Current release: 8.3 – September 1st, 2018
Changelog Entries:
September 1st, 2018
[bdubbs] - Release of BLFS-8.3.
August 30th, 2018
[ibdubbs] - Archive icedtea-web.
August 30th, 2018
August 28th, 2018
[renodr] - Update to libva-2.2.0 and intel driver. Fixes #10944.
August 27th, 2018
August 26th, 2018
[ken] - Final changes re search.cpan.org going away. Fixes #10869.
[bdubbs] - Update to ImageMagick-6.9.10-10. Leaving open #7859.
[ken] - Remainder of changes in perl-modules to use metacpan.org instead of search.cpan.org. Completes most of #10869.
[dj] - Update to Fop-2.3. Fixes #10811.
[dj] - Fix build issue with junit-4.12. Fixes #10777.
[dj] - Update to Apache-Maven-3.5.4. Fixes #11062.
[dj] - Update to Apache-Ant-1.10.4. Fixes #10896.
[dj] - Update to OpenJDK-10.0.2. Fixes #10959.
August 25th, 2018
August 24th, 2018
[bdubbs] - Add a patch for MPlayer.
[bdubbs] - Update to gparted-0.32.0. Fixes #11056.
[bdubbs] - Archive midori.
[bdubbs] - Archive opal and ekiga.
[bdubbs] - Update xterm to install .desktop files.
[bdubbs] - Update plasma to properly link to .desktop file.
August 23rd, 2018
[bdubbs] - Update to qemu-3.0.0. Fixes #11015.
[bdubbs] - Remove --disable-compositor from xfwm4. Fixes #10994.
[bdubbs] - Update wpa_supplicant-2.6-upstream_fixes patch. Fixes #10994.
[bdubbs] - Update to tigervnc-1.9.0. Fixes #10956.
[dj] - Update to gdb-8.1.1. Fixes #10981.
[ken] - Update to gimp-2.10.6. Fixes #11038.
[ken] - external perl modules: initial changes to point to metacpan.org instead of search.cpan.org. Addresses #10869.
[thomas] - Update to mousepad-0.4.1. Fixes #10843.
August 22nd, 2018
[bdubbs] - Update to wireshark-2.6.2. Fixes #10962.
[bdubbs] - Update to xscreensaver-5.40. Fixes #11012.
[bdubbs] - Update to node-v9.11.2. Fixes #10867.
[renodr] - Update to gnumeric-1.12.43. Fixes #11003.
[renodr] - Update to goffice-0.10.43. Fixes #11002.
[renodr] - Update to libgsf-1.14.44. Fixes #10995.
[renodr] - Update to epiphany-<IP_ADDRESS>. Note that this update contains two critical vulnerability fixes. Fixes #10685.
[ken] - gimp-help: recommend gvfs to access online help, use new snapshot for local help but explain the issues. Addresses #11007.
[bdubbs] - Update to plasma-5.13.4. Fixes #10859.
[renodr] - Update to gnome-terminal-3.28.2. Fully fixes #10649.
[renodr] - Update to gnome-system-monitor-3.28.2. Partially fixes #10649.
[renodr] - Update to EOG-3.28.3. Partially fixes #10649.
[renodr] - Update to evince-3.28.2. Partially fixes #10649.
[renodr] - Update to gtksourceview-3.24.8. Fixes #10877.
[renodr] - Update to file-roller-3.28.1. Partially fixes #10649.
[renodr] - Update to gnome-calculator-3.28.2. Partially fixes #10649.
[renodr] - Add fix for glibc-2.28 to dvd+rw-tools.
August 21st, 2018
[bdubbs] - Update to ntp-4.2.8p12. Fixes #11020.
[bdubbs] - Update to gegl-0.4.8. Fixes #10970.
[bdubbs] - Update to ffmpeg-4.0.2. Fixes #10874.
[ken] - Update to ImageMagick-7.0.8-10. Fixes #11041.
[bdubbs] - Update to libX11-1.6.6.tar.bz2 (xorg library). Fixes #11046.
[renodr] - Update to yelp-3.28.1. Finishes #10648.
[ken] - Update to firefox-61.0.2. Fixes #11013.
[bdubbs] - Update to poppler-0.67.0. Fixes #10883.
[bdubbs] - Update to mlt-6.10.0. Fixes #10914.
[bdubbs] - Update to graphite2-1.3.12. Fixes #11017.
[bdubbs] - Update to kf5-apps-18.08.0. Fixes #10853.
[bdubbs] - Update to opencv-3.4.2. Fixes #10913.
August 20th, 2018
[renodr] - Update to network-manager-applet-1.8.16. Partially fixes #10649.
[renodr] - Update to ibus-1.5.19. Fixes #10996.
[renodr] - Fix NetworkManager build with libnm-glib.
[bdubbs] - Update to kf5-5.49.0. Includes oxygen-icons5, extra-cmake-modules, and breeze-icons. Fixes #10842.
[ken] - Update to boost_1_68_0. Fixes #11000.
[bdubbs] - Update to mariadb-10.3.9. Fixes #10913.
[bdubbs] - Update to Archive-Zip-1.62 (Perl Module). Fixes #11036.
August 19th, 2018
[renodr] - Update to gnome-keyring-3.28.2. Partially fixes #10648.
[renodr] - Update to nautilus-3.28.1. Partially fixes #10648.
[renodr] - Update to gvfs-1.36.2. Partially fixes #10648.
[bdubbs] - Update to latest snapshot x264-snapshot-20180819-2245-stable. See #7555.
[ken] - Update to unixODBC-2.3.7. Fixes #11005.
[bdubbs] - Update to qpdf-8.2.1. Fixes #11029.
[thomas] - Update to php-7.2.9. Fixes #11026.
August 18th, 2018
[renodr] - Update to udisks-2.8.0. Fixes #10917.
[renodr] - Update to samba-4.8.4. Fixes #11021. Note that this fixes four critical vulnerabilities, upgrading is suggested.
[bdubbs] - Update to babl-0.1.56. Fixes #10969.
[bdubbs] - Update to xapian-core-1.4.7. Fixes #10910.
[bdubbs] - Update to feh-2.27.1. Fixes #10901.
[bdubbs] - Update to libpcap-1.9.0. Fixes #10973.
[bdubbs] - Update to bluez-5.50. Fixes #10837.
[bdubbs] - Update to libical-3.0.4. Fixes #11016.
[ken] - Update to pulseaudio-12.2. Fixes #10889.
[dj] - Update to gcc-8.2.0. Fixes #10730.
[thomas] - Update to cmake-3.12.1. Fixes #11001.
[thomas] - Update to llvm-6.0.1. Fixes #10897.
August 17th, 2018
[bdubbs] - Update to libjpeg-turbo-2.0.0. Fixes #10576.
[bdubbs] - Update to pciutils-3.6.2. Fixes #11010.
[bdubbs] - Update to xterm-335. Fixes #11023.
[bdubbs] - Update to mesa-18.1.6. Fixes #11022.
[bdubbs] - Update to harfbuzz-1.8.8. Fixes #11018.
[renodr] - Update to NetworkManager-1.12.2. Note: This version could possibly cause incompatibilites due to the removal of several libraries and API interfaces. Fixes #10876.
[renodr] - Update to gnome-desktop-3.28.2. Fixes #10648.
[renodr] - Update to geocode-glib-3.26.0. Fixes #10854.
[renodr] - Update to vte-0.52.2. Partially fixes #10648.
[renodr] - Update to totem-pl-parser-3.26.1. Partially fixes #10648.
[bdubbs] - Update to openssl-1.0.2p. Fixes #11014.
August 16th, 2018
[renodr] - Update to WebKitGTK+-2.20.5. Fixes #10866.
[ken] - Revert Berkeley-DB to 5.3.28. Fixes #10989.
[bdubbs] - Update to libatomic_ops-7.6.6. Fixes #10993.
[bdubbs] - Update to git-2.18.0. Fixes #10886.
[bdubbs] - Update to libblockdev-2.19. Fixes #10885.
[bdubbs] - Update to libbytesize-1.4. Fixes #10987.
[ken] - Update to cups-filters-1.20.4. Fixes #10945.
[bdubbs] - Update to mercurial-4.7. Fixes #10856.
[bdubbs] - Update to lxml-4.2.2. Fixes #10892.
[bdubbs] - Update to Text-CSV-1.96. Fixes #11019.
[renodr] - Update to gjs-1.52.3. Partially fixes #10648.
[renodr] - Update to libmbim-1.16.2. Fixes #11008.
[renodr] - Update to libqmi-1.20.2. Fixes #11009.
[renodr] - Update to ModemManager-1.8.0. Fixes #10840.
[renodr] - Update to geoclue-2.4.11. Fixes #10977.
[ken] - Update to unbound-1.7.3. Fixes #10865.
[renodr] - Update gstreamer and plugins to 1.14.2. Fixes #10974.
[ken] - Update to icu4c-62_1. Fixes #10884.
[renodr] - Add a patch to allow building v4l-utils with glibc-2.28.
August 15th, 2018
[bdubbs] - Update to btrfs-progs-4.17.1. Fixes #10903.
[bdubbs] - Update to sshfs-3.4.0. Fixes #10903.
[bdubbs] - Update to stunnel-5.48. Fixes #10894.
[bdubbs] - Update to cryptsetup-2.0.4. Fixes #10991.
[bdubbs] - Update to xfsprogs-4.17.0. Fixes #10904.
[renodr] - Fix alsa-oss to build with glibc-2.28.
[ken] - Revert Berkeley-DB to 5.3.28. Fixes #10989.
[ken] - Update to libreoffice-<IP_ADDRESS>. Fixes #10458.
[ken] - Update to postgresql-10.5 (security fix). Fixes #10999.
[dj] - Update to p11-kit-0.23.13. Fixes #11004.
[dj] - Update to dbus-1.12.10. Fixes #10988.
August 14th, 2018
[renodr] - Update to qpdf-8.1.0. Fixes #10895.
[ken] - Update to (intel) microcode-20180807. Fixes #10930. Also mark the AMD examples as 'historic', at least until someone can provide details for a current machine where new microcode is available.
[renodr] - Update to gsl-2.5. Fixes #10871.
[renodr] - Update to libsoup-2.62.3. Fixes #11006.
[renodr] - Update to pango-1.42.3. Fixes #10963.
[timtas] - Update to thunderbird-60.0. Fixes #10997.
[dj] - Update to xterm-334. Fixes #11011.
August 13th, 2018
[ken] - Patch Qt5 to build with glibc-2.28.
[renodr] - Update to atk-2.29.2. Fixes #10843. DJ says this is required for gnome in the ticket.
August 10th, 2018
August 9th, 2018
[renodr] - Update to harfbuzz-1.8.7. Fixes #10982.
[renodr] - Update to libdrm-2.4.93. Fixes #10983.
[renodr] - Update to talloc-2.1.14. Fixes #10942.
[renodr] - Update to vala-0.40.8. Fixes #10668.
[renodr] - Update to yaml-0.2.1. Fixes #10923.
[renodr] - Update to shared-mime-info-1.10. Fixes #10905.
[timtas] - Update to audacious-3.10. Fixes #10998.
[renodr] - Update to highlight-3.44. Fixes #10972.
[renodr] - Update to lua-5.3.5. Fixes #10935.
August 8th, 2018
[renodr] - Add patch to facilitate building sg3_utils with glibc-2.28.
[renodr] - Update to unrar-5.6.5. Fixes #10900.
[renodr] - Implement a build fix for sharutils related to glibc-2.28.
August 6th, 2018
[timtas] - Update to qemu-2.12.1. Fixes #10986.
August 4th, 2018
August 3rd, 2018
[ken] - Python-2.7.15 no longer installs the _ssl module, remove the ineffective sed and instead require libssh2 in rustc. Fixes #10899.
[ken] - patch libreoffice to build with recent LFS, the problem was apparently caused by python-3.7.
[ken] - Fix postfix to build against Berkeley DB-18. Minimally tested, but without grokking what changed from DB-6 to DB-18 there may possibly be breakage for some usage. Addresses #10984.
August 2nd, 2018
[thomas] - Update to dhcpcd-7.0.7. Bug fix on host routes. Fixes #10976.
August 1st, 2018
[ken] - Fixes for iptables-1.8.0. Thanks to Ryan Marsaw for the report.
[renodr] - Update to curl-7.61.0. Security fix for SMTP users. Fixes #10940.
July 31st, 2018
[bdubbs] - Update to fuse3-3.2.5. Fixes #10939.
[bdubbs] - Update to volume_key-0.3.11. Fixes #10957.
[bdubbs] - Update to nss-3.38. Fixes #10890.
[bdubbs] - Update to iptables-1.8.0. Fixes #10931.
[bdubbs] - Update to gnutls-3.5.18. Fixes #10951.
[bdubbs] - Update to gnupg-2.2.9. Fixes #10860.
[bdubbs] - Update to db-18.1.25. Fixes #10875.
[renodr] - Update to guile-2.2.4. Fixes #10912.
July 30th, 2018
July 28th, 2018
[bdubbs] - Update to npth-1.6. Fixes #10952.
[bdubbs] - Update to libgpg-error-1.32. Fixes #10941.
[bdubbs] - Update to gptfdisk-1.0.4. Fixes #10926.
[bdubbs] - Update to libpng-1.6.35. Fixes #10953.
[bdubbs] - Update to fribidi-1.0.5. Fixes #10971.
[bdubbs] - Update to PyYAML-3.13 (Python Module). Fixes #10927.
[bdubbs] - Update to scour-0.37 (Python Module). Fixes #10920.
[bdubbs] - Update to pygobject3-3.28.3 (Python Module). Fixes #10836.
[bdubbs] - Update to pycairo-1.17.1 (Python Module). Fixes #10928.
[bdubbs] - Update to subversion-1.10.2. Fixes #10966.
[bdubbs] - Remove chromium and lxqt.
July 28th, 2018
[bdubbs] - Update to xf86-input-libinput-0.28.0. Fixes #10937.
[bdubbs] - Update to libinput-1.11.3. Fixes #10908.
[bdubbs] - Update to acpid-2.0.30. Fixes #10961.
[bdubbs] - Update to mesa-18.1.5. Fixes #10873.
[bdubbs] - Update to wayland-protocols-1.15. Fixes #10922.
[bdubbs] - Update to Beaker-1.10.0 (Python Module). Fixes #10848.
[bdubbs] - Update to libXinerama-1.1.4 (Xorrg library). Fixes #10925.
[bdubbs] - Update to libXScrnSaver-1.2.3 (Xorg library). Fixes #10924.
[bdubbs] - Update to harfbuzz-1.8.4. Fixes #10916.
[bdubbs] - Update to python3-3.7.0. Fixes #10902.
[bdubbs] - Update to Business-ISMN-1.132 (Perl Module). Fixes #10947.
[bdubbs] - Update to Net-DNS-1.16 (Perl Module). Fixes #10954.
