| Title: | Simulation of Plasmodium genetic data |
|---|---|
| Description: | A basic Plasmodium simulator. Contains functions to simulate epidemiological and genetic data from a simple model of Plasmodium falciparum transmission. |
| Authors: | Bob Verity [aut, cre] |
| Maintainer: | Bob Verity <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.0.0 |
| Built: | 2024-06-09 03:26:41 UTC |
| Source: | https://github.com/mrc-ide/PlasmoSim |
Simple function to check that PlasmoSim package has loaded successfully. Prints "PlasmoSim loaded successfully!" if so.
check_PlasmoSim_loaded()check_PlasmoSim_loaded()
Compare two sets of haplotypes (matrices), and return the proportion of identical sites over all pairwise comparisons. Values can be any numeric value; for example if values represent ancestry then this function returns the average identity by descent, or if values represent alleles then it returns the average identity by state.
get_haplotype_identity(mat1, mat2)get_haplotype_identity(mat1, mat2)
mat1, mat2
|
matrices representing sets of haplotypes to compare. Haplotypes are in rows and loci are in columns. |
Calculates pairwise genetic identity between all samples. If
deme_level = TRUE this is averaged over all individuals within a
deme, to produce average pairwise relatedness within and between demes.
Each time point in the sample is considered independently, and output as a
list.
get_identity_matrix(sim_output, deme_level = FALSE)get_identity_matrix(sim_output, deme_level = FALSE)
sim_output |
simulation output from |
deme_level |
if |
Get great circle distance between spatial points.
get_spatial_distance(lat, lon)get_spatial_distance(lat, lon)
lat |
vector of latitudes. |
lon |
vector of longitudes. |
Calculate great circle distance and bearing between spatial coordinates.
lonlat_to_bearing(origin_lon, origin_lat, dest_lon, dest_lat)lonlat_to_bearing(origin_lon, origin_lat, dest_lon, dest_lat)
origin_lon |
The origin longitude |
origin_lat |
The origin latitude |
dest_lon |
The destination longitude |
dest_lat |
The destination latitude |
# one degree longitude should equal approximately 111km at the equator lonlat_to_bearing(0, 0, 1, 0)# one degree longitude should equal approximately 111km at the equator lonlat_to_bearing(0, 0, 1, 0)
A basic Plasmodium simulator. Contains functions to simulate epidemiological and genetic data from a simple model of Plasmodium falciparum transmission.
Import file from the inst/extdata folder of this package
plasmosim_file(name)plasmosim_file(name)
name |
name of file. |
Simulate genetic data from a simple model of P. falciparum epidemiology and genetics.
sim_falciparum( a = 0.3, p = 0.9, mu = -log(p), u = 12, v = 10, g = 10, prob_infection = 0.1, duration_infection = dgeom(1:500, 1/100), infectivity = 0.1, max_infections = 5, H = 1000, seed_infections = 100, M = 1000, mig_matrix = diag(length(M)), L = 24, mean_oocysts = 2, mean_products = 5, recomb_prob = 0.1, max_time = max(sample_dataframe$time), sample_dataframe = data.frame(deme = 1, time = 365, n = 100), report_progress = TRUE )sim_falciparum( a = 0.3, p = 0.9, mu = -log(p), u = 12, v = 10, g = 10, prob_infection = 0.1, duration_infection = dgeom(1:500, 1/100), infectivity = 0.1, max_infections = 5, H = 1000, seed_infections = 100, M = 1000, mig_matrix = diag(length(M)), L = 24, mean_oocysts = 2, mean_products = 5, recomb_prob = 0.1, max_time = max(sample_dataframe$time), sample_dataframe = data.frame(deme = 1, time = 365, n = 100), report_progress = TRUE )
a |
human blood feeding rate. The proportion of mosquitoes that feed on humans each day. |
p |
mosquito probability of surviving one day. |
mu |
mosquito instantaneous death rate. mu = -log(p) unless otherwise specified. |
u |
intrinsic incubation period. The number of days from infection to blood-stage infection in a human host. |
v |
extrinsic incubation period. The number of days from infection to becoming infectious in a mosquito. |
g |
lag time between human blood-stage infection and production of gametocytes. |
prob_infection |
probability a human becomes infected after being bitten by an infected mosquito. |
duration_infection |
vector specifying probability distribution of time (in days) of a malaria episode. |
infectivity |
probability a mosquito becomes infected after biting an infective human host. |
max_infections |
maximum number of infections that an individual can hold simultaneously. |
H |
human population size, which is assumed to be the same in every deme. |
seed_infections |
vector specifying the initial number of infected humans in each deme. |
M |
vector specifying mosquito population size (strictly the number of adult female mosquitoes) in each deme. |
mig_matrix |
migration matrix specifing the daily probability of migrating from each deme to each other deme. Migration must be equal in both directions, meaning this matrix must be symmetric. |
L |
number of loci. The maximum number of loci is 1000, as at higher numbers haplotypes begin to exceed integer representation (2^L). |
mean_oocysts |
the average number of viable oocysts generated from gametocytes upon biting an infective host. The actual number of oocysts is generated from a zero-truncated Poisson distribution with this mean. |
mean_products |
parasite genotypes are passed from mosquito to host by
sampling N times with replacement from the available oocysts products (the
available number of products is 4 times the number of oocysts). N is drawn
independently for each infection from a zero-truncated Poisson distribution
with mean given by |
recomb_prob |
the probability of a recombination breakpoint between any sequential pair of loci. Assumed to be the same for all loci. |
max_time |
number of days in the simulation. |
sample_dataframe |
a dataframe specifying outputs from the model. Must contain the following three columns:
|
report_progress |
if |