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.FOI
BVSV 0.4784689 0.0001392 0.0001475 0.5609756 0.0011659 0.0016162
CL 0.5289515 0.0002305 0.0002533 0.6315789 0.0011569 0.0015709
CM 0.4490644 0.0001645 0.0001757 0.6363636 0.0014661 0.0020324
MQBA 0.4482759 0.0002460 0.0002739 0.5116279 0.0009724 0.0011829

Environment and Habitat Values Table

Annual.Precipitation Wettest Driest NDVIMean NDVIMedian NDVIMax NDVIMin LSTMean LSTMedian LSTMax LSTMin EvapoMean EvapoMedian EvapoMax EvapoMin Cult.2.growth Cult.trees Open.Woodland Savanna
ABCHAC 2545 465 23 71171480 72124656 83807144 39128224 300.5819 300.8271 303.0098 296.1200 31.48407 30.30290 50.20264 14.176617 0.1666667 0.8333333 0.0000000 0.0000000
BCVN 2712 513 19 68978590 74344300 88563360 23014351 301.3609 301.3182 302.7504 299.6700 34.04578 32.61080 59.02321 13.396487 NA NA NA NA
BMCA 2565 472 21 76365818 81642252 89359640 22570000 301.6482 301.5077 303.9783 300.3395 40.50005 39.14014 71.94923 15.479762 0.3333333 0.6666667 0.0000000 0.0000000
BVSV 2675 502 22 66396028 71211897 80306307 35999860 301.2537 301.3463 302.7621 300.0952 32.44249 29.98976 51.49193 10.128520 NA NA NA NA
CD 2533 463 21 67193928 70285952 85833000 33270751 301.3924 301.0569 303.1886 299.6663 28.59371 27.74046 52.54673 8.543652 NA NA NA NA
CL 2804 536 16 61414923 63564123 77102720 21825432 300.6765 300.5820 302.5384 298.4493 1479.88998 1479.22331 1488.55842 1472.834867 NA NA NA NA
CM 2506 457 21 71262930 75586501 85088944 21250836 302.0870 302.1326 303.5665 300.4409 34.06431 31.96171 54.65224 13.881584 NA NA NA NA
FDR 2484 448 23 59531105 67846856 83440456 10942584 299.9074 299.8832 301.1968 299.0244 618.75475 619.07491 632.48888 597.756224 NA NA NA NA
JUCACH 2492 451 22 76857983 83674620 90319288 11576548 300.0859 300.0298 302.0617 298.6659 35.28196 36.10414 51.93369 11.716193 NA NA NA NA
MARU 2549 467 22 68922772 76347064 87785160 14878260 301.0485 301.0889 302.8358 298.0121 38.78923 38.19121 67.12448 15.347358 NA NA NA NA
MGROS 2548 469 20 59298448 64433116 78529904 12650532 303.4854 303.2383 305.1004 301.9213 28.18515 24.99208 49.68626 11.888706 0.0000000 0.0000000 0.0000000 1.0000000
MQBA 2751 522 17 68256453 73206280 82936463 31080920 301.2487 301.2910 303.3614 299.2475 255.44454 255.16791 277.84252 236.315641 1.0000000 0.0000000 0.0000000 0.0000000
PABE 2608 484 21 57434785 55752292 83119800 24896600 302.8574 302.5098 305.1974 301.4247 26.73978 24.50969 47.55969 11.947536 0.0588235 0.0000000 0.7058824 0.2352941
PD 2595 480 22 74303323 76214741 83793944 43079578 300.5899 301.1789 302.7252 293.0273 38.08400 36.30581 58.62634 14.902667 0.1818182 0.8181818 0.0000000 0.0000000
PF 2742 520 17 72026454 75880300 86175296 34324358 301.3940 301.3448 303.0893 299.5918 33.13820 31.46552 59.30126 8.860002 NA NA NA NA
SM 2506 455 21 67031112 73060000 83226112 13844195 300.1174 300.0407 301.8558 298.2349 3274.23554 3274.23863 3274.24589 3274.221180 NA NA NA NA
VC 2634 491 23 74922352 76383299 83954072 51465236 301.0097 300.9769 303.6098 299.6946 33.92231 33.79157 53.97996 13.031496 0.8750000 0.1250000 0.0000000 0.0000000
VUPD 2586 477 22 68107798 70802201 79956392 17223452 301.1254 301.6835 303.3354 295.1025 30.39886 31.15986 49.19620 14.207052 0.6250000 0.0000000 0.3750000 0.0000000

Infection Correlation Matrices

Environment and Infection Correlations Matrix

PCA between Infection and Environment

#Environment and Habitat Analysis

##RDA Screeplot

##RDA Output

#Environment Analysis

##RDA Screeplot

RDA Output

## 
## Call:
## rda(formula = infection_values ~ Annual.Precipitation + Wettest +      Driest + NDVIMean + NDVIMedian + NDVIMax + NDVIMin + LSTMean +      LSTMedian + LSTMax + LSTMin + EvapoMean + EvapoMedian + EvapoMax +      EvapoMin, data = environment_values, scale = TRUE, na.action = na.omit) 
## 
## Partitioning of correlations:
##               Inertia Proportion
## Total               6          1
## Constrained         6          1
## Unconstrained       0          0
## 
## Eigenvalues, and their contribution to the correlations 
## 
## Importance of components:
##                         RDA1   RDA2   RDA3
## Eigenvalue            3.7362 1.5371 0.7267
## Proportion Explained  0.6227 0.2562 0.1211
## Cumulative Proportion 0.6227 0.8789 1.0000
## 
## Accumulated constrained eigenvalues
## Importance of components:
##                         RDA1   RDA2   RDA3
## Eigenvalue            3.7362 1.5371 0.7267
## Proportion Explained  0.6227 0.2562 0.1211
## Cumulative Proportion 0.6227 0.8789 1.0000
## 
## Scaling 2 for species and site scores
## * Species are scaled proportional to eigenvalues
## * Sites are unscaled: weighted dispersion equal on all dimensions
## * General scaling constant of scores:  2.059767 
## 
## 
## Species scores
## 
##                     RDA1    RDA2    RDA3
## MST.Prevalence  -0.05238 0.69788 -0.4662
## MST.Incidence   -0.69760 0.35361  0.3089
## MST.FOI         -0.70609 0.34040  0.3044
## Sero.Prevalence  0.59903 0.57838  0.1173
## Sero.Incidence   0.79106 0.09783  0.2679
## Sero.FOI         0.81813 0.12191  0.1514
## 
## 
## Site scores (weighted sums of species scores)
## 
##         RDA1    RDA2    RDA3
## BVSV  0.4600 -0.8722 -1.4865
## CL   -0.2894  1.7178 -0.3840
## CM    1.3170 -0.1282  1.1963
## MQBA -1.4876 -0.7173  0.6742
## 
## 
## Site constraints (linear combinations of constraining variables)
## 
##         RDA1    RDA2    RDA3
## BVSV  0.4600 -0.8722 -1.4865
## CL   -0.2894  1.7178 -0.3840
## CM    1.3170 -0.1282  1.1963
## MQBA -1.4876 -0.7173  0.6742
## 
## 
## Biplot scores for constraining variables
## 
##                         RDA1    RDA2    RDA3
## Annual.Precipitation -0.8045  0.4072 -0.4324
## Wettest              -0.8043  0.4054 -0.4345
## Driest                0.7481 -0.6276 -0.2155