[bdubbs] - Update to libwww-perl-6.35 (Perl module). Fixes #10955.
July 24th, 2018
July 16th, 2018
[ken] - Update to mutt-1.10.1 (security fix). Fixes #10950.
July 14th, 2018
[thomas] - Update to pciutils-3.6.1. Fixes #10943.
July 13th, 2018
July 11th, 2018
July 10th, 2018
July 09th, 2018
July 07th, 2018
July 06th, 2018
[timtas] - Update to cups-2.2.8. Fixes #10855.
July 05th, 2018
July 04th, 2018
[timtas] - Update to dovecot-2.3.2. Fixes #10907.
July 03rd, 2018
June 28th, 2018
[ken] - Update to libinput-1.11.0. Fixes #10851.
[ken] - Remove obsolete text from valgrind re symlinking ld-linux to a .dbg version of ld. In April 2017 LFS changed the strip commands. That file now only contains debug symbols and is loaded when needed: making the symlink breaks the system. Remove related text from curl.
June 28th, 2018
June 26th, 2018
[ken] - Update to libwww-perl-6.34 (perl module). Fixes #10849.
[ken] - Update to harfbuzz-1.8.1. Fixes #10847.
[ken] - Update to qt-everywhere-src-5.11.1. Fixes #10882.
[ken] - Update to firefox-61.0. Stylo is no-longer optional, therefore Clang is now required. Fixes #10898.
[ken] - Update to sqlite-3.24.0. Fixes #10850.
June 20th, 2018
June 17th, 2018
[thomas] - Update to nano-2.9.8. Fixes #10839.
June 15th, 2018
June 12th, 2018
[bdubbs] - Archive juffed, QScintilla-gpl, and chrpath.
June 11th, 2018
[ken] - Update to firefox-60.0.2 (security fix). Fixes #10863.
June 7th, 2018
[ken] - Update to (intel) microcode-20180425 (this only affects some Broadwell E machines (previous microcode withdrawn) and Gemini Lake Pentium/Celeron (new microcode). Fixes #10844.
June 5th, 2018
May 31st, 2018
[ken] - Fix inkscape for changes in poppler-0.65.0.
[ken] - Fix vlc build for QT-5.11 API changes.
May 31st, 2018
May 30th, 2018
[ken] - Update to git-2.17.1 (security fix). Fixes #10830.
May 29th, 2018
[bdubbs] - Update to gstreamer-1.14.1 and plugins. Fixes #10787.
[bdubbs] - Update to rpcsvc-proto-1.4. Fixes #10820.
[bdubbs] - Update to xf86-input-synaptics-1.9.1. Fixes #10822.
[bdubbs] - Update to xf86-input-evdev-2.10.6. Fixes #10821.
[bdubbs] - Update to xf86-video-vmware-13.3.0. Fixes #10786.
[bdubbs] - Update to NetworkManager-1.10.6. Fixes #10764.
[bdubbs] - Update to krb5-1.16.1. Fixes #10738.
May 28th, 2018
[bdubbs] - Update to qtwebengine-everywhere-src-5.11.0.
[ken] - Update to mutt-1.10.0. Fixes #10796.
[ken] - Update to libunistring-1.9.10. Fixes #10813.
[bdubbs] - Update to qt-everywhere-src-5.11.0. Fixes #10805.
[bdubbs] - Update to postfix-3.3.1. Fixes #10799.
[bdubbs] - Update to thunderbird-52.8.0. Fixes #10793.
[bdubbs] - Update to postgresql-10.4. Fixes #10765.
[bdubbs] - Update to seamonkey-2.49.3. Fixes #10733.
[thomas] - Update to bind-9.13.0. Fixes #10791.
May 27th, 2018
May 26th, 2018
May 25th, 2018
[bdubbs] - Update to curl-7.60.0. Fixes #10781.
[bdubbs] - Update to x265-2.8. Fixes #10804.
[bdubbs] - Update to glib-networking-2.56.1. Fixes #10803.
[bdubbs] - Update to cryptsetup-2.0.3. Fixes #10737.
[bdubbs] - Update to gnumeric-1.12.41. Fixes #10729.
[bdubbs] - Update to webkitgtk-2.20.2. Fixes #10756.
[bdubbs] - Update to geoclue-2.4.10. Fixes #10732.
[bdubbs] - Update to php-7.2.6. Fixes #10709.
[bdubbs] - Update to vim-8.1. Fixes #10783.
May 24th, 2018
[bdubbs] - Update to volume_key-0.3.10. Fixes #10802.
[bdubbs] - Update to goffice-0.10.41. Fixes #10719.
[bdubbs] - Update to libidn2-2.0.5. Fixes #10790.
[bdubbs] - Update to libidn-1.35. Fixes #10763.
[bdubbs] - Update to fribidi-1.0.3. Fixes #10778.
[bdubbs] - Update to php-7.2.5. Fixes #10709.
[bdubbs] - Update to wireshark-2.6.1. Fixes #10704.
[bdubbs] - Fix failures with xfwm and xorg-xerver-1.20.0. Fixes #10772.
[bdubbs] - Update to Error-0.17026 (Perl Module). Fixes #10808.
May 22nd, 2018
May 21st, 2018
[ken] - Update gimp-help snapshot to 2018-05-19-f8fb93ed2.
[bdubbs] - Update to libepoxy-1.5.2. Fixes #10797.
[bdubbs] - Update to cmake-3.11.2. Fixes #10784.
[bdubbs] - Update to cdrdao-1.2.4. Fixes #10782.
[bdubbs] - Update to c-ares-1.14.0. Fixes #10780.
[bdubbs] - Update to gegl-0.4.2. Fixes #10779.
[bdubbs] - Update to xfce4-terminal-<IP_ADDRESS>. Fixes #10776.
[bdubbs] - Update to usbutils-010. Fixes #10775.
[bdubbs] - Update to babl-0.1.50. Fixes #10774.
[bdubbs] - Update to nano-2.9.7. Fixes #10773.
[bdubbs] - Update to libdmx-1.1.4 (Xorg library). Fixes #10770.
[bdubbs] - Update to unrar-5.6.4. Fixes #10769.
[bdubbs] - Update to mlt-6.8.0. Fixes #10768.
[bdubbs] - Update to xdg-utils-1.1.3. Fixes #10767.
[bdubbs] - Update to feh-2.26.3. Fixes #10766.
[bdubbs] - Update to nghttp2-1.32.0. Fixes #10755.
[bdubbs] - Update to libsoup-2.62.2. Fixes #10752.
[bdubbs] - Update to gnupg-2.2.7. Fixes #10728.
May 20th, 2018
[bdubbs] - Update to sshfs-3.3.2. Fixes #10718.
[bdubbs] - Update to fuse-3.2.3. Fixes #10762.
[bdubbs] - Update to libfm and libfm-extra-<IP_ADDRESS>. Fixes #10716.
[bdubbs] - Update to phonon-4.10.1. Fixes #10714.
[bdubbs] - Update to xfsprogs-4.16.1. Fixes #10707.
[bdubbs] - Update to links-2.16. Fixes #10759.
[bdubbs] - Update to Business-ISSN-1.003 (Perl Module). Fixes #10757.
[bdubbs] - Update to dbus-python-1.2.8. Fixes #10743.
[bdubbs] - Update to LibRaw-0.18.11. Fixes #10740.
[bdubbs] - Update to dash-<IP_ADDRESS>. Fixes #10739.
[bdubbs] - Update to libinput-1.10.7. Fixes #10726.
[bdubbs] - Update to highlight-3.43. Fixes #10723.
[bdubbs] - Update to libgpg-error-1.31. Fixes #10722.
[bdubbs] - Update to btrfs-progs-4.16.1. Fixes #10700.
May 18th, 2018
May 17th, 2018
May 16th, 2018
[pierre] - Fix building Apache-Maven with Java 10. Fixes #10771.
May 13th, 2018
May 12th, 2018
[bdubbs] - Add a patch to xf86-video-vmware for gcc8 and xorg-server-1.20.0 changes.
[bdubbs] - Update to xterm-333. Fixes #10742.
May 11th, 2018
[bdubbs] - Update to xorg-server-1.20.0. Fixes #10760.
[bdubbs] - Update to libepoxy-1.5.1. Fixes #10706.
[bdubbs] - Update to mesa-18.0.3. Fixes #10715.
[bdubbs] - Update to wayland-protocols-1.14. Fixes #10751.
[bdubbs] - Update to libuv-v1.20.3. Fixes #10750.
[bdubbs] - Update to libdrm-2.4.92. Fixes #10758.
[bdubbs] - Update to dbus-1.12.8. Fixes #10724.
[bdubbs] - Update to freetype-2.9.1. Fixes #10729.
[bdubbs] - Update to nss-3.37. Fixes #10749.
[bdubbs] - Update to shadow-4.6. Fixes #10717.
[bdubbs] - Update to wget-1.19.5. Fixes #10748.
[bdubbs] - Update to python2-2.7.15. Fixes #10725.
[bdubbs] - Update to sudo-1.8.23. Fixes #10721.
[thomas] - Update to nano-2.9.6. Fixes #10713.
May 8th, 2018
[ken] - Update to firefox-60.0. Fixes #10754.
May 7th, 2018
[ken] - change gentoo ftp repo to one which still works. Fixes #10736.
[ken] - webkitgtk: demote enchant to recommended. Fixes #10745.
[ken] - gvfs: move libsecret and libsoup2 to required. Fixes #10744.
[ken] - Update to gimp-2.10.0 and gegl-0.4.0, with libmypaint-1.3.0 and mypaint-brushes-1.3.0. Fixes #10711 and #10708.
May 3rd, 2018
[ken] - Update to xine-lib-1.2.9. Fixes #10734.
[pierre] - Remove version from OpenJDK .desktop files.
May 2nd, 2018
[ken] - Update to texlive-20180414 and 2018 install-tl-unx. Fixes #10712.
[ken] - Update external perl modules used by biber for changed dependencies as at 30th April (File::Copy::Recursive now uses Test::Warnings instead of Test::Warn, DateTime::Locale adds IPC::System::Simple).
April 26th, 2018
April 25th, 2018
April 24th, 2018
April 23rd, 2018
April 22nd, 2018
April 21st, 2018
April 20th, 2018
[bdubbs] - Update to feh-2.26. Fixes #10686.
[bdubbs] - Update to libgsf-1.14.43. Fixes #10684.
[bdubbs] - Update to libbytesize-1.3. Fixes #10683.
[bdubbs] - Update to libinput-1.10.5. Fixes #10682.
[bdubbs] - Update to colord-1.4.3. Fixes #10681.
[bdubbs] - Update to libuv-1.20.1. Fixes #10680.
[bdubbs] - Update to mesa-18.0.1. Fixes #10590.
[pierre] - gptfdisk-1.0.3 has usable tests. Add them.
[pierre] - Update convenience patch for gptfdisk-1.0.3: the ICU switch is not needed, and the POPT switch is superfluous. Only the “install” target is kept.
April 18th, 2018
April 17th, 2018
April 16th, 2018
April 15th, 2018
[ken] Fixes for problems people have encountered with my rustc instructions. In particular, in llvm add -DLLVM_LINK_LLVM_DYLIB=ON which I have been using for ages but was not in the current book, and in rustc add RUSTFLAGS to ensure that libffi is linked. Also simplify the rustc install. Particular thanks to 'balducci' for the RUSTFLAGS.
[bdubbs] - Update to subversion-1.10.0. Fixes #10658.
[bdubbs] - Update to gegl-0.3.32. Fixes #10664.
April 13th, 2018
April 12th, 2018
[bdubbs] - Update to webkitgtk-2.20.1. Fixes #10654.
[bdubbs] - Update to epiphany-3.28.1. Fixes #10655.
[bdubbs] - Update to QScintilla_gpl-2.10.4. Fixes #10653.
[bdubbs] - Update to sqlite-autoconf-3.23.1. Fixes #10652.
[bdubbs] - Update to parole-1.0.1. Fixes #10657.
[bdubbs] - Update to libgpg-error-1.29. Fixes #10656.
[bdubbs] - Update to babl-0.1.46. Fixes #10651.
[bdubbs] - Update to libsoup-2.62.1. Fixes #10645.
April 11th, 2018
[bdubbs] - Update to libinput-1.10.4. Fixes #10646.
[bdubbs] - Update to xf86-input-libinput-0.27.1. Fixes #10647.
[bdubbs] - Update to Beaker-1.9.1 (Python Module). Fixes #10644.
[bdubbs] - Update to wayland-1.15.0. Fixes #10643.
[bdubbs] - Update to gobject-introspection-1.56.1. Fixes #10642.
[bdubbs] - Update to nss-3.36.1. Fixes #10641.
[bdubbs] - Update xfburn dependencies.
[bdubbs] - Remove obsolete note in gtk+3.
[bdubbs] - Update to gnupg-2.2.6. Fixes #10640.
[bdubbs] - Update gnome-screenshot instructions. Fixes #10``2.
April 10th, 2018
[ken] - Thunderbird requires gtk2 as well as gtk3. Reported by 'rhubarbpieguy'.
April 9th, 2018
April 8th, 2018
[timtas] - Update to alsa-1.1.6 (alsa-lib, alsa-plugins, alsa-utils,alsa-tools, ALSA OSS). Fixes #10623.
[bdubbs] - Update to pango-1.42.1. Fixes #10636.
[bdubbs] - Update to gdk-pixbuf-2.36.12. Fixes #10635.
[bdubbs] - Update to glib-2.56.1. Fixes #10634.
[bdubbs] - Update to pidgin-2.13.0. Fixes #10499.
[bdubbs] - Update to btrfs-progs-v4.16. Fixes #10631.
[bdubbs] - Update to sysstat-11.6.3. Fixes #10632.
[bdubbs] - Update to xf86-video-amdgpu-18.0.1 (built only). Fixes #10462.
[bdubbs] - Update to dhcpcd-7.0.3. Fixes #10633.
[bdubbs] - Update to mercurial-4.5.3. Fixes #10629.
[bdubbs] - Update to node.js-9.11.2. Fixes #10627.
[bdubbs] - Update to wireshark-2.4.6. Fixes #10622.
[bdubbs] - Update to git-2.17.0. Fixes #10621.
April 7th, 2018
[bdubbs] - Update to talloc-2.1.13. Fixes #10630.
[bdubbs] - Update to accountsservice-0.6.46. Fixes #10628.
[bdubbs] - Update to sqlite-autoconf-3230000. Fixes #10618.
[bdubbs] - Update to libuv-v1.20.0. Fixes #10617.
[bdubbs] - Update to openssh-7.7p1. Fixes #10616.
[bdubbs] - Update to tripwire-<IP_ADDRESS>. Fixes #10606.
[bdubbs] - Update to unrar-5.6.2. Fixes #10610.
[bdubbs] - Update to libidn-1.34. Fixes #10609.
[bdubbs] - Update to fuse-3.2.2. Fixes #10607.
