applescript" | sed -e "s/WINX/$WINX/g" -e "s/WINY/$WINY/g" -e "s/WINW/$WINW/g" -e "s/WINH/$WINH/g" -e "s/BACKGROUND_CLAUSE/$BACKGROUND_CLAUSE/g" -e "s/ICON_SIZE/$ICON_SIZE/g" | perl -pe "s/POSITION_CLAUSE/$POSITION_CLAUSE/g" >"$APPLESCRIPT" +echo APPLESCRIPT=$APPLESCRIPT + +# echo "Running Applescript: ./AdiumApplescriptRunner \"${APPLESCRIPT}\" process_disk_image \"${VOLUME_NAME}\"" +# "$AUX_PATH/AdiumApplescriptRunner" "${APPLESCRIPT}" process_disk_image "${VOLUME_NAME}" || true +#echo "Done running the applescript..." +#sleep 4 + +# make sure it's not world writeable +echo "Fixing permissions..." +chmod -Rf go-w "${MOUNT_DIR}" || true +echo "Done fixing permissions." + +# make the top window open itself on mount: +if [ -x /usr/local/bin/openUp ]; then + echo "Applying openUp..." + /usr/local/bin/openUp "${MOUNT_DIR}" +fi + +# unmount +echo "Unmounting disk image..." +hdiutil detach "${DEV_NAME}" + +# compress image +echo "Compressing disk image..." +hdiutil convert "${DMG_TEMP_NAME}" -format UDZO -imagekey zlib-level=9 -o "${DMG_DIR}/${DMG_NAME}" +rm -f "${DMG_TEMP_NAME}" + +# adding EULA resources +if [ ! -z "${EULA_RSRC}" -a "${EULA_RSRC}" != "-null-" ]; then + echo "adding EULA resources" + hdiutil unflatten "${DMG_DIR}/${DMG_NAME}" + /Developer/Tools/ResMerger -a "${EULA_RSRC}" -o "${DMG_DIR}/${DMG_NAME}" + hdiutil flatten "${DMG_DIR}/${DMG_NAME}" +fi + +echo "Disk image done" +exit 0 diff --git a/distributions/osx/createdmg.sh b/distributions/osx/createdmg.sh new file mode 100644 index 0000000..b10c62c --- /dev/null +++ b/distributions/osx/createdmg.sh @@ -0,0 +1,43 @@ +#!/bin/bash +set -x +# +# Creates a disk image (dmg) on Mac OS X from the command line. +# usage: +# mkdmg +# +# Where is the name to use for the mounted image, is the version +# number of the volume and is where the contents to put on the dmg are. +# +# The result will be a file called -.dmg + +if [ $# != 3 ]; then + echo "usage: mkdmg.sh volname vers srcdir" + exit 0 +fi + +VOL="$1" +VER="$2" +FILES="$3" + +DMG="tmp-$VOL.dmg" + +# create temporary disk image and format, ejecting when done +#SIZE=`du -sk ${FILES} | sed -n '/^[0-9]*/s/([0-9]*).*/\1/p'` +SIZE=`du -sk ${FILES} | sed -n 's/^\([0-9]*\).*/\1/p'` +echo SIZE=$SIZE +SIZE=$((${SIZE}/1000+1)) +hdiutil create "$DMG" -megabytes ${SIZE} -ov -type UDIF +DISK=`hdid -nomount "$DMG" | sed -ne ' /Apple_partition_scheme/ s|^/dev/\([^ ]*\).*$|\1|p'` +newfs_hfs -v "$VOL" /dev/r${DISK}s2 +hdiutil eject $DISK + +# mount and copy files onto volume +hdid "$DMG" +cp -R "${FILES}"/* "/Volumes/$VOL" +hdiutil eject $DISK +osascript -e "tell application "Finder" to eject disk "$VOL"" && + +# convert to compressed image, delete temp image +rm -f "${VOL}-${VER}.dmg" +hdiutil convert "$DMG" -format UDZO -o "${VOL}-${VER}.dmg" +rm -f "$DMG" diff --git a/distributions/osx/createdmg3.sh b/distributions/osx/createdmg3.sh new file mode 100755 index 0000000..8ae3118 --- /dev/null +++ b/distributions/osx/createdmg3.sh @@ -0,0 +1,149 @@ +#!/bin/bash +set -x +LANG=C # Otherwise du gives french comma and can't sum! +# borrowed to Andy Maloney +# http://asmaloney.com/2013/07/howto/packaging-a-mac-os-x-application-using-a-dmg/ + +# make sure we are in the correct dir when we double-click a .command file +dir=${0%/*} +if [ -d "$dir" ]; then + cd "$dir" +fi + +# set up your app name, version number, and background image file name +#APP_NAME="imach" +APP_NAME=$4 +VERSION=$5 +#"0.98nT" +DMG_BACKGROUND_IMG="Background.png" + +# you should not need to change these +#APP_EXE="/Users/nbrouard/Documents/imachcvs/NetBeans/imach/src +#APP_EXE="${APP_NAME}.app/Contents/MacOS/${APP_NAME}" +APP_EXE="${APP_NAME}.app/Contents/MacOS/applet" + +#VOL_NAME="${APP_NAME} ${VERSION}" # volume name will be "SuperCoolApp 1.0.0" +VOL_NAME=$2 # volume name will be "SuperCoolApp 1.0.0" +#DMG_FINAL="${VOL_NAME}.dmg" # final DMG name will be "SuperCoolApp 1.0.0.dmg" +DMG_FINAL=$3 # final DMG name will be "SuperCoolApp 1.0.0.dmg" +DMG_TMP="${VOL_NAME}-temp.dmg" +STAGING_DIR="./Install" # we copy all our stuff into this dir + +# Check the background image DPI and convert it if it isn't 72x72 +_BACKGROUND_IMAGE_DPI_H=`sips -g dpiHeight ${DMG_BACKGROUND_IMG} | grep -Eo '[0-9]+\.[0-9]+'` +_BACKGROUND_IMAGE_DPI_W=`sips -g dpiWidth ${DMG_BACKGROUND_IMG} | grep -Eo '[0-9]+\.[0-9]+'` + +if [ $(echo " $_BACKGROUND_IMAGE_DPI_H != 72.0 " | bc) -eq 1 -o $(echo " $_BACKGROUND_IMAGE_DPI_W != 72.0 " | bc) -eq 1 ]; then + echo "WARNING: The background image's DPI is not 72. This will result in distorted backgrounds on Mac OS X 10.7+." + echo " I will convert it to 72 DPI for you." + + _DMG_BACKGROUND_TMP="${DMG_BACKGROUND_IMG%.*}"_dpifix."${DMG_BACKGROUND_IMG##*.}" + + sips -s dpiWidth 72 -s dpiHeight 72 ${DMG_BACKGROUND_IMG} --out ${_DMG_BACKGROUND_TMP} + + DMG_BACKGROUND_IMG="${_DMG_BACKGROUND_TMP}" +fi + +# clear out any old data +rm -rf "${STAGING_DIR}" "${DMG_TMP}" "${DMG_FINAL}" + +# copy over the stuff we want in the final disk image to our staging dir +mkdir -p "${STAGING_DIR}" +cp -rpf "${APP_NAME}.app" "${STAGING_DIR}" +# ... cp anything else you want in the DMG - documentation, etc. + +pushd "${STAGING_DIR}" + +# strip the executable +echo "Stripping ${APP_EXE}..." +strip -u -r "${APP_EXE}" + +# compress the executable if we have upx in PATH +# UPX: http://upx.sourceforge.net/ +if hash upx 2>/dev/null; then + echo "Compressing (UPX) ${APP_EXE}..." + upx -9 "${APP_EXE}" +fi + +# ... perform any other stripping/compressing of libs and executables + +popd + +# figure out how big our DMG needs to be +# assumes our contents are at least 1M! +SIZE=`du -sh "${STAGING_DIR}" | sed 's/\([0-9\.]*\)M\(.*\)/\1/'` +#SIZE=`du -sm "${STAGING_DIR}" | sed 's/\([0-9\.]*\)m\(.*\)/\1/'` +SIZE=`echo "${SIZE} + 1.0" | bc | awk '{print int($1+0.5)}'` +#SIZE=1 + +if [ $? -ne 0 ]; then + echo "Error: Cannot compute size of staging dir" + exit +fi + +# create the temp DMG file +hdiutil create -srcfolder "${STAGING_DIR}" -volname "${VOL_NAME}" -fs HFS+ \ + -format UDRW -size ${SIZE}M "${DMG_TMP}" +# -fsargs "-c c=64,a=16,e=16" -format UDRW -size ${SIZE}M "${DMG_TMP}" + +echo "Created DMG: ${DMG_TMP}" + +# mount it and save the device +# works and I verified that it keeps the hml subdirectory. +DEVICE=$(hdiutil attach -readwrite -noverify "${DMG_TMP}" | \ + egrep '^/dev/' | sed 1q | awk '{print $1}') + +sleep 2 + +# add a link to the Applications dir +echo "Add link to /Applications" +pushd /Volumes/"${VOL_NAME}" +ln -s /Applications +popd + +# add a background image +mkdir /Volumes/"${VOL_NAME}"/.background +cp "${DMG_BACKGROUND_IMG}" /Volumes/"${VOL_NAME}"/.background/ + +# tell the Finder to resize the window, set the background, +# change the icon size, place the icons in the right position, etc. +echo ' + tell application "Finder" + tell disk "'${VOL_NAME}'" + open + set current view of container window to icon view + set toolbar visible of container window to false + set statusbar visible of container window to false + set the bounds of container window to {400, 100, 920, 440} + set viewOptions to the icon view options of container window + set arrangement of viewOptions to not arranged + set icon size of viewOptions to 72 + set background picture of viewOptions to file ".background:'${DMG_BACKGROUND_IMG}'" + set position of item "'${APP_NAME}'.app" of container window to {160, 205} + set position of item "Applications" of container window to {360, 205} + close + open + update without registering applications + delay 2 + end tell + end tell +' | osascript + +sync + +# unmount it +hdiutil detach "${DEVICE}" + +# now make the final image a compressed disk image +echo "Creating compressed image" +hdiutil convert "${DMG_TMP}" -format UDZO -imagekey zlib-level=9 -o "${DMG_FINAL}" + +# clean up +pwd +sleep 2 +rm -rf "${DMG_TMP}" +rm -rf "${STAGING_DIR}" + +echo 'Done.' + +exit diff --git a/distributions/windows/CMakeLists.txt b/distributions/windows/CMakeLists.txt new file mode 100644 index 0000000..e0d4b0f --- /dev/null +++ b/distributions/windows/CMakeLists.txt @@ -0,0 +1 @@ +# ADD_SUBDIRECTORY(windows) \ No newline at end of file diff --git a/html/CMakeLists.txt b/html/CMakeLists.txt new file mode 100644 index 0000000..7d218b9 --- /dev/null +++ b/html/CMakeLists.txt @@ -0,0 +1 @@ +# html diff --git a/html/doc/CMakeLists.txt b/html/doc/CMakeLists.txt new file mode 100644 index 0000000..d98d442 --- /dev/null +++ b/html/doc/CMakeLists.txt @@ -0,0 +1 @@ +# doc diff --git a/html/doc/biaspar-cov.htm b/html/doc/biaspar-cov.htm index e69de29..2968b3f 100644 --- a/html/doc/biaspar-cov.htm +++ b/html/doc/biaspar-cov.htm @@ -0,0 +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=
+ +

