We need the following packages:
> library(magrittr)
> library(dplyr)
> library(purrr)
> library(car)
> library(irr)Let’s load and clean a bit the data:
> data <- "PathogenData130619.csv" %>%
+ read.csv() %>%
+ mutate_at(c("Prostration", "Respiratory", "Diarrhea", "CNS", "Joints", "Anemia"), `>`, 0) %>%
+ mutate_at(vars(ends_with("FINAL")), `>`, 0) %>%
+ mutate_at(vars(ends_with("y.n")), `>`, 0)A key issue in multivariate analyses is when the \(x\) variables are not independent (or colinear), which may cause confounding effects in your analysis, meaning that some effect that you detect between \(y\) and \(x\) may not reflect a true direct association between \(y\) and \(x\) but instead reflects the fact that both \(x\) and \(y\) are associated to a third variable. In such conditions, we thus need to find a way to correct for these potential confounding effects due to colinearities. One powerful option is the so-called Type-II partial tests (see here for example). The car R package has the function Anova() that computes Type-II partial tests for many classical models, including the logistic regression that you want to use here. The function below uses the car::Anova() function to compute significativity tests and summarises the results a multivariate logistic regression in a table that contains estimates of Odds Ratio, their confidence interval and their level of significativity, corrected for the potential confounding effect due to the other \(x\) variables.
> make_table <- function(model) {
+ out <- cbind(exp(cbind(coef(model), confint(model))),
+ rbind(rep(NA, 2), as.data.frame(car::Anova(model))))
+ names(out)[1] <- "Estimate"
+ out
+ }Let’s try it on a simple multivariate analysis:
> model1 <- glm(AVI.FINAL ~ Prostration + Respiratory + Diarrhea + CNS + Joints + Anemia, binomial, data)The results of which are:
> make_table(model1)
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 1.2488700 0.15312261 11.046709 NA NA NA
ProstrationTRUE 1.5208240 0.23618089 9.189364 0.2136974 1 0.64388471
RespiratoryTRUE 2.3575087 0.77284144 7.624603 2.2610415 1 0.13266482
DiarrheaTRUE 0.5262251 0.13421906 1.815648 1.0067839 1 0.31567456
CNSTRUE 0.3249811 0.01456772 3.119398 0.9135985 1 0.33916142
JointsTRUE 10.8473401 0.89229708 481.335267 3.4441172 1 0.06347732
AnemiaTRUE 0.2786208 0.04534223 1.427960 2.3477664 1 0.12546266We aim to explain the presence of these 8 pathogens:
> (xs <- paste0(c("AVI", "ORT", "PM", "MG", "IBV", "IBD", "FLU", "E.COLI"), ".FINAL"))
[1] "AVI.FINAL" "ORT.FINAL" "PM.FINAL" "MG.FINAL" "IBV.FINAL" "IBD.FINAL" "FLU.FINAL" "E.COLI.FINAL"Note that we have to drop ND.FINAL that is never present in the data set:
> tmp <- data %>%
+ select(ends_with("FINAL")) %>%
+ sapply(table)
> tmp %>%
+ reduce(bind_rows) %>%
+ as.data.frame() %>%
+ `rownames<-`(names(tmp))
FALSE TRUE
AVI.FINAL 24 39
ORT.FINAL 55 8
PM.FINAL 55 8
MG.FINAL 47 16
IBV.FINAL 49 14
IBD.FINAL 48 15
ND.FINAL 63 NA
FLU.FINAL 60 3
E.COLI.FINAL 53 10Below is the list of co-variables that we will consider in order to explain the presence of each of the above pathogens:
> ys <- c("Prostration", "Respiratory", "Diarrhea", "CNS", "Joints", "Anemia",
+ "Age.weeks.", "Helminth.Y.N", "Nematodes.y.n", "Cestodes.Y.N")Let’s explore the agreements between the boolean variables in ys (i.e. all except Age.weeks.). For that, the following function computes a matrix of Cohen’s kappa p values:
> kappa_mat <- function(df) {
+ nb <- ncol(df)
+ vn <- names(df)
+ expand.grid(1:nb, 1:nb) %>%
+ t() %>%
+ as.data.frame() %>%
+ sapply(function(x) irr::kappa2(data.frame(df[, x[1]], df[, x[2]]))$p) %>%
+ matrix(nb) %>%
+ round(2) %>%
+ as.data.frame(vn) %>%
+ setNames(vn) %>%
+ `rownames<-`(vn)
+ }Let’s run it:
> data %>%
+ select(ys, -Age.weeks.) %>%
+ kappa_mat()
Prostration Respiratory Diarrhea CNS Joints Anemia Helminth.Y.N Nematodes.y.n Cestodes.Y.N
Prostration 0.00 0.06 0.63 0.18 0.18 0.88 0.27 0.27 0.19
Respiratory 0.06 0.00 0.94 1.00 0.42 0.53 0.83 0.83 0.37
Diarrhea 0.63 0.94 0.00 0.10 0.44 0.07 0.53 0.53 0.46
CNS 0.18 1.00 0.10 0.00 0.00 0.02 0.11 0.11 0.00
Joints 0.18 0.42 0.44 0.00 0.00 0.25 0.11 0.11 0.04
Anemia 0.88 0.53 0.07 0.02 0.25 0.00 0.04 0.04 0.00
Helminth.Y.N 0.27 0.83 0.53 0.11 0.11 0.04 0.00 0.00 0.00
Nematodes.y.n 0.27 0.83 0.53 0.11 0.11 0.04 0.00 0.00 0.00
Cestodes.Y.N 0.19 0.37 0.46 0.00 0.04 0.00 0.00 0.00 0.00Anemia appears pretty associated with CNS, and the presence of worms and CNS appears associated with the presence of joints pain and cestodes. So, it’s not all super associated but there are some associations. Let’s now look at how these variables are associated with age:
> data %>%
+ select(ys, -Age.weeks.) %>%
+ sapply(function(y)anova(glm(y ~ data$Age.weeks., binomial), test = "LRT")$P[2])
Prostration Respiratory Diarrhea CNS Joints Anemia Helminth.Y.N Nematodes.y.n Cestodes.Y.N
0.2015742 0.8857427 0.0204409 0.3710758 0.2774946 0.2170100 0.1617669 0.1617669 0.5823138 Only Diarrhea seems to decrease with age:
> summary(glm(Diarrhea ~ Age.weeks., binomial, data))
Call:
glm(formula = Diarrhea ~ Age.weeks., family = binomial, data = data)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.9895 -1.0750 0.6352 0.8495 1.2474
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 2.1625 0.6895 3.136 0.00171 **
Age.weeks. -0.1661 0.0761 -2.183 0.02903 *
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 77.138 on 62 degrees of freedom
Residual deviance: 71.764 on 61 degrees of freedom
AIC: 75.764
Number of Fisher Scoring iterations: 4Let’s now run the multivariate logisitc models corrected for confounding effects in order to explain the presence of all the pathogens. Because there is not much data and there is multiple infections in most of the cases, we’ll also include the presence of the other pathogens in the co-variables of the multivariable logistic regression:
> for(i in seq_along(xs)) {
+ print(xs[i])
+ print(make_table(glm(formula(paste(xs[i], "~", paste(c(xs[-i], ys), collapse = " + "))), binomial, data)))
+ cat("------------------------------------------------------------------\n")
+ }
[1] "AVI.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 5.404864e-01 1.569007e-02 17.4134356 NA NA NA
ORT.FINALTRUE 3.904266e+06 1.903205e-40 NA 0.64003104 1 0.423699556
PM.FINALTRUE 2.102398e+01 1.032619e+00 1522.3806728 3.93187557 1 0.047379075
MG.FINALTRUE 4.161304e+00 5.190024e-01 56.4314915 1.73841103 1 0.187340286
IBV.FINALTRUE 6.024741e-01 8.219732e-02 4.0748587 0.27584798 1 0.599435604
IBD.FINALTRUE 2.595261e+00 4.763316e-01 17.5953627 1.18291150 1 0.276764068
FLU.FINALTRUE 6.153678e-01 7.415723e-03 37.2989688 0.05439162 1 0.815590489
E.COLI.FINALTRUE 4.866229e+00 5.686867e-01 63.3141869 2.04432547 1 0.152774688
ProstrationTRUE 3.114521e-01 1.750326e-02 4.2896038 0.75629866 1 0.384489334
RespiratoryTRUE 3.921657e+00 7.529136e-01 26.4213842 2.60461944 1 0.106552733
DiarrheaTRUE 4.005415e-01 6.582074e-02 2.0666988 1.18319086 1 0.276707356
CNSTRUE 5.739047e-02 2.479215e-04 1.9450140 2.40022104 1 0.121318107
JointsTRUE 2.382591e+01 5.758207e-01 6841.0358657 2.60102575 1 0.106794575
AnemiaTRUE 4.636979e-02 2.450275e-03 0.4915133 6.74280728 1 0.009412639
Age.weeks. 1.294961e+00 1.013970e+00 1.7346827 4.31698263 1 0.037733776
Helminth.Y.NTRUE 5.321384e-01 8.661481e-02 2.7031370 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 3.891965e+00 2.548087e-01 84.5319910 0.93723586 1 0.332989723