[bdubbs] - Update to LMDB_0.9.22. Fixes #10605.
[bdubbs] - Update to libusb-1.0.22. Fixes #10604.
[bdubbs] - Update to lsof_4.91. Fixes #10603.
[bdubbs] - Update to php-7.2.4. Fixes #10601.
April 6th, 2018
April 5th, 2018
April 4th, 2018
[bdubbs] - Update to gucharmap-10.0.4. Fixes #10527.
[bdubbs] - Update to gnome-apps-2.28 baobab cheese eog evince file-roller gnome-calculator gnome-color-manager gnome-disk-utility gnome-logs gnome-maps gnome-system-monitor gnome-terminal. Fixes #10525.
[bdubbs] - Update to evolution-3.28.0. Fixes #10482.
[bdubbs] - Update to libwacom-0.29. Fixes #10473.
[pierre] - Move Little-CMS2 to recommended dependency of poppler, since cups-filters needs it.
[pierre] - Move Linux-PAM to recommended dependency of cups, since upstream will make it required in a forthcoming version.
[pierre] - Update to dovecot-2.3.1. Fixes #10588.
[pierre] - Update to apache-ant-1.10.3. Fixes #10586.
[pierre] - Update to vala-0.40.2. Fixes #10582.
[pierre] - Update to icu-61.1. Add a switch to allow building libreoffice with this version of icu. Fixes #10581.
[timtas] - Update to cups-filters-1.20.2. Fixes #10612.
April 2nd, 2018
April 1st, 2018
[bdubbs] - Update to GNOME platform packages gcr, gjs, gnome-backgrounds, gnome-bluetooth, gnome-desktop, gnome-keyring, gnome-online-accounts, gnome-settings-daemon, gsettings-desktop-schemas, libgweather, libsecret, nautilus, yelp-xsl, and zenity. Partially fixes #10502.
[bdubbs] - Update to evolution-data-server-3.28.0. Partially fixes #10482.
[bdubbs] - Update to gvfs-1.36.0. Fixes #10483.
[bdubbs] - Update to systemd-238. Fixes #10575.
[timtas] - Update to glibmm-2.56.0. Fixes #10608.
[timtas] - Update to tumbler-0.2.1. Fixes #10611.
March 31st, 2018
March 30th, 2018
[bdubbs] - Update to Unicode-LineBreak-2018.003 (Perl Module). Fixes #10600.
[bdubbs] - Update to OpenSSL-1.0.2n Libraries. Fixes #10593.
[bdubbs] - Update to cups-2.2.7. Fixes #10591.
[bdubbs] - Update to mariadb-10.2.14. Fixes #10589.
[bdubbs] - Update to webkitgtk-2.20.0. Fixes #10523.
[bdubbs] - Update to gtksourceview-3.24.7. Fixes #10542.
[bdubbs] - Update to libsoup-2.62.0. Fixes #10519.
[bdubbs] - Update to colord-1.4.2. Fixes #10515.
March 29th, 2018
March 28th, 2018
[bdubbs] - Update to pygobject-3.28.2. Fixes #10587.
[bdubbs] - Update to libinput-1.10.3. Fixes #10541.
[bdubbs] - Update to libatomic_ops-7.6.4. Fixes #10585.
[bdubbs] - Update to ibus-1.5.18. Fixes #10461.
[bdubbs] - Archive obex-data-server and openobex. Fixes #10500.
[timtas] - Update to thunderbird-52.7.0. Fixes #10574.
[timtas] - Update to dhcpcd-7.0.2. Fixes #10583.
[timtas] - Update to ghostscript-9.23. Fixes #10569.
March 27th, 2018
[bdubbs] - Update to glib-networking-2.56.0. Fixes #10506.
[bdubbs] - Revert to stable gnutls-3.5.18.
March 26th, 2018
[bdubbs] - Update to mesa-17.3.7. Fixes #10467.
[bdubbs] - Update to llvm-6.0.0. Fixes #10503.
[bdubbs] - Update to gegl-0.3.30. Fixes #10571.
[bdubbs] - Update to libdvdcss-1.4.2. Fixes #10568.
[bdubbs] - Update to git-2.16.3. Fixes #10566.
[bdubbs] - Update to talloc-2.1.12. Fixes #10565.
[bdubbs] - Update to node.js-9.9.0. Fixes #10564.
[bdubbs] - Update to nmap-7.70. Fixes #10563.
[bdubbs] - Use LWP::Protocol::https for ntp dependency. Fixes #10570.
[bdubbs] - Update to hdparm-9.56. Fixes (again) #10545.
[timtas] - Update to poppler-0.63.0. Fixes #10555.
March 25th, 2018
[bdubbs] - Update to pcre-8.42. Fixes #10562.
[bdubbs] - Update to gparted-0.31.0. Fixes #10560.
[bdubbs] - Update to xf86-input-libinput-0.27.0. Fixes #10559.
[bdubbs] - Update to fribidi-1.0.2. Fixes #10554.
[bdubbs] - Update to links-2.15. Fixes #10580.
[bdubbs] - Update to pygobject-3.28.1. Fixes #10579.
[bdubbs] - Update to lxml-4.2.1 (python module). Fixes #10578.
[bdubbs] - Update to gtk-doc-1.28. Fixes #10577.
[bdubbs] - Update to cmake-3.10.3. Fixes #10550.
March 24th, 2018
[timtas] - Update to inkscape-0.92.3. Fixes #10573.
[bdubbs] - Update to imlib2-1.5.1. Fixes #10553.
[bdubbs] - Update to libvorbis-1.3.6. Fixes #10551.
[bdubbs] - Update to hdparm-9.55. Fixes #10545.
[bdubbs] - Update to libtirpc-1.0.3. Fixes #10540.
[bdubbs] - Update to XML-Simple-2.25 (Perl module). Fixes #10552.
[bdubbs] - Update to lxml-4.2.0 (python module). Fixes #10530.
[bdubbs] - Update to gobject-introspection-1.56.0. Fixes #10528.
[bdubbs] - Update to pygobject-3.28.0. Fixes #10517.
[pierre] - Samba: promote libtirpc to required, and pass
-ltirpc to
LDFLAGS
instead of
CFLAGS
.
March 23rd, 2018
[timtas] - Update to openldap-2.4.46. Fixes #10567.
March 22nd, 2018
March 21st, 2018
[timtas] - Update to cifs-utils-6.8. Fixes #10531.
[timtas] - Add rpcsvc-proto as a required dependency of samba, as reported by Ryan Marsaw.
[pierre] - Update to unbound-1.7.0. Fixes #10546.
[pierre] - Update to xbitmaps-1.1.2. Fixes #10543.
[pierre] - Update to xdg-user-dirs-0.17. Fixes #10537.
[pierre] - Update to libgpg-error-1.28. Fixes #10529.
[timtas] - Update to samba-4.8.0. Fixes #10532.
March 20th, 2018
[timtas] - Update to gstreamer-1.14.0 (including updates to gstreamer-vaapi gst-libav gst-plugins-base gst-plugins-good gst-plugins-bad gst-plugins-ugly). Fixes #10561.
[timtas] - Update to unixODBC-2.3.6. Fixes #10558.
[ken] - Fixes in firefox: the icon location changed in firefox-59, and the old text about using configure --help has been wrong since firefox-58 required ./mach. Thanks to Wayne for the report.
March 19th, 2018
[bdubbs] - Update to vala-0.40.0. Fixes #10511.
[bdubbs] - Update to unrar-5.6.1. Fixes #10510.
[bdubbs] - Update to hexchat-2.14.1. Fixes #10509.
[pierre] - Update to Junit-4.12 (using maven for building). Fixes #10422.
[pierre] - Add Apache-Maven-3.5.3. Part of #10422.
[ken] - Update to firefox-59.0.1 (security fix). Fixes #10557.
[timtas] - Update to NetworkManager-1.10.6. Fixes #10518.
[timtas] - Update to xfce4-settings-4.12.3. Fixes #10556.
[timtas] - Add libnsl as a required dependency of vsftpd.
March 18th, 2018
[bdubbs] - Update to clutter-gst-3.0.26. Fixes #10508.
[bdubbs] - Update to gtk+3-3.22.29. Fixes #10521.
[bdubbs] - Update to pango-1.42.0. Fixes #10522.
[bdubbs] - Added rpcsvc-proto as a required dependency of autofs. Fixes #10512.
[bdubbs] - Update to at-spi2-core-2.28.0 and at-spi2-atk-2.26.2. Fixes #10520.
[bdubbs] - Update to atk-2.28.1. Fixes #10524.
March 17th, 2018
March 16th, 2018
[bdubbs] - Update to cryptsetup-2.0.2. Fixes #10504.
[bdubbs] - Update to mercurial-4.5.2. Fixes #10488.
[bdubbs] - Update to exempi-2.4.5. Fixes #10486.
[bdubbs] - Update to nspr-4.19. Fixes #10475.
[bdubbs] - Update to libical-3.0.3. Fixes #10472.
[bdubbs] - Update to nss-3.36. Fixes #10470.
[bdubbs] - Update to slang-2.3.2. Fixes #10465.
[bdubbs] - Update to graphite-1.3.11. Fixes #10464.
[timtas] - Upgrade to xfce4-terminal-<IP_ADDRESS>. Fixes #10547.
[timtas] - Upgrade to VTE-0.52.0. Fixes #10526.
[thomas] - Upgrade to bind-9.12.1. Fixes #10538.
March 15th, 2018
[bdubbs] - Upgrade to fdk-aac-0.1.6. Fixes #10496.
[bdubbs] - Upgrade to mpg123-1.25.10. Fixes #10484.
[bdubbs] - Upgrade to libxml2-2.9.8. Fixes #10474.
[bdubbs] - Upgrade to nghttp2-1.31.0. Fixes #10441.
[bdubbs] - Upgrade to p11-kit-0.23.10. Fixes #10438.
[bdubbs] - Upgrade to feh-2.25.1. Fixes #10432.
[bdubbs] - Upgrade to balsa-2.5.5. Fixes #10431.
[bdubbs] - Upgrade to xfsprogs-4.15.1. Fixes #10438.
[bdubbs] - Upgrade to LibRaw-0.18.8. Fixes #10417.
[bdubbs] - Upgrade to node-9.8.0. Fixes #10414.
[pierre] - Move the instructions to install the CA certificates for Java to "Configuring the Java environment", so that a "cacerts" file can be passed to OpenJDK's configure. Also host the jtreg bundle on anduin.
[thomas] - Upgrade to json-c-0.13.1. Fixes #10471.
[ken] - Update intel microcode to 20180312 (spectre v2 mitigation for SandyBridge and later). Please note that for some models, particularly Skylake, currently-available kernels may disregard the mitigation because of issues with the previous (now withdrawn) version. That will hopefully be fixed in a few days, but will then require a kernel upgrade. Fixes #10300.
[timtas] - Explain how to build network-manager-applet without gobject-introspection and gtk-doc.
March 14th, 2018
[bdubbs] - Update to mkfontscale-1.1.3 (Xorg app).
[bdubbs] - Update to xcursor-themes-1.0.5.
[thomas] - Update to nano-2.9.4. Fixes #10498.
March 13th, 2018
[bdubbs] - Update to xinit-1.4.0 and 12 Xorg apps. Fixes #10501.
[bdubbs] - Update to twm-1.0.10. Fixes #10492.
[bdubbs] - Update to libinput-1.10.2. Fixes #10490.
[bdubbs] - Update to libevdev-1.5.9. Fixes #10489.
[bdubbs] - Update to harfbuzz-1.7.6. Fixes #10487.
[ken] - Update to firefox-59.0 (security fix). Fixes
#10507.
Please note that the libraries are now installed in an
unversioned /usr/lib/firefox/
directory.
March 12th, 2018
[ken] - Update to mutt-1.9.4. Fixes #10507.
March 11th, 2018
[pierre] - Update configuration instructions for OpenLDAP: Mention the new slapd-config method, and account for possibly removed .la files in the module directory.
March 10th, 2018
[thomas] - Update to libuv-1.19.2. Fixes #10409.
March 9th, 2018
March 8th, 2018
[pierre] - Update to php-7.2.3. Fixes #10455.
[pierre] - Update to dovecot-<IP_ADDRESS>. Fixes #10450.
[pierre] - Update to gnupg-2.2.5. Fixes #10413.
[timtas] - Update to parole-1.0.0. Fixes #10497.
[thomas] - Update to postfix-3.3.0. Fixes #10411.
[thomas] - Update to dhcp-4.4.1. Fixes #10449.
[thomas] - Update to ntp-4.2.8p11. Fixes #10440.
March 7th, 2018
[pierre] - Update to libdrm-2.4.91. Fixes #10481.
[pierre] - Update to xcb-proto-1.13. Fixes #10480.
[pierre] - Update to libxcb-1.13. Fixes #10479.
[pierre] - Update to fontconfig-2.13.0. Fixes #10476.
[pierre] - New Xorg protocols bundle xorgproto-2018.4. Remove the previous page. Thanks to Ken for help. Fixes #10347.
[timtas] - Update to imlib2-1.5.0. Fixes #10419.
[timtas] - Update to SDL2-2.0.8. Fixes #10459.
March 5th, 2018
[bdubbs] - Update to dbus-1.12.6. Fixes #10454.
[bdubbs] - Update to phonon-backend-vlc-0.10.1. Fixes #10444.
[bdubbs] - Update to vlc-3.0.1. Fixes #10445.
[bdubbs] - Update to iceauth-1.0.8 (xorg app). Fixes #10466.
[bdubbs] - Update to util-macros-1.19.2. Fixes #10468.
[bdubbs] - Update to libepoxy-1.5.0. Fixes #10451.
[bdubbs] - Update to libinput-1.10.1. Fixes #10442.
[bdubbs] - Update to x265_2.7. Fixes #10412.
[bdubbs] - Update to babl-0.1.44. Fixes #10403.
[bdubbs] - Update to libdrm-2.4.90. Fixes #10401.
[bdubbs] - Update to libical-3.0.2. Fixes #10400.
March 4th, 2018
[bdubbs] - Update to opencv-3.4.1. Fixes #10448.
[bdubbs] - Update to mesa-17.3.5. Fixes #10404.
[bdubbs] - Update to xfce4-notifyd-0.4.2. Fixes #10452.
[bdubbs] - Update to xfce4-settings-4.12.2. Fixes #10453.
[bdubbs] - Update to pycairo-1.16.3 (Python module). Fixes #10408.
[bdubbs] - Update to File-Slurper-0.012 (Perl module). Fixes #10408.
[bdubbs] - Update to libxshmfence-1.3 (xorg lib). Fixes #10430.
[bdubbs] - Update to xkbcomp-1.4.1 (xorg app). Fixes #10457.
[bdubbs] - Update to libwww-perl-6.33. Fixes #10407.
[bdubbs] - Update to XML-LibXSLT-1.96. Fixes #10410.