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.
+ +
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 +
+ \ No newline at end of file diff --git a/html/doc/biaspar.gp b/html/doc/biaspar.gp index e69de29..b7d94c7 100644 --- a/html/doc/biaspar.gp +++ b/html/doc/biaspar.gp @@ -0,0 +1,271 @@ + +# 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 +# biaspar.gp +set datafile missing 'NaNq' +cd "/Users/nbrouard/Documents/imach/cvs/imach/build/osx/html/doc" + +# 1st: Period (stable) prevalence with CI: 'vpl' files + +set out "biaspar/vbiaspar1_1.png" + +#set out "vbiaspar1_1.png" +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 out "vbiaspar2_1.png" +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 out "biaspar/ebiaspar1.png" +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 xlabel "Age" +set ylabel "Probability" +set ter png small size 320, 240 +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 + +# +# +#CV preval stable (period): 'pij' files, cov=1 state=2 +set out "biaspar/pbiaspar2_1.png" +set xlabel "Age" +set ylabel "Probability" +set ter png small size 320, 240 +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 + +############## +#MLE estimated parameters +############# +# initial state 1 +# current state 2 +p1=-12.202711; p2=0.091764; +# current state 3 +p3=-10.299238; p4=0.056626; +# initial state 2 +# current state 1 +p5=-1.545619; p6=-0.035395; +# current state 3 +p7=-5.565963; p8=0.016951; +############## +# + +############## +#Graphics of 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)+...) +# +# ng=1 +# jk=1 to 2^0=1 +# jk=1 + +set out "biaspar/pebiaspar1_1.png" + +set title "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 + +set out "biaspar/pebiaspar1_2.png" + +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" +# 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 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 +# 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 +# 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 +# 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 +# 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 +# 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 +# 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 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 +# 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 +# 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 +# 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 +# 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 +# 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 +# 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 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 +# 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 +# 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 +# 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 +# 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 +# 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 +# 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 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 +# 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 +# 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 +# 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 +# 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 +# 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 +# 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 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 +# 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 +# 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 +# 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 +# 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 +# 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 +# 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 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 +# 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 +# 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 +# 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 +# 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 +# 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 +# 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; +# Routine varevsij +unset parametric;unset label; set ter png small size 320, 240 + 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; diff --git a/html/doc/biaspar.htm b/html/doc/biaspar.htm index 2d47bd0..a7b053f 100644 --- a/html/doc/biaspar.htm +++ b/html/doc/biaspar.htm @@ -1,18 +1,58 @@ - -IMaCh biaspar.htm - Imach version 0.98q2, April 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=
- -
- -
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
- -
File of contributions to the likelihood: biaspar/ilkrbiaspar.txt
+ +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=
+ +
+ +
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
+ +
File of contributions to the likelihood: biaspar/ilkrbiaspar.txt
+

  • Result files (first order: no variance)

    + - Observed prevalence in each state (during the period defined between 1/1/1984 and 1/6/1988): biaspar/prbiaspar.txt
    + - Estimated transition probabilities over 1 (stepm) months: biaspar/pijrbiaspar.txt
    + - Period (stable) prevalence in each health state: biaspar/plrbiaspar.txt
    + - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm= 1 months): biaspar/erbiaspar.txt
    + - Population projections by age and states: biaspar/frbiaspar.txt
    +
    • +
    • Graphs


      • - Pij or Conditional probabilities to be observed in state j being in state i, 1 (stepm) months before: biaspar/pebiaspar1_1.png

      - Pij or Conditional probabilities to be observed in state j being in state i 1 (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: biaspar/pebiaspar1_2.png

      - Convergence to period (stable) prevalence in state 1. Or probability to be in state 1 being in state (1 to 2) at different ages. biaspar/pbiaspar1_1.png

      - Convergence to period (stable) prevalence in state 2. Or probability to be in state 2 being in state (1 to 2) at different ages. biaspar/pbiaspar2_1.png
      +
      - Life expectancy by health state (1) at initial age and its decomposition into health expectancies in each alive state (1 to 2) : biaspar/expbiaspar11.png
      +
      - Life expectancy by health state (2) at initial age and its decomposition into health expectancies in each alive state (1 to 2) : biaspar/expbiaspar21.png

    +

  • Result files (second order: variances)

    + - Parameter file with estimated parameters and covariance matrix: rbiaspar.imach
    - 95% confidence intervals and T statistics are in the log file.
    + - Standard deviation of one-step probabilities: biaspar/probrbiaspar.txt
    + - Variance-covariance of one-step probabilities: biaspar/probcovrbiaspar.txt
    + - Correlation matrix of one-step probabilities: biaspar/probcorrbiaspar.txt
    + - Variances and covariances of health expectancies by age and initial health status (cov(eij,ekl)(estepm= 1 months): biaspar/cverbiaspar.txt
    +
    • - (a) Health expectancies by health status at initial age (eij) and standard errors (in parentheses) (b) life expectancies and standard errors (ei.=ei1+ei2+...)(estepm= 1 months): biaspar/stderbiaspar.txt
    + - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=1 months): biaspar/vrbiaspar.txt
    + - Total life expectancy and total health expectancies to be spent in each health state e.j with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=1 months): biaspar/trbiaspar.txt
    + - Standard deviation of period (stable) prevalences: biaspar/vplrbiaspar.txt
    +
    • Graphs


      • - Observed (cross-sectional) and period (incidence based) prevalence (with 95% confidence interval) in state (1): biaspar/vbiaspar1_1.png

      - Observed (cross-sectional) and period (incidence based) prevalence (with 95% confidence interval) in state (2): biaspar/vbiaspar2_1.png
      +
      - Total life expectancy by age and health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) true period expectancies (those weighted with period prevalences are also drawn in addition to the population based expectancies computed using observed and cahotic prevalences: biaspar/ebiaspar1.png

    +

  • Computing and drawing one step probabilities with their confidence intervals

    • + + +

  • Matrix of variance-covariance of pairs of step probabilities (drawings)

    • + +

  • Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)

    • + +
    -stablbased-
    + +
    File (multiple files are possible if covariates are present): biaspar/prmorprev1-stablbased-rbiaspar.txt + +
    Probability is computed over estepm=1 months.

