Initial commit
This commit is contained in:
commit
e398e85416
8
.gitignore
vendored
Normal file
8
.gitignore
vendored
Normal file
@ -0,0 +1,8 @@
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|||||||
|
.idea/
|
||||||
|
*.iws
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||||||
|
out/
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||||||
|
.gradle
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||||||
|
build/
|
||||||
|
|
||||||
|
|
||||||
|
!gradle-wrapper.jar
|
39
build.gradle.kts
Normal file
39
build.gradle.kts
Normal file
@ -0,0 +1,39 @@
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|||||||
|
import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
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|
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|
plugins {
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|
kotlin("jvm") version "1.4.10"
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|
application
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|
}
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|
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|
group = "ru.mipt.npm"
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|
version = "1.0-SNAPSHOT"
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||||||
|
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||||||
|
repositories {
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|
jcenter()
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|
mavenCentral()
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}
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|
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|
dependencies {
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|
implementation("kscience.plotlykt:plotlykt-server:0.2.0") {
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exclude(module = "kotlinx-io")
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|
}
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|
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|
implementation("org.apache.commons:commons-math3:3.6.1")
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|
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|
testImplementation(kotlin("test-junit5"))
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|
testImplementation("org.junit.jupiter:junit-jupiter-api:5.6.0")
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|
testRuntimeOnly("org.junit.jupiter:junit-jupiter-engine:5.6.0")
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|
}
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|
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|
tasks.test {
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|
useJUnitPlatform()
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|
}
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|
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|
tasks.withType<KotlinCompile>() {
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|
kotlinOptions.jvmTarget = "11"
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|
}
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|
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|
application {
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|
mainClassName = "ru.mipt.npm.sim.epidemics.MainKt"
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|
}
|
1
gradle.properties
Normal file
1
gradle.properties
Normal file
@ -0,0 +1 @@
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|
kotlin.code.style=official
|
BIN
gradle/wrapper/gradle-wrapper.jar
vendored
Normal file
BIN
gradle/wrapper/gradle-wrapper.jar
vendored
Normal file
Binary file not shown.
5
gradle/wrapper/gradle-wrapper.properties
vendored
Normal file
5
gradle/wrapper/gradle-wrapper.properties
vendored
Normal file
@ -0,0 +1,5 @@
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|||||||
|
distributionBase=GRADLE_USER_HOME
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|
distributionPath=wrapper/dists
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|
distributionUrl=https\://services.gradle.org/distributions/gradle-6.3-bin.zip
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||||||
|
zipStoreBase=GRADLE_USER_HOME
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|
zipStorePath=wrapper/dists
|
183
gradlew
vendored
Normal file
183
gradlew
vendored
Normal file
@ -0,0 +1,183 @@
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|||||||
|
#!/usr/bin/env sh
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|
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|
#
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|
# Copyright 2015 the original author or authors.
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|
#
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|
# Licensed under the Apache License, Version 2.0 (the "License");
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|
# you may not use this file except in compliance with the License.
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||||||
|
# You may obtain a copy of the License at
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||||||
|
#
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|
# https://www.apache.org/licenses/LICENSE-2.0
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||||||
|
#
|
||||||
|
# Unless required by applicable law or agreed to in writing, software
|
||||||
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
# See the License for the specific language governing permissions and
|
||||||
|
# limitations under the License.
|
||||||
|
#
|
||||||
|
|
||||||
|
##############################################################################
|
||||||
|
##
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|
## Gradle start up script for UN*X
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||||||
|
##
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||||||
|
##############################################################################
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||||||
|
|
||||||
|
# Attempt to set APP_HOME
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|
# Resolve links: $0 may be a link
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|
PRG="$0"
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|
# Need this for relative symlinks.
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|
while [ -h "$PRG" ] ; do
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|
ls=`ls -ld "$PRG"`
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|
link=`expr "$ls" : '.*-> \(.*\)$'`
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|
if expr "$link" : '/.*' > /dev/null; then
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|
PRG="$link"
|
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|
else
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|
PRG=`dirname "$PRG"`"/$link"
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|
fi
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|
done
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|
SAVED="`pwd`"
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|
cd "`dirname \"$PRG\"`/" >/dev/null
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|
APP_HOME="`pwd -P`"
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|
cd "$SAVED" >/dev/null
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|
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||||||
|
APP_NAME="Gradle"