------------------------------------------------------------------
[1] "ORT.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 5.374583e-89 0.000000e+00 Inf NA NA NA
AVI.FINALTRUE 2.803769e-01 0.000000e+00 Inf -3.467271e-11 1 1.000000e+00
PM.FINALTRUE 9.642629e+20 0.000000e+00 Inf 4.378533e-10 1 9.999833e-01
MG.FINALTRUE 1.751056e+27 0.000000e+00 Inf 2.585799e-09 1 9.999594e-01
IBV.FINALTRUE 3.122875e+15 0.000000e+00 Inf 3.675842e-10 1 9.999847e-01
IBD.FINALTRUE 1.329903e+27 0.000000e+00 Inf 1.867114e-09 1 9.999655e-01
FLU.FINALTRUE 3.415398e-65 NA Inf 2.438272e-09 1 9.999606e-01
E.COLI.FINALTRUE 1.753230e+03 0.000000e+00 NA -1.738343e-11 1 1.000000e+00
ProstrationTRUE 4.035164e-31 0.000000e+00 Inf 2.152631e-09 1 9.999630e-01
RespiratoryTRUE 7.497032e-27 0.000000e+00 Inf 7.240017e-10 1 9.999785e-01
DiarrheaTRUE 6.239875e+16 0.000000e+00 Inf 6.292358e-10 1 9.999800e-01
CNSTRUE 4.631599e-77 0.000000e+00 Inf 1.783535e-09 1 9.999663e-01
JointsTRUE 1.085680e+05 0.000000e+00 Inf 3.204637e-11 1 9.999955e-01
AnemiaTRUE 1.353386e+05 0.000000e+00 NA 1.520295e-11 1 9.999969e-01
Age.weeks. 1.069853e+09 7.170412e-270 7.884419e+281 1.996654e+01 1 7.880919e-06
Helminth.Y.NTRUE 1.952502e-08 0.000000e+00 Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 7.956916e+64 0.000000e+00 Inf 3.524157e-09 1 9.999526e-01
------------------------------------------------------------------
[1] "PM.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 2.705115e-11 NA 7.261780e+109 NA NA NA
AVI.FINALTRUE 2.137489e+01 4.432138e-01 5.727307e+04 2.100795e+00 1 0.1472226
ORT.FINALTRUE 3.657294e+01 4.386059e-01 2.262621e+04 2.466594e+00 1 0.1162897
MG.FINALTRUE 5.604501e+00 1.602232e-01 3.603282e+02 9.635976e-01 1 0.3262821
IBV.FINALTRUE 1.240826e+01 2.660359e-01 1.521493e+03 1.680123e+00 1 0.1949081
IBD.FINALTRUE 2.248408e+00 1.211135e-01 7.508058e+01 3.083506e-01 1 0.5786941
FLU.FINALTRUE 3.459492e-06 NA 3.899483e+220 5.729872e-03 1 0.9396610
E.COLI.FINALTRUE 1.174326e+00 2.876995e-02 1.933143e+01 1.096810e-02 1 0.9165911
ProstrationTRUE 1.490999e+08 1.833189e-120 NA 2.563753e+00 1 0.1093387
RespiratoryTRUE 2.369693e-01 4.005757e-03 4.970064e+00 8.103058e-01 1 0.3680298
DiarrheaTRUE 2.810052e+00 1.542604e-01 1.396276e+02 4.516111e-01 1 0.5015709
CNSTRUE 8.822928e+01 1.278406e-01 6.188941e+05 1.784679e+00 1 0.1815759
JointsTRUE 1.012131e+00 1.201388e-02 4.164006e+01 4.074979e-05 1 0.9949067
AnemiaTRUE 5.106275e+01 3.553578e-01 2.086026e+05 2.287700e+00 1 0.1304030
Age.weeks. 8.961956e-01 5.408557e-01 1.397067e+00 2.512032e-01 1 0.6162292
Helminth.Y.NTRUE 8.212072e-02 3.444854e-04 3.159342e+00 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 1.401503e+00 1.322976e-02 1.380762e+02 2.557714e-02 1 0.8729374
------------------------------------------------------------------
[1] "MG.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 8.693888e-02 1.289117e-03 3.597971e+00 NA NA NA
AVI.FINALTRUE 1.497905e+01 1.389841e+00 5.022245e+02 5.1616020 1 0.02309159
ORT.FINALTRUE 3.742810e+01 9.439915e-01 4.965224e+03 3.7076985 1 0.05416203
PM.FINALTRUE 3.258713e+00 1.174240e-01 8.759497e+01 0.5260944 1 0.46825348
IBV.FINALTRUE 9.759750e+00 1.116509e+00 1.474915e+02 4.2646159 1 0.03891405
IBD.FINALTRUE 3.435944e-01 3.452857e-02 2.512368e+00 1.0783841 1 0.29905933
FLU.FINALTRUE 1.861830e-07 NA 5.815732e+57 0.5527790 1 0.45718441
E.COLI.FINALTRUE 1.457720e+00 1.415406e-01 1.354360e+01 0.1121486 1 0.73771112
ProstrationTRUE 1.779451e+00 1.304072e-01 3.352765e+01 0.1818453 1 0.66979220
RespiratoryTRUE 3.152167e-01 2.659551e-02 2.578922e+00 1.1238332 1 0.28909456
DiarrheaTRUE 4.366404e-01 4.134652e-02 4.431197e+00 0.5281734 1 0.46737581
CNSTRUE 2.797821e-03 1.839222e-06 6.132224e-01 4.6915799 1 0.03031076
JointsTRUE 1.804403e+01 4.263299e-01 1.177575e+03 2.2864831 1 0.13050534
AnemiaTRUE 2.425157e+00 8.438896e-02 6.023178e+01 0.3034681 1 0.58171637
Age.weeks. 7.469839e-01 4.765044e-01 1.065934e+00 2.5394831 1 0.11103113
Helminth.Y.NTRUE 6.469189e+00 8.137168e-01 8.452461e+01 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 1.817206e-01 2.808182e-03 5.745399e+00 0.8948573 1 0.34416441
------------------------------------------------------------------
[1] "IBV.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 2.165014e-01 0.005137763 6.777820e+00 NA NA NA
AVI.FINALTRUE 1.349378e+00 0.197573886 1.002538e+01 0.09548589 1 0.7573155
ORT.FINALTRUE 1.437459e+00 0.078213120 2.843786e+01 0.06153539 1 0.8040854
PM.FINALTRUE 5.090138e+00 0.287836114 1.236276e+02 1.26144848 1 0.2613771
MG.FINALTRUE 4.193955e+00 0.686106061 2.843362e+01 2.42572595 1 0.1193579
IBD.FINALTRUE 6.425573e-01 0.073114753 4.211794e+00 0.20496507 1 0.6507427
FLU.FINALTRUE 3.583203e-07 NA 1.380993e+58 0.34933598 1 0.5544893
E.COLI.FINALTRUE 6.453210e-01 0.048931398 5.820036e+00 0.14192020 1 0.7063795
ProstrationTRUE 3.212344e-01 0.030649485 2.987524e+00 1.01240142 1 0.3143282
RespiratoryTRUE 3.068364e+00 0.564717568 2.390331e+01 1.63824252 1 0.2005668
DiarrheaTRUE 1.085999e+00 0.172084747 8.253220e+00 0.00749658 1 0.9310031
CNSTRUE 1.466625e+00 0.048597874 2.595579e+01 0.06470370 1 0.7992103
JointsTRUE 9.849185e-02 0.002721591 1.728271e+00 2.47823619 1 0.1154316
AnemiaTRUE 4.763620e-01 0.024424674 6.308125e+00 0.31203922 1 0.5764315
Age.weeks. 8.873629e-01 0.630834987 1.206970e+00 0.57464672 1 0.4484183
Helminth.Y.NTRUE 4.479369e+00 0.698899395 3.608395e+01 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 3.365812e-01 0.014217690 5.025726e+00 0.60055877 1 0.4383649
------------------------------------------------------------------
[1] "IBD.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 1.385457e+00 0.03127715 4.228781e+01 NA NA NA
AVI.FINALTRUE 1.381109e+00 0.29252531 7.038540e+00 0.165471958 1 0.68416778
ORT.FINALTRUE 7.609574e+00 0.36812623 1.597242e+02 1.790848128 1 0.18082286
PM.FINALTRUE 9.329892e-01 0.06680518 1.004703e+01 0.003222499 1 0.95473075
MG.FINALTRUE 5.397819e-01 0.05918339 3.581342e+00 0.390180363 1 0.53220461
IBV.FINALTRUE 6.452596e-01 0.06922966 4.284986e+00 0.193692298 1 0.65986115
FLU.FINALTRUE 2.050323e-07 NA 1.554238e+50 0.641278808 1 0.42324810
E.COLI.FINALTRUE 1.128939e+00 0.16992335 6.896086e+00 0.017378942 1 0.89511938
ProstrationTRUE 1.720125e+00 0.13097176 5.249041e+01 0.151434688 1 0.69716807
RespiratoryTRUE 3.798028e-01 0.08205173 1.588342e+00 1.757585564 1 0.18492596
DiarrheaTRUE 1.263654e+00 0.24403769 8.167991e+00 0.074108926 1 0.78544552
CNSTRUE 1.152072e+00 0.03288969 2.588741e+01 0.007939940 1 0.92899740
JointsTRUE 7.476421e-01 0.02302319 1.084889e+01 0.040769749 1 0.83998302
AnemiaTRUE 6.265126e-01 0.01978473 7.973987e+00 0.112346422 1 0.73748842
Age.weeks. 8.073624e-01 0.61562063 1.023967e+00 3.094821640 1 0.07854176
Helminth.Y.NTRUE 5.951413e-01 0.10920049 2.954281e+00 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 8.059503e-01 0.04395353 1.206689e+01 0.024757921 1 0.87497177
------------------------------------------------------------------
[1] "FLU.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 1.181799e-20 0.0000000 Inf NA NA NA
AVI.FINALTRUE 3.201600e+08 0.0000000 Inf 2.911291e-09 1 0.9999569
ORT.FINALTRUE 1.727392e+06 0.0000000 Inf 1.375823e-08 1 0.9999064
PM.FINALTRUE 1.042214e+15 0.0000000 Inf 5.460783e-10 1 0.9999814
MG.FINALTRUE 1.543973e-18 0.0000000 Inf 9.599440e-09 1 0.9999218
IBV.FINALTRUE 4.131783e-08 0.0000000 Inf 8.318040e-10 1 0.9999770