    +
    Local time at start Tue Aug 18 18:20:44 2015 +
    Local time at end Tue Aug 18 18:26:33 2015 +
    + \ No newline at end of file diff --git a/html/doc/biaspar.imach b/html/doc/biaspar.imach index 3dabb24..e5f82a5 100644 --- a/html/doc/biaspar.imach +++ b/html/doc/biaspar.imach @@ -2,11 +2,11 @@ title=1st_example datafile=data1.txt lastobs=8600 firstpass=1 lastpass=4 ftol=1.000000e-008 stepm=1 ncovcol=2 nlstate=2 ndeath=1 maxwav=4 mle=1 weight=0 model=1+age+. -# Parameters -12 0. 0. -13 0. 0. -21 0. 0. -23 0. 0. +#q Parameters +12 -12.245240 0.092358 +13 -10.671890 0.060969 +21 -2.645345 -0.022325 +23 -4.773317 0.007859 # Scales 12 0. 0. 13 0. 0. diff --git a/html/doc/biaspar.log b/html/doc/biaspar.log index d750318..629627b 100644 --- a/html/doc/biaspar.log +++ b/html/doc/biaspar.log @@ -1,140 +1,266 @@ -Log filename:biaspar.log - -Imach version 0.98q2, April 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015 -$Revision$ $Date$ -Enter the parameter file name: -pathimach=Z:\imachcvs\NetBeans\imach\src\ -pathtot=Z:\imachcvs\NetBeans\imach\html\doc\biaspar.imach - path=Z:\imachcvs\NetBeans\imach\html\doc\ - optionfile=biaspar.imach - optionfilext=imach - optionfilefiname='biaspar' -Compiled with: Intel ICC/ICPC Microsoft Visual Studio for Windows (x64 and x86) 32-bitThe programm is not running under WOW64 (i.e probably on a 64bit Windows). -Local time (at start): Tue May 05 11:13:23 2015 +Log filename:biaspar.log + +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 +$Revision$ $Date$ +Enter the parameter file name: +pathimach=/Users/nbrouard/Documents/imach/cvs/imach/build/osx/ +pathtot=html/doc/biaspar.imach + path=html/doc/ + optionfile=biaspar.imach + optionfilext=imach + optionfilefiname='biaspar' +Local time (at start): Tue Aug 18 18:20:44 2015 # Imach version 0.98q2, April 2015, INED-EUROREVES -title=1st_example datafile=data1.txt lastobs=8600 firstpass=1 lastpass=4 -ftol=1.000000e-008 stepm=1 ncovcol=2 nlstate=2 ndeath=1 maxwav=4 mle=1 weight=0 -model=1+age+. -# Parameters -11 0.000000 0.000000 -12 0.000000 0.000000 -21 0.000000 0.000000 -22 0.000000 0.000000 +title=1st_example datafile=data1.txt lastobs=8600 firstpass=1 lastpass=4 +ftol=1.000000e-08 stepm=1 ncovcol=2 nlstate=2 ndeath=1 maxwav=4 mle=1 weight=0 +model=1+age+. +#q Parameters +12 -12.245240 0.092358 +13 -10.671890 0.060969 +21 -2.645345 -0.022325 +23 -4.773317 0.007859 # Scales -12 0.000000e+000 0.000000e+000 -13 0.000000e+000 0.000000e+000 -21 0.000000e+000 0.000000e+000 -23 0.000000e+000 0.000000e+000 +12 0.000000e+00 0.000000e+00 +13 0.000000e+00 0.000000e+00 +21 0.000000e+00 0.000000e+00 +23 0.000000e+00 0.000000e+00 #covariance matrix# -121 0.00000e+000 -122 0.00000e+000 0.00000e+000 -131 0.00000e+000 0.00000e+000 0.00000e+000 -132 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 -211 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 -212 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 -231 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 -232 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 0.00000e+000 - -Total number of individuals= 8270, Agemin = 70.00, Agemax= 104.17 - -Delay (in months) between two waves Min=1 (for indiviudal 6017) Max=74 (5168) Mean=24.040080 - - Age 70 1.=665 loss[1]=5.1% 2.=0 loss[2]=NaNQ% 1.=631 prev[1]=100.0% 2.=0 prev[2]=0.0% 1-1=34 11=563 12=33 13=35 33=6 -Age 71 1.=663 loss[1]=5.7% 2.=2 loss[2]=0.0% 1.=625 prev[1]=99.7% 2.=2 prev[2]=0.3% 1-1=38 11=530 12=47 13=48 21=1 22=1 3-1=2 33=31 -Age 72 1.=1181 loss[1]=5.6% 2.=35 loss[2]=5.7% 1.=1115 prev[1]=97.1% 2.=33 prev[2]=2.9% 1-1=66 11=969 12=70 13=76 2-1=2 21=9 22=18 23=6 3-1=2 33=87 -Age 73 1.=1119 loss[1]=5.1% 2.=48 loss[2]=8.3% 1.=1062 prev[1]=96.0% 2.=44 prev[2]=4.0% 1-1=57 11=912 12=71 13=79 2-1=4 21=12 22=26 23=6 3-1=12 33=94 -Age 74 1.=1563 loss[1]=4.2% 2.=90 loss[2]=4.4% 1.=1497 prev[1]=94.6% 2.=86 prev[2]=5.4% 1-1=66 11=1277 12=104 13=116 2-1=4 21=30 22=41 23=15 3-1=4 33=125 -Age 75 1.=1463 loss[1]=6.2% 2.=98 loss[2]=7.1% 1.=1372 prev[1]=93.8% 2.=91 prev[2]=6.2% 1-1=91 11=1155 12=98 13=119 2-1=7 21=15 22=55 23=21 3-1=4 33=124 -Age 76 1.=1390 loss[1]=4.5% 2.=112 loss[2]=3.6% 1.=1328 prev[1]=92.5% 2.=108 prev[2]=7.5% 1-1=62 11=1090 12=111 13=127 2-1=4 21=25 22=54 23=29 3-1=4 33=142 -Age 77 1.=1271 loss[1]=5.0% 2.=101 loss[2]=5.9% 1.=1208 prev[1]=92.7% 2.=95 prev[2]=7.3% 1-1=63 11=962 12=131 13=115 2-1=6 21=24 22=52 23=19 3-1=7 33=145 -Age 78 1.=1166 loss[1]=4.9% 2.=122 loss[2]=4.1% 1.=1109 prev[1]=90.5% 2.=117 prev[2]=9.5% 1-1=57 11=894 12=111 13=104 2-1=5 21=21 22=75 23=21 3-1=4 33=146 -Age 79 1.=1045 loss[1]=5.7% 2.=133 loss[2]=5.3% 1.=985 prev[1]=88.7% 2.=126 prev[2]=11.3% 1-1=60 11=773 12=109 13=103 2-1=7 21=31 22=68 23=27 3-1=8 33=136 -Age 80 1.=986 loss[1]=4.1% 2.=128 loss[2]=3.1% 1.=946 prev[1]=88.4% 2.=124 prev[2]=11.6% 1-1=40 11=718 12=140 13=88 2-1=4 21=21 22=71 23=32 3-1=6 33=121 -Age 81 1.=872 loss[1]=4.9% 2.=130 loss[2]=3.8% 1.=829 prev[1]=86.9% 2.=125 prev[2]=13.1% 1-1=43 11=629 12=102 13=98 2-1=5 21=24 22=74 23=27 3-1=5 33=126 -Age 82 1.=803 loss[1]=4.4% 2.=146 loss[2]=4.1% 1.=768 prev[1]=84.6% 2.=140 prev[2]=15.4% 1-1=35 11=546 12=131 13=91 2-1=6 21=15 22=77 23=48 3-1=11 33=100 -Age 83 1.=726 loss[1]=6.5% 2.=116 loss[2]=0.9% 1.=679 prev[1]=85.5% 2.=115 prev[2]=14.5% 1-1=47 11=456 12=124 13=99 2-1=1 21=19 22=71 23=25 3-1=8 33=133 -Age 84 1.=622 loss[1]=5.6% 2.=147 loss[2]=4.1% 1.=587 prev[1]=80.6% 2.=141 prev[2]=19.4% 1-1=35 11=394 12=112 13=81 2-1=6 21=18 22=82 23=41 3-1=5 33=114 -Age 85 1.=526 loss[1]=4.4% 2.=127 loss[2]=6.3% 1.=503 prev[1]=80.9% 2.=119 prev[2]=19.1% 1-1=23 11=315 12=122 13=66 2-1=8 21=13 22=67 23=39 3-1=4 33=137 -Age 86 1.=464 loss[1]=5.2% 2.=130 loss[2]=6.2% 1.=440 prev[1]=78.3% 2.=122 prev[2]=21.7% 1-1=24 11=271 12=103 13=66 2-1=8 21=18 22=70 23=34 3-1=3 33=112 -Age 87 1.=372 loss[1]=4.8% 2.=143 loss[2]=2.8% 1.=354 prev[1]=71.8% 2.=139 prev[2]=28.2% 1-1=18 11=219 12=79 13=56 2-1=4 21=15 22=71 23=53 3-1=1 33=81 -Age 88 1.=283 loss[1]=3.9% 2.=164 loss[2]=6.7% 1.=272 prev[1]=64.0% 2.=153 prev[2]=36.0% 1-1=11 11=172 12=63 13=37 2-1=11 21=25 22=84 23=44 3-1=8 33=102 -Age 89 1.=227 loss[1]=3.5% 2.=152 loss[2]=4.6% 1.=219 prev[1]=60.2% 2.=145 prev[2]=39.8% 1-1=8 11=135 12=45 13=39 2-1=7 21=21 22=73 23=51 3-1=2 33=77 -Age 90 1.=181 loss[1]=3.9% 2.=143 loss[2]=4.9% 1.=174 prev[1]=56.1% 2.=136 prev[2]=43.9% 1-1=7 11=104 12=41 13=29 2-1=7 21=18 22=82 23=36 3-1=1 33=75 -Age 91 1.=146 loss[1]=4.1% 2.