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|
APP_BASE_NAME=`basename "$0"`
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|
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||||||
|
# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
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|
DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
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|
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|
# Use the maximum available, or set MAX_FD != -1 to use that value.
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|
MAX_FD="maximum"
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|
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|
warn () {
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|
echo "$*"
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||||||
|
}
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|
|
||||||
|
die () {
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|
echo
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||||||
|
echo "$*"
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||||||
|
echo
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|
exit 1
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|
}
|
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|
|
||||||
|
# OS specific support (must be 'true' or 'false').
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|
cygwin=false
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|
msys=false
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|
darwin=false
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|
nonstop=false
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|
case "`uname`" in
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|
CYGWIN* )
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|
cygwin=true
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|
;;
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|
Darwin* )
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|
darwin=true
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|
;;
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|
MINGW* )
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|
msys=true
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|
;;
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|
NONSTOP* )
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|
nonstop=true
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|
;;
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|
esac
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||||||
|
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||||||
|
CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
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||||||
|
|
||||||
|
# Determine the Java command to use to start the JVM.
|
||||||
|
if [ -n "$JAVA_HOME" ] ; then
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|
if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
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||||||
|
# IBM's JDK on AIX uses strange locations for the executables
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||||||
|
JAVACMD="$JAVA_HOME/jre/sh/java"
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||||||
|
else
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|
JAVACMD="$JAVA_HOME/bin/java"
|
||||||
|
fi
|
||||||
|
if [ ! -x "$JAVACMD" ] ; then
|
||||||
|
die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
|
||||||
|
|
||||||
|
Please set the JAVA_HOME variable in your environment to match the
|
||||||
|
location of your Java installation."
|
||||||
|
fi
|
||||||
|
else
|
||||||
|
JAVACMD="java"
|
||||||
|
which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
|
||||||
|
|
||||||
|
Please set the JAVA_HOME variable in your environment to match the
|
||||||
|
location of your Java installation."
|
||||||
|
fi
|
||||||
|
|
||||||
|
# Increase the maximum file descriptors if we can.
|
||||||
|
if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
|
||||||
|
MAX_FD_LIMIT=`ulimit -H -n`
|
||||||
|
if [ $? -eq 0 ] ; then
|
||||||
|
if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
|
||||||
|
MAX_FD="$MAX_FD_LIMIT"
|
||||||
|
fi
|
||||||
|
ulimit -n $MAX_FD
|
||||||
|
if [ $? -ne 0 ] ; then
|
||||||
|
warn "Could not set maximum file descriptor limit: $MAX_FD"
|
||||||
|
fi
|
||||||
|
else
|
||||||
|
warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
|
||||||
|
fi
|
||||||
|
fi
|
||||||
|
|
||||||
|
# For Darwin, add options to specify how the application appears in the dock
|
||||||
|
if $darwin; then
|
||||||
|
GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
|
||||||
|
fi
|
||||||
|
|
||||||
|
# For Cygwin or MSYS, switch paths to Windows format before running java
|
||||||
|
if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
