Package index • ramp.micro

Adult Mosquito Models

Methods to set up and compute adult mosquito models

adult_dynamics(): Update States for an Adult Mosquito Model

save_states_M(): Store State Variables for an Adult Mosquito Model

init_states_M(): Save state variables

init_adult_model(): Set Initial Values for **M** Module

compute_diffs_M(): The some of squared differences between two sets of variables

setup_adult_model(): Setup Adult Mosquito Module

BQ

Methods to setup and compute the BQ model

adult_dynamics(<BQ>): Update States for the `BQ` model

save_states_M(<BQ>): Save the state variables in a vector

init_states_M(<BQ>): Save the state variables in a vector

init_adult_model(<BQ>): Set initial values for the BQ model

init_adult_model_BQ(): Set initial values for the BQ model

compute_diffs_M(<BQ>): The sum of squared differences between two sets of variables

setup_dispersal_BQ(): Dispersal parameters for the BQ model

make_Psi_BQ(): Make dispersal matrices for the BQS model

setup_bionomics_BQ(): Bionomic parameters set for the BQ model

make_demography_BQ(): Make the demographic matrices for the BQ model

setup_adult_model(<BQ>): Setup a BQ model for adult mosquitoes

BQS

Methods to setup and compute the BQS model

adult_dynamics(<BQS>): Update States for the `BQS` model: one time step

save_states_M(<BQS>): Store the state variables for the BQS model

init_states_M(<BQS>): Save the state variables in a vector

init_adult_model(<BQS>): Set initial values for the BQS model

init_adult_model_BQS(): Set initial values for the BQ model

compute_diffs_M(<BQS>): The sum of squared differences between the state and putative steady state

setup_dispersal_BQS(): Dispersal parameters for the BQS model

make_Psi_BQS(): Make dispersal matrices for the BQS model

setup_bionomics_BQS(): Bionomic parameters set for the BQ model

make_demography_BQS(): Make the demographic matrices for the BQS model

setup_adult_model(<BQS>): Setup a BQS model for adult mosquitoes

Aquatic Mosquito Models

Methods to set up and compute aquatic mosquito models

aquatic_dynamics(): Aquatic Dynamics

save_states_L(): Save state variables

init_states_L(): Initialize the Lstates

init_aquatic_model(): Set initial values for

compute_diffs_L(): The some of squared differences between two sets of variables

setup_aquatic_model(): Setup an aquatic model

the basicL model

Methods to setup and compute basicL

aquatic_dynamics(<basicL>): Aquatic Dynamics

save_states_L(<basicL>): Save state variables

init_states_L(<basicL>): Save the state variables in a vector

init_aquatic_model(<basicL>): Set initial values for the BQ model

init_aquatic_model_basicL(): Set initial values for

compute_diffs_L(<basicL>): The some of squared differences between two sets of variables

setup_aquatic_model(<basicL>): Setup an aquatic model

setup_aquatic_model_basicL(): Set up the aquatic population model of class basicL

Setup

Functions

Point Sets

Utilities to generate point sets

unif_xy(): Make a random point set, xy

lattice(): Set up a lattice with n x n points

clusters_xy(): Use a set of `xy` values as seeds for clusters

clusters_nm(): Setup n clusters with m points per cluster

Kernels

Functions to compute search weights by distance

make_kF_exp(): Make an exponential function for weight by distance

make_kF_pwr(): Make an power function to weight points by distance

make_kF_mix(): Make an power function that combines an exponential and power function

Dispersal Matrices (Psi)