=109 loss[2]=8.3% 1.=140 prev[1]=58.3% 2.=100 prev[2]=41.7% 1-1=6 11=78 12=36 13=26 2-1=9 21=11 22=51 23=38 3-1=3 33=77 -Age 92 1.=114 loss[1]=6.1% 2.=101 loss[2]=2.0% 1.=107 prev[1]=51.9% 2.=99 prev[2]=48.1% 1-1=7 11=47 12=43 13=17 2-1=2 21=11 22=52 23=36 3-1=2 33=61 -Age 93 1.=78 loss[1]=3.8% 2.=89 loss[2]=12.4% 1.=75 prev[1]=49.0% 2.=78 prev[2]=51.0% 1-1=3 11=36 12=25 13=14 2-1=11 21=10 22=46 23=22 3-1=2 33=62 -Age 94 1.=51 loss[1]=3.9% 2.=71 loss[2]=1.4% 1.=49 prev[1]=41.2% 2.=70 prev[2]=58.8% 1-1=2 11=24 12=8 13=17 2-1=1 21=4 22=39 23=27 3-1=1 33=37 -Age 95 1.=38 loss[1]=5.3% 2.=57 loss[2]=5.3% 1.=36 prev[1]=40.0% 2.=54 prev[2]=60.0% 1-1=2 11=16 12=13 13=7 2-1=3 21=4 22=31 23=19 3-1=1 33=39 -Age 96 1.=25 loss[1]=4.0% 2.=43 loss[2]=4.7% 1.=24 prev[1]=36.9% 2.=41 prev[2]=63.1% 1-1=1 11=11 12=9 13=4 2-1=2 21=2 22=22 23=17 3-1=2 33=25 -Age 97 1.=11 loss[1]=0.0% 2.=36 loss[2]=8.3% 1.=11 prev[1]=25.0% 2.=33 prev[2]=75.0% 11=4 12=7 2-1=3 21=2 22=22 23=9 33=23 -Age 98 1.=5 loss[1]=0.0% 2.=21 loss[2]=0.0% 1.=5 prev[1]=19.2% 2.=21 prev[2]=80.8% 11=1 12=4 21=1 22=13 23=7 3-1=1 33=17 -Age 99 1.=6 loss[1]=0.0% 2.=14 loss[2]=0.0% 1.=6 prev[1]=30.0% 2.=14 prev[2]=70.0% 11=3 12=1 13=2 21=2 22=2 23=10 33=6 -Age 100 1.=2 loss[1]=0.0% 2.=9 loss[2]=0.0% 1.=2 prev[1]=18.2% 2.=9 prev[2]=81.8% 11=1 12=1 21=2 22=5 23=2 33=2 -Age 101 1.=2 loss[1]=50.0% 2.=0 loss[2]=NaNQ% 1.=1 prev[1]=100.0% 2.=0 prev[2]=0.0% 1-1=1 12=1 3-1=1 33=3 -Age 102 1.=2 loss[1]=0.0% 2.=1 loss[2]=0.0% 1.=2 prev[1]=66.7% 2.=1 prev[2]=33.3% 12=2 22=1 33=1 -Age 103 1.=0 loss[1]=NaNQ% 2.=0 loss[2]=NaNQ% 1.=0 prev[1]=NaNQ% 2.=0 prev[2]=NaNQ% -Age 104 1.=0 loss[1]=NaNQ% 2.=0 loss[2]=NaNQ% 1.=0 prev[1]=NaNQ% 2.=0 prev[2]=NaNQ% -Age 105 1.=0 loss[1]=NaNQ% 2.=0 loss[2]=NaNQ% 1.=0 prev[1]=NaNQ% 2.=0 prev[2]=NaNQ% -Age 106 1.=0 loss[1]=NaNQ% 2.=0 loss[2]=NaNQ% 1.=0 prev[1]=NaNQ% 2.=0 prev[2]=NaNQ% -1-1=69 -11=718 -12=195 -13=261 -Total 1.=18068 loss[1]=5.0% 2.=2818 loss[2]=4.9% 1.=17161 prev[1]=86.5% 2.=2681 prev[2]=13.5% -1-1=69 -11=718 -12=195 -13=261 1-1=907 11=13305 12=2097 13=1759 2-1=137 21=424 22=1496 23=761 3-1=114 33=2567 -Powell - -Powell iter=1 -2*LL=429817.002238171520 0 sec. 0 sec. 1 0.000000000000 2 0.000000000000 3 0.000000000000 4 0.000000000000 5 0.000000000000 6 0.000000000000 7 0.000000000000 8 0.000000000000 - -Considering the time needed for this last iteration #1: 0 seconds, - - if your program needs 10 iterations to converge, convergence will be - reached in 0 day(s) 0 hour(s) 0 minute(s) 0 second(s) i.e. - on Tue May 05 11:13:34 2015 (current time is Tue May 05 11:13:34 2015); - - if your program needs 20 iterations to converge, convergence will be - reached in 0 day(s) 0 hour(s) 0 minute(s) 0 second(s) i.e. - on Tue May 05 11:13:34 2015 (current time is Tue May 05 11:13:34 2015); - - if your program needs 30 iterations to converge, convergence will be - reached in 0 day(s) 0 hour(s) 0 minute(s) 0 second(s) i.e. - on Tue May 05 11:13:34 2015 (current time is Tue May 05 11:13:34 2015); -1.....2................3..........4.....................5.....6............7........8..............................Gaining to use new average direction of P0 P8 instead of biggest increase direction 5 : - -Powell iter=2 -2*LL=61164.969498491329 14 sec. 0 sec. 1 10.361177425153 2 -0.000405752275 3 -0.426051135866 4 0.000411058449 5 3.199377281172 6 -0.000133628129 7 -0.817385555710 8 0.000414645460 - -Considering the time needed for this last iteration #2: 14 seconds, - - if your program needs 10 iterations to converge, convergence will be - reached in 0 day(s) 0 hour(s) 1 minute(s) 52 second(s) i.e. - on Tue May 05 11:15:40 2015 (current time is Tue May 05 11:13:48 2015); - - if your program needs 20 iterations to converge, convergence will be - reached in 0 day(s) 0 hour(s) 4 minute(s) 12 second(s) i.e. - on Tue May 05 11:18:00 2015 (current time is Tue May 05 11:13:48 2015); - - if your program needs 30 iterations to converge, convergence will be - reached in 0 day(s) 0 hour(s) 6 minute(s) 32 second(s) i.e. - on Tue May 05 11:20:20 2015 (current time is Tue May 05 11:13:48 2015); -1............2....................3......4..................5..................6.................7..........8........ -Powell iter=3 -2*LL=58792.325287399166 43 sec. 0 sec. 1 5.025320473019 2 -0.001271522649 3 -2.292075301862 4 0.005675436950 5 3.064920310602 6 -0.003614340923 7 -1.082612744376 8 -0.006929410302 - -Considering the time needed for this last iteration #3: 43 seconds, - - if your program needs 10 iterations to converge, convergence will be - reached in 0 day(s) 0 hour(s) 5 minute(s) 1 second(s) i.e. - on Tue May 05 11:19:32 2015 (current time is Tue May 05 11:14:31 2015); - - if your program needs 20 iterations to converge, convergence will be - reached in 0 day(s) 0 hour(s) 12 minute(s) 11 second(s) i.e. - on Tue May 05 11:26:42 2015 (current time is Tue May 05 11:14:31 2015); - - if your program needs 30 iterations to converge, convergence will be - reached in 0 day(s) 0 hour(s) 19 minute(s) 21 second(s) i.e. - on Tue May 05 11:33:52 2015 (current time is Tue May 05 11:14:31 2015); -1.........2....................3.........4....................5..................6.................7...........8...............Gaining to use new average direction of P0 P8 instead of biggest increase direction 1 : - -Powell iter=4 -2*LL=51671.511989744839 13 sec. 0 sec. 1 -0.738171836654 2 -0.005095967053 3 -6.249885480035 4 0.018850231372 5 2.760427678775 6 0.002137535586 7 -0.810125973911 8 -0.019962106000 -1........2................3..........4..................5.................6................7.................8.......... -Powell iter=5 -2*LL=51564.973406501369 13 sec. 0 sec. 1 -0.640102693049 2 -0.004671488059 3 -6.355728607893 4 0.019354535332 5 2.794272826941 6 2.309115769305 7 1.799068527323 8 -4.254984576420 -1........2.............3.........4..................5.................6.................7.................8.......... -Powell iter=6 -2*LL=51512.620168158559 12 sec. 0 sec. 1 -0.707671793492 2 -0.004043840434 3 -6.235710935103 4 0.019694131082 5 2.772348672077 6 4.883902697129 7 4.421901023083 8 -1.637606955042 -1........2.............3...................4..................5.................6...............7.................8.......... -Powell iter=7 -2*LL=51497.973086223668 13 sec. 0 sec. 1 -0.748745600049 2 -0.003548201851 3 -6.280610560550 4 0.020192016944 5 2.776035786301 