|
||||||
|
APP_HOME=`cygpath --path --mixed "$APP_HOME"`
|
||||||
|
CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
|
||||||
|
JAVACMD=`cygpath --unix "$JAVACMD"`
|
||||||
|
|
||||||
|
# We build the pattern for arguments to be converted via cygpath
|
||||||
|
ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
|
||||||
|
SEP=""
|
||||||
|
for dir in $ROOTDIRSRAW ; do
|
||||||
|
ROOTDIRS="$ROOTDIRS$SEP$dir"
|
||||||
|
SEP="|"
|
||||||
|
done
|
||||||
|
OURCYGPATTERN="(^($ROOTDIRS))"
|
||||||
|
# Add a user-defined pattern to the cygpath arguments
|
||||||
|
if [ "$GRADLE_CYGPATTERN" != "" ] ; then
|
||||||
|
OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
|
||||||
|
fi
|
||||||
|
# Now convert the arguments - kludge to limit ourselves to /bin/sh
|
||||||
|
i=0
|
||||||
|
for arg in "$@" ; do
|
||||||
|
CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
|
||||||
|
CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
|
||||||
|
|
||||||
|
if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
|
||||||
|
eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
|
||||||
|
else
|
||||||
|
eval `echo args$i`="\"$arg\""
|
||||||
|
fi
|
||||||
|
i=`expr $i + 1`
|
||||||
|
done
|
||||||
|
case $i in
|
||||||
|
0) set -- ;;
|
||||||
|
1) set -- "$args0" ;;
|
||||||
|
2) set -- "$args0" "$args1" ;;
|
||||||
|
3) set -- "$args0" "$args1" "$args2" ;;
|
||||||
|
4) set -- "$args0" "$args1" "$args2" "$args3" ;;
|
||||||
|
5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
|
||||||
|
6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
|
||||||
|
7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
|
||||||
|
8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
|
||||||
|
9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
|
||||||
|
esac
|
||||||
|
fi
|
||||||
|
|
||||||
|
# Escape application args
|
||||||
|
save () {
|
||||||
|
for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
|
||||||
|
echo " "
|
||||||
|
}
|
||||||
|
APP_ARGS=`save "$@"`
|
||||||
|
|
||||||
|
# Collect all arguments for the java command, following the shell quoting and substitution rules
|
||||||
|
eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
|
||||||
|
|
||||||
|
exec "$JAVACMD" "$@"
|
103
gradlew.bat
vendored
Normal file
103
gradlew.bat
vendored
Normal file
@ -0,0 +1,103 @@
|
|||||||
|
@rem
|
||||||
|
@rem Copyright 2015 the original author or authors.
|
||||||
|
@rem
|
||||||
|
@rem Licensed under the Apache License, Version 2.0 (the "License");
|
||||||
|
@rem you may not use this file except in compliance with the License.
|
||||||
|
@rem You may obtain a copy of the License at
|
||||||
|
@rem
|
||||||
|
@rem https://www.apache.org/licenses/LICENSE-2.0
|
||||||
|
@rem
|
||||||
|
@rem Unless required by applicable law or agreed to in writing, software
|
||||||
|
@rem distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
@rem See the License for the specific language governing permissions and
|
||||||
|
@rem limitations under the License.
|
||||||
|
@rem
|
||||||
|
|
||||||
|
@if "%DEBUG%" == "" @echo off
|
||||||
|
@rem ##########################################################################
|
||||||
|
@rem
|
||||||
|
@rem Gradle startup script for Windows
|
||||||
|
@rem
|
||||||
|
@rem ##########################################################################
|
||||||
|
|
||||||
|
@rem Set local scope for the variables with windows NT shell
|
||||||
|
if "%OS%"=="Windows_NT" setlocal
|
||||||
|
|
||||||
|
set DIRNAME=%~dp0
|
||||||
|
if "%DIRNAME%" == "" set DIRNAME=.
|
||||||
|
set APP_BASE_NAME=%~n0
|
||||||
|
set APP_HOME=%DIRNAME%
|
||||||
|
|
||||||
|
@rem Resolve any "." and ".." in APP_HOME to make it shorter.
|
||||||
|
for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
|
||||||
|
|
||||||
|
@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
|
||||||
|
set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
|
||||||
|
|
||||||
|
@rem Find java.exe
|
||||||
|
if defined JAVA_HOME goto findJavaFromJavaHome
|
||||||
|
|
||||||
|
set JAVA_EXE=java.exe
|
||||||
|
%JAVA_EXE% -version >NUL 2>&1
|
||||||
|
if "%ERRORLEVEL%" == "0" goto init
|
||||||
|
|
||||||
|
echo.
|
||||||
|
echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
|
||||||
|
echo.
|
||||||
|
echo Please set the JAVA_HOME variable in your environment to match the
|
||||||
|
echo location of your Java installation.
|
||||||
|
|
||||||
|
goto fail
|
||||||
|
|
||||||
|
:findJavaFromJavaHome
|
||||||
|
set JAVA_HOME=%JAVA_HOME:"=%
|
||||||
|
set JAVA_EXE=%JAVA_HOME%/bin/java.exe
|
||||||
|
|
||||||
|
if exist "%JAVA_EXE%" goto init
|
||||||
|
|
||||||
|
echo.
|
||||||
|
echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
|
||||||
|
echo.
|
||||||
|
echo Please set the JAVA_HOME variable in your environment to match the
|
||||||
|
echo location of your Java installation.