[thomas] - Update to postgresql-10.3. Fixes #10456.
March 2nd, 2018
[bdubbs] - Release of BLFS-8.2.
Last updated on 2018-09-01 14:35:46 -0700


(You
can search any file or page on this web site by following the steps found by
clicking on Search.)
Descendants of Isaac Agin
[ Click on the red arrow for a shortcut to
the list of family trees on this site
s Click on the
blue question mark for assistance in navigating among family trees
1 Isaac Agin
... + Matilda (Tilda) J. Fisher
.. 2
.. 2 Fred Agin b: April 19, 1884
..... + Elma Jean (or Jane) Turner b: Dec. 8, 1884
....... 3
Phyllis
Elizabeth Agin b: Oct. 2, 1911 1930s, 1960s
.......... + James
(Doc)
............ 4 James
Forrest Moore b: 1932 1950, 1955, 1970
............... + ?
................. 5
Jackie Moore
.. 2 Jno Gilbert Agin b: Nov. 22, 1885
.. 2 Ella Ann Agin b: Nov. 28, 1888
Provided by: e-mail:
Jackie
Moore
Click here for the Short-Cut Table of Contents


Mode of transmisison: respiratory droplets
Incubation: 2-10d - commonly 3-4d
Period of infectivity: therapy with rifampicin, ceftriaxone, cipro eradicates N.meningitidis within 24hrs
Vaccines:
MenCCV (conjugate)
MCV4D
4vMenPV (polysaccharide)
Schedule: funded; splenectomy, hiv, close contacts of cases, bone marrow, immunosuppression, oslid organ transplatn
recommend; adolescent and young aduls communal accom., travellers (Hajj), microbiolists/lab workers
efficacy: conjugate > polysaccharide
precaution; individuals with history of Guillain Barre whoare considering immunisation with MCV4-D
Herd:
-
Nisseria meningitisis
- gram negative
Clinical
-
sepsis syndrome
-
nausea
-
vomiting
-
meningism
-
rash
-
petechial
-
purpuric
-
maculopapular
-
-
sleep/difficult to rous
-
arthralgia/myalgia
-
young infants
-
bulging fontanelle
-
tachycardia
-
altered responsiveness
-
irriatbiliyt and/or floppiness
-
refusing drinks or feeds
-
poor peripheral perfusion
-
-
Benzylpenicillin:
-
Adult: 1.2g IV/IM at least 6hourly
-
Children: 25-50mg/kg IV/IM at least 6hours
-
-
Amoxyl
-
1-2g IV or IM
-
50-100mg/kg IV/IM
-
-
chemoprophylaxis
-
Rifampicin
-
10mg/kg every 12hr for 2d
- \<4wk = 5mg/kg
-
-
Ceftriaxone
-
single dose IM
-
125mg \<12yrs
-
250mg >12yrs
-
-
-
Ciprofloxacin
-
500-750mg single oral dose
-
preferred on OCP
-
larrge groups
-
not for pregnant/lactating woemn
-
-


.equ locat, 0x8000 ;Location for this program .org locat .db 0xA5,0xE5,0xE0,0xA5 ;signiture bytes .db 35,255,0,0 ;id (35=prog) .db 0,0,0,0 ;prompt code vector .db 0,0,0,0 ;reserved .db 0,0,0,0 ;reserved .db 0,0,0,0 ;reserved .db 0,0,0,0 ;user defined .db 255,255,255,255 ;length and checksum (255=unused) .db "Program Name",0 ;max 31 characters, plus the zero .org locat+64 ;executable code begins hereAdmittedly using the Run Command instead of the Jump Command isn't a big advantage. The most compelling reason to use the normal program header is because it is later quite easy to change it into the startup header.
Startup programs are really only useful when used with nonvolatile memory. With Flash ROM, programs may be written via the Download command, but they will remain in memory.
Instead of replacing PAULMON2 (at 0000), the final application program can be turned into a startup program by changing a byte in it's header. If Flash ROM is used, the board will always startup to the intended program. The lines to add to define a startup header should look like this:
.equ locat, 0x8000 ;Location for this program .org locat .db 0xA5,0xE5,0xE0,0xA5 ;signiture bytes .db 253,255,0,0 ;id (253=startup) .db 0,0,0,0 ;prompt code vector .db 0,0,0,0 ;reserved .db 0,0,0,0 ;reserved .db 0,0,0,0 ;reserved .db 0,0,0,0 ;user defined .db 255,255,255,255 ;length and checksum (255=unused) .db "Program Name",0 ;max 31 characters, plus the zero .org locat+64 ;executable code begins herePAULMON2 has a feature where an erase pin may be defined. If this pin is held low after a reset as PAULMON2 starts up, it will attempt to erase the Flash ROM. By providing a jumper which pulls this pin low when installed, the application program (in Flash ROM) may be deleted and a new version may be downloaded without having to pull the EPROM, as would be necessary in a system without PAULMON2 and Flash ROM. The default erase pin is P3.5 (T1, pin 15).
The startup program header feature is intended work together with Flash ROM to provide a quick and easy way to make the application under development permanent, without pulling any chips, without having to worry if the program will correctly initialize the hardware without having run PAULMON2 first, and with a simple (and well tested) mechanism to erase and download a new version of the permanent startup program should changes become necessary.
It should be noted that startup programs are run after the baud rate and serial port is configured, so that they may perform serial I/O. In most permanent applications, the automatic baud rate detection (requiring a carriage return after power is first applied) is not desirable, so it will probably be necessary to customize PAULMON2 with a fixed baud rate for use the hardware's crystal frequency.
In some cases, it may be desirable to install a startup program which initializes hardware or performs some startup function but then allows PAULMON2 to begin normally. In this case, the startup program must terminate with a RET instruction to return back to PAULMON2. Obviously the stack must point to the return address which PAULMON2 originally pushed before running the startup program.
.equ locat, 0x8000 ;Location for this program .org locat .db 0xA5,0xE5,0xE0,0xA5 ;signiture bytes .db 254,'A',0,0 ;id (254=command, key='A') .db 0,0,0,0 ;prompt code vector .db 0,0,0,0 ;reserved .db 0,0,0,0 ;reserved .db 0,0,0,0 ;reserved .db 0,0,0,0 ;user defined .db 255,255,255,255 ;length and checksum (255=unused) .db "Command Name",0 ;max 31 characters, plus the zero .org locat+64 ;executable code begins hereIn this example, the command will be executed when the user presses the 'A' key. The specified character must be uppercase, because PAULMON2 calls the upper function to make the user interface case insensitive.
For more detailed information about Adding Commands to PAULMON2, and some examples, please refer to that section.


| ( $* ) [Sparse] |
Shorthand for
mul_scalar x a , i.e., x $* a
|
| ( $* ) [Dense] |
Shorthand for
mul_scalar x a , i.e., x $* a
|
| ( *$ ) [Sparse] |
Shorthand for
mul_scalar x a , i.e., x *$ a
|
| ( *$ ) [Dense] |
Shorthand for
mul_scalar x a , i.e., x *$ a
|
| ( **@ ) [Sparse] |
Shorthand for
power x a , i.e., x **@ a
|
| ( **@ ) [Dense] |
Shorthand for
power x a , i.e., x **@ a
|
| ( *@ ) [Sparse] |
Shorthand for
mul x y , i.e., x *@ y
|
| ( *@ ) [Dense] |
Shorthand for
mul x y , i.e., x *@ y
|
| ($+) [Dense] |
Shorthand for
add_scalar x a , i.e., a $+ x
|
| ($-) [Dense] |
Shorthand for
sub_scalar x a , i.e., a -$ x
|
| ($/) [Sparse] |
Shorthand for
div_scalar x a , i.e., x $/ a
|
| ($/) [Dense] |
Shorthand for
div_scalar x a , i.e., x $/ a
|
| ($@) [Sparse] |
Shorthand for
dot x y , i.e., x $@ y
|
| ($@) [Dense] |
Shorthand for
dot x y , i.e., x $@ y
|
| (+$) [Dense] |
Shorthand for
add_scalar x a , i.e., x +$ a
|
| (+@) [Sparse] |
Shorthand for
add x y , i.e., x +@ y
|
| (+@) [Dense] |
Shorthand for
add x y , i.e., x +@ y
|
| (-$) [Dense] |
Shorthand for
sub_scalar x a , i.e., x -$ a
|
| (-@) [Sparse] |
Shorthand for
sub x y , i.e., x -@ y
|
| (-@) [Dense] |
Shorthand for
sub x y , i.e., x -@ y
|
| (/$) [Sparse] |
Shorthand for
div_scalar x a , i.e., x /$ a
|
| (/$) [Dense] |
Shorthand for
div_scalar x a , i.e., x /$ a
|
| (/@) [Sparse] |
Shorthand for
div x y , i.e., x /@ y
|
| (/@) [Dense] |
Shorthand for
div x y , i.e., x /@ y
|
| (<<) [Dense] |
Shorthand for
copy_to y x , i.e., x << y
|
| (<=@) [Sparse] |
Shorthand for
equal_or_smaller x y , i.e., x <=@ y
|
| (<=@) [Dense] |
Shorthand for
equal_or_smaller x y , i.e., x <=@ y
|
| (<>@) [Sparse] |
Shorthand for
is_unequal x y , i.e., x <>@ y
|
| (<>@) [Dense] |
Shorthand for
is_unequal x y , i.e., x <>@ y
|
| (<@) [Sparse] |
Shorthand for
is_smaller x y , i.e., x <@ y
|
| (<@) [Dense] |
Shorthand for
is_smaller x y , i.e., x <@ y
|
| (=@) [Sparse] |
Shorthand for
is_equal x y , i.e., x =@ y
|
| (=@) [Dense] |
Shorthand for
is_equal x y , i.e., x =@ y
|
| (>=@) [Sparse] |
Shorthand for
equal_or_greater x y , i.e., x >=@ y
|
| (>=@) [Dense] |
Shorthand for
equal_or_greater x y , i.e., x >=@ y
|
| (>>) [Dense] |
Shorthand for
copy_to x y , i.e., x >> y
|
| (>@) [Sparse] |
Shorthand for
is_greater x y , i.e., x >@ y
|
| (>@) [Dense] |
Shorthand for
is_greater x y , i.e., x >@ y
|
| (@=) [Dense] |
Shorthand for
concat_vertical x y , i.e., x @= y
|
| (@@) [Dense] |
Shorthand for
map f x , i.e., f @@ x
|
| (@||) [Dense] |
Shorthand for
concat_horizontal x y , i.e., x @|| y
|
A | |
| abs [Maths] | |
| abs [Sparse] | abs x returns a new matrix where each element has the absolute value of
that in the original matrix x .
|
| abs [Dense] | abs x returns a new matrix where each element has the absolute value of
that in the original matrix x .
|
| absdev [Stats] | |
| acos [Maths] | |
| acosh [Maths] | |
| acot [Maths] | |
| add [Sparse] | add x y adds two matrices x and y .
|
| add [Dense] | add x y adds two matrices x and y .
|
| add_diag [Dense] | add_diag x a adds a constant a to all the diagonal elements in x .
|
| add_scalar [Dense] | add_scalar x a adds every element in x by a constant factor a .
|
| airy_Ai [Maths] | |
| airy_Ai_deriv [Maths] | |
| airy_Ai_scaled [Maths] | |
| airy_Bi [Maths] | |
| airy_Bi_deriv [Maths] | |
| airy_Bi_scaled [Maths] | |
| airy_zero_Ai [Maths] | |
| airy_zero_Bi [Maths] | |
| angle_restrict_pos [Maths] | |
| angle_restrict_symm [Maths] | |
| asin [Maths] | |
| asinh [Maths] | |
| atan [Maths] | |
| atanh [Maths] | |
| atanint [Maths] | |
| autocorrelation [Stats] | |
| average [Sparse] | average x returns the average value of all the elements in x .
|
| average [Dense] | average x returns the average value of all the elements in x .
|
| average_cols [Sparse] | average_cols x returns the average value of all column vectors in x .
|
| average_cols [Dense] | average_cols x returns the average value of all column vectors in x .
|
| average_rows [Sparse] | average_rows x returns the average value of all row vectors in x .
|
| average_rows [Dense] | average_rows x returns the average value of all row vectors in x .
|
B | |
| bernoulli [Stats.Pdf] | |
| bernoulli [Stats.Rnd] | |
| bessel_I0 [Maths] | |
| bessel_I0_scaled [Maths] | |
| bessel_I1 [Maths] | |
| bessel_I1_scaled [Maths] | |
| bessel_In [Maths] | |
| bessel_In_array [Maths] | |
| bessel_In_scaled [Maths] | |
| bessel_In_scaled_array [Maths] | |
| bessel_Inu [Maths] | |
| bessel_Inu_scaled [Maths] | |
| bessel_J0 [Maths] | |
| bessel_J1 [Maths] | |
| bessel_Jn [Maths] | |
| bessel_Jn_array [Maths] | |
| bessel_Jnu [Maths] | |
| bessel_K0 [Maths] | |
| bessel_K0_scaled [Maths] | |
| bessel_K1 [Maths] | |
| bessel_K1_scaled [Maths] | |
| bessel_Kn [Maths] | |
| bessel_Kn_array [Maths] | |
| bessel_Kn_scaled [Maths] | |
| bessel_Kn_scaled_array [Maths] | |
| bessel_Knu [Maths] | |
| bessel_Knu_scaled [Maths] | |
| bessel_Y0 [Maths] | |
| bessel_Y1 [Maths] | |
| bessel_Yn [Maths] | |
| bessel_Yn_array [Maths] | |
| bessel_Ynu [Maths] | |
| bessel_i0_scaled [Maths] | |
| bessel_i1_scaled [Maths] | |
| bessel_il_array_scaled [Maths] | |
| bessel_il_scaled [Maths] | |
| bessel_j0 [Maths] | |
| bessel_j1 [Maths] | |
| bessel_j2 [Maths] | |
| bessel_jl [Maths] | |
| bessel_jl_array [Maths] | |
| bessel_jl_steed_array [Maths] | |
| bessel_k0_scaled [Maths] | |
| bessel_k1_scaled [Maths] | |
| bessel_kl_array_scaled [Maths] | |
| bessel_kl_scaled [Maths] | |
| bessel_lnKnu [Maths] | |
| bessel_y0 [Maths] | |
| bessel_y1 [Maths] | |
| bessel_y2 [Maths] | |
| bessel_yl [Maths] | |
| bessel_yl_array [Maths] | |
| bessel_zero_J0 [Maths] | |
| bessel_zero_J1 [Maths] | |
| bessel_zero_Jnu [Maths] | |
| beta [Stats.Pdf] | |
| beta [Stats.Rnd] | |
| beta_P [Stats.Cdf] | |
| beta_Pinv [Stats.Cdf] | |
| beta_Q [Stats.Cdf] | |
| beta_Qinv [Stats.Cdf] | |
| beta_inc [Maths] | |
| betaf [Maths] | |
| bidiag [Linalg] | |
| binary [Sparse] | binary m n creates an m by n random matrix where 10% ~ 15% elements are 1.
