Publications by Katie Farnes
FOI Model Fitting
This presents the parameter fitting for my FOI models. This is based on age prevalence data from Human MST scores. Model Functions get_catalytic_result = function(lambda, a){ z = 1 - exp(-lambda*a) return(z) } get_variable_result = function(lambda,P, a){ z = P*(1-exp(-lambda*a)) return(z) } get_reverse_result = function(lam...
1333 sym R (12478 sym/12 pcs) 14 img
Remote Sensing
Set Up memory.limit(560000) setwd("C:/Users/katie/OneDrive/Marajo Project/") load("C:/Users/katie/OneDrive/Marajo Project/ndvilist.RData") x <- c("rgdal", "rgeos", "maptools", "sp", 'sf', "raster", "MODIS",'tidyverse', "gdalUtils", "ggplot2", "RColorBrewer") lapply(x, library, character.only = TRUE) tif.dir <- "C:/Users/katie...
724 sym R (12693 sym/36 pcs) 17 img
Marajo Mapping NDVI
Set Up rm(list = ls()) setwd("C:/Users/katie/OneDrive/Marajo Project") x <- c("sp", "rgdal", "rgeos", "maptools", "sp", "sf", "raster", "MODIS", "gdalUtils", "ggplot2", "RColorBrewer", "ggmap", "mapview", "openxlsx", "leaflet", "tidyverse", "mapedit") lapply(x, library, character.only = TRUE) register_google(key = "AIzaSyDnw8wZ...
138 sym R (2151 sym/6 pcs) 2 img
Correlations between FOI and Environmental Risk Factors
Maps of Villages by Environment Human FOI Correlation Annual Precipitation ## `geom_smooth()` using formula 'y ~ x' ## ## Call: ## lm(formula = HumanRevGroupModLambda ~ `Annual Precipitation`, ## data = HumEnviroVardf) ## ## Coefficients: ## (Intercept) `Annual Precipitation` ## -0.2506439 ...
473 sym R (24561 sym/91 pcs) 34 img
PCA Villages
Set Up Infection Values Data Frame Prev.Pos.Dogs.T1 = Prevalence of positive Dog Serology from original data at time point 1 Prev.Pos.Dogs.T3 = Prevalence of positive Dog Serology from original data at time point 3 Inc.MST2 = Incidence of positive Human MST from original data Mean.Max.Saliva = I calculated the maximum saliva test for each dog an...
1092 sym R (7740 sym/14 pcs) 4 img
Enviro Factors
Maps of Villages by Environment Human FOI Correlation Annual Precipitation ## `geom_smooth()` using formula 'y ~ x' ## ## Call: ## lm(formula = HumanRevGroupModLambda ~ `Annual Precipitation`, ## data = HumEnviroVardf) ## ## Coefficients: ## (Intercept) `Annual Precipitation` ## -0.2506439 ...
586 sym R (33595 sym/115 pcs) 45 img
Vegan PC and RDA
Infection Values Data Frame Prev.Pos.Dogs.T1 = Prevalence of positive Dog Serology from original data at time point 1 Prev.Pos.Dogs.T3 = Prevalence of positive Dog Serology from original data at time point 3 Inc.MST2 = Incidence of positive Human MST from original data Mean.Max.Saliva = I calculated the maximum saliva test for each dog and found ...
2355 sym R (33355 sym/34 pcs) 1 img
Comparing Environmental Factors
Combine 1993-1995 data with 2004-2006 data Compare Environmental Variables Precipitation Min NDVI Mean NDVI Max NDVI Min Temp Max Temp ...
163 sym 6 img
RDA Analysis
Redundancy Analysis of infection scores and environmental factors This script takes the prevalence and incidence of human and dog infection in marajo by village and looks at how this is correlated with environmental factors and habitats Infection Values Table MST.Prevalence MST.Incidence MST.FOI Sero.Prevalence Sero.Incidence Sero.FO...
553 sym R (2347 sym/1 pcs) 5 img 2 tbl