6 6.512481518851 7 7.040490669592 8 0.979620465528 -1........2.............3..........4..................5.................6..................7.................8........................Gaining to use new average direction of P0 P8 instead of biggest increase direction 8 : - -Powell iter=8 -2*LL=51469.726224868631 15 sec. 0 sec. 1 -0.833574313562 2 -0.002535454468 3 -6.362935045791 4 0.021191220259 5 2.782030172908 6 6.608886952762 7 12.367555241042 8 6.303685589096 -1........2.............3..........4..................5.......6....................7..................8............... -Powell iter=9 -2*LL=51460.597638570471 14 sec. 0 sec. 1 -0.819597388038 2 -0.001927771721 3 -6.366922190899 4 0.021608735010 5 2.788633894031 6 6.715764216787 7 11.126986364695 8 6.426838468958 -1........2.............3.........4..................5..........6.........7.....................8..................................Gaining to use new average direction of P0 P8 instead of biggest increase direction 2 : - -Powell iter=10 -2*LL=51437.479784084469 17 sec. 0 sec. 1 -0.893774665883 2 -0.000533885740 3 -6.429458703340 4 0.022581850422 5 2.770188936631 6 6.798189075056 7 12.797974488056 8 6.485900015773 -1................2..............3.........4..................5..............6...................7..................8.............................. -Powell iter=11 -2*LL=51420.437001909391 42 sec. 0 sec. 1 -0.950697588560 2 -0.000527484177 3 -6.481470925397 4 0.022923641821 5 2.752623141516 6 6.798366227492 7 11.189519918460 8 6.148112871371 -1...................2....................... \ No newline at end of file +121 0.00000e+00 +122 0.00000e+00 0.00000e+00 +131 0.00000e+00 0.00000e+00 0.00000e+00 +132 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 +211 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 +212 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 +231 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 +232 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 + +Total number of individuals= 8270, Agemin = 70.00, Agemax= 104.17 + +Delay (in months) between two waves Min=1 (for indiviudal 6017) Max=74 (5168) Mean=24.040080 + + Age 70 1.=665 loss[1]=5.1% 2.=0 loss[2]=NaNQ% 1.=631 prev[1]=100.0% 2.=0 prev[2]=0.0% 1-1=34 11=563 12=33 13=35 33=6 +Age 71 1.=663 loss[1]=5.7% 2.=2 loss[2]=0.0% 1.=625 prev[1]=99.7% 2.=2 prev[2]=0.3% 1-1=38 11=530 12=47 13=48 21=1 22=1 3-1=2 33=31 +Age 72 1.=1181 loss[1]=5.6% 2.=35 loss[2]=5.7% 1.=1115 prev[1]=97.1% 2.=33 prev[2]=2.9% 1-1=66 11=969 12=70 13=76 2-1=2 21=9 22=18 23=6 3-1=2 33=87 +Age 73 1.=1119 loss[1]=5.1% 2.=48 loss[2]=8.3% 1.=1062 prev[1]=96.0% 2.=44 prev[2]=4.0% 1-1=57 11=912 12=71 13=79 2-1=4 21=12 22=26 23=6 3-1=12 33=94 +Age 74 1.=1563 loss[1]=4.2% 2.=90 loss[2]=4.4% 1.=1497 prev[1]=94.6% 2.=86 prev[2]=5.4% 1-1=66 11=1277 12=104 13=116 2-1=4 21=30 22=41 23=15 3-1=4 33=125 +Age 75 1.=1463 loss[1]=6.2% 2.=98 loss[2]=7.1% 1.=1372 prev[1]=93.8% 2.=91 prev[2]=6.2% 1-1=91 11=1155 12=98 13=119 2-1=7 21=15 22=55 23=21 3-1=4 33=124 +Age 76 1.=1390 loss[1]=4.5% 2.=112 loss[2]=3.6% 1.=1328 prev[1]=92.5% 2.=108 prev[2]=7.5% 1-1=62 11=1090 12=111 13=127 2-1=4 21=25 22=54 23=29 3-1=4 33=142 +Age 77 1.=1271 loss[1]=5.0% 2.=101 loss[2]=5.9% 1.=1208 prev[1]=92.7% 2.=95 prev[2]=7.3% 1-1=63 11=962 12=131 13=115 2-1=6 21=24 22=52 23=19 3-1=7 33=145 +Age 78 1.=1166 loss[1]=4.9% 2.=122 loss[2]=4.1% 1.=1109 prev[1]=90.5% 2.=117 prev[2]=9.5% 1-1=57 11=894 12=111 13=104 2-1=5 21=21 22=75 23=21 3-1=4 33=146 +Age 79 1.=1045 loss[1]=5.7% 2.=133 loss[2]=5.3% 1.=985 prev[1]=88.7% 2.=126 prev[2]=11.3% 1-1=60 11=773 12=109 13=103 2-1=7 21=31 22=68 23=27 3-1=8 33=136 +Age 80 1.=986 loss[1]=4.1% 2.=128 loss[2]=3.1% 1.=946 prev[1]=88.4% 2.=124 prev[2]=11.6% 1-1=40 11=718 12=140 13=88 2-1=4 21=21 22=71 23=32 3-1=6 33=121 +Age 81 1.=872 loss[1]=4.9% 2.=130 loss[2]=3.8% 1.=829 prev[1]=86.9% 2.=125 prev[2]=13.1% 1-1=43 11=629 12=102 13=98 2-1=5 21=24 22=74 23=27 3-1=5 33=126 +Age 82 1.=803 loss[1]=4.4% 2.=146 loss[2]=4.1% 1.=768 prev[1]=84.6% 2.=140 prev[2]=15.4% 1-1=35 11=546 12=131 13=91 2-1=6 21=15 22=77 23=48 3-1=11 33=100 +Age 83 1.=726 loss[1]=6.5% 2.=116 loss[2]=0.9% 1.=679 prev[1]=85.5% 2.=115 prev[2]=14.5% 1-1=47 11=456 12=124 13=99 2-1=1 21=19 22=71 23=25 3-1=8 33=133 +Age 84 1.=622 loss[1]=5.6% 2.=147 loss[2]=4.1% 1.=587 prev[1]=80.6% 2.=141 prev[2]=19.4% 1-1=35 11=394 12=112 13=81 2-1=6 21=18 22=82 23=41 3-1=5 33=114 +Age 85 1.=526 loss[1]=4.4% 2.=127 loss[2]=6.3% 1.=503 prev[1]=80.9% 2.=119 prev[2]=19.1% 1-1=23 11=315 12=122 13=66 2-1=8 21=13 22=67 23=39 3-1=4 33=137 +Age 86 1.=464 loss[1]=5.2% 2.=130 loss[2]=6.2% 1.=440 prev[1]=78.3% 2.=122 prev[2]=21.7% 1-1=24 11=271 12=103 13=66 2-1=8 21=18 22=70 23=34 3-1=3 33=112 +Age 87 1.=372 loss[1]=4.8% 2.=143 loss[2]=2.8% 1.=354 prev[1]=71.8% 2.=139 prev[2]=28.2% 1-1=18 11=219 12=79 13=56 2-1=4 21=15 22=71 23=53 3-1=1 33=81 +Age 88 1.=283 loss[1]=3.9% 2.=164 loss[2]=6.7% 1.=272 prev[1]=64.0% 2.=153 prev[2]=36.0% 1-1=11 11=172 12=63 13=37 2-1=11 21=25 22=84 23=44 3-1=8 33=102 +Age 89 1.=227 loss[1]=3.5% 2.=152 loss[2]=4.6% 1.=219 prev[1]=60.2% 2.=145 prev[2]=39.8% 1-1=8 11=135 12=45 13=39 2-1=7 21=21 22=73 23=51 3-1=2 33=77 +Age 90 1.=181 loss[1]=3.9% 2.=143 loss[2]=4.9% 1.=174 prev[1]=56.1% 2.=136 prev[2]=43.9% 1-1=7 11=104 12=41 13=29 2-1=7 21=18 22=82 23=36 3-1=1 33=75 +Age 91 1.=146 loss[1]=4.1% 2.=109 loss[2]=8.3% 1.=140 prev[1]=58.3% 2.=100 prev[2]=41.7% 1-1=6 11=78 12=36 13=26 2-1=9 21=11 22=51 23=38 3-1=3 33=77 +Age 92 1.=114 loss[1]=6.1% 2.=101 loss[2]=2.0% 1.=107 prev[1]=51.9% 2.=99 prev[2]=48.1% 1-1=7 11=47 12=43 13=17 2-1=2 21=11 22=52 23=36 3-1=2 33=61 +Age 93 1.=78 loss[1]=3.8% 2.=89 loss[2]=12.4% 1.=75 prev[1]=49.0% 2.=78 prev[2]=51.0% 1-1=3 11=36 12=25 13=14 2-1=11 21=10 22=46 23=22 3-1=2 33=62 +Age 94 1.=51 loss[1]=3.9% 2.=71 loss[2]=1.4% 1.=49 prev[1]=41.2% 2.=70 prev[2]=58.8% 1-1=2 11=24 12=8 13=17 2-1=1 21=4 22=39 23=27 3-1=1 33=37 +Age 95 1.=38 loss[1]=5.3% 2.=57 loss[2]=5.3% 1.=36 prev[1]=40.0% 2.=54 prev[2]=60.0% 1-1=2 11=16 12=13 13=7 2-1=3 21=4 22=31 23=19 3-1=1 33=39 +Age 96 1.=25 loss[1]=4.0% 2.=43 loss[2]=4.7% 1.=24 prev[1]=36.9% 2.=41 prev[2]=63.1% 1-1=1 11=11 12=9 13=4 2-1=2 21=2 22=22 23=17 3-1=2 33=25 +Age 97 1.=11 loss[1]=0.0% 2.=36 loss[2]=8.3% 1.=11 prev[1]=25.0% 2.=33 prev[2]=75.0% 11=4 12=7 2-1=3 21=2 22=22 23=9 33=23 +Age 98 1.=5 loss[1]=0.0% 2.=21 loss[2]=0.0% 1.=5 prev[1]=19.2% 2.