IBD.FINALTRUE 1.104422e-10 0.0000000 Inf 5.051090e-09 1 0.9999433
E.COLI.FINALTRUE 1.480758e-08 0.0000000 Inf 7.578399e-02 1 0.7830943
ProstrationTRUE 1.253101e+02 0.0000000 Inf 2.094556e-10 1 0.9999885
RespiratoryTRUE 4.138974e-18 0.0000000 Inf 4.925923e-01 1 0.4827732
DiarrheaTRUE 1.271943e-08 0.0000000 Inf 3.495815e-09 1 0.9999528
CNSTRUE 1.712503e-27 0.0000000 Inf 1.259537e-09 1 0.9999717
JointsTRUE 1.546652e+00 0.0000000 Inf -6.933965e-11 1 1.0000000
AnemiaTRUE 1.354932e-07 0.0000000 Inf 5.346581e-10 1 0.9999816
Age.weeks. 1.402909e+00 0.1816134 31.40271 1.103948e-01 1 0.7396952
Helminth.Y.NTRUE 1.368272e+24 0.0000000 Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 8.896048e-09 0.0000000 Inf 1.597137e-09 1 0.9999681
------------------------------------------------------------------
[1] "E.COLI.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 4.865070e-10 NA 6.550080e+145 NA NA NA
AVI.FINALTRUE 2.260969e+00 2.880738e-01 2.318060e+01 0.59543983 1 0.44032325
ORT.FINALTRUE 3.569188e+01 9.250582e-01 5.803338e+03 3.66781892 1 0.05547273
PM.FINALTRUE 1.370574e+00 7.555235e-02 1.992802e+01 0.05423650 1 0.81584891
MG.FINALTRUE 2.091896e+00 1.941408e-01 2.259296e+01 0.39928717 1 0.52745762
IBV.FINALTRUE 1.273424e+00 4.612844e-02 2.455157e+01 0.02609822 1 0.87166067
IBD.FINALTRUE 6.586180e-01 8.160626e-02 4.284460e+00 0.18586341 1 0.66638200
FLU.FINALTRUE 2.203102e+00 2.710134e-02 1.323436e+02 0.14615023 1 0.70224182
ProstrationTRUE 1.086576e+09 9.682549e-160 NA 4.55334500 1 0.03285450
RespiratoryTRUE 2.474713e-01 1.406780e-02 2.247137e+00 1.48276849 1 0.22334187
DiarrheaTRUE 4.880491e-01 5.633634e-02 5.136823e+00 0.41292862 1 0.52048678
CNSTRUE 4.676377e-09 NA 4.796818e+131 1.42549590 1 0.23250092
JointsTRUE 8.304826e+00 8.818148e-02 5.318047e+02 0.98274684 1 0.32152160
AnemiaTRUE 1.022457e-08 NA 1.247700e+122 1.51151797 1 0.21890760
Age.weeks. 8.922786e-01 6.498033e-01 1.195778e+00 0.58884014 1 0.44286798
Helminth.Y.NTRUE 1.580622e+00 1.375805e-01 1.632494e+01 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 4.534110e-02 9.508181e-05 3.932238e+00 1.68197567 1 0.19466214
------------------------------------------------------------------It shows that
Of note: this confounder effect correction is to unraveal “biological” relationships between in order to understand how things works. But that doesn’t have much of practical benefit in a particular situation. If instead you aim at predicting the etiology (or simply the presence of a pathogen), then rerun the above model, without including the pathogens in the \(x\) variables:
> for(i in seq_along(xs)) {
+ print(xs[i])
+ print(make_table(glm(formula(paste(xs[i], "~", paste(ys, collapse = " + "))), binomial, data)))
+ cat("------------------------------------------------------------------\n")
+ }
[1] "AVI.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.6254003 0.043812735 8.8010135 NA NA NA
ProstrationTRUE 0.7257343 0.086700906 5.3002080 0.0999329 1 0.75191017
RespiratoryTRUE 2.0938104 0.642051658 7.1721057 1.4980228 1 0.22097584
DiarrheaTRUE 0.6955445 0.158942125 2.8018478 0.2596047 1 0.61039185
CNSTRUE 0.1379565 0.004290178 1.8547825 2.1761637 1 0.14016346
JointsTRUE 9.8353965 0.635099782 529.6508648 2.5276037 1 0.11186999
AnemiaTRUE 0.1298929 0.012037934 0.8844019 4.3727864 1 0.03651723
Age.weeks. 1.1986870 1.006661956 1.4736918 4.1582021 1 0.04143336
Helminth.Y.NTRUE 0.8420943 0.219139051 3.1262048 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 4.5113671 0.511276881 68.5631037 1.7710359 1 0.18325393
------------------------------------------------------------------
[1] "ORT.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 3.671823e-04 9.703369e-08 9.774825e-02 NA NA NA
ProstrationTRUE 1.341162e-01 2.345440e-03 6.659063e+00 1.11619724 1 0.2907387623
RespiratoryTRUE 3.478991e+00 2.677423e-01 8.373674e+01 0.87833182 1 0.3486589875
DiarrheaTRUE 1.885786e+00 2.023433e-01 3.047690e+01 0.28931734 1 0.5906583296
CNSTRUE 7.599665e-02 5.375567e-04 2.346018e+00 2.04733607 1 0.1524727739
JointsTRUE 1.601586e+00 4.541568e-02 5.486588e+01 0.07428086 1 0.7852028803
AnemiaTRUE 2.464279e-01 8.686285e-03 4.092913e+00 0.91134071 1 0.3397589381
Age.weeks. 1.606373e+00 1.194983e+00 2.450763e+00 11.37603291 1 0.0007439784
Helminth.Y.NTRUE 4.644652e+00 2.356561e-01 2.711723e+02 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 6.641275e+01 2.894920e+00 5.251781e+03 7.31065861 1 0.0068546799
------------------------------------------------------------------
[1] "PM.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 4.835114e-09 NA 6.425899e+72 NA NA NA
ProstrationTRUE 9.591958e+06 8.435411e-85 NA 1.09285963 1 0.2958385
RespiratoryTRUE 5.560054e-01 7.898462e-02 3.236518e+00 0.42797763 1 0.5129830
DiarrheaTRUE 2.314515e+00 3.430180e-01 2.778294e+01 0.67647007 1 0.4108049
CNSTRUE 7.647128e-01 2.603029e-02 1.597803e+01 0.02995426 1 0.8625941
JointsTRUE 2.300501e+00 1.292278e-01 3.630601e+01 0.36000986 1 0.5485008
AnemiaTRUE 2.725811e+00 2.370855e-01 2.686010e+01 0.70804660 1 0.4000931
Age.weeks. 1.023063e+00 7.686396e-01 1.311041e+00 0.02955637 1 0.8635007
Helminth.Y.NTRUE 1.117848e+00 1.169701e-01 1.067194e+01 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 4.805506e+00 4.426796e-01 6.960678e+01 1.67606803 1 0.1954477
------------------------------------------------------------------
[1] "MG.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.14919318 0.007375739 2.304795 NA NA NA
ProstrationTRUE 0.70304787 0.094741785 5.968965 0.1158081 1 0.73362622
RespiratoryTRUE 1.41790914 0.365864930 5.800285 0.2565196 1 0.61252140
DiarrheaTRUE 1.22739805 0.273738515 6.200826 0.0696929 1 0.79178445
CNSTRUE 0.06850305 0.001118038 1.204518 3.2878971 1 0.06979235
JointsTRUE 6.13540251 0.507309650 167.892899 1.9802559 1 0.15936345
AnemiaTRUE 1.36048607 0.185918488 9.136227 0.1012481 1 0.75033693
Age.weeks. 0.95689905 0.784995127 1.144732 0.2234231 1 0.63644401
Helminth.Y.NTRUE 4.44237432 1.000442934 25.191764 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 1.69730503 0.225343490 13.496321 0.2711258 1 0.60257754
------------------------------------------------------------------
[1] "IBV.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.1449621 0.005497502 2.966725 NA NA NA
ProstrationTRUE 0.2925335 0.037624785 2.087117 1.52857089 1 0.21632706
RespiratoryTRUE 3.8806398 0.859956130 22.622692 3.08687121 1 0.07892643
DiarrheaTRUE 1.9903256 0.387444520 13.502983 0.64265537 1 0.42275088
CNSTRUE 0.7354356 0.026851916 10.012266 0.04954470 1 0.82385743
JointsTRUE 0.2459319 0.008321399 3.322265 1.05977916 1 0.30326556
AnemiaTRUE 0.8159679 0.082389320 6.802606 0.03572886 1 0.85007652
Age.weeks. 0.9259039 0.736952360 1.133039 0.53394163 1 0.46495441
Helminth.Y.NTRUE 5.2782902 1.093815239 33.114406 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 0.6893780 0.065214901 5.707652 0.11527485 1 0.73421690
------------------------------------------------------------------
[1] "IBD.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.9454030 0.02524097 21.360133 NA NA NA
ProstrationTRUE 1.7830503 0.17238287 44.623240 0.20864765 1 0.6478294
RespiratoryTRUE 0.4034798 0.09837363 1.507912 1.81255950 1 0.1782015
DiarrheaTRUE 1.3764174 0.29729354 7.744846 0.16014225 1 0.6890256
CNSTRUE 0.8514412 0.03000908 12.946388 0.01277492 1 0.9100098
JointsTRUE 1.2353753 0.05051543 13.937569 0.02538432 1 0.8734132
AnemiaTRUE 0.5509003 0.02267103 5.238017 0.23254629 1 0.6296422