|
| binomial [Stats.Pdf] | |
| binomial [Stats.Rnd] | |
| binomial_P [Stats.Cdf] | |
| binomial_Q [Stats.Cdf] | |
| bivariate_gaussian [Stats.Pdf] | bivariate_gaussian x y sigma_x sigma_y rho returns the probability
density p(x,y) at (x,y) for a bivariate Gaussian distribution with standard
deviations sigma_x, sigma_y and correlation coefficient rho.
|
| bivariate_gaussian [Stats.Rnd] | bivariate_gaussian sigma_x sigma_y rho returns a pair of correlated
gaussian variates, with mean zero, correlation coefficient rho -1, 1 and
standard deviations sigma_x and sigma_y in the x and y directions.
|
C | |
| cauchy [Stats.Pdf] | |
| cauchy [Stats.Rnd] | |
| cauchy_P [Stats.Cdf] | |
| cauchy_Pinv [Stats.Cdf] | |
| cauchy_Q [Stats.Cdf] | |
| cauchy_Qinv [Stats.Cdf] | |
| central_moment [Stats] | |
| chi [Maths] | |
| chisq [Stats.Pdf] | |
| chisq [Stats.Rnd] | |
| chisq_P [Stats.Cdf] | |
| chisq_Pinv [Stats.Cdf] | |
| chisq_Q [Stats.Cdf] | |
| chisq_Qinv [Stats.Cdf] | |
| cholesky [Linalg] | |
| choose [Stats] | choose x n draw n samples from x without replecement.
|
| ci [Maths] | |
| clausen [Maths] | |
| clone [Sparse] | clone x makes an exact copy of matrix x .
|
| clone [Dense] | clone x returns a copy of matrix x .
|
| col [Sparse] | col x j returns the column j of x .
|
| col [Dense] | col x j returns the column j of x .
|
| col_num [Sparse] | col_num x returns the number of columns in matrix x .
|
| col_num [Dense] | col_num x returns the number of columns in matrix x .
|
| col_num_nz [Sparse] | col_num_nz x returns the number of non-zero columns in matrix x .
|
| cols [Sparse] |
Similar to
rows , cols x a returns the columns (specified in array a )
of x in a new sparse matrix.
|
| cols [Dense] |
Similar to
rows , cols x a returns the columns (specified in array a )
of x in a new sparse matrix.
|
| combination [Maths] | |
| concat_horizontal [Dense] | concat_horizontal x y concats two matrices x and y horizontally,
therefore their row numbers must be the same.
|
| concat_vertical [Dense] | concat_vertical x y concats two matrices x and y vertically,
therefore their column numbers must be the same.
|
| copy_col_to [Dense] | copy_col_to v x j copies an 1 by n column vector v to the j th
column in an m by n matrix x .
|
| copy_row_to [Dense] | copy_row_to v x i copies an 1 by n row vector v to the i th row
in an m by n matrix x .
|
| copy_to [Dense] | copy_to x y copies the elements of x to y .
|
| correlation [Stats] | |
| cos [Maths] | |
| cosh [Maths] | |
| cot [Maths] | |
| covariance [Stats] | |
| create [Dense] | create m n a creates an m by n matrix and all the elements of x are
initialised with the value a .
|
| csc [Maths] | |
D | |
| dawson [Maths] | |
| debye_1 [Maths] | |
| debye_2 [Maths] | |
| debye_3 [Maths] | |
| debye_4 [Maths] | |
| debye_5 [Maths] | |
| debye_6 [Maths] | |
| density [Sparse] | density x returns the density of non-zero element.
|
| det [Linalg] | det x computes the determinant of a matrix x from its LU decomposition.
|
| diag [Sparse] | diag x returns the diagonal elements of x .
|
| diag [Dense] | diag x returns the diagonal elements of x .
|
| dilog [Maths] | |
| dir_2d [Stats.Rnd] | |
| dir_2d_trig_method [Stats.Rnd] | |
| dir_3d [Stats.Rnd] | |
| dir_nd [Stats.Rnd] | |
| dirichlet [Stats.Pdf] | |
| dirichlet [Stats.Rnd] | |
| dirichlet_lnpdf [Stats.Pdf] | |
| div [Sparse] | div x y performs an element-wise division, so both x and y
must have the same dimensions.
|
| div [Dense] | div x y performs an element-wise division, so both x and y
must have the same dimensions.
|
| div_scalar [Sparse] | div_scalar x a divides every element in x by a constant factor a .
|
| div_scalar [Dense] | div_scalar x a divides every element in x by a constant factor a .
|
| dot [Sparse] | dot x y calculates the dot product of an m by n matrix x and
another n by p matrix y .
|
| dot [Dense] | dot x y calculates the dot product of an m by n matrix x and
another n by p matrix y .
|
| double_factorial [Maths] | |
| draw_cols [Sparse] | draw_cols x m draws m cols randomly from x .
|
| draw_cols [Dense] | draw_cols x m draws m cols randomly from x .
|
| draw_rows [Sparse] | draw_rows x m draws m rows randomly from x .
|
| draw_rows [Dense] | draw_rows x m draws m rows randomly from x .
|
E | |
| ellint_D [Maths] | |
| ellint_Dcomp [Maths] | |
| ellint_E [Maths] | |
| ellint_Ecomp [Maths] | |
| ellint_F [Maths] | |
| ellint_Kcomp [Maths] | |
| ellint_P [Maths] | |
| ellint_Pcomp [Maths] | |
| ellint_RC [Maths] | |
| ellint_RD [Maths] | |
| ellint_RF [Maths] | |
| ellint_RJ [Maths] | |
| empty [Dense] | empty m n creates an m by n matrix without initialising the values of
elements in x .
|
| equal_or_greater [Sparse] | equal_or_greater x y returns true if all the elements in x are not
smaller than the corresponding elements in y .
|
| equal_or_greater [Dense] | equal_or_greater x y returns true if all the elements in x are not
smaller than the corresponding elements in y .
|
| equal_or_smaller [Sparse] | equal_or_smaller x y returns true if all the elements in x are not
greater than the corresponding elements in y .
|
| equal_or_smaller [Dense] | equal_or_smaller x y returns true if all the elements in x are not
greater than the corresponding elements in y .
|
| eta [Maths] | |
| eta_int [Maths] | |
| exists [Sparse] | exists f x checks all the elements in x using f .
|
| exists [Dense] | exists f x checks all the elements in x using f .
|
| exists_nz [Sparse] | exists_nz f x is similar to exists but only checks non-zero elements.
|
| exp [Maths] | |
| exp [Dense] | exp x applies exp function to each element in matrix x .
|
| exp_mult [Maths] | |
| expint_3 [Maths] | |
| expint_E1 [Maths] | |
| expint_E1_scaled [Maths] | |
| expint_E2 [Maths] | |
| expint_E2_scaled [Maths] | |
| expint_Ei [Maths] | |
| expint_Ei_scaled [Maths] | |
| expm1 [Maths] | |
| exponential [Regression] |
Exponential regression:
exponential x y fits the measurements x and the
observations y into a exponential model: y = a * exp^(-lambda * x) + b .
|
| exponential [Stats.Pdf] | exponential x mu returns the probability density at x
|
| exponential [Stats.Rnd] | exponential mu return a random value that follows exponential distribution.
|
| exponential_P [Stats.Cdf] | |
| exponential_Pinv [Stats.Cdf] | |
| exponential_Q [Stats.Cdf] | |
| exponential_Qinv [Stats.Cdf] | |
| exppow [Stats.Pdf] | |
| exppow [Stats.Rnd] | |
| exppow_P [Stats.Cdf] | |
| exppow_Q [Stats.Cdf] | |
| exprel [Maths] | |
| eye [Sparse] | eye m creates an m by m identity matrix.
|
| eye [Dense] | eye m creates an m by m identity matrix.
|
F | |
| factorial [Maths] | |
| fdist [Stats.Pdf] | |
| fdist [Stats.Rnd] | |
| fdist_P [Stats.Cdf] | |
| fdist_Pinv [Stats.Cdf] | |
| fdist_Q [Stats.Cdf] | |
| fdist_Qinv [Stats.Cdf] | |
| fermi_dirac_0 [Maths] | |
| fermi_dirac_1 [Maths] | |
| fermi_dirac_2 [Maths] | |
| fermi_dirac_3half [Maths] | |
| fermi_dirac_half [Maths] | |
| fermi_dirac_inc_0 [Maths] | |
| fermi_dirac_int [Maths] | |
| fermi_dirac_m1 [Maths] | |
| fermi_dirac_mhalf [Maths] | |
| filter [Sparse] |
Similar to
filteri , but the coordinates of the elements are not passed to
the function f : float -> bool .
|
| filter [Dense] |
Similar to
filteri , but the coordinates of the elements are not passed to
the function f : float -> bool .
|
| filter_cols [Dense] |
Similar to
filteri_cols except that the column indices are not passed to f .
|
| filter_nz [Sparse] | filter_nz f x is similar to filteri_nz except that the coordinates of
matrix elements are not passed to f .
|
| filter_rows [Dense] |
Similar to
filteri_rows except that the row indices are not passed to f .
|
| filteri [Sparse] | filteri f x uses f : int -> int -> float -> bool to filter out certain
elements in x .
|
| filteri [Dense] | filteri f x uses f : int -> int -> float -> bool to filter out certain
elements in x .
|
| filteri_cols [Dense] | filteri_cols f x uses function f : int -> dsmat -> bool to check each
column in x , then returns an int array containing the indices of those
columns which satisfy the function f .
|
| filteri_nz [Sparse] | filteri_nz f x is similar to filter f x but only applies f to
non-zero elements in x .
|
| filteri_rows [Dense] | filteri_rows f x uses function f : int -> dsmat -> bool to check each
row in x , then returns an int array containing the indices of those rows
which satisfy the function f .
|
| flat [Stats.Pdf] | |
| flat [Stats.Rnd] | flat a b draws a random number from the interval [a,b) with a uniform
distribution.
|
| flat_P [Stats.Cdf] | |
| flat_Pinv [Stats.Cdf] | |
| flat_Q [Stats.Cdf] | |
| flat_Qinv [Stats.Cdf] | |
| fold [Sparse] | fold f a x folds all the elements in x with the function
f : 'a -> float -> 'a .
|
| fold [Dense] | fold f a x folds all the elements in x with the function
f : 'a -> float -> 'a .
|
| fold_cols [Sparse] | fold_cols f a x folds all the columns in x using function f .
|
| fold_cols [Dense] | fold_cols f a x folds all the columns in x using function f .
|
| fold_cols_nz [Sparse] | fold_cols_nz f a x is similar to fold_cols but only folds non-zero
columns in x using function f .
|
| fold_nz [Sparse] | fold_nz f a x is similar to fold f a x but only applies to non-zero
rows in x .
|
| fold_rows [Sparse] | fold_rows f a x folds all the rows in x using function f .
|
| fold_rows [Dense] | fold_rows f a x folds all the rows in x using function f .
|
| fold_rows_nz [Sparse] | fold_rows_nz f a x is similar to fold_rows but only folds non-zero
rows in x using function f .
|
| for_all [Sparse] | for_all f x checks all the elements in x , the function returns true
if and only if all the elements pass the check of function f .
|
| for_all [Dense] | for_all f x checks all the elements in x , the function returns true
if and only if all the elements pass the check of function f .
|
| for_all_nz [Sparse] | for_all_nz f x is similar to for_all_nz but only checks non-zero elements.
|
G | |
| gamma [Stats.Pdf] | |
| gamma [Stats.Rnd] | |
| gamma [Maths] | |
| gamma_P [Stats.Cdf] | |
| gamma_Pinv [Stats.Cdf] | |
| gamma_Q [Stats.Cdf] | |
| gamma_Qinv [Stats.Cdf] | |
| gamma_inc [Maths] | |
| gamma_inc_P [Maths] | |
| gamma_inc_Q [Maths] | |
| gammainv [Maths] | |
| gammastar [Maths] | |
| gaussian [Stats.Pdf] | gaussian_pdf x sigma returns the probability density at x
|
| gaussian [Stats.Rnd] | gaussian ~sigma:s () returns the value of a random variable that
follows Normal distribution of sigma = s .
|
| gaussian [Dense] | gaussian m n creates an m by n matrix where all the elements in x
follow a Gaussian distribution with specified sigma.
|
| gaussian_P [Stats.Cdf] | |
| gaussian_Pinv [Stats.Cdf] | |
| gaussian_Q [Stats.Cdf] | |
| gaussian_Qinv [Stats.Cdf] | |
| gaussian_tail [Stats.Pdf] | gaussian_tail_pdf x a sigma returns the probability density at x given
a gaussian tail distribution of N(a, sigma)
|
| gaussian_tail [Stats.Rnd] | gaussian_tail a x sigma returns a random value of a gaussian tail
distribution.
|
| geometric [Stats.Pdf] | |
| geometric [Stats.Rnd] | |
| geometric_P [Stats.Cdf] | |
| geometric_Q [Stats.Cdf] | |
| get [Sparse] | get x i j returns the value of element (i,j) of x .
|
| get [Dense] | get x i j returns the value of element (i,j) of x .
|
| gibbs_sampling [Stats] |
TODO:
gibbs_sampling f p n is Gibbs sampler.
|
| gsl_col [Dense] | |
| gumbel1 [Stats.Pdf] | |
| gumbel1 [Stats.Rnd] | |
| gumbel1_P [Stats.Cdf] | |
| gumbel1_Pinv [Stats.Cdf] | |
| gumbel1_Q [Stats.Cdf] | |
| gumbel1_Qinv [Stats.Cdf] | |
| gumbel2 [Stats.Pdf] | |
| gumbel2 [Stats.Rnd] | |
| gumbel2_P [Stats.Cdf] | |
| gumbel2_Pinv [Stats.Cdf] | |
| gumbel2_Q [Stats.Cdf] | |
| gumbel2_Qinv [Stats.Cdf] | |
H | |
| histogram [Plot] | |
| hypergeometric [Stats.Pdf] | |
| hypergeometric [Stats.Rnd] | |
| hypergeometric_P [Stats.Cdf] | |
| hypergeometric_Q [Stats.Cdf] | |
| hypot [Maths] | |
| hzeta [Maths] | |
I | |
| inv [Linalg] |
A general square matrix A has an LU decomposition into upper and lower triangular matrices,
P A = L U where P is a permutation matrix, L is unit lower triangular matrix and U is upper triangular matrix.
|
| is_equal [Sparse] | is_equal x y returns true if two matrices x and y are equal.
|
| is_equal [Dense] | is_equal x y returns true if two matrices x and y are equal.
|
| is_greater [Sparse] | is_greater x y returns true if all the elements in x are greater than
the corresponding elements in y .
