alisonfowler / enkf_seir Goto Github PK
View Code? Open in Web Editor NEWThis project forked from geirev/enkf_seir
EnKF_seir
License: MIT License
This project forked from geirev/enkf_seir
EnKF_seir
License: MIT License
NOTE IN THIS RELEASE: infile.in has changed: There are three reproduction factors for the three periods. There are Rmatrix_01.in, Rmatrix_02.in, and Rmatrix_03.in generated with numbers 1.00 at first run. These matrices can be edited to set different reproduction factors between different agegroups. They are read into Rmat(:,:,1:3). The effective R between agegroups i and j, for the period k, is then R(i,j) = p%R(k) * Rmat(i,j,k) This modificaiton provides a significantly improved flexibilty, and adds uncertainty to simulations after the second intervention. EnKF_seir code # 1a. Simple installation: # Make a directory where you will install the following git clone [email protected]:geirev/EnKF_seir.git git clone [email protected]:geirev/EnKF_analysis.git git clone [email protected]:geirev/EnKF_sampling.git #1b. Best installation option # - Make a personal github account unless you already have one. # Fork the three repositorys listed above replacing the userid with your github account id. # Next clone the repositories and set upstream to the original repositories git clone [email protected]:<userid>/EnKF_seir.git cd EnKF_seir; git remote add upstream https://github.com/geirev/EnKF_seir git clone [email protected]:<userid>/EnKF_analysis.git cd EnKF_analysis; git remote add upstream https://github.com/geirev/EnKF_analysis git clone [email protected]:<userid>/EnKF_sampling.git cd EnKF_sampling; git remote add upstream https://github.com/geirev/EnKF_sampling # If you are new to git read the README_GIT file # 2. Install blas, lapack, libfftw3, and Fortran95 sudo apt-get update sudo apt-get install libblas-dev liblapack-dev libfftw3-dev gfortran # 3. Compile the EnKF_analysis library cd EnKF_analysis/lib # in the makefile: change build dir to dir where EnKF_seir will be build" # BUILD = ../../EnKF_seir/build # This will put all the .o files as well as libanalysis.a in the same dir as you will use when compiling EnKF_seir make # 4. Compile the EnKF_sampling library cd EnKF_sampling/lib # in the makefile: change build dir to dir where EnKF_seir will be build" # BUILD = ../../EnKF_seir/build # This will put all the .o files as well as libanalysis.a in the same dir as you will use when compiling EnKF_seir make cd 5. EnKF_seir/src # change target install dir which is currently $HOME/bin to where you want it to reside make cd ../run seir For some plotting options check python/enkf_seir/plot plot.py covid.ipynb good luck and ask when you get stuck. ################################################################################ # If you plan to change the code note the follwing: I always define subroutines in new modules: module m_name_of_routine ! define global variables here contains subroutine name_of_sub ! define local variables here end subroutine end module in the main program you write program seir use m_name_of_routine call name_of_routine end program The main program then has access to all the global variables defined in the module, and knows the header of the subroutine and the compiler checks the consistency between the call and the subroutine definition. make new -> updates the dependencies for the makefile make tags -> runs ctags (useful if you use vim) For this to work install the scripts in the ./bin in your path and install ctags ################################################################################
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.