|
||||||
|
|
||||||
|
goto fail
|
||||||
|
|
||||||
|
:init
|
||||||
|
@rem Get command-line arguments, handling Windows variants
|
||||||
|
|
||||||
|
if not "%OS%" == "Windows_NT" goto win9xME_args
|
||||||
|
|
||||||
|
:win9xME_args
|
||||||
|
@rem Slurp the command line arguments.
|
||||||
|
set CMD_LINE_ARGS=
|
||||||
|
set _SKIP=2
|
||||||
|
|
||||||
|
:win9xME_args_slurp
|
||||||
|
if "x%~1" == "x" goto execute
|
||||||
|
|
||||||
|
set CMD_LINE_ARGS=%*
|
||||||
|
|
||||||
|
:execute
|
||||||
|
@rem Setup the command line
|
||||||
|
|
||||||
|
set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
|
||||||
|
|
||||||
|
@rem Execute Gradle
|
||||||
|
"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
|
||||||
|
|
||||||
|
:end
|
||||||
|
@rem End local scope for the variables with windows NT shell
|
||||||
|
if "%ERRORLEVEL%"=="0" goto mainEnd
|
||||||
|
|
||||||
|
:fail
|
||||||
|
rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
|
||||||
|
rem the _cmd.exe /c_ return code!
|
||||||
|
if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
|
||||||
|
exit /b 1
|
||||||
|
|
||||||
|
:mainEnd
|
||||||
|
if "%OS%"=="Windows_NT" endlocal
|
||||||
|
|
||||||
|
:omega
|
3
settings.gradle.kts
Normal file
3
settings.gradle.kts
Normal file
@ -0,0 +1,3 @@
|
|||||||
|
|
||||||
|
rootProject.name = "epidemics-sim"
|
||||||
|
|
34
src/main/kotlin/ru/mipt/npm/sim/epidemics/Behavior.kt
Normal file
34
src/main/kotlin/ru/mipt/npm/sim/epidemics/Behavior.kt
Normal file
@ -0,0 +1,34 @@
|
|||||||
|
package ru.mipt.npm.sim.epidemics
|
||||||
|
|
||||||
|
import org.apache.commons.math3.random.RandomGenerator
|
||||||
|
|
||||||
|
interface Behavior {
|
||||||
|
/**
|
||||||
|
* Generate daily contact for given [subject]
|
||||||
|
*/
|
||||||
|
fun generateDailyContacts(generator: RandomGenerator, subject: Subject, date: Int): List<Int>
|
||||||
|
}
|
||||||
|
|
||||||
|
object DefaultBehavior : Behavior {
|
||||||
|
|
||||||
|
@OptIn(ExperimentalStdlibApi::class)
|
||||||
|
override fun generateDailyContacts(
|
||||||
|
generator: RandomGenerator,
|
||||||
|
subject: Subject,
|
||||||
|
date: Int
|
||||||
|
): List<Int> = buildList {
|
||||||
|
subject.closeContacts.forEach { contact ->
|
||||||
|
if (generator.nextDouble() < 0.5) {
|
||||||
|
add(contact)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
subject.otherContacts.forEach { contact ->
|
||||||
|
if (generator.nextDouble() < 0.1) {
|
||||||
|
add(contact)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -0,0 +1,98 @@
|
|||||||
|
package ru.mipt.npm.sim.epidemics
|
||||||
|
|
||||||
|
import org.apache.commons.math3.random.JDKRandomGenerator
|
||||||
|
import org.apache.commons.math3.random.RandomGenerator
|
||||||
|
|
||||||
|
typealias Population = Map<Int, SubjectState>
|
||||||
|
|
||||||
|
|
||||||
|
interface EpidemicsModel {
|
||||||
|
fun generatePopulation(generator: RandomGenerator, size: Int = 1000): Population
|
||||||
|
fun propagateSubjectState(generator: RandomGenerator, subjectState: SubjectState, date: Int): SubjectState
|
||||||
|
fun propagate(generator: RandomGenerator, population: Population, date: Int): Population
|
||||||
|
}
|
||||||
|
|
||||||
|
//TODO add model parametrization
|
||||||
|
object DefaultEpidemicsModel : EpidemicsModel {
|
||||||
|
|
||||||
|
override fun generatePopulation(generator: RandomGenerator, size: Int): Population {
|
||||||
|
//TODO add custom distributions
|
||||||
|