Age.weeks. 0.8604061 0.68394217 1.043768 2.25575771 1 0.1331183
Helminth.Y.NTRUE 0.4565090 0.09711881 1.894312 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 2.0226795 0.17641087 20.703550 0.35424862 1 0.5517179
------------------------------------------------------------------
[1] "FLU.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 3.796834e-20 0.000000e+00 0.000000e+00 NA NA NA
ProstrationTRUE 2.758315e+06 0.000000e+00 Inf 5.017197e-03 1 0.94353132
RespiratoryTRUE 1.171673e-10 6.632153e-255 3.516521e+225 4.207015e+00 1 0.04025712
DiarrheaTRUE 1.766541e+00 1.953656e-04 5.151652e+06 1.660425e-02 1 0.89747041
CNSTRUE 2.563083e-10 0.000000e+00 Inf 1.470024e-11 1 0.99999694
JointsTRUE 5.886062e-01 0.000000e+00 Inf 7.514700e-11 1 0.99999308
AnemiaTRUE 7.201134e-10 0.000000e+00 Inf 1.262466e-10 1 0.99999104
Age.weeks. 2.733158e+00 1.073585e+00 5.043833e+01 5.028613e+00 1 0.02493186
Helminth.Y.NTRUE 2.486032e+08 Inf Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 1.823710e-01 0.000000e+00 Inf 1.153628e-10 1 0.99999143
------------------------------------------------------------------
[1] "E.COLI.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 2.302718e-09 NA 1.456324e+100 NA NA NA
ProstrationTRUE 8.545651e+07 7.179660e-112 NA 2.83430826 1 0.09227053
RespiratoryTRUE 7.475316e-01 1.415100e-01 3.678613e+00 0.12962337 1 0.71882286
DiarrheaTRUE 6.955886e-01 1.180898e-01 5.093507e+00 0.14921681 1 0.69928493
CNSTRUE 8.311884e-09 NA 1.655843e+173 2.37501884 1 0.12329011
JointsTRUE 5.764171e+00 1.521996e-01 2.425676e+02 1.02529027 1 0.31126742
AnemiaTRUE 2.486534e-08 NA 1.263225e+137 2.17695462 1 0.14009143
Age.weeks. 1.046550e+00 8.609505e-01 1.284642e+00 0.21395993 1 0.64368120
Helminth.Y.NTRUE 2.075306e+00 4.102579e-01 1.122597e+01 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 6.391344e-01 1.338542e-02 1.335479e+01 0.07629837 1 0.78237787
------------------------------------------------------------------> symptoms <- c("RESPIRATORY.SIGNS", "DIARRHOEA", "JOINT.FOOT.PROBLEMS", "ABNORMAL.EGGS",
+ "NERVOUS.SIGNS", "ANAEMIA", "REDUCTION.IN.FEED.CONSUMPTION....")
> data2 <- "summary data.csv" %>%
+ read.csv() %>%
+ mutate_at(symptoms, `>`, 0) %>%
+ mutate_at(vars(contains("FINAL")), `>`, 0) %>%
+ mutate(Helminth.Y.N = Helminth.Y.N == "Yes") %>%
+ mutate_at(vars(ends_with("y.n")), `>`, 0)> xs <- grep("FINAL", names(data2), value = TRUE) %>%
+ grep("ND", ., invert = TRUE, value = TRUE) %>%
+ grep("FLU", ., invert = TRUE, value = TRUE)No log transformation:
> ys <- c("Age.weeks.", "Nochicks", "Proportion.of.morbidity..per.100.", "Cumulative.mortality", "Days.onset", "Ratio.of.weight.standard.weight")
> for(i in seq_along(xs)) {
+ print(xs[i])
+ print(make_table(glm(formula(paste(xs[i], "~", paste(ys, collapse = " + "))), binomial, data2)))
+ cat("------------------------------------------------------------------\n")
+ }
[1] "AVI.FINAL..PCR.CULTURE."
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.09353626 0.009008902 0.7289286 NA NA NA
Age.weeks. 1.14222238 0.965397640 1.3900559 2.3560553 1 0.12479740
Nochicks 0.99869123 0.995459142 1.0018569 0.6824186 1 0.40875513
Proportion.of.morbidity..per.100. 1.01542817 0.996397679 1.0387976 2.4624774 1 0.11659475
Cumulative.mortality 0.97814090 0.944617433 1.0120932 1.6620578 1 0.19732571
Days.onset 1.08994848 0.960297726 1.2733353 1.7178665 1 0.18996791
Ratio.of.weight.standard.weight 11.26239977 1.191242668 159.6980687 4.5036166 1 0.03382324
------------------------------------------------------------------
[1] "ORT.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.0164595 0.0003619115 0.3027945 NA NA NA
Age.weeks. 1.3365713 1.0758749441 1.7659714 7.18162939 1 0.007365379
Nochicks 1.0010213 0.9967414177 1.0049971 0.25259937 1 0.615250702
Proportion.of.morbidity..per.100. 0.9934367 0.9612179666 1.0183568 0.23826018 1 0.625465535
Cumulative.mortality 0.9867229 0.9393800547 1.0309735 0.37328004 1 0.541221774
Days.onset 1.0236007 0.8266677913 1.2129008 0.06079338 1 0.805246334
Ratio.of.weight.standard.weight 0.5956785 0.0177460076 13.3039236 0.10259247 1 0.748740472
------------------------------------------------------------------
[1] "PM.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.03908796 0.001349326 0.6710339 NA NA NA
Age.weeks. 1.03725612 0.853917299 1.2492349 0.14850112 1 0.6999719
Nochicks 0.99900495 0.993253204 1.0033144 0.17407185 1 0.6765181
Proportion.of.morbidity..per.100. 1.01202435 0.988564575 1.0348289 1.07592053 1 0.2996120
Cumulative.mortality 0.99771773 0.963326042 1.0309021 0.01898317 1 0.8904147
Days.onset 1.05627098 0.910958656 1.2087609 0.59632437 1 0.4399839
Ratio.of.weight.standard.weight 1.79933545 0.090416639 28.7008598 0.16784316 1 0.6820358
------------------------------------------------------------------
[1] "MG.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.1252043 0.01225616 0.9994243 NA NA NA
Age.weeks. 0.9493176 0.79914351 1.1088613 0.416855628 1 0.51851021
Nochicks 0.9999054 0.99651458 1.0029878 0.003475069 1 0.95299216
Proportion.of.morbidity..per.100. 1.0016419 0.98238687 1.0195275 0.031101003 1 0.86001524
Cumulative.mortality 0.9867647 0.94925803 1.0186220 0.641488276 1 0.42317238
Days.onset 1.1197513 0.99577811 1.2694929 3.573497789 1 0.05870853
Ratio.of.weight.standard.weight 3.8816576 0.46045814 34.5800902 1.577558088 1 0.20911278
------------------------------------------------------------------
[1] "IBV.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.1778530 0.01351153 1.925582 NA NA NA
Age.weeks. 0.8923384 0.72225324 1.069206 1.4696310 1 0.22540393
Nochicks 0.9984436 0.99373220 1.002179 0.6033084 1 0.43731852
Proportion.of.morbidity..per.100. 1.0124532 0.99254143 1.032471 1.5405933 1 0.21452951
Cumulative.mortality 0.9726907 0.92277551 1.010061 1.9443140 1 0.16320089
Days.onset 1.1740497 1.03156028 1.362828 5.9442404 1 0.01476545
Ratio.of.weight.standard.weight 1.9744702 0.16118449 24.161553 0.2992893 1 0.58432833
------------------------------------------------------------------
[1] "GUM.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 1.4399699 0.1306758 18.4749269 NA NA NA
Age.weeks. 0.7725407 0.5841349 0.9579286 5.7732678 1 0.01627175
Nochicks 0.9983919 0.9939146 1.0020641 0.6725745 1 0.41215545
Proportion.of.morbidity..per.100. 0.9919529 0.9672883 1.0129162 0.5274428 1 0.46768394
Cumulative.mortality 1.0132389 0.9768595 1.0528852 0.5206829 1 0.47055053
Days.onset 0.9273814 0.7713640 1.0655837 1.0504854 1 0.30539532
Ratio.of.weight.standard.weight 5.7431558 0.6108693 68.2060184 2.3235402 1 0.12742972
------------------------------------------------------------------
[1] "E.COLI.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.04336807 0.002024215 0.5304076 NA NA NA
Age.weeks. 0.98971495 0.811501693 1.1944866 0.01179437 1 0.91351827
Nochicks 1.00367184 0.999729149 1.0082036 3.34271415 1 0.06750318
Proportion.of.morbidity..per.100. 0.98926513 0.948772821 1.0168628 0.49864102 1 0.48009786
Cumulative.mortality 1.03832686 0.998888135 1.0945711 3.61093167 1 0.05740095
Days.onset 1.08131392 0.938192230 1.2478652 1.23102903 1 0.26720701
Ratio.of.weight.standard.weight 0.48784173 0.012612862 10.8812840 0.18936849 1 0.66344274
------------------------------------------------------------------With log transformations:
> yslog <- ys %>%
+ paste0("log(", ., ")") %>%
+ sub("mortality)$", "mortality + 1)", .)