Generate the single bout dispersal matrices

make_Psi_xy(): Make Psi from a source point set to a destination point set

make_Psi_xx(): Make Psi from a source point set to a destination point set

Setup Model

Utilities for setting up Models

setup_model(): Setup a behavioral state, micro-simulation model

make_model_squareLattice(): Setup a square lattice model with one point set offset and nested within the other

make_model_unif(): Setup a model on a random uniform set of points

Simulation

Utilities for setting up Models

SIM(): Simulate population dynamics

steady_state(): Run the model until it has reached a steady state

Analysis of Dispersal

Utilities for analyzing movement

dispersal_PMF(): Compute distances dispersed

compute_KGV(): Compute net dispersal matrix to blood feed within one feeding cycle

basic_analysis(): Basic analysis

Compute K Matrices

Generate matrices describing feeding or egg laying within a single feeding cycle

compute_Kqb(): Compute dispersal matrix to lay eggs within one feeding cycle

compute_Kqb(<BQ>): Compute net dispersal matrix to blood feed within one feeding cycle

compute_Kqb(<BQS>): Compute dispersal to lay eggs within one feeding cycle

compute_Kbq(): Compute dispersal matrix to blood feed within one feeding cycle

compute_Kbq(<BQ>): Compute dispersal matrix to lay eggs within one feeding cycle

compute_Kbq(<BQS>): Compute net dispersal matrix to blood feed within one feeding cycle

compute_Kbb(): Compute dispersal matrix to lay eggs within one feeding cycle

compute_Kqq(): Compute dispersal matrix to lay eggs within one feeding cycle

Compute Dispersal of Eggs

Compute matrices describing net dispersal of Eggs

compute_G(): Compute the dispersion of eggs after one feeding cycle

compute_G(<BQ>): Compute the dispersion of eggs after one feeding cycle for the BQ model

compute_G(<BQS>): Compute the dispersion of eggs after one feeding cycle for the BQ model

compute_GG(): Compute the dispersion of eggs after one feeding cycle for the BQ model

Compute Potential Transmission

Compute matrices describing net dispersal of Eggs

compute_V(): Compute the potential dispersion of parasites after one feeding cycle

compute_V(<BQ>): Compute the potential dispersion of parasites after one feeding cycle for the BQ model

compute_V(<BQS>): Compute the potential dispersion of parasites after one feeding cycle for the BQS model

compute_VC(): Compute the potential dispersion of parasites after one feeding cycle for the BQS model

Compute Distances Dispersed

Methods to compute the PMF and CMF for distances dispersed

plotDDpmf(): Plot the PMF for distances dispersed

plotDDcmf(): Plot the CMF for distances dispersed

Network Analysis

Methods to set up and analyze communities

Graphs

Make Graphs

make_graph_obj(): Make graph object

make_common_graphs(): Make all of the graphs

make_all_graphs(): Make graphs

make_all_graphs(<BQ>): Make graphs for a BQ model

make_all_graphs(<BQS>): Make graphs for a BQS model

net2patches(): Use communities to define patches

Tesselate

Methods to compute and visualize using Delauney / Dirichlet methods

make_tiles(): Make a set of tiles that tesselate space

make_tiles(<BQ>): Make a set of tiles that tesselate space for the BQ model

make_tiles(<BQS>): Make a set of tiles that tesselate space for the BQS model

Convex Hulls

Methods to compute and visualize convex hulls around communities

make_convex_hulls(): Make a set of convex hulls to visualize the community

make_convex_hull_i(): Make the convex hull for the i^th community

make_convex_hull_xy(): Make the convex hull for the i^th community

Visualization

Visualize Point Sets

Utilities to visualize point sets

plot_points(): Plot point sets for a model

plot_points(<BQ>): Plot point sets for a model for a BQ model

plot_points(<BQS>): Plot point sets for a model for a BQS model

plot_points_bq(): Plot point sets for a bq model

plot_points_bqs(): Plot point sets for a model for a BQS model

frame_bq(): Set up a frame to plot points for a model

frame_bqs(): Set up a frame to plot points for a BQS model

add_points_b(): Add blood feeding points to a frame

outline_points_b(): Add blood feeding points to a frame

add_points_bb(): Add blood feeding sites with and without the self loop

add_points_q(): Add habitats to a frame

outline_points_q(): Add habitats to a frame

add_points_qq(): Add habitats with and without the self loop

add_points_s(): Add sugar feeding sites to a frame

outline_points_s(): Add habitats to a frame

add_points_ss(): Add sugar feeding sites with and without the self loop

Visualize Matrices

Visualize a generic dispersal matrix

plot_matrix_xy(): Visualize a dispersal matrix among two point sets

plot_matrix_xx(): Visualize a dispersal matrix from one point set to itself

add_arrows_xy(): Draw arrows from one point set to another

add_arrows_xx(): Draw arrows from a point set to itself

add_one_arrow(): Draw an arrow from (x_i, y_i) to (x_j, y_j)