=21 prev[2]=80.8% 11=1 12=4 21=1 22=13 23=7 3-1=1 33=17 +Age 99 1.=6 loss[1]=0.0% 2.=14 loss[2]=0.0% 1.=6 prev[1]=30.0% 2.=14 prev[2]=70.0% 11=3 12=1 13=2 21=2 22=2 23=10 33=6 +Age 100 1.=2 loss[1]=0.0% 2.=9 loss[2]=0.0% 1.=2 prev[1]=18.2% 2.=9 prev[2]=81.8% 11=1 12=1 21=2 22=5 23=2 33=2 +Age 101 1.=2 loss[1]=50.0% 2.=0 loss[2]=NaNQ% 1.=1 prev[1]=100.0% 2.=0 prev[2]=0.0% 1-1=1 12=1 3-1=1 33=3 +Age 102 1.=2 loss[1]=0.0% 2.=1 loss[2]=0.0% 1.=2 prev[1]=66.7% 2.=1 prev[2]=33.3% 12=2 22=1 33=1 +Age 103 1.=0 loss[1]=NaNQ% 2.=0 loss[2]=NaNQ% 1.=0 prev[1]=NaNQ% 2.=0 prev[2]=NaNQ% +Age 104 1.=0 loss[1]=NaNQ% 2.=0 loss[2]=NaNQ% 1.=0 prev[1]=NaNQ% 2.=0 prev[2]=NaNQ% +Age 105 1.=0 loss[1]=NaNQ% 2.=0 loss[2]=NaNQ% 1.=0 prev[1]=NaNQ% 2.=0 prev[2]=NaNQ% +Age 106 1.=0 loss[1]=NaNQ% 2.=0 loss[2]=NaNQ% 1.=0 prev[1]=NaNQ% 2.=0 prev[2]=NaNQ% -1-1=69 -11=718 -12=195 -13=261 +Total 1.=18068 loss[1]=5.0% 2.=2818 loss[2]=4.9% 1.=17161 prev[1]=86.5% 2.=2681 prev[2]=13.5% -1-1=69 -11=718 -12=195 -13=261 1-1=907 11=13305 12=2097 13=1759 2-1=137 21=424 22=1496 23=761 3-1=114 33=2567 +Powell + +Powell iter=1 -2*LL=46542.394740741831 0 sec. 1 sec. 1 -12.245240000000 2 0.092358000000 3 -10.671890000000 4 0.060969000000 5 -2.645345000000 6 -0.022325000000 7 -4.773317000000 8 0.007859000000 + +Considering the time needed for this last iteration #1: 0 seconds, + - if your program needs 10 iterations to converge, convergence will be + reached in 0 day(s) 0 hour(s) 0 minute(s) 0 second(s) i.e. + on Tue Aug 18 18:20:45 2015 (current time is Tue Aug 18 18:20:45 2015); + - if your program needs 20 iterations to converge, convergence will be + reached in 0 day(s) 0 hour(s) 0 minute(s) 0 second(s) i.e. + on Tue Aug 18 18:20:45 2015 (current time is Tue Aug 18 18:20:45 2015); + - if your program needs 30 iterations to converge, convergence will be + reached in 0 day(s) 0 hour(s) 0 minute(s) 0 second(s) i.e. + on Tue Aug 18 18:20:45 2015 (current time is Tue Aug 18 18:20:45 2015); +1.............2.....................3...............4...................5..........6.............7...............8.................. +Powell iter=2 -2*LL=46542.366177077667 23 sec. 24 sec. 1 -12.245474667968 2 0.092360078052 3 -10.671718090206 4 0.060967648859 5 -2.641226372487 6 -0.022378298324 7 -4.773347352998 8 0.007897501084 + +Considering the time needed for this last iteration #2: 23 seconds, + - if your program needs 10 iterations to converge, convergence will be + reached in 0 day(s) 0 hour(s) 3 minute(s) 4 second(s) i.e. + on Tue Aug 18 18:24:12 2015 (current time is Tue Aug 18 18:21:08 2015); + - if your program needs 20 iterations to converge, convergence will be + reached in 0 day(s) 0 hour(s) 6 minute(s) 54 second(s) i.e. + on Tue Aug 18 18:28:02 2015 (current time is Tue Aug 18 18:21:08 2015); + - if your program needs 30 iterations to converge, convergence will be + reached in 0 day(s) 0 hour(s) 10 minute(s) 44 second(s) i.e. + on Tue Aug 18 18:31:52 2015 (current time is Tue Aug 18 18:21:08 2015); +1............2.................3............4...................5..........6.............7..........8.........................Gaining to use new average direction of P0 P8 instead of biggest increase direction 8 : + +Powell iter=3 -2*LL=46542.180101184662 22 sec. 46 sec. 1 -12.243554549912 2 0.092379481639 3 -10.687240979880 4 0.060948425212 5 -2.601681584093 6 -0.022889573696 7 -4.797716971796 8 0.008263023171 + +Considering the time needed for this last iteration #3: 22 seconds, + - if your program needs 10 iterations to converge, convergence will be + reached in 0 day(s) 0 hour(s) 2 minute(s) 34 second(s) i.e. + on Tue Aug 18 18:24:04 2015 (current time is Tue Aug 18 18:21:30 2015); + - if your program needs 20 iterations to converge, convergence will be + reached in 0 day(s) 0 hour(s) 6 minute(s) 14 second(s) i.e. + on Tue Aug 18 18:27:44 2015 (current time is Tue Aug 18 18:21:30 2015); + - if your program needs 30 iterations to converge, convergence will be + reached in 0 day(s) 0 hour(s) 9 minute(s) 54 second(s) i.e. + on Tue Aug 18 18:31:24 2015 (current time is Tue Aug 18 18:21:30 2015); +1.................2.................3..........4....................5..........6.............7..........8....... +Powell iter=4 -2*LL=46541.944882756965 20 sec. 66 sec. 1 -12.242484543366 2 0.092391161272 3 -10.684956992257 4 0.060933369989 5 -2.571767476006 6 -0.023216409131 7 -4.817698692685 8 0.008460497128 +1.........2..................3..........4....................5..........6.............7..........8..............Gaining to use new average direction of P0 P8 instead of biggest increase direction 3 : + +Powell iter=5 -2*LL=46538.155159115864 21 sec. 87 sec. 1 -12.277818683456 2 0.092782784461 3 -10.606927524558 4 0.060433498790 5 -1.636618302422 6 -0.034173907116 7 -5.415159199358 8 0.015209892785 +1.........2..............3........4...................5.........6..............7..........8........directest= 3.559482495482, t= -1.587615025675, f1= 46538.155159115864,f2= 46537.965437599931,f3= 46541.605702231980, del= 0.135251826250 +f1-2f2+f3= 3.829986147983, f1-f2-del= 0.054469689683, f1-f3= -3.450543116116 + +Powell iter=6 -2*LL=46537.965437599931 17 sec. 104 sec. 1 -12.286824634318 2 0.092796946661 3 -10.605118146544 4 0.060392081785 5 -1.601001695625 6 -0.034696856573 7 -5.445686958604 8 0.015541650236 +1............2...............3..........4...........................5.........6.............7.................8........ +Powell iter=7 -2*LL=46537.953896904983 21 sec. 125 sec. 1 -12.288663475348 2 0.092794258423 3 -10.602520523521 4 0.060372798332 5 -1.596765949187 6 -0.034763087057 7 -5.450260084532 8 0.015582787665 +1...........2...............3........4...................5..........6..............7............8.............Gaining to use new average direction of P0 P8 instead of biggest increase direction 4 : + +Powell iter=8 -2*LL=46537.933555419499 20 sec. 145 sec. 1 -12.288754155703 2 0.092753643773 3 -10.588920461186 4 0.060230465648 5 -1.588742425574 6 -0.034884297842 7 -5.460441275653 8 0.015679980832 +1..........2................3..........4.........5...........6..............7...........8............Gaining to use new average direction of P0 P8 instead of biggest increase direction 1 : + +Powell iter=9 -2*LL=46537.891454595432 19 sec. 164 sec. 1 -12.283266439012 2 0.092658255416 3 -10.562891684762 4 0.059948818330 5 -1.581316871784 6 -0.034987633432 7 -5.472744984969 8 0.015801808619 +1.....2..............3........4............5............6..............7...........8...........Gaining to use new average direction of P0 P8 instead of biggest increase direction 8 : + +Powell iter=10 -2*LL=46537.765677731819 18 sec. 182 sec. 1 -12.262794789308 2 0.092367916069 3 -10.470813624311 4 0.058882333788 5 -1.562236459514 6 -0.035239826239 7 -5.510520845667 8 0.016209203343 +1......2.......................3.......4........5............6..............7............8............Gaining to use new average direction of P0 P8 instead of biggest increase direction 8 : + +Powell iter=11 -2*LL=46537.498821119196 19 sec. 201 sec. 1 -12.214937649099 2 0.091832303757 3 -10.310758734665 4 0.056891524738 5 -1.540234661352 6 -0.035490430955 7 -5.566745000929 8 0.016892295483 +1.....2..............3.......4........5.................6...............7..............8....... +Powell iter=12 -2*LL=46537.411404609535 18 sec. 219 sec. 1 -12.203395121992 2 0.091768319083 3 -10.300995242801 4 0.056661013905 5 -1.545167229526 6 -0.035400936285 7 -5.565324661507 8 0.016938176004 +1............2..................3..........4............5..................6..............7.............8.....................Gaining to use new average direction of P0 P8 instead of biggest increase direction 3 : + +Powell iter=13 -2*LL=46537.410703925241 22 sec. 241 sec. 1 -12.202513270154 2 0.091761198901 3 -10.299418789414 4 0.056628413435 5 -1.545343667372 6 -0.035398382663 7 -5.565921175501 8 0.016950736226 +1.........2................3............4.............5..........6....................7..............8........#Number of iterations & function calls = 13 & 1694, -2 Log likelihood = 46537.410262065809 +# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ... +12 -12.2027105 0.0917637 +13 -10.2992383 0.0566262 +21 -1.5456185 -0.0353950 +23 -5.5659628 0.0169512 + +Calculation of the hessian matrix. Wait... +12345678.12.13.14.15.16.17.18.23.24.25.26.27.28.34.35.36.37.38.45.46.47.48.56.57.58.67.68.78 + +Inverting the hessian to get the covariance matrix. Wait... + +#Hessian matrix# +2.301e+03 1.898e+05 3.980e+02 3.280e+04 -3.628e+02 -3.007e+04 -3.111e+02 -2.563e+04 +1.898e+05 1.574e+07 3.252e+04 2.694e+06 -3.003e+04 -2.503e+06 -2.554e+04 -2.114e+06 +3.980e+02 3.252e+04 8.499e+02 6.839e+04 -8.040e+01 -6.688e+03 3.773e+02 3.120e+04 +3.280e+04 2.694e+06 6.839e+04 5.532e+06 -6.734e+03 -5.639e+05 3.117e+04 2.590e+06 +-3.628e+02 -3.003e+04 -8.040e+01 -6.734e+03 4.570e+02 3.818e+04 4.994e+01 4.126e+03 +-3.007e+04 -2.503e+06 -6.688e+03 -5.639e+05 3.818e+04 3.208e+06 4.126e+03 3.421e+05 +-3.111e+02 -2.554e+04 3.773e+02 3.117e+04 4.994e+01 4.126e+03 1.024e+03 8.867e+04 +-2.563e+04 -2.114e+06 3.120e+04 2.590e+06 4.126e+03 3.421e+05 8.867e+04 7.720e+06 +Parameters, T and confidence intervals +12 -12.2027105 T= -36.632 CI=[ -12.8689514 ; -11.5364696] 0.0917637 T= 22.911 CI=[ 0.0837533 ; 0.0997740] +13 -10.2992383 T= -18.738 CI=[ -11.3985038 ; -9.1999728] 0.0566262 T= 8.316 CI=[ 0.0430080 ; 0.0702444] +21 -1.5456185 T= -2.259 CI=[ -2.9142844 ; -0.1769526] -0.0353950 T= -4.335 CI=[ -0.0517251 ; -0.0190649] +23 -5.5659628 T= -11.196 CI=[ -6.5602821 ; -4.5716434] 0.0169512 T= 2.998 CI=[ 0.0056422 ; 0.0282603] +# Scales (for hessian or gradient estimation) +12 1.00000e-04 1.00000e-06 +13 1.00000e-04 1.00000e-06 +21 1.00000e-04 1.00000e-06 +23 3.00000e-04 1.00000e-06 +# Covariance matrix +# 121 Var(a12) +# 122 Cov(b12,a12) Var(b12) +# ... +# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23) +#121 Var(a12) +#122 Cov(b12,a12) Var(b12) +#131 Cov(a13,a12) Cov(a13,b12) Var(a13) +#132 Cov(b13,a12) Cov(b13,b12) Cov(b13,a13) Var(b13) +#211 Cov(a21,a12) Cov(a21,b12) Cov(a21,a13) Cov(a21,b13) Var(a21) +#212 Cov(b21,a12) Cov(b21,b12) Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21) +#231 Cov(a23,a12) Cov(a23,b12) Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23) +#232 Cov(b23,a12) Cov(b23,b12) Cov(b23,a13) Cov(b23,b13) Cov(b23,a21) Cov(b23,b21) Cov(b23,a23) Var(b23) +121 1.10969e-01 +122 -1.33029e-03 1.60415e-05 +131 -5.53768e-02 6.77306e-04 3.02096e-01 +132 6.58106e-04 -8.12775e-06 -3.73026e-03 4.63642e-05 +211 7.59223e-02 -9.02778e-04 2.53226e-02 -3.27358e-04 4.68312e-01 +212 -9.05016e-04 1.08138e-05 -3.15929e-04 4.09141e-06 -5.57262e-03 6.66682e-05 +231 5.24440e-02 -5.95206e-04 -8.93872e-02 1.00357e-03 6.06408e-03 -7.39139e-05 2.47168e-01 +232 -5.95756e-04 6.80630e-06 1.05928e-03 -1.20524e-05 -6.07266e-05 7.34461e-07 -2.80315e-03 3.19737e-05 +begin-prev-date=1/1/1984 end-prev-date=1/6/1988 mov_average=0 +pop_based=0 +prevforecast=0 starting-proj-date=1/1/2000 final-proj-date=1/1/2000 mobil_average=0 +Computing period (stable) prevalence: result on file 'plrbiaspar.txt' + +#************ +Computing pij: result on file 'pijrbiaspar.txt' +Computing standard deviation of one-step probabilities: result on file 'probrbiaspar.txt' +Computing matrix of variance covariance of one-step probabilities: result on file 'probcovrbiaspar.txt' +and correlation matrix of one-step probabilities: result on file 'probcorrbiaspar.txt' +65 13-12 mu 1.5972e-02 2.3367e-02 Var 3.3236e-06 3.1628e-06 cor -0.338 cov -1.0950e-06 Eig 4.341e-06 2.145e-06 1stv 0.733 -0.681 tan -0.929 +70 13-12 mu 2.1166e-02 3.6913e-02 Var 3.1497e-06 4.5213e-06 cor -0.360 cov -1.3581e-06 Eig 5.357e-06 2.314e-06 1stv 0.524 -0.852 tan -1.625 +75 13-12 mu 2.8027e-02 5.8265e-02 Var 2.6312e-06 5.5954e-06 cor -0.404 cov -1.5492e-06 Eig 6.257e-06 1.969e-06 1stv 0.393 -0.920 tan -2.341 +80 13-12 mu 3.7067e-02 9.1858e-02 Var 2.7234e-06 6.5867e-06 cor -0.456 cov -1.9326e-06 Eig 7.387e-06 1.923e-06 1stv 0.383 -0.924 tan -2.413 +85 13-12 mu 4.8930e-02 1.4455e-01 Var 7.0008e-06 1.4795e-05 cor -0.418 cov -4.2498e-06 Eig 1.666e-05 5.132e-06 1stv 0.403 -0.915 tan -2.274 +90 13-12 mu 6.4406e-02 2.2681e-01 Var 2.5605e-05 7.2563e-05 cor -0.359 cov -1.5484e-05 Eig 7.721e-05 2.096e-05 1stv 0.287 -0.958 tan -3.333 +95 13-12 mu 8.4408e-02 3.5434e-01 Var 8.3580e-05 3.5679e-04 cor -0.341 cov -5.8808e-05 Eig 3.689e-04 7.146e-05 1stv 0.202 -0.979 tan -4.852 +65 21-12 mu 2.4815e-01 2.3367e-02 Var 1.5081e-03 3.1628e-06 cor 0.333 cov 2.3009e-05 Eig 1.509e-03 2.811e-06 1stv 1.000 0.015 tan 0.015 +70 21-12 mu 2.0839e-01 3.6913e-02 Var 6.2123e-04 4.5213e-06 cor 0.332 cov 1.7587e-05 Eig 6.217e-04 4.020e-06 1stv 1.000 0.028 tan 0.028 +75 21-12 mu 1.7490e-01 5.8265e-02 Var 2.2058e-04 5.5954e-06 cor 0.326 cov 1.1456e-05 Eig 2.212e-04 4.987e-06 1stv 0.999 0.053 