> for(i in seq_along(xs)) {
+ print(xs[i])
+ print(make_table(glm(formula(paste(xs[i], "~", paste(yslog, collapse = " + "))), binomial, data2)))
+ cat("------------------------------------------------------------------\n")
+ }
[1] "AVI.FINAL..PCR.CULTURE."
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 1.9284890 0.003116089 1289.376738 NA NA NA
log(Age.weeks.) 1.4351054 0.469079993 4.293742 0.4176757 1 0.51809911
log(Nochicks) 0.7495341 0.301756314 1.848732 0.4020105 1 0.52605277
log(Proportion.of.morbidity..per.100.) 1.4205595 0.758363412 2.846441 1.1782876 1 0.27770488
log(Cumulative.mortality + 1) 0.7445997 0.369519028 1.452037 0.7471793 1 0.38737076
log(Days.onset) 2.3197520 0.968050486 6.347708 3.5491500 1 0.05957596
log(Ratio.of.weight.standard.weight) 5.4568571 1.440263023 26.632274 6.4256321 1 0.01124849
------------------------------------------------------------------
[1] "ORT.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 3.135521e-05 6.898546e-10 0.1695293 NA NA NA
log(Age.weeks.) 1.327212e+01 1.638895e+00 267.5473711 6.412729069 1 0.01133051
log(Nochicks) 1.661085e+00 5.084828e-01 5.9705851 0.714199946 1 0.39805305
log(Proportion.of.morbidity..per.100.) 9.189103e-01 3.394429e-01 2.1502325 0.035826922 1 0.84987336
log(Cumulative.mortality + 1) 7.237723e-01 2.583806e-01 1.9388523 0.429253154 1 0.51235564
log(Days.onset) 2.012840e+00 5.208625e-01 8.4893476 1.048924164 1 0.30575499
log(Ratio.of.weight.standard.weight) 9.404006e-01 1.116162e-01 9.3680561 0.003110314 1 0.95552488
------------------------------------------------------------------
[1] "PM.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.02976893 4.935109e-06 126.121042 NA NA NA
log(Age.weeks.) 0.88096511 2.669308e-01 3.212609 0.042607269 1 0.8364665
log(Nochicks) 0.94655747 2.621943e-01 3.118049 0.008062208 1 0.9284543
log(Proportion.of.morbidity..per.100.) 1.43697386 5.163350e-01 3.894767 0.529505145 1 0.4668150
log(Cumulative.mortality + 1) 1.26812422 5.451815e-01 3.238755 0.300489099 1 0.5835760
log(Days.onset) 1.45067241 4.995670e-01 4.251517 0.489763932 1 0.4840326
log(Ratio.of.weight.standard.weight) 1.60213434 2.398702e-01 11.999663 0.238307762 1 0.6254310
------------------------------------------------------------------
[1] "MG.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.4370582 0.001026811 197.592561 NA NA NA
log(Age.weeks.) 0.7087752 0.248948634 1.970010 0.448742520 1 0.50293272
log(Nochicks) 0.9755818 0.406495751 2.302499 0.003226307 1 0.95470404
log(Proportion.of.morbidity..per.100.) 1.0855335 0.523758508 2.148003 0.053955568 1 0.81631792
log(Cumulative.mortality + 1) 0.7665611 0.363821989 1.589068 0.523227671 1 0.46946809
log(Days.onset) 2.5052455 1.046990759 6.561692 4.263227373 1 0.03894586
log(Ratio.of.weight.standard.weight) 3.0112580 0.773783125 13.816849 2.499173507 1 0.11390606
------------------------------------------------------------------
[1] "IBV.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 6.3466317 0.007218555 10443.262392 NA NA NA
log(Age.weeks.) 0.4071975 0.119140739 1.215581 2.5885909 1 0.1076361
log(Nochicks) 0.5954578 0.204889655 1.543470 1.1112493 1 0.2918105
log(Proportion.of.morbidity..per.100.) 1.1607908 0.497242961 2.527194 0.1335782 1 0.7147506
log(Cumulative.mortality + 1) 0.7139014 0.301001356 1.629489 0.6543525 1 0.4185608
log(Days.onset) 3.0786196 1.169389339 9.206282 5.2257148 1 0.0222553
log(Ratio.of.weight.standard.weight) 1.9542339 0.464575036 9.644875 0.8175182 1 0.3659068
------------------------------------------------------------------
[1] "GUM.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 35.5874217 0.03561008 89035.490671 NA NA NA
log(Age.weeks.) 0.3416962 0.09300820 1.038387 3.5774809 1 0.0585679
log(Nochicks) 0.7577228 0.26087088 2.041535 0.2955498 1 0.5866858
log(Proportion.of.morbidity..per.100.) 0.6803916 0.26476210 1.467316 0.9014951 1 0.3423811
log(Cumulative.mortality + 1) 1.6364912 0.76102558 4.070261 1.5341526 1 0.2154903
log(Days.onset) 0.6626054 0.24259687 1.642874 0.7709627 1 0.3799194
log(Ratio.of.weight.standard.weight) 3.2700809 0.79678367 16.617458 2.6663109 1 0.1024933
------------------------------------------------------------------
[1] "E.COLI.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 3.319336e-05 3.342783e-10 0.4434172 NA NA NA
log(Age.weeks.) 8.495481e-01 1.732033e-01 4.1100106 0.04363109 1 0.83454147
log(Nochicks) 3.257588e+00 8.865816e-01 14.8501740 3.15113894 1 0.07587399
log(Proportion.of.morbidity..per.100.) 5.266733e-01 1.050242e-01 1.6813442 1.04484734 1 0.30669678
log(Cumulative.mortality + 1) 3.785138e+00 1.266587e+00 18.9830950 6.02218005 1 0.01412719
log(Days.onset) 2.388314e+00 8.098860e-01 8.1846470 2.47493765 1 0.11567403
log(Ratio.of.weight.standard.weight) 1.331136e+00 1.508840e-01 13.0208456 0.06720893 1 0.79544479
------------------------------------------------------------------With some log transformations:
> sel <- c(1, 3, 6)
> for(i in seq_along(xs)) {
+ print(xs[i])
+ print(make_table(glm(formula(paste(xs[i], "~", paste(c(ys[sel], yslog[-sel]), collapse = " + "))), binomial, data2)))
+ cat("------------------------------------------------------------------\n")
+ }
[1] "AVI.FINAL..PCR.CULTURE."