|
| is_greater [Dense] | is_greater x y returns true if all the elements in x are greater than
the corresponding elements in y .
|
| is_negative [Sparse] | is_negative x returns true if all the elements in x are negative.
|
| is_negative [Dense] | is_negative x returns true if all the elements in x are negative.
|
| is_nonnegative [Sparse] | is_nonnegative returns true if all the elements in x are non-negative.
|
| is_nonnegative [Dense] | is_nonnegative returns true if all the elements in x are non-negative.
|
| is_posdef [Linalg] | is_posdef x checks whether x is a positive semi-definite matrix.
|
| is_positive [Sparse] | is_positive x returns true if all the elements in x are positive.
|
| is_positive [Dense] | is_positive x returns true if all the elements in x are positive.
|
| is_smaller [Sparse] | is_smaller x y returns true if all the elements in x are smaller than
the corresponding elements in y .
|
| is_smaller [Dense] | is_smaller x y returns true if all the elements in x are smaller than
the corresponding elements in y .
|
| is_unequal [Sparse] | is_unequal x y returns true if there is at least one element in x is
not equal to that in y .
|
| is_unequal [Dense] | is_unequal x y returns true if there is at least one element in x is
not equal to that in y .
|
| is_zero [Sparse] | is_zero x returns true if all the elements in x are zeros.
|
| is_zero [Dense] | is_zero x returns true if all the elements in x are zeros.
|
| iter [Sparse] | iter f x is the same as as iteri f x except the coordinates of the
current element is not passed to the function f : float -> 'a
|
| iter [Dense] | iter f x is the same as as iteri f x except the coordinates of the
current element is not passed to the function f : float -> 'a
|
| iter_cols [Sparse] |
Similar to
iteri_cols except col number is not passed to f .
|
| iter_cols [Dense] |
Similar to
iteri_cols except col number is not passed to f .
|
| iter_cols_nz [Sparse] |
Similar to
iteri_cols_nz except that column numbers are not passed to f .
|
| iter_nz [Sparse] |
Similar to
iter_nz except the coordinates of elements are not passed to f .
|
| iter_rows [Sparse] |
Similar to
iteri_rows except row number is not passed to f .
|
| iter_rows [Dense] |
Similar to
iteri_rows except row number is not passed to f .
|
| iter_rows_nz [Sparse] |
Similar to
iteri_rows_nz except that row numbers are not passed to f .
|
| iteri [Sparse] | iteri f x iterates all the elements in x and applies the user defined
function f : int -> int -> float -> 'a .
|
| iteri [Dense] | iteri f x iterates all the elements in x and applies the user defined
function f : int -> int -> float -> 'a .
|
| iteri_cols [Sparse] | iteri_cols f x iterates every column in x and applies function
f : int -> spmat -> unit to each of them.
|
| iteri_cols [Dense] | iteri_cols f x iterates every column in x and applies function
f : int -> dsmat -> unit to each of them.
|
| iteri_cols_nz [Sparse] | iteri_cols_nz f x is similar to iteri_cols but only applies f to
non-zero columns in x .
|
| iteri_nz [Sparse] | iteri_nz f x iterates all the non-zero elements in x by applying the
function f : int -> int -> float -> 'a .
|
| iteri_rows [Sparse] | iteri_rows f x iterates every row in x and applies function
f : int -> spmat -> unit to each of them.
|
| iteri_rows [Dense] | iteri_rows f x iterates every row in x and applies function
f : int -> dsmat -> unit to each of them.
|
| iteri_rows_nz [Sparse] | iteri_rows_nz f x is similar to iteri_rows but only applies f to
non-zero rows in x .
|
K | |
| kendall_tau [Stats] | |
| kmeans [Regression] |
K-means clustering:
kmeans x c divides x which is a row-based matrix
into c clusters.
|
| kurtosis [Stats] | |
L | |
| laguerre_1 [Maths] | |
| laguerre_2 [Maths] | |
| laguerre_3 [Maths] | |
| laguerre_n [Maths] | |
| lambert_w0 [Maths] | |
| lambert_w1 [Maths] | |
| landau [Stats.Pdf] | |
| landau [Stats.Rnd] | |
| laplace [Stats.Pdf] | |
| laplace [Stats.Rnd] | |
| laplace_P [Stats.Cdf] | |
| laplace_Pinv [Stats.Cdf] | |
| laplace_Q [Stats.Cdf] | |
| laplace_Qinv [Stats.Cdf] | |
| lasso [Regression] |
LASSO regression: in
lasso ~i ~a x y , i : whether or not to include
intercept bias in parameters, the default is true ; a : the weight on the
regularisation term; x is the measurements, and y is the observations.
|
| legendre_P1 [Maths] | |
| legendre_P2 [Maths] | |
| legendre_P3 [Maths] | |
| legendre_Pl [Maths] | |
| legendre_Pl_array [Maths] | |
| legendre_Q0 [Maths] | |
| legendre_Q1 [Maths] | |
| legendre_Ql [Maths] | |
| levy [Stats.Rnd] | |
| levy_skew [Stats.Rnd] | |
| linear [Regression] |
Linear regression:
linear ~i x y fits the measurements x and the
observations y into a linear model.
|
| linspace [Sparse] | linspace a b n linearly divides the interval [a,b] into n pieces by
creating an m by 1 row vector.
|
| linspace [Dense] | linspace a b n linearly divides the interval [a,b] into n pieces by
creating an m by 1 row vector.
|
| ln [Maths] | |
| ln1p [Maths] | |
| ln_abs [Maths] | |
| ln_combination [Maths] | |
| ln_double_factorial [Maths] | |
| ln_factorial [Maths] | |
| lnbeta [Maths] | |
| lncosh [Maths] | |
| lngamma [Maths] | |
| lnpoch [Maths] | |
| lnsinh [Maths] | |
| load [Sparse] | load f loads a sparse matrix from file f .
|
| load [Dense] | load f loads a sparse matrix from file f .
|
| load_txt [Dense] | load_txt f load a text file f into a matrix.
|
| log [Maths] | |
| log [Dense] | log x applies log function to each element in matrix x .
|
| log10 [Maths] | |
| log10 [Dense] | log10 x applies log10 function to each element in matrix x .
|
| log2 [Maths] | |
| logarithmic [Stats.Pdf] | |
| logarithmic [Stats.Rnd] | |
| logistic [Regression] |
Logistic regression: in
logistic ~i x y , i : whether or not to include
intercept bias in parameters, the default is true ; ; x is the
measurements, and y is the observations.
|
| logistic [Stats.Pdf] | |
| logistic [Stats.Rnd] | |
| logistic_P [Stats.Cdf] | |
| logistic_Pinv [Stats.Cdf] | |
| logistic_Q [Stats.Cdf] | |
| logistic_Qinv [Stats.Cdf] | |
| lognormal [Stats.Pdf] | |
| lognormal [Stats.Rnd] | |
| lognormal_P [Stats.Cdf] | |
| lognormal_Pinv [Stats.Cdf] | |
| lognormal_Q [Stats.Cdf] | |
| lognormal_Qinv [Stats.Cdf] | |
M | |
| map [Sparse] | map f x is similar to mapi f x except the coordinates of the
current element is not passed to the function f : float -> float
|
| map [Dense] | map f x is similar to mapi f x except the coordinates of the
current element is not passed to the function f : float -> float
|
| map_at_col [Dense] | map_at_col f x i is similar to mapi_at_col except that the coordinates
of an element is not passed to f .
|
| map_at_row [Dense] | map_at_row f x i is similar to mapi_at_row except that the coordinates
of an element is not passed to f .
|
| map_by_col [Dense] | map_by_col f x i is similar to mapi_by_col except that the column
indices are not passed to f .
|
| map_by_row [Dense] | map_by_row f x i is similar to mapi_by_row except that the row indices
are not passed to f .
|
| map_cols [Sparse] |
Similar to
mapi_cols except column number is not passed to f .
|
| map_cols [Dense] |
Similar to
mapi_cols except column number is not passed to f .
|
| map_cols_nz [Sparse] |
Similar to
mapi_cols_nz , but columns numbers are not passed to f .
|
| map_nz [Sparse] |
Similar to
mapi_nz except the coordinates of elements are not passed to f .
|
| map_rows [Sparse] |
Similar to
mapi_rows except row number is not passed to f .
|
| map_rows [Dense] |
Similar to
mapi_rows except row number is not passed to f .
|
| map_rows_nz [Sparse] |
Similar to
mapi_rows_nz , but row numbers are not passed to f .
|
| mapi [Sparse] | mapi f x maps each element in x to a new value by applying
f : int -> int -> float -> float .
|
| mapi [Dense] | mapi f x maps each element in x to a new value by applying
f : int -> int -> float -> float .
|
| mapi_at_col [Dense] | mapi_at_col f x j creates a new matrix by applying function f only to
the j th column in matrix x .
|
| mapi_at_row [Dense] | mapi_at_row f x i creates a new matrix by applying function f only to
the i th row in matrix x .
|
| mapi_by_col [Dense] | mapi_by_col f x applies f to each column of x , then uses the returned
column vectors to assemble a new matrix.
|
| mapi_by_row [Dense] | mapi_by_row f x applies f to each row of x , then uses the returned
row vectors to assemble a new matrix.
|
| mapi_cols [Sparse] | mapi_cols f x maps every column in x to a type 'a value by applying
function f : int -> spmat -> 'a .
|
| mapi_cols [Dense] | mapi_cols f x maps every column in x to a type 'a value by applying
function f : int -> dsmat -> 'a .
|
| mapi_cols_nz [Sparse] | mapi_cols_nz f x applies f only to the non-zero columns in x .
|
| mapi_nz [Sparse] | mapi_nz f x is similar to mapi f x but only applies f to non-zero
elements in x .
|
| mapi_rows [Sparse] | mapi_rows f x maps every row in x to a type 'a value by applying
function f : int -> spmat -> 'a to each of them.
|
| mapi_rows [Dense] | mapi_rows f x maps every row in x to a type 'a value by applying
function f : int -> dsmat -> 'a to each of them.
|
| mapi_rows_nz [Sparse] | mapi_rows_nz f x applies f only to the non-zero rows in x .
|
| max [Stats] | |
| max [Sparse] | max x returns the maximum value of all elements in x .
|
| max [Dense] | max x returns the maximum value of all elements in x .
|
| max_cols [Dense] | min_cols x returns the minimum value in each column along with their coordinates.
|
| max_i [Stats] | |
| max_rows [Dense] | max_rows x returns the maximum value in each row along with their coordinates.
|
| mean [Stats] | |
| mesh [Plot] | |
| meshgrid [Dense] | meshgrid a1 b1 a2 b2 n1 n2 is similar to the meshgrid function in
Matlab.
|
| meshup [Dense] | meshup x y creates mesh grids by using two row vectors x and y .
|
| metropolis_hastings [Stats] |
TODO:
metropolis_hastings f p n is Metropolis-Hastings MCMC algorithm.
|
| min [Stats] | |
| min [Sparse] | min x returns the minimum value of all elements in x .
|
| min [Dense] | min x returns the minimum value of all elements in x .
|
| min_cols [Dense] | min_cols x returns the minimum value in each column along with their coordinates.
|
| min_i [Stats] | |
| min_rows [Dense] | min_rows x returns the minimum value in each row along with their coordinates.
|
| minmax [Stats] | |
| minmax [Sparse] | minmax x returns both the minimum and minimum values in x .
|
| minmax [Dense] | minmax x returns both the minimum and minimum values in x .
|
| minmax_i [Stats] | |
| mul [Sparse] | mul x y performs an element-wise multiplication, so both x and y
must have the same dimensions.
|
| mul [Dense] | mul x y performs an element-wise multiplication, so both x and y
must have the same dimensions.
|
| mul_scalar [Sparse] | mul_scalar x a multiplies every element in x by a constant factor a .
|
| mul_scalar [Dense] | mul_scalar x a multiplies every element in x by a constant factor a .
|
| multinomial [Stats.Pdf] | |
| multinomial [Stats.Rnd] | |
| multinomial_lnpdf [Stats.Pdf] | |
N | |
| neg [Sparse] | neg x returns a new matrix where each element has the negative value of
that in the original matrix x .
|
| neg [Dense] | neg x returns a new matrix where each element has the negative value of
that in the original matrix x .
|
| negative_binomial [Stats.Pdf] | |
| negative_binomial [Stats.Rnd] | |
| negative_binomial_P [Stats.Cdf] | |
| negative_binomial_Q [Stats.Cdf] | |
| nnz [Sparse] | nnz x returns the number of non-zero elements in matrix x .
|
| nnz_cols [Sparse] | nnz_cols x returns the number of non-zero cols in matrix x .
|
| nnz_rows [Sparse] | nnz_rows x returns the number of non-zero rows in matrix x .
|
| nonlinear [Regression] |
Nonlinear regression:
nonlinear f p x y fits the measurements x and the
observations y into a user-defined nonlinear model.
|
| not_exists [Sparse] | not_exists f x checks all the elements in x , the function returns
true only if all the elements fail to satisfy f : float -> bool .
|
| not_exists [Dense] | not_exists f x checks all the elements in x , the function returns
true only if all the elements fail to satisfy f : float -> bool .
|
| not_exists_nz [Sparse] | not_exists_nz f x is similar to not_exists but only checks non-zero elements.
|
| numel [Sparse] | numel x returns the number of elements in matrix x .
|
| numel [Dense] | numel x returns the number of elements in matrix x .
|
O | |
| of_array [Dense] | of_array x m n converts a float array x into an m by n matrix.
|
| of_arrays [Dense] | of_arrays x converts an array of m float arrays (of length n ) in to
an m by n matrix.
|
| of_dense [Sparse] | of_dense x returns a sparse matrix from the dense matrix x .
|
| ols [Regression] |
Ordinary Least Square regression: in
ols ~i x y , i : whether or not to
include intercept bias in parameters, the default is true ; ; x is the
measurements, and y is the observations.
|
| ones [Sparse] | ones m n creates an m by n matrix where all the elements are ones.
|
| ones [Dense] | ones m n creates an m by n matrix where all the elements are ones.
|
P | |
| pareto [Stats.Pdf] | |
| pareto [Stats.Rnd] | |
| pareto_P [Stats.Cdf] | |
| pareto_Pinv [Stats.Cdf] | |
| pareto_Q [Stats.Cdf] | |
| pareto_Qinv [Stats.Cdf] | |
| pascal [Stats.Pdf] | |
| pascal [Stats.Rnd] | |
| pascal_P [Stats.Cdf] | |
| pascal_Q [Stats.Cdf] | |
| pearson_r [Stats] | |
| permutation_matrix [Sparse] | permutation_matrix m returns an m by m permutation matrix.