return generatePopulation(generator, size, 3, 10)
|
||||||
|
}
|
||||||
|
|
||||||
|
@OptIn(ExperimentalStdlibApi::class)
|
||||||
|
fun generatePopulation(
|
||||||
|
generator: RandomGenerator,
|
||||||
|
size: Int,
|
||||||
|
closeContactsNum: Int,
|
||||||
|
otherContactsNum: Int
|
||||||
|
): Population {
|
||||||
|
return (0 until size).associateWith { subjectId ->
|
||||||
|
val closeContacts = buildList<Int> {
|
||||||
|
repeat(closeContactsNum) {
|
||||||
|
val id = generator.nextInt(size)
|
||||||
|
if (id != subjectId) {
|
||||||
|
add(id)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
val otherContacts = buildList<Int> {
|
||||||
|
repeat(otherContactsNum) {
|
||||||
|
val id = generator.nextInt(size)
|
||||||
|
if (id != subjectId) {
|
||||||
|
add(id)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
val subject = Subject(subjectId, closeContacts, otherContacts)
|
||||||
|
return@associateWith SubjectState(subject)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
override fun propagateSubjectState(generator: RandomGenerator, subjectState: SubjectState, date: Int): SubjectState {
|
||||||
|
when (subjectState.state) {
|
||||||
|
InfectionState.SUSCEPTIBLE, InfectionState.RECOVERED -> {
|
||||||
|
//do nothing
|
||||||
|
}
|
||||||
|
InfectionState.EXPOSED -> {
|
||||||
|
//TODO add custom distributions
|
||||||
|
if (date - subjectState.exposedDate!! >= 3) {
|
||||||
|
subjectState.infect(date)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
InfectionState.INFECTIOUS -> {
|
||||||
|
if (generator.nextDouble() < 0.1) {
|
||||||
|
subjectState.recover(date)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return subjectState
|
||||||
|
}
|
||||||
|
|
||||||
|
val behavior = DefaultBehavior
|
||||||
|
|
||||||
|
override fun propagate(generator: RandomGenerator, population: Population, date: Int): Population {
|
||||||
|
//TODO check population health and change behavior
|
||||||
|
population.values.forEach {
|
||||||
|
propagateSubjectState(generator, it, date)
|
||||||
|
}
|
||||||
|
population.forEach { (_, subj) ->
|
||||||
|
val contacts: List<Int> = behavior.generateDailyContacts(generator, subj.subject, date)
|
||||||
|
contacts.forEach { contactId ->
|
||||||
|
val otherContact = population[contactId]
|
||||||
|
?: error("Undefined subject with id $contactId")
|
||||||
|
|
||||||
|
if (subj.state == InfectionState.INFECTIOUS && generator.nextDouble() < 0.25) {
|
||||||
|
otherContact.expose(date)
|
||||||
|
}
|
||||||
|
|
||||||
|
if (otherContact.state == InfectionState.INFECTIOUS && generator.nextDouble() < 0.25) {
|
||||||
|
subj.expose(date)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return population
|
||||||
|
}
|
||||||
|
}
|
51
src/main/kotlin/ru/mipt/npm/sim/epidemics/Subject.kt
Normal file
51
src/main/kotlin/ru/mipt/npm/sim/epidemics/Subject.kt
Normal file
@ -0,0 +1,51 @@
|
|||||||
|
package ru.mipt.npm.sim.epidemics
|
||||||
|
|
||||||
|
enum class InfectionState {
|
||||||
|
SUSCEPTIBLE,
|
||||||
|
EXPOSED,
|
||||||
|
INFECTIOUS,
|
||||||
|
RECOVERED
|
||||||
|
}
|
||||||
|
|
||||||
|
class Subject(
|
||||||
|
val id: Int,
|
||||||
|
val closeContacts: List<Int>,
|
||||||
|
val otherContacts: List<Int>
|
||||||
|
)
|
||||||
|
|
||||||
|
class SubjectState(
|
||||||
|
val subject: Subject
|
||||||
|
) {
|
||||||
|
var state: InfectionState = InfectionState.SUSCEPTIBLE
|
||||||
|
private set
|
||||||
|
|
||||||
|
var exposedDate: Int? = null
|
||||||