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.3401150 0.001302839 74.365874 NA NA NA
Age.weeks. 1.0962229 0.922052209 1.330798 1.0501358 1 0.30547582
Proportion.of.morbidity..per.100. 1.0152745 0.995792129 1.038033 2.3131881 1 0.12828070
Ratio.of.weight.standard.weight 11.6564475 1.256790247 161.251404 4.7212159 1 0.02979267
log(Nochicks) 0.7098479 0.289986747 1.693498 0.6041792 1 0.43698791
log(Cumulative.mortality + 1) 0.7409912 0.384316132 1.377891 0.8916256 1 0.34503717
log(Days.onset) 2.3316119 0.945744057 6.587530 3.3626772 1 0.06668957
------------------------------------------------------------------
[1] "ORT.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.0009240876 2.961755e-07 0.7824741 NA NA NA
Age.weeks. 1.3038823246 1.052157e+00 1.7069869 6.05023280 1 0.01390446
Proportion.of.morbidity..per.100. 0.9968997681 9.644614e-01 1.0240576 0.04606026 1 0.83006630
Ratio.of.weight.standard.weight 0.6587002747 1.836905e-02 16.0707029 0.06369533 1 0.80074787
log(Nochicks) 1.6929520006 5.535978e-01 5.9786800 0.83723094 1 0.36018992
log(Cumulative.mortality + 1) 0.6790696188 2.461037e-01 1.7295120 0.66128655 1 0.41610611
log(Days.onset) 1.9125604885 4.835042e-01 8.0018894 0.88525407 1 0.34676666
------------------------------------------------------------------
[1] "PM.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.03046102 1.595212e-05 46.976969 NA NA NA
Age.weeks. 1.01943928 8.440372e-01 1.225730 0.04351242 1 0.8347634
Proportion.of.morbidity..per.100. 1.00639990 9.800362e-01 1.030904 0.25263765 1 0.6152239
Ratio.of.weight.standard.weight 1.55464837 6.666658e-02 28.411672 0.08595979 1 0.7693777
log(Nochicks) 0.92285770 2.604838e-01 3.016660 0.01762979 1 0.8943696
log(Cumulative.mortality + 1) 1.39672557 6.441711e-01 3.245537 0.71157309 1 0.3989221
log(Days.onset) 1.35204250 4.483298e-01 4.001655 0.30788959 1 0.5789781
------------------------------------------------------------------
[1] "MG.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.08083852 0.0003531159 14.925407 NA NA NA
Age.weeks. 0.92674765 0.7782185994 1.079803 0.9189974058 1 0.33773836
Proportion.of.morbidity..per.100. 1.00340282 0.9828395262 1.022995 0.1135953202 1 0.73608746
Ratio.of.weight.standard.weight 4.39811073 0.5063255885 41.191047 1.8206494077 1 0.17723600
log(Nochicks) 0.99209252 0.4209431288 2.318538 0.0003430408 1 0.98522294
log(Cumulative.mortality + 1) 0.78766506 0.3984317235 1.503068 0.5232599041 1 0.46945440
log(Days.onset) 2.58236942 1.0687256705 6.821526 4.4513981568 1 0.03487268
------------------------------------------------------------------
[1] "IBV.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 1.3736898 0.003398763 747.015958 NA NA NA
Age.weeks. 0.8558313 0.683345048 1.026347 2.7566491 1 0.09685091
Proportion.of.morbidity..per.100. 1.0168535 0.995176740 1.039571 2.3399236 1 0.12609574
Ratio.of.weight.standard.weight 2.1568992 0.173178719 27.773219 0.3728521 1 0.54145372
log(Nochicks) 0.6118139 0.212603121 1.600091 0.9856755 1 0.32080162
log(Cumulative.mortality + 1) 0.6040278 0.269024417 1.231478 1.8947107 1 0.16867156
log(Days.onset) 3.2762073 1.214849202 10.119808 5.5508155 1 0.01847208
------------------------------------------------------------------
[1] "GUM.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 1.2372023 0.002039708 991.4462400 NA NA NA
Age.weeks. 0.7863401 0.604195171 0.9657326 5.4449864 1 0.01962457
Proportion.of.morbidity..per.100. 0.9831013 0.955291309 1.0063963 1.9477985 1 0.16282428
Ratio.of.weight.standard.weight 6.4381086 0.647554145 78.7075143 2.5197088 1 0.11243135
log(Nochicks) 0.8301716 0.286059004 2.2946467 0.1284443 1 0.72005053
log(Cumulative.mortality + 1) 1.8099744 0.886889118 4.0932420 2.6271908 1 0.10504743
log(Days.onset) 0.6756262 0.241348627 1.7203697 0.6604686 1 0.41639457
------------------------------------------------------------------
[1] "E.COLI.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 3.396303e-06 7.247073e-11 0.01246413 NA NA NA
Age.weeks. 1.011677e+00 8.245801e-01 1.24212806 0.01320726 1 0.90850626
Proportion.of.morbidity..per.100. 9.728916e-01 9.279340e-01 1.00677629 2.32101416 1 0.12763679
Ratio.of.weight.standard.weight 1.180487e+00 2.554752e-02 42.59415404 0.00821109 1 0.92779846
log(Nochicks) 3.627341e+00 9.935278e-01 17.34175451 3.80135707 1 0.05121106
log(Cumulative.mortality + 1) 4.357144e+00 1.537088e+00 18.50349011 8.53356045 1 0.00348657
log(Days.onset) 2.102290e+00 6.728473e-01 7.60977932 1.62741044 1 0.20206160
------------------------------------------------------------------> additional_variables <- c(grep("y.n", names(data2), TRUE, value = TRUE), symptoms)No log transformation:
> for(i in seq_along(xs)) {
+ print(xs[i])
+ print(make_table(glm(formula(paste(xs[i], "~", paste(c(ys, additional_variables), collapse = " + "))), binomial, data2)))
+ cat("------------------------------------------------------------------\n")
+ }
[1] "AVI.FINAL..PCR.CULTURE."
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 4.039669e-07 3.128297e-16 1.240000e-02 NA NA NA
Age.weeks. 1.033060e+00 6.988975e-01 1.824014e+00 0.02388638 1 0.8771743688
Nochicks 9.919837e-01 9.801577e-01 9.994875e-01 4.44692618 1 0.0349641267
Proportion.of.morbidity..per.100. 1.126487e+00 1.036214e+00 1.361758e+00 12.28304550 1 0.0004570918
Cumulative.mortality 9.141046e-01 7.690414e-01 1.001551e+00 3.70191058 1 0.0543502000
Days.onset 1.047728e+00 8.081557e-01 1.415648e+00 0.13038312 1 0.7180351379
Ratio.of.weight.standard.weight 2.970473e+07 2.732856e+02 8.741070e+17 13.79231902 1 0.0002041692
Helminth.Y.NTRUE 1.037271e+03 2.287899e+00 6.271744e+07 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 2.923578e+00 5.217553e-02 3.193042e+02 0.27755979 1 0.5983050971
RESPIRATORY.SIGNSTRUE 3.782043e+00 7.331542e-02 2.851639e+02 0.45212994 1 0.5013252124
DIARRHOEATRUE 2.558351e-01 3.457049e-03 6.358315e+00 0.68566013 1 0.4076444658
JOINT.FOOT.PROBLEMSTRUE 8.613997e-03 3.571640e-06 2.302838e+00 2.77724570 1 0.0956124682
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 4.494685e+03 8.662511e+00 1.462754e+08 8.17684314 1 0.0042428535
ANAEMIATRUE 2.970274e-03 1.465770e-06 1.364895e-01 11.39845359 1 0.0007350527
REDUCTION.IN.FEED.CONSUMPTION....TRUE 3.774317e+00 1.160400e-01 4.141462e+02 0.51036710 1 0.4749799846
------------------------------------------------------------------
[1] "ORT.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 1.625435e-130 0.000000e+00 Inf NA NA NA
Age.weeks. 5.320547e+03 4.114688e-288 3.152803e+300 5.040698e-07 1 9.994335e-01
Nochicks 1.130341e+00 7.623670e-04 3.661972e+02 4.410262e-09 1 9.999470e-01
Proportion.of.morbidity..per.100. 3.421933e-01 8.446436e-49 1.386339e+47 2.084005e-09 1 9.999636e-01
Cumulative.mortality 6.109283e-01 8.055470e-181 3.129544e+205 2.528378e-11 1 9.999960e-01
Days.onset 1.178891e+01 NA Inf 6.468994e-10 1 9.999797e-01
Ratio.of.weight.standard.weight 3.898562e+54 0.000000e+00 Inf 5.736289e-09 1 9.999396e-01
Helminth.Y.NTRUE 1.583760e+46 0.000000e+00 Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 1.802777e+53 0.000000e+00 Inf 1.693480e+01 1 3.868578e-05
RESPIRATORY.SIGNSTRUE 1.105819e-21 0.000000e+00 Inf 4.700313e-09 1 9.999453e-01
DIARRHOEATRUE 2.762779e+23 0.000000e+00 Inf 1.178477e-09 1 9.999726e-01
JOINT.FOOT.PROBLEMSTRUE 2.174042e+16 0.000000e+00 Inf 8.061494e-10 1 9.999773e-01