|
| plot [Plot] | |
| plot_fun [Plot] | |
| poch [Maths] | |
| pochrel [Maths] | |
| poisson [Stats.Pdf] | |
| poisson [Stats.Rnd] | |
| poisson_P [Stats.Cdf] | |
| poisson_Q [Stats.Cdf] | |
| polar_of_rect [Maths] | |
| polynomial [Regression] |
polynomial regression:
polynomial x y d fits the measurements x and the
observations y into a polynomial model.
|
| pow [Maths] | |
| power [Sparse] | power x a calculates the power of a of each element in x .
|
| power [Dense] | power x a calculates the power of a of each element in x .
|
| pp_dsmat [Dense] | pp_spmat x pretty prints matrix x with headings.
|
| pp_spmat [Sparse] | pp_spmat x pretty prints matrix x with headings.
|
| print [Sparse] | print x pretty prints matrix x without headings.
|
| print [Dense] | print x pretty prints matrix x without headings.
|
| psi [Maths] | |
| psi_1 [Maths] | |
| psi_1_pint [Maths] | |
| psi_1piy [Maths] | |
| psi_int [Maths] | |
| psi_n [Maths] | |
Q | |
| qr [Linalg] | qr x calculates QR decomposition for an m by n matrix x as
x = Q R .
|
| qr_lssolve [Linalg] | |
| qr_sqsolve [Linalg] | |
R | |
| rank [Stats] | rank x translates each element in x to its ranking.
|
| rayleigh [Stats.Pdf] | |
| rayleigh [Stats.Rnd] | |
| rayleigh_P [Stats.Cdf] | |
| rayleigh_Pinv [Stats.Cdf] | |
| rayleigh_Q [Stats.Cdf] | |
| rayleigh_Qinv [Stats.Cdf] | |
| rect_of_polar [Maths] | |
| replace_col [Dense] | replace_col v x j uses the column vector v to replace the j th column
in the matrix x .
|
| replace_row [Dense] | replace_row v x i uses the row vector v to replace the i th row in
the matrix x .
|
| reset [Sparse] | reset x resets all the elements in x to 0 .
|
| reshape [Dense] | reshape m n x creates a new m by n matrix from the m' by n'
matrix x .
|
| ridge [Regression] |
Ridge regression: in
ridge ~i ~a x y , i : whether or not to include
intercept bias in parameters, the default is true ; a : the weight on the
regularisation term; x is the measurements, and y is the observations.
|
| row [Sparse] | row x i returns the row i of x .
|
| row [Dense] | row x i returns the row i of x .
|
| row_num [Sparse] | row_num x returns the number of rows in matrix x .
|
| row_num [Dense] | row_num x returns the number of rows in matrix x .
|
| row_num_nz [Sparse] | row_num_nz x returns the number of non-zero rows in matrix x .
|
| rows [Sparse] | rows x a returns the rows (defined in an int array a ) of x .
|
| rows [Dense] | rows x a returns the rows (defined in an int array a ) of x .
|
S | |
| same_shape [Dense] | same_shape x y returns true if two matrics have the same shape.
|
| sample [Stats] | sample x n draw n samples from x with replacement.
|
| save [Sparse] | save x f saves the matrix x to a file with the name f .
|
| save [Dense] | save x f saves the matrix x to a file with the name f .
|
| save_txt [Dense] | save_txt x f save the matrix x into a text file f .
|
| scatter [Plot] | |
| sec [Maths] | |
| seed [Stats] | seed x sets x as seed for the internal random number generator.
|
| semidef [Dense] | semidef n returns an random n by n positive semi-definite matrix.
|
| sequential [Dense] | sequential m n creates an m by n matrix.
|
| set [Sparse] | set x i j a sets the element (i,j) of x to value a .
|
| set [Dense] | set x i j a sets the element (i,j) of x to value a .
|
| shape [Sparse] |
If
x is an m by n matrix, shape x returns (m,n) , i.e., the size
of two dimensions of x .
|
| shape [Dense] |
If
x is an m by n matrix, shape x returns (m,n) , i.e., the size
of two dimensions of x .
|
| shi [Maths] | |
| shuffle [Stats] | shuffle x return a new array of the shuffled x .
|
| shuffle [Sparse] | shuffle x shuffles all the elements in x by first shuffling along the
rows then shuffling along columns.
|
| shuffle [Dense] | shuffle x shuffles all the elements in x by first shuffling along the
rows then shuffling along columns.
|
| shuffle_cols [Sparse] | shuffle_cols x shuffles all the columns in matrix x .
|
| shuffle_cols [Dense] | shuffle_cols x shuffles all the columns in matrix x .
|
| shuffle_rows [Sparse] | shuffle_rows x shuffles all the rows in matrix x .
|
| shuffle_rows [Dense] | shuffle_rows x shuffles all the rows in matrix x .
|
| si [Maths] | |
| sigmoid [Dense] | sigmoid x applies sigmoid function to each element in matrix x .
|
| sin [Maths] | |
| sinc [Maths] | |
| sinh [Maths] | |
| skew [Stats] | |
| sort [Stats] | |
| spearman_rho [Stats] | |
| sqrt [Maths] | |
| std [Stats] | |
| sub [Sparse] | sub x y subtracts the matrix x from y .
|
| sub [Dense] | sub x y subtracts the matrix x from y .
|
| sub_scalar [Dense] | sub_scalar x a subtracts every element in x by a constant factor a .
|
| sum [Sparse] | sum x returns the summation of all the elements in x .
|
| sum [Dense] | sum x returns the summation of all the elements in x .
|
| sum_cols [Sparse] | sum_cols returns the summation of all the column vectors in x .
|
| sum_cols [Dense] | sum_cols returns the summation of all the column vectors in x .
|
| sum_rows [Sparse] | sum_rows x returns the summation of all the row vectors in x .
|
| sum_rows [Dense] | sum_rows x returns the summation of all the row vectors in x .
|
| svd [Linalg] | svd x calculates the singular value decomposition of x , and returns a
tuple (u,s,v) .
|
| svm [Regression] |
Support Vector Machine regression: in
svm ~i p x y , i : whether or not
to include intercept bias in parameters, the default is true ; p : the
initial guess of the model; x is the measurements, and y is the observations.
|
| symm_tridiag_solve [Linalg] | |
| symmtd [Linalg] | |
| synchrotron_1 [Maths] | |
| synchrotron_2 [Maths] | |
T | |
| tan [Maths] | |
| taylorcoeff [Maths] | |
| tdist [Stats.Pdf] | |
| tdist [Stats.Rnd] | |
| tdist_P [Stats.Cdf] | |
| tdist_Pinv [Stats.Cdf] | |
| tdist_Q [Stats.Cdf] | |
| tdist_Qinv [Stats.Cdf] | |
| to_array [Dense] | to_array x flattens an m by n matrix x then returns x as an
float array of length (numel x) .
|
| to_arrays [Dense] | to arrays x returns an array of float arrays, wherein each row in x
becomes an array in the result.
|
| to_dense [Sparse] | to_dense x converts x into a dense matrix.
|
| trace [Sparse] | trace x returns the sum of diagonal elements in x .
|
| trace [Dense] | trace x returns the sum of diagonal elements in x .
|
| transport_2 [Maths] | |
| transport_3 [Maths] | |
| transport_4 [Maths] | |
| transport_5 [Maths] | |
| transpose [Sparse] | transpose x transposes an m by n matrix to n by m one.
|
| transpose [Dense] | transpose x transposes an m by n matrix to n by m one.
|
| tridiag_solve [Linalg] | |
U | |
| uniform [Stats.Rnd] | uniform returns a random float number within [0,1) , including 0
but excluding 1.
|
| uniform [Sparse] | uniform m n creates an m by n matrix where 10% ~ 15% elements
follow a uniform distribution in (0,1) interval.
|
| uniform [Dense] | uniform m n creates an m by n matrix where all the elements
follow a uniform distribution in (0,1) interval.
|
| uniform_int [Stats.Rnd] | uniform_int a b returns a random int between a and b inclusive,
i.e., a random int in a, b
|
| uniform_int [Sparse] | uniform ~a ~b m n creates an m by n matrix where 10% ~ 15% elements
follow a uniform distribution in [a, b] interval.
|
| uniform_int [Dense] | uniform ~a ~b m n creates an m by n matrix where all the elements
follow a uniform distribution in [a, b] interval.
|
V | |
| variance [Stats] | |
| vector [Dense] | vector m returns an 1 by m row vector x without initialising the
values in x .
|
| vector_ones [Dense] | vector_ones m returns an 1 by m row vector x by initialising the
all values in x to ones.
|
| vector_uniform [Dense] | vector_zeros m returns an 1 by m row vector x and the values are
drawn from the interval (0,1) with a uniform distribution.
|
| vector_zeros [Dense] | vector_zeros m returns an 1 by m row vector x by initialising the
all values in x to zeros.
|
W | |
| weibull [Stats.Pdf] | |
| weibull [Stats.Rnd] | |
| weibull_P [Stats.Cdf] | |
| weibull_Pinv [Stats.Cdf] | |
| weibull_Q [Stats.Cdf] | |
| weibull_Qinv [Stats.Cdf] | |
Z | |
| zeros [Sparse] | zeros m n creates an m by n matrix where all the elements are zeros.
|
| zeros [Dense] | zeros m n creates an m by n matrix where all the elements are
initialised to zeros.
|
| zeta [Maths] | |
| zeta_int [Maths] |


11 Basic statistical analyses
Let us start by illustrating how to peform simple statistical data analyses using different resources. Here, we will use data from three studies that are available in our Opal demo repository. The three databases are called CNSIM1, CNSIM2, CNSIM3 and are available as three different resources: mySQL database, SPSS file and CSV file (see Figure 6.2). This example mimics real situations where different hospitals or research centers manage their own databases containing harmonized data. Data correspond to three simulated datasets with different numbers of observations of 11 harmonized variables. They contain synthetic data based on a model derived from the participants of the 1958 Birth Cohort, as part of an obesity methodological development project. This dataset does contain some NA values. The available variables are:
| Variable | Description | Type | Note |
|---|---|---|---|
| LAB_TSC | Total Serum Cholesterol | numeric | mmol/L |
| LAB_TRIG | Triglycerides | numeric | mmol/L |
| LAB_HDL | HDL Cholesterol | numeric | mmol/L |
| LAB_GLUC_ADJUSTED | Non-Fasting Glucose | numeric | mmol/L |
| PM_BMI_CONTINUOUS | Body Mass Index (continuous) | numeric | kg/m2 |
| DIS_CVA | History of Stroke | factor | 0 = Never had stroke; 1 = Has had stroke |
| MEDI_LPD | Current Use of Lipid Lowering Medication (from categorical assessment item) | factor | 0 = Not currently using lipid lowering medication; 1 = Currently using lipid lowering medication |
| DIS_DIAB | History of Diabetes | factor | 0 = Never had diabetes; 1 = Has had diabetes |
| DIS_AMI | History of Myocardial Infarction | factor | 0 = Never had myocardial infarction; 1 = Has had myocardial infarction |
| GENDER | Gender | factor | 0 = Female |
| PM_BMI_CATEGORICAL | Body Mass Index (categorical) | factor | 1 = Less than 25 kg/m2; 2 = 25 to 30 kg/m2; 3 = Over 30 kg/m2 |
The analyses that are described here, can also be found in the DataSHIELD Tutorial where these resources here uploaded to the Opal server as three tables, an inferior approach since data have to be moved from their original repositories.
11.1 Analysis from a single study
Let us start by illustrating how to analyze one data set (CNSIM2).
library(DSOpal)
library(dsBaseClient)
# prepare login data and resource to assign
builder <- DSI::newDSLoginBuilder()
builder$append(server = "study1", url = "https://opal-demo.obiba.org",
user = "dsuser", password = "password",
resource = "RSRC.CNSIM1", driver = "OpalDriver")
logindata <- builder$build()
# login and assign resource
conns <- DSI::datashield.login(logins = logindata, assign = TRUE,
symbol = "res")
# coerce ResourceClient objects to a data.frame called 'D'
datashield.assign.expr(conns, symbol = "D",
expr = quote(as.resource.data.frame(res, strict=TRUE)))
Then we can inspect the type of data we have
$study1
[1] "data.frame"
$study1
[1] "id" "LAB_TSC" "LAB_TRIG"
[4] "LAB_HDL" "LAB_GLUC_ADJUSTED" "PM_BMI_CONTINUOUS"
[7] "DIS_CVA" "MEDI_LPD" "DIS_DIAB"
[10] "DIS_AMI" "GENDER" "PM_BMI_CATEGORICAL"
Perform some data descriptive analyses
Data in all studies were valid
Study 1 : No errors reported from this study
$output.list
$output.list$TABLE_rvar.by.study_row.props
study
D$DIS_DIAB 1
0 1
1 1
$output.list$TABLE_rvar.by.study_col.props
study
D$DIS_DIAB 1
0 0.98613037
1 0.01386963
$output.list$TABLE_rvar.by.study_counts
study
D$DIS_DIAB 1
0 2133
1 30
$output.list$TABLES.COMBINED_all.sources_proportions
D$DIS_DIAB
0 1
0.9860 0.0139
$output.list$TABLES.COMBINED_all.sources_counts
D$DIS_DIAB
0 1
2133 30
$validity.message
[1] "Data in all studies were valid"
Data in all studies were valid
Study 1 : No errors reported from this study
$output.list
$output.list$TABLE.STUDY.1_row.props
D$GENDER
D$DIS_DIAB 0 1
0 0.502 0.498
1 0.700 0.300
$output.list$TABLE.STUDY.1_col.props
D$GENDER
D$DIS_DIAB 0 1
0 0.9810 0.9920
1 0.0192 0.0084
$output.list$TABLES.COMBINED_all.sources_row.props
D$GENDER
D$DIS_DIAB 0 1
0 0.502 0.498
1 0.700 0.300
$output.list$TABLES.COMBINED_all.sources_col.props
D$GENDER
D$DIS_DIAB 0 1
0 0.9810 0.9920
1 0.0192 0.0084
$output.list$TABLE_STUDY.1_counts
D$GENDER
D$DIS_DIAB 0 1
0 1071 1062
1 21 9
$output.list$TABLES.COMBINED_all.sources_counts
D$GENDER
D$DIS_DIAB 0 1
0 1071 1062
1 21 9
$validity.message
[1] "Data in all studies were valid"
Or even some statistical modelling. In this case we want to assess whether sex (GENDER) or trigrycerids (LAB_TRIG) are risk factors for diabetes (DIS_DIAB)
Estimate Std. Error z-value p-value low0.95CI.LP
(Intercept) -5.1696619 0.4549328 -11.363572 6.349427e-30 -6.0613138
LAB_TRIG 0.3813891 0.1037611 3.675647 2.372471e-04 0.1780211
GENDER -0.2260851 0.4375864 -0.516664 6.053908e-01 -1.0837387
high0.95CI.LP P_OR low0.95CI.P_OR high0.95CI.P_OR
(Intercept) -4.2780099 0.005654338 0.002325913 0.01368049
LAB_TRIG 0.5847570 1.464317247 1.194850574 1.79455494
GENDER 0.6315685 0.797650197 0.338328242 1.88055787
As usual the connection must be closed
11.2 Analysis from a multiple studies
Now, let us illustrate a similar analysis with multiple studies. In this case we see results aggregated across all three studies.