tan 0.053 +80 21-12 mu 1.4670e-01 9.1858e-02 Var 7.0767e-05 6.5867e-06 cor 0.304 cov 6.5593e-06 Eig 7.143e-05 5.923e-06 1stv 0.995 0.101 tan 0.101 +85 21-12 mu 1.2299e-01 1.4455e-01 Var 3.9227e-05 1.4795e-05 cor 0.276 cov 6.6547e-06 Eig 4.092e-05 1.310e-05 1stv 0.969 0.247 tan 0.255 +90 21-12 mu 1.0307e-01 2.2681e-01 Var 5.4893e-05 7.2563e-05 cor 0.289 cov 1.8261e-05 Eig 8.401e-05 4.344e-05 1stv 0.531 0.847 tan 1.595 +95 21-12 mu 8.6343e-02 3.5434e-01 Var 8.2297e-05 3.5679e-04 cor 0.302 cov 5.1723e-05 Eig 3.662e-04 7.287e-05 1stv 0.179 0.984 tan 5.489 +65 23-12 mu 1.3378e-01 2.3367e-02 Var 3.1221e-04 3.1628e-06 cor 0.364 cov 1.1447e-05 Eig 3.126e-04 2.739e-06 1stv 0.999 0.037 tan 0.037 +70 23-12 mu 1.4596e-01 3.6913e-02 Var 2.3686e-04 4.5213e-06 cor 0.388 cov 1.2697e-05 Eig 2.376e-04 3.829e-06 1stv 0.999 0.054 tan 0.054 +75 23-12 mu 1.5914e-01 5.8265e-02 Var 1.6142e-04 5.5954e-06 cor 0.423 cov 1.2709e-05 Eig 1.625e-04 4.566e-06 1stv 0.997 0.081 tan 0.081 +80 23-12 mu 1.7343e-01 9.1858e-02 Var 9.6292e-05 6.5867e-06 cor 0.449 cov 1.1306e-05 Eig 9.769e-05 5.184e-06 1stv 0.992 0.123 tan 0.124 +85 23-12 mu 1.8890e-01 1.4455e-01 Var 5.6832e-05 1.4795e-05 cor 0.356 cov 1.0309e-05 Eig 5.922e-05 1.240e-05 1stv 0.974 0.226 tan 0.232 +90 23-12 mu 2.0566e-01 2.2681e-01 Var 6.4965e-05 7.2563e-05 cor 0.255 cov 1.7485e-05 Eig 8.666e-05 5.087e-05 1stv 0.628 0.779 tan 1.241 +95 23-12 mu 2.2383e-01 3.5434e-01 Var 1.5120e-04 3.5679e-04 cor 0.238 cov 5.5313e-05 Eig 3.707e-04 1.373e-04 1stv 0.244 0.970 tan 3.969 +65 21-13 mu 2.4815e-01 1.5972e-02 Var 1.5081e-03 3.3236e-06 cor 0.047 cov 3.3259e-06 Eig 1.508e-03 3.316e-06 1stv 1.000 0.002 tan 0.002 +70 21-13 mu 2.0839e-01 2.1166e-02 Var 6.2123e-04 3.1497e-06 cor 0.037 cov 1.6580e-06 Eig 6.212e-04 3.145e-06 1stv 1.000 0.003 tan 0.003 +75 21-13 mu 1.7490e-01 2.8027e-02 Var 2.2058e-04 2.6312e-06 cor 0.024 cov 5.6775e-07 Eig 2.206e-04 2.630e-06 1stv 1.000 0.003 tan 0.003 +80 21-13 mu 1.4670e-01 3.7067e-02 Var 7.0767e-05 2.7234e-06 cor 0.024 cov 3.3537e-07 Eig 7.077e-05 2.722e-06 1stv 1.000 0.005 tan 0.005 +85 21-13 mu 1.2299e-01 4.8930e-02 Var 3.9227e-05 7.0008e-06 cor 0.078 cov 1.2860e-06 Eig 3.928e-05 6.950e-06 1stv 0.999 0.040 tan 0.040 +90 21-13 mu 1.0307e-01 6.4406e-02 Var 5.4893e-05 2.5605e-05 cor 0.100 cov 3.7654e-06 Eig 5.537e-05 2.513e-05 1stv 0.992 0.126 tan 0.127 +95 21-13 mu 8.6343e-02 8.4408e-02 Var 8.2297e-05 8.3580e-05 cor 0.097 cov 8.0750e-06 Eig 9.104e-05 7.484e-05 1stv 0.679 0.735 tan 1.083 +65 23-13 mu 1.3378e-01 1.5972e-02 Var 3.1221e-04 3.3236e-06 cor -0.409 cov -1.3182e-05 Eig 3.128e-04 2.762e-06 1stv 0.999 -0.043 tan -0.043 +70 23-13 mu 1.4596e-01 2.1166e-02 Var 2.3686e-04 3.1497e-06 cor -0.453 cov -1.2362e-05 Eig 2.375e-04 2.498e-06 1stv 0.999 -0.053 tan -0.053 +75 23-13 mu 1.5914e-01 2.8027e-02 Var 1.6142e-04 2.6312e-06 cor -0.528 cov -1.0874e-05 Eig 1.622e-04 1.890e-06 1stv 0.998 -0.068 tan -0.068 +80 23-13 mu 1.7343e-01 3.7067e-02 Var 9.6292e-05 2.7234e-06 cor -0.585 cov -9.4784e-06 Eig 9.724e-05 1.773e-06 1stv 0.995 -0.100 tan -0.100 +85 23-13 mu 1.8890e-01 4.8930e-02 Var 5.6832e-05 7.0008e-06 cor -0.513 cov -1.0241e-05 Eig 5.885e-05 4.978e-06 1stv 0.981 -0.194 tan -0.198 +90 23-13 mu 2.0566e-01 6.4406e-02 Var 6.4965e-05 2.5605e-05 cor -0.434 cov -1.7707e-05 Eig 7.176e-05 1.881e-05 1stv 0.934 -0.358 tan -0.384 +95 23-13 mu 2.2383e-01 8.4408e-02 Var 1.5120e-04 8.3580e-05 cor -0.363 cov -4.0852e-05 Eig 1.704e-04 6.436e-05 1stv 0.905 -0.426 tan -0.470 +65 23-21 mu 1.3378e-01 2.4815e-01 Var 3.1221e-04 1.5081e-03 cor -0.015 cov -1.0342e-05 Eig 1.508e-03 3.121e-04 1stv 0.009 -1.000 tan -115.645 +70 23-21 mu 1.4596e-01 2.0839e-01 Var 2.3686e-04 6.2123e-04 cor -0.013 cov -4.8257e-06 Eig 6.213e-04 2.368e-04 1stv 0.013 -1.000 tan -79.662 +75 23-21 mu 1.5914e-01 1.7490e-01 Var 1.6142e-04 2.2058e-04 cor -0.014 cov -2.7177e-06 Eig 2.207e-04 1.613e-04 1stv 0.046 -0.999 tan -21.813 +80 23-21 mu 1.7343e-01 1.4670e-01 Var 9.6292e-05 7.0767e-05 cor -0.029 cov -2.3931e-06 Eig 9.651e-05 7.054e-05 1stv 0.996 -0.093 tan -0.093 +85 23-21 mu 1.8890e-01 1.2299e-01 Var 5.6832e-05 3.9227e-05 cor -0.061 cov -2.8869e-06 Eig 5.729e-05 3.877e-05 1stv 0.987 -0.158 tan -0.160 +90 23-21 mu 2.0566e-01 1.0307e-01 Var 6.4965e-05 5.4893e-05 cor -0.062 cov -3.6726e-06 Eig 6.616e-05 5.370e-05 1stv 0.951 -0.310 tan -0.326 +95 23-21 mu 2.2383e-01 8.6343e-02 Var 1.5120e-04 8.2297e-05 cor -0.040 cov -4.5038e-06 Eig 1.515e-04 8.200e-05 1stv 0.998 -0.065 tan -0.065 +Computing Health Expectancies: result on file 'erbiaspar.txt' +65|66|67|68|69|70|71|72|73|74|75|76|77|78|79|80|81|82|83|84|85|86|87|88|89|90|91|92|93|94|95| +Computing Total Life expectancies with their standard errors: file 'trbiaspar.txt' +Computing Health Expectancies and standard errors: result on file 'stderbiaspar.txt' +Computing Covar. of Health Expectancies: result on file 'cverbiaspar.txt' +Computing Variance-covariance of DFLEs: file 'vrbiaspar.txt' +65|66|67|68|69|70|71|72|73|74|75|76|77|78|79|80|81|82|83|84|85|86|87|88|89|90|91|92|93|94|95| +Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file 'prmorprev1-stablbased-rbiaspar.txt' +End of Imach +Local time at start Tue Aug 18 18:20:44 2015 + +Local time at end Tue Aug 18 18:26:33 2015 + +Total time used 0 day(s) 0 hour(s) 5 minute(s) 49 second(s) +Total time was 349 Sec. diff --git a/html/doc/mypar.imach b/html/doc/mypar.imach index b3f8e5d..2ca37f8 100755 --- a/html/doc/mypar.imach +++ b/html/doc/mypar.imach @@ -1,9 +1,9 @@ # MLE 1984-1990 # -title=MLE datafile=..\doc\data\mydata.txt lastobs=3000 firstpass=1 lastpass=4 +title=MLE datafile=../doc/data/mydata.txt lastobs=3000 firstpass=1 lastpass=4 ftol=1e-8 stepm=24 ncovcol=2 nlstate=2 ndeath=1 maxwav=4 mle=1 weight=0 -model=. -# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ... +model=1+age+. +#q Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ... 12 0. 0. 13 0. 0. 21 0. 0. @@ -24,8 +24,8 @@ model=. 232 0. 0. 0. 0. 0. 0. 0. 0. # agemin agemax for lifexpectancy, bage fage (if mle==0 ie no data nor Max likelihood). agemin=70 agemax=100 bage=50 fage=100 estepm=24 -# Observed prevalence period +#Observed prevalence period begin-prev-date=1/1/1984 end-prev-date=1/6/1988 mov_average=0 # Population or status based pop_based=0 -prevforecast=1 starting-proj-date=1/1/1984 final-proj-date=1/1/2000 mobil_average=1 \ No newline at end of file +prevforecast=1 starting-proj-date=1/1/1984 final-proj-date=1/1/2000 mobil_average=1 -- 2.43.0