add_nth_arrow_xy(): Add the nth arrow from a list of locations and indices

add_nth_arrow_xx(): Plot the n^th arrow

add_nth_segment(): Add the nth segment

add_bent_arrows_xy(): Draw bent arrows from one point set to another

add_bent_arrows_xx(): Title

Visualize Populations

Visualize Mosquito Populations

make_movie(): Make a movie

make_movie(<BQ>): Make a movie of a simulation with a BQ model

make_movie(<BQS>): Make a movie of a simulation with a BQS model

Visualize Psi Matrices

Plot the single bout dispersal matrices

plot_Psi_bb(): Visualize the one-bout dispersal matrices for a BQ model

plot_Psi_bq(): Visualize the one-bout dispersal matrices for a BQ model

plot_Psi_bs(): Visualize the dispersal matrix to b from s

plot_Psi_qb(): Visualize the one-bout dispersal matrices for a BQ model

plot_Psi_qq(): Visualize the one-bout dispersal matrices for a BQ model

plot_Psi_qs(): Visualize the one-bout dispersal matrices for a BQ model

plot_Psi_sb(): Visualize the one-bout dispersal matrices for a BQ model

plot_Psi_sq(): Visualize the one-bout dispersal matrices for a BQ model

plot_Psi_ss(): Visualize the one-bout dispersal matrices for a Bs model

plot_all_Psi(): Visualize the one-bout dispersal matrices

plot_all_Psi(<BQ>): Visualize the one-bout dispersal matrices for a BQ model

plot_all_Psi_BQ(): Visualize the one-bout dispersal matrices for a BQ model

plot_all_Psi(<BQS>): Visualize the one-bout dispersal matrices for a BQS model

plot_all_Psi_BQS(): Visualize the one-bout dispersal matrices for a BQS model

Visualize K Matrices

Plot matrices describing feeding or egg laying within a single feeding cycle

plot_Kbq(): Plot the matrix \(K_{b \leftarrow q}\): dispersal from \(\left\{q\right\}\) to \(\left\{b\right\}\)

plot_Kqb(): Plot the matrix \(K_{q \leftarrow b}\) dispersal from \(\left\{b\right\}\) to \(\left\{q\right\}\)

plot_Kbb(): Plot the matrix \(K_{b \leftarrow b}\)

plot_Kqq(): Plot the matrix \(K_{q \leftarrow q}\)

Visualize Egg Dispersal

Methods to compute and visualize egg dispersal across a mosquito generation

plot_dispersal_G(): Plot lifetime egg dispersal, per mosquito

plot_dispersal_GG(): Plot lifetime egg dispersal by a mosquito population

Visualize Transmission Potential

Methods to compute and visualize parasite transmission potential

plot_dispersal_V(): Visualize lifetime transmission from a site, per mosquito

plot_dispersal_VV(): Visualize lifetime transmission from a site by mosquito populations

Visualize Networks

Methods to set up and analyze communities

plot_graph(): Plot the ouptuts of a graph using

plot_convex_hulls(): Add the convex hulls to a framed plot

add_convex_hulls(): Add convex hulls around the points in a community

stretch_convex_hull(): Stretch (or shrink) the convex hull for plotting

add_hulls(): Plot the ouptuts of a graph using

plot_meta(): Plot the ouptuts of a graph using

plot_subgraph(): Plot the ouptuts of a graph using

Visualize Metapopulation

Metapopulations

plot_patches(): Visualize the patchespopulation approximation

Utilites

Methods to help streamline matrix visualization

decompM(): Decompose Matrix

cutoffValue(): Define a cutoff that includes a fraction of the total mass (e.g. 90 percent)

edgeSubset_fracMass(): Subset Edges

edgeSubset(): Subset Edges

get_matrix(): Choose one of the matrices describing movement

get_graph(): Choose one of the networks describing dispersion