library(DSOpal)
library(dsBaseClient)
# prepare login data and resources to assign
builder <- DSI::newDSLoginBuilder()
builder$append(server = "study1", url = "https://opal-demo.obiba.org",
user = "dsuser", password = "password",
resource = "RSRC.CNSIM1", driver = "OpalDriver")
builder$append(server = "study2", url = "https://opal-demo.obiba.org",
user = "dsuser", password = "password",
resource = "RSRC.CNSIM2", driver = "OpalDriver")
builder$append(server = "study3", url = "https://opal-demo.obiba.org",
user = "dsuser", password = "password",
resource = "RSRC.CNSIM3", driver = "OpalDriver")
logindata <- builder$build()
# login and assign resources
conns <- datashield.login(logins = logindata, assign = TRUE, symbol = "res")
# assigned objects are of class ResourceClient (and others)
ds.class("res")
$study1
[1] "SQLResourceClient" "ResourceClient" "R6"
$study2
[1] "TidyFileResourceClient" "FileResourceClient" "ResourceClient"
[4] "R6"
$study3
[1] "TidyFileResourceClient" "FileResourceClient" "ResourceClient"
[4] "R6"
# coerce ResourceClient objects to data.frames
# (DataSHIELD config allows as.resource.data.frame() assignment function for the purpose of the demo)
datashield.assign.expr(conns, symbol = "D",
expr = quote(as.resource.data.frame(res, strict = TRUE)))
ds.class("D")
$study1
[1] "data.frame"
$study2
[1] "data.frame"
$study3
[1] "data.frame"
$study1
$study1$class
[1] "numeric"
$study1$length
[1] 2163
$study1$`quantiles & mean`
5% 10% 25% 50% 75% 90% 95% Mean
0.875240 1.047400 1.300000 1.581000 1.844500 2.090000 2.210900 1.569416
$study2
$study2$class
[1] "numeric"
$study2$length
[1] 3088
$study2$`quantiles & mean`
5% 10% 25% 50% 75% 90% 95% Mean
0.850280 1.032200 1.294000 1.563000 1.840000 2.077000 2.225000 1.556648
$study3
$study3$class
[1] "numeric"
$study3$length
[1] 4128
$study3$`quantiles & mean`
5% 10% 25% 50% 75% 90% 95% Mean
0.876760 1.039200 1.304000 1.589000 1.856000 2.098800 2.244200 1.574687
# vector types are not necessarily the same depending on the data reader that was used
ds.class('D$GENDER')
$study1
[1] "integer"
$study2
[1] "haven_labelled" "vctrs_vctr" "double"
$study3
[1] "numeric"
$all.unique.levels
[1] "0" "1"
$return.message
[1] "Data object <GENDER> correctly created in all specified data sources"
$study1
$study1$class
[1] "factor"
$study1$length
[1] 2163
$study1$categories
[1] "0" "1"
$study1$`count of '0'`
[1] 1092
$study1$`count of '1'`
[1] 1071
$study2
$study2$class
[1] "factor"
$study2$length
[1] 3088
$study2$categories
[1] "0" "1"
$study2$`count of '0'`
[1] 1585
$study2$`count of '1'`
[1] 1503
$study3
$study3$class
[1] "factor"
$study3$length
[1] 4128
$study3$categories
[1] "0" "1"
$study3$`count of '0'`
[1] 2091
$study3$`count of '1'`
[1] 2037
Estimate Std. Error z-value p-value low0.95CI.LP
(Intercept) -4.7792110 0.21081170 -22.670521 8.755236e-114 -5.1923944
LAB_TRIG 0.3035931 0.05487436 5.532514 3.156737e-08 0.1960414
GENDER -0.4455989 0.20797931 -2.142516 3.215202e-02 -0.8532309
high0.95CI.LP P_OR low0.95CI.P_OR high0.95CI.P_OR
(Intercept) -4.36602770 0.00833261 0.005527953 0.01254229
LAB_TRIG 0.41114488 1.35471774 1.216577226 1.50854390
GENDER -0.03796695 0.64044060 0.426036242 0.96274475


2023/05/15
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We have 2 papers accepted by ACMMM 2022 !2022/04/18
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2018/06/18
2017/10/22


Class: Aws::WAFV2::Types::FieldToMatch
| Relationships & Source Files | |
| Super Chains via Extension / Inclusion / Inheritance | |
|
Class Chain:
self,
Struct
|
|
|
Instance Chain:
self,
::Aws::Structure ,
Struct
|
|
| Inherits: |
Struct
|
| Defined in: | gems/aws-sdk-wafv2/lib/aws-sdk-wafv2/types.rb |
Overview
The part of the web request that you want ::Aws::WAF
to inspect. Include the
single FieldToMatch
type that you want to inspect, with additional
specifications as needed, according to the type. You specify a single
request component in FieldToMatch
for each rule statement that
requires it. To inspect more than one component of the web request,
create a separate rule statement for each component.
Example JSON for a QueryString
field to match:
"FieldToMatch": \{ "QueryString": \{\} \}
Example JSON for a Method
field to match specification:
"FieldToMatch": \{ "Method": \{ "Name": "DELETE" \} \}
Constant Summary
Instance Attribute Summary
-
#all_query_arguments ⇒ Types::AllQueryArguments
rw
Inspect all query arguments.
-
#body ⇒ Types::Body
rw
Inspect the request body as plain text.
-
#cookies ⇒ Types::Cookies
rw
Inspect the request cookies.
-
#header_order ⇒ Types::HeaderOrder
rw
Inspect a string containing the list of the request's header names, ordered as they appear in the web request that
::Aws::WAF
receives for inspection. -
#headers ⇒ Types::Headers
rw
Inspect the request headers.
-
#json_body ⇒ Types::JsonBody
rw
Inspect the request body as JSON.
-
#method ⇒ Types::Method
rw
Inspect the HTTP method.
-
#query_string ⇒ Types::QueryString
rw
Inspect the query string.
-
#single_header ⇒ Types::SingleHeader
rw
Inspect a single header.
-
#single_query_argument ⇒ Types::SingleQueryArgument
rw
Inspect a single query argument.
-
#uri_path ⇒ Types::UriPath
rw
Inspect the request URI path.
Instance Method Summary
::Aws::Structure
- Included
| #to_hash | Alias for Structure#to_h. |
Instance Attribute Details
#all_query_arguments ⇒ Types::AllQueryArguments (rw)
Inspect all query arguments.
# File 'gems/aws-sdk-wafv2/lib/aws-sdk-wafv2/types.rb', line 2364
class FieldToMatch < Struct.new( :single_header, :single_query_argument, :all_query_arguments, :uri_path, :query_string, :body, :method, :json_body, :headers, :, :header_order) SENSITIVE = [] include Aws::Structure end
#body ⇒ Types::Body (rw)
Inspect the request body as plain text. The request body immediately follows the request headers. This is the part of a request that contains any additional data that you want to send to your web server as the HTTP request body, such as data from a form.
A limited amount of the request body is forwarded to ::Aws::WAF
for
inspection by the underlying host service. For regional resources,
the limit is 8 KB (8,192 kilobytes) and for ::Aws::CloudFront
distributions, the limit is 16 KB (16,384 kilobytes). For CloudFront
distributions, you can increase the limit in the web ACL's
AssociationConfig
, for additional processing fees.
For information about how to handle oversized request bodies, see
the Body
object configuration.
# File 'gems/aws-sdk-wafv2/lib/aws-sdk-wafv2/types.rb', line 2364
class FieldToMatch < Struct.new( :single_header, :single_query_argument, :all_query_arguments, :uri_path, :query_string, :body, :method, :json_body, :headers, :, :header_order) SENSITIVE = [] include Aws::Structure end
#cookies ⇒ Types::Cookies (rw)
Inspect the request cookies. You must configure scope and pattern
matching filters in the Cookies
object, to define the set of
cookies and the parts of the cookies that ::Aws::WAF
inspects.
Only the first 8 KB (8192 bytes) of a request's cookies and only
the first 200 cookies are forwarded to ::Aws::WAF
for inspection by the
underlying host service. You must configure how to handle any
oversize cookie content in the Cookies
object. ::Aws::WAF
applies the
pattern matching filters to the cookies that it receives from the
underlying host service.
# File 'gems/aws-sdk-wafv2/lib/aws-sdk-wafv2/types.rb', line 2364
class FieldToMatch < Struct.new( :single_header, :single_query_argument, :all_query_arguments, :uri_path, :query_string, :body, :method, :json_body, :headers, :, :header_order) SENSITIVE = [] include Aws::Structure end
#header_order ⇒ Types::HeaderOrder (rw)
Inspect a string containing the list of the request's header names,
ordered as they appear in the web request that ::Aws::WAF
receives for
inspection. ::Aws::WAF
generates the string and then uses that as the field
to match component in its inspection. ::Aws::WAF
separates the header names
in the string using colons and no added spaces, for example
host:user-agent:accept:authorization:referer
.
# File 'gems/aws-sdk-wafv2/lib/aws-sdk-wafv2/types.rb', line 2364
class FieldToMatch < Struct.new( :single_header, :single_query_argument, :all_query_arguments, :uri_path, :query_string, :body, :method, :json_body, :headers, :, :header_order) SENSITIVE = [] include Aws::Structure end
#headers ⇒ Types::Headers (rw)
Inspect the request headers. You must configure scope and pattern
matching filters in the Headers
object, to define the set of
headers to and the parts of the headers that ::Aws::WAF
inspects.
Only the first 8 KB (8192 bytes) of a request's headers and only
the first 200 headers are forwarded to ::Aws::WAF
for inspection by the
underlying host service. You must configure how to handle any
oversize header content in the Headers
object. ::Aws::WAF
applies the
pattern matching filters to the headers that it receives from the
underlying host service.
# File 'gems/aws-sdk-wafv2/lib/aws-sdk-wafv2/types.rb', line 2364
class FieldToMatch < Struct.new( :single_header, :single_query_argument, :all_query_arguments, :uri_path, :query_string, :body, :method, :json_body, :headers, :, :header_order) SENSITIVE = [] include Aws::Structure end
#json_body ⇒ Types::JsonBody (rw)
Inspect the request body as JSON. The request body immediately follows the request headers. This is the part of a request that contains any additional data that you want to send to your web server as the HTTP request body, such as data from a form.
A limited amount of the request body is forwarded to ::Aws::WAF
for
inspection by the underlying host service. For regional resources,
the limit is 8 KB (8,192 kilobytes) and for ::Aws::CloudFront
distributions, the limit is 16 KB (16,384 kilobytes). For CloudFront
distributions, you can increase the limit in the web ACL's
AssociationConfig
, for additional processing fees.
For information about how to handle oversized request bodies, see
the JsonBody
object configuration.
# File 'gems/aws-sdk-wafv2/lib/aws-sdk-wafv2/types.rb', line 2364
class FieldToMatch < Struct.new( :single_header, :single_query_argument, :all_query_arguments, :uri_path, :query_string, :body, :method, :json_body, :headers, :, :header_order) SENSITIVE = [] include Aws::Structure end
#method ⇒ Types::Method (rw)
Inspect the HTTP method. The method indicates the type of operation that the request is asking the origin to perform.
# File 'gems/aws-sdk-wafv2/lib/aws-sdk-wafv2/types.rb', line 2364
class FieldToMatch < Struct.new( :single_header, :single_query_argument, :all_query_arguments, :uri_path, :query_string, :body, :method, :json_body, :headers, :, :header_order) SENSITIVE = [] include Aws::Structure end
#query_string ⇒ Types::QueryString (rw)
Inspect the query string. This is the part of a URL that appears
after a ?
character, if any.
# File 'gems/aws-sdk-wafv2/lib/aws-sdk-wafv2/types.rb', line 2364
class FieldToMatch < Struct.new( :single_header, :single_query_argument, :all_query_arguments, :uri_path, :query_string, :body, :method, :json_body, :headers, :, :header_order) SENSITIVE = [] include Aws::Structure end
#single_header ⇒ Types::SingleHeader (rw)
Inspect a single header. Provide the name of the header to inspect,
for example, User-Agent
or Referer
. This setting isn't case
sensitive.
Example JSON: "SingleHeader": \{ "Name": "haystack" \}
Alternately, you can filter and inspect all headers with the
Headers
FieldToMatch
setting.
# File 'gems/aws-sdk-wafv2/lib/aws-sdk-wafv2/types.rb', line 2364
class FieldToMatch < Struct.new( :single_header, :single_query_argument, :all_query_arguments, :uri_path, :query_string, :body, :method, :json_body, :headers, :, :header_order) SENSITIVE = [] include Aws::Structure end
#single_query_argument ⇒ Types::SingleQueryArgument (rw)
Inspect a single query argument. Provide the name of the query argument to inspect, such as UserName or SalesRegion. The name can be up to 30 characters long and isn't case sensitive.
Example JSON: "SingleQueryArgument": \{ "Name": "myArgument" \}
# File 'gems/aws-sdk-wafv2/lib/aws-sdk-wafv2/types.rb', line 2364
class FieldToMatch < Struct.new( :single_header, :single_query_argument, :all_query_arguments, :uri_path, :query_string, :body, :method, :json_body, :headers, :, :header_order) SENSITIVE = [] include Aws::Structure end
#uri_path ⇒ Types::UriPath (rw)
Inspect the request URI path. This is the part of the web request
that identifies a resource, for example, /images/daily-ad.jpg
.
# File 'gems/aws-sdk-wafv2/lib/aws-sdk-wafv2/types.rb', line 2364
class FieldToMatch < Struct.new( :single_header, :single_query_argument, :all_query_arguments, :uri_path, :query_string, :body, :method, :json_body, :headers, :, :header_order) SENSITIVE = [] include Aws::Structure end


Purchases is the client SDK for RevenueCat.
com.revenuecat.purchases
Package that contains all the SDK classes.
com.revenuecat.purchases.interfaces


{% extends 'account/login_base.html' %} {% load staticfiles %} {% block page-content %}
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TIFF CHANGE INFORMATION
This document describes the changes made to the software between the
previous and current versions (see above).
If you don't find something listed here, then it was not done in this
timeframe, or it was not considered important enough to be mentioned.
The following information is located here:
CHANGES IN THE SOFTWARE CONFIGURATION:
- support was added installing the HTML documentation
- support was added for building the library as a DSO under FreeBSD
CHANGES IN LIBTIFF:
- the interface to the mkversion program was restored to
the form used prior to v3.4beta034
- several portability problems for 16-bit systems were fixed
TIFF home page.
Sam Leffler /<EMAIL_ADDRESS>Last updated $Date: 2016-09-25 20:05:45 $.