|
private set
|
||||||
|
|
||||||
|
var infectedDate: Int? = null
|
||||||
|
private set
|
||||||
|
|
||||||
|
var recoveryDate: Int? = null
|
||||||
|
private set
|
||||||
|
|
||||||
|
|
||||||
|
fun expose(date: Int) {
|
||||||
|
if (state == InfectionState.SUSCEPTIBLE) {
|
||||||
|
state = InfectionState.EXPOSED
|
||||||
|
exposedDate = date
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
fun infect(date: Int) {
|
||||||
|
if (state != InfectionState.EXPOSED) error("Expected 'EXPOSED' state")
|
||||||
|
state = InfectionState.INFECTIOUS
|
||||||
|
infectedDate = date
|
||||||
|
}
|
||||||
|
|
||||||
|
fun recover(date: Int) {
|
||||||
|
if (state != InfectionState.INFECTIOUS) error("Expected 'EXPOSED' state")
|
||||||
|
state = InfectionState.RECOVERED
|
||||||
|
recoveryDate = date
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
26
src/main/kotlin/ru/mipt/npm/sim/epidemics/main.kt
Normal file
26
src/main/kotlin/ru/mipt/npm/sim/epidemics/main.kt
Normal file
@ -0,0 +1,26 @@
|
|||||||
|
package ru.mipt.npm.sim.epidemics
|
||||||
|
|
||||||
|
import org.apache.commons.math3.random.JDKRandomGenerator
|
||||||
|
|
||||||
|
fun main() {
|
||||||
|
val generator = JDKRandomGenerator()
|
||||||
|
val population = DefaultEpidemicsModel.generatePopulation(generator)
|
||||||
|
var date = 0
|
||||||
|
|
||||||
|
val patientZero = generator.nextInt(population.size)
|
||||||
|
population[patientZero]?.expose(0)
|
||||||
|
|
||||||
|
while (
|
||||||
|
!population.values.all {
|
||||||
|
it.state == InfectionState.RECOVERED || it.state == InfectionState.SUSCEPTIBLE
|
||||||
|
}
|
||||||
|
) {
|
||||||
|
date++
|
||||||
|
DefaultEpidemicsModel.propagate(generator, population, date)
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
println("Epidemics ended at $date")
|
||||||
|
println(population.count { it.value.state == InfectionState.RECOVERED })
|
||||||
|
population.show()
|
||||||
|
}
|
40
src/main/kotlin/ru/mipt/npm/sim/epidemics/visualization.kt
Normal file
40
src/main/kotlin/ru/mipt/npm/sim/epidemics/visualization.kt
Normal file
@ -0,0 +1,40 @@
|
|||||||
|
package ru.mipt.npm.sim.epidemics
|
||||||
|
|
||||||
|
import kscience.plotly.*
|
||||||
|
|
||||||
|
|
||||||
|
data class PopulationState(val infected: Int, val recovered: Int)
|
||||||
|
|
||||||
|
@OptIn(ExperimentalStdlibApi::class)
|
||||||
|
fun Population.collectData(): Map<Int, PopulationState>{
|
||||||
|
val maxRecoveryDate = values.map{ it.recoveryDate ?: 0 }.max() ?: 1
|
||||||
|
return (0..maxRecoveryDate).associateWith {date->
|
||||||
|
val infected = values.count {
|
||||||
|
(it.exposedDate ?: Int.MAX_VALUE) <= date && it.recoveryDate?:Int.MAX_VALUE > date
|
||||||
|
}
|
||||||
|
val recovered = values.count { (it.recoveryDate ?: Int.MAX_VALUE) <= date }
|
||||||
|
PopulationState(infected,recovered)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
fun Population.show(): Plot {
|
||||||
|
val data = collectData()
|
||||||
|
|
||||||
|
val plot = Plotly.plot {
|
||||||
|
trace {
|
||||||
|
name = "infected"
|
||||||
|
x.set(data.keys.toIntArray())
|
||||||
|
y.set(data.values.map { it.infected })
|
||||||
|
}
|
||||||
|
trace{
|
||||||
|
name = "recovered"
|
||||||
|
x.set(data.keys.toIntArray())
|
||||||
|
y.set(data.values.map { it.recovered })
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
plot.makeFile()
|
||||||
|
|
||||||
|
return plot
|
||||||
|
}
|
Loading…
Reference in New Issue
Block a user