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 8.253705e-55 0.000000e+00 Inf 2.767591e-08 1 9.998673e-01
ANAEMIATRUE 1.056726e-12 0.000000e+00 Inf 1.266992e-09 1 9.999716e-01
REDUCTION.IN.FEED.CONSUMPTION....TRUE 2.039146e-25 0.000000e+00 Inf 1.802258e-09 1 9.999661e-01
------------------------------------------------------------------
[1] "PM.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 9.923189e-168 0.000000e+00 Inf NA NA NA
Age.weeks. 6.607929e+00 4.498550e-177 1.814440e+169 2.673633e-09 1 0.9999587
Nochicks 1.086010e+00 5.628162e-05 2.095564e+04 1.326372e-09 1 0.9999709
Proportion.of.morbidity..per.100. 8.065996e-01 1.695065e-36 7.732183e+36 2.627707e-10 1 0.9999871
Cumulative.mortality 2.467126e+01 2.564010e-59 1.058666e+60 1.092623e-08 1 0.9999166
Days.onset 4.442451e+01 8.395834e-253 3.302709e+268 1.242122e-09 1 0.9999719
Ratio.of.weight.standard.weight 1.221925e+81 0.000000e+00 Inf 1.522619e-08 1 0.9999015
Helminth.Y.NTRUE 8.671254e+59 0.000000e+00 Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 2.401085e+23 0.000000e+00 Inf 1.810906e-09 1 0.9999660
RESPIRATORY.SIGNSTRUE 2.781158e-29 0.000000e+00 Inf 1.914102e-09 1 0.9999651
DIARRHOEATRUE 9.836563e-03 0.000000e+00 Inf 8.034196e-11 1 0.9999928
JOINT.FOOT.PROBLEMSTRUE 1.687020e-56 0.000000e+00 Inf 2.652914e-09 1 0.9999589
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 8.104629e+25 0.000000e+00 Inf 1.529144e-09 1 0.9999688
ANAEMIATRUE 1.550992e+38 0.000000e+00 Inf 1.810419e-09 1 0.9999661
REDUCTION.IN.FEED.CONSUMPTION....TRUE 3.583699e+24 0.000000e+00 Inf 1.664674e-09 1 0.9999674
------------------------------------------------------------------
[1] "MG.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 1.888314e-03 3.404690e-06 1.940715e-01 NA NA NA
Age.weeks. 9.721703e-01 7.480517e-01 1.237310e+00 0.053483382 1 0.81710913
Nochicks 9.981974e-01 9.905227e-01 1.003725e+00 0.365013287 1 0.54573508
Proportion.of.morbidity..per.100. 1.002132e+00 9.712236e-01 1.031150e+00 0.021301448 1 0.88396074
Cumulative.mortality 1.019355e+00 9.544817e-01 1.116369e+00 0.299352031 1 0.58428892
Days.onset 1.200300e+00 9.685246e-01 1.597268e+00 2.725572488 1 0.09875271
Ratio.of.weight.standard.weight 1.103712e+02 2.008975e+00 2.645836e+04 5.464259754 1 0.01940927
Helminth.Y.NTRUE 8.494896e+00 6.978746e-01 1.941670e+02 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 1.376307e+01 6.004057e-01 8.258134e+02 2.637539533 1 0.10436506
RESPIRATORY.SIGNSTRUE 1.290849e-01 7.485860e-03 1.256500e+00 3.081966071 1 0.07916478
DIARRHOEATRUE 2.383644e-01 1.097137e-02 2.839753e+00 1.227579308 1 0.26787832
JOINT.FOOT.PROBLEMSTRUE 9.598985e+00 4.099096e-01 5.523078e+02 1.953085340 1 0.16225476
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 2.833294e-02 1.607370e-05 2.714013e+00 2.079911529 1 0.14924883
ANAEMIATRUE 1.077252e+00 7.903962e-02 1.243463e+01 0.003659219 1 0.95176420
REDUCTION.IN.FEED.CONSUMPTION....TRUE 4.989366e+00 3.068115e-01 1.870241e+02 1.200296568 1 0.27326241
------------------------------------------------------------------
[1] "IBV.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.0710628 0.0005646338 5.877820 NA NA NA
Age.weeks. 0.7310948 0.4346224752 1.003760 3.73308080 1 0.05334492
Nochicks 0.9963575 0.9872543560 1.002883 1.08550792 1 0.29746866
Proportion.of.morbidity..per.100. 1.0195833 0.9878246120 1.058036 1.45523464 1 0.22768986
Cumulative.mortality 1.0206723 0.9575222841 1.090620 0.43817572 1 0.50800427
Days.onset 1.1026934 0.9107401869 1.379860 0.98529626 1 0.32089473
Ratio.of.weight.standard.weight 33.7076196 0.4997741274 15873.646148 2.58124941 1 0.10813628
Helminth.Y.NTRUE 29.9369413 1.0912670071 5384.998760 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 0.2002272 0.0043694826 4.129129 1.05512380 1 0.30432997
RESPIRATORY.SIGNSTRUE 0.6093941 0.0669072447 5.887348 0.20033150 1 0.65445340
DIARRHOEATRUE 0.1375755 0.0057629183 1.592890 2.49383907 1 0.11429263
JOINT.FOOT.PROBLEMSTRUE 0.4800680 0.0060655346 17.509299 0.15082041 1 0.69775257
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 2.9857967 0.0353577233 150.092975 0.29075105 1 0.58973964
ANAEMIATRUE 0.7908532 0.0371210525 11.637698 0.03000079 1 0.86248843
REDUCTION.IN.FEED.CONSUMPTION....TRUE 0.4399400 0.0315823788 5.349117 0.44217490 1 0.50607459
------------------------------------------------------------------
[1] "GUM.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 4.120385e+05 0.000000e+00 Inf NA NA NA
Age.weeks. 6.143604e-05 1.265046e-214 2.983598e+205 1.128384e-08 1 9.999152e-01
Nochicks 9.591767e-01 7.135065e-05 1.101753e+04 7.637476e-09 1 9.999303e-01
Proportion.of.morbidity..per.100. 3.086932e-01 4.424096e-20 4.469780e+18 2.914240e-07 1 9.995693e-01
Cumulative.mortality 1.085896e+00 5.232158e-25 5.781571e+24 -1.966249e-11 1 1.000000e+00
Days.onset 1.672533e-01 1.980648e-67 2.703879e+66 2.183635e-09 1 9.999627e-01
Ratio.of.weight.standard.weight 5.617125e+139 0.000000e+00 Inf 2.387502e+01 1 1.027970e-06
Helminth.Y.NTRUE 7.938232e-23 0.000000e+00 Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 2.395780e+88 0.000000e+00 Inf 7.208731e+02 1 8.645946e-159
RESPIRATORY.SIGNSTRUE 1.331989e-103 0.000000e+00 Inf 2.705296e+01 1 1.979564e-07
DIARRHOEATRUE 7.702072e+45 0.000000e+00 Inf 1.623779e+01 1 5.586851e-05
JOINT.FOOT.PROBLEMSTRUE 1.557265e+02 0.000000e+00 Inf 1.717551e-10 1 9.999895e-01
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 1.529012e-114 0.000000e+00 Inf 1.802973e+01 1 2.174822e-05
ANAEMIATRUE 2.915837e-96 0.000000e+00 Inf 1.275374e-08 1 9.999099e-01
REDUCTION.IN.FEED.CONSUMPTION....TRUE 2.033973e-70 0.000000e+00 Inf 2.459655e+01 1 7.067803e-07
------------------------------------------------------------------
[1] "E.COLI.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 9.666934e-198 0.000000e+00 Inf NA NA NA
Age.weeks. 6.662051e+01 0.000000e+00 Inf 7.508194e-10 1 0.9999781
Nochicks 9.661426e-01 5.994301e-25 2.301805e+26 1.588050e-10 1 0.9999899
Proportion.of.morbidity..per.100. 3.398474e+00 4.971350e-63 1.413184e+61 1.840331e-09 1 0.9999658
Cumulative.mortality 4.079699e+01 1.859456e-127 2.666030e+125 4.969708e-09 1 0.9999438
Days.onset 1.797681e+03 0.000000e+00 Inf 8.314898e-09 1 0.9999272
Ratio.of.weight.standard.weight 9.722440e+41 0.000000e+00 Inf 2.145289e-09 1 0.9999630
Helminth.Y.NTRUE 1.022036e+90 0.000000e+00 Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 5.403999e+25 0.000000e+00 Inf 2.958140e-10 1 0.9999863
RESPIRATORY.SIGNSTRUE 9.941915e-62 0.000000e+00 Inf 9.758504e-09 1 0.9999212
DIARRHOEATRUE 4.750115e-36 0.000000e+00 Inf 5.077068e-10 1 0.9999820
JOINT.FOOT.PROBLEMSTRUE 7.830613e+50 0.000000e+00 Inf 7.125305e-10 1 0.9999787
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 4.560612e+16 0.000000e+00 Inf 1.842576e-08 1 0.9998917
ANAEMIATRUE 7.615857e-83 0.000000e+00 Inf 4.382740e-09 1 0.9999472
REDUCTION.IN.FEED.CONSUMPTION....TRUE 7.984368e+59 0.000000e+00 Inf 1.052064e-09 1 0.9999741
------------------------------------------------------------------With log transformations:
> for(i in seq_along(xs)) {
+ print(xs[i])
+ print(make_table(glm(formula(paste(xs[i], "~", paste(c(yslog, additional_variables), collapse = " + "))), binomial, data2)))
+ cat("------------------------------------------------------------------\n")
+ }
[1] "AVI.FINAL..PCR.CULTURE."
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 64.49847827 0.0003940010 3.657984e+07 NA NA NA
log(Age.weeks.) 0.88422669 0.0732060263 1.164603e+01 0.009725893 1 0.921440034
log(Nochicks) 0.46633020 0.0620365450 2.424038e+00 0.822929777 1 0.364324958
log(Proportion.of.morbidity..per.100.) 4.51361133 1.0965423919 3.733171e+01 4.432829294 1 0.035254023
log(Cumulative.mortality + 1) 0.41966283 0.0766954450 1.670340e+00 1.500167581 1 0.220645579
log(Days.onset) 1.63178572 0.2723922846 1.076056e+01 0.303393451 1 0.581762811
log(Ratio.of.weight.standard.weight) 285.74151150 4.5443122936 2.439552e+05 10.487504176 1 0.001201846
Helminth.Y.NTRUE 8.49023099 0.3547238891 4.131553e+02 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 1.87026134 0.1024428419 4.626630e+01 0.186277356 1 0.666033172
RESPIRATORY.SIGNSTRUE 2.09040545 0.0914525784 4.160350e+01 0.252109331 1 0.615593733
DIARRHOEATRUE 1.07273964 0.1363046167 9.936955e+00 0.004503317 1 0.946496716
JOINT.FOOT.PROBLEMSTRUE 0.20000034 0.0024646601 2.063766e+01 0.546960706 1 0.459562214
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 197.74481520 1.7129758632 2.064682e+05 4.891215956 1 0.026993668
ANAEMIATRUE 0.01524197 0.0002023898 2.735405e-01 9.086797417 1 0.002574613
REDUCTION.IN.FEED.CONSUMPTION....TRUE 0.43398464 0.0336341045 4.341371e+00 0.516401853 1 0.472380598
------------------------------------------------------------------
[1] "ORT.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 8.845264e-106 0 Inf NA NA NA
log(Age.weeks.) 4.551564e+21 0 Inf 5.009913e-09 1 0.9999435251
log(Nochicks) 2.106486e+09 0 Inf 1.357447e-09 1 0.9999706031
log(Proportion.of.morbidity..per.100.) 5.772900e-08 0 Inf 5.134302e-10 1 0.9999819207
log(Cumulative.mortality + 1) 5.518630e+04 0 Inf 2.321459e-10 1 0.9999878432
log(Days.onset) 3.808867e+02 0 Inf 1.537570e-11 1 0.9999968713
log(Ratio.of.weight.standard.weight) 6.044493e+29 0 Inf 1.038860e-09 1 0.9999742831
Helminth.Y.NTRUE 2.586044e+30 0 Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 1.123665e+40 0 Inf 1.385852e+01 1 0.0001971008
RESPIRATORY.SIGNSTRUE 3.378211e-14 0 Inf 9.738255e-10 1 0.9999751011
DIARRHOEATRUE 1.477234e+03 0 Inf 2.766587e-11 1 0.9999958033
JOINT.FOOT.PROBLEMSTRUE 2.172039e-03 0 NA 4.070078e-12 1 0.9999983903
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 9.070839e-36 0 Inf 3.534432e-09 1 0.9999525649
ANAEMIATRUE 1.124907e-03 0 Inf 5.014167e-11 1 0.9999943501
REDUCTION.IN.FEED.CONSUMPTION....TRUE 9.503567e-10 NA Inf 5.455569e-10 1 0.9999813637
------------------------------------------------------------------
[1] "PM.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 2.613042e-192 0 Inf NA NA NA
log(Age.weeks.) 6.556608e-07 0 Inf 1.869439e-09 1 0.9999655
log(Nochicks) 1.152557e+26 0 Inf 2.956523e-09 1 0.9999566
log(Proportion.of.morbidity..per.100.) 1.673973e-12 0 Inf 6.373972e-10 1 0.9999799
log(Cumulative.mortality + 1) 1.396608e+27 0 Inf 2.193937e-08 1 0.9998818
log(Days.onset) 4.784508e-13 0 Inf 1.167819e-09 1 0.9999727
log(Ratio.of.weight.standard.weight) 6.000337e+37 0 Inf 1.268733e-09 1 0.9999716
Helminth.Y.NTRUE 3.209246e+83 0 Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 7.553018e+32 0 Inf 2.846954e-09 1 0.9999574
RESPIRATORY.SIGNSTRUE 1.807871e-17 0 Inf 1.213372e-10 1 0.9999912
DIARRHOEATRUE 6.573565e-05 0 Inf 1.438920e-10 1 0.9999904
JOINT.FOOT.PROBLEMSTRUE 9.753372e-53 0 Inf 3.436835e-09 1 0.9999532
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 6.820814e+00 0 Inf 1.866285e-11 1 0.9999966
ANAEMIATRUE 1.104123e+31 0 Inf 9.215832e-09 1 0.9999234
REDUCTION.IN.FEED.CONSUMPTION....TRUE 6.014953e+03 0 Inf -2.925216e-12 1 1.0000000
------------------------------------------------------------------
[1] "MG.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 0.76013376 1.561904e-04 4334.647510 NA NA NA
log(Age.weeks.) 0.75590290 1.524846e-01 3.454126 0.13740994 1 0.71086959
log(Nochicks) 0.74337039 1.713128e-01 2.834837 0.18999092 1 0.66292418
log(Proportion.of.morbidity..per.100.) 0.87865578 2.290775e-01 3.146860 0.04019424 1 0.84110129
log(Cumulative.mortality + 1) 1.13276110 2.660379e-01 4.992460 0.02983515 1 0.86286481
log(Days.onset) 3.03330544 5.063390e-01 34.070376 1.36348190 1 0.24293495
log(Ratio.of.weight.standard.weight) 20.29930035 1.426144e+00 825.165402 5.14317131 1 0.02333798
Helminth.Y.NTRUE 7.05744797 5.364810e-01 174.961358 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 9.93070871 5.712847e-01 423.793674 2.42948459 1 0.11907204
RESPIRATORY.SIGNSTRUE 0.12666039 6.184824e-03 1.390915 2.82263839 1 0.09294351
DIARRHOEATRUE 0.44814397 3.613284e-02 4.063418 0.50219338 1 0.47853795
JOINT.FOOT.PROBLEMSTRUE 6.66165905 3.253087e-01 317.860467 1.46222294 1 0.22657676
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 0.02835584 2.312421e-05 2.932190 2.05777370 1 0.15143127
ANAEMIATRUE 1.16751195 1.040067e-01 11.622743 0.01797715 1 0.89334020
REDUCTION.IN.FEED.CONSUMPTION....TRUE 4.02663352 3.445161e-01 114.164684 1.12598047 1 0.28863434
------------------------------------------------------------------
[1] "IBV.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 534.1707520 0.02038027 2.220974e+08 NA NA NA
log(Age.weeks.) 0.2068258 0.01663157 1.024965e+00 3.708337283 1 0.0541413
log(Nochicks) 0.3978720 0.06388785 1.751408e+00 1.461598419 1 0.2266760
log(Proportion.of.morbidity..per.100.) 1.0453350 0.30472498 3.175179e+00 0.006037670 1 0.9380647
log(Cumulative.mortality + 1) 1.1828856 0.29879892 4.574002e+00 0.065181776 1 0.7984858
log(Days.onset) 1.5484169 0.35300271 7.742913e+00 0.340705998 1 0.5594220
log(Ratio.of.weight.standard.weight) 4.6642940 0.60950276 7.830065e+01 2.115543342 1 0.1458103
Helminth.Y.NTRUE 7.2174144 0.61314247 1.835754e+02 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 0.2364520 0.00923309 3.429474e+00 1.085650985 1 0.2974368
RESPIRATORY.SIGNSTRUE 0.6828441 0.07388745 6.957657e+00 0.114732775 1 0.7348190
DIARRHOEATRUE 0.3114043 0.02601365 2.390851e+00 1.229555221 1 0.2674936
JOINT.FOOT.PROBLEMSTRUE 0.8650429 0.01834439 2.321531e+01 0.007556482 1 0.9307287
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 1.3855673 0.01966095 5.500671e+01 0.029046051 1 0.8646728
ANAEMIATRUE 0.7215721 0.05668536 7.131092e+00 0.077360236 1 0.7809071
REDUCTION.IN.FEED.CONSUMPTION....TRUE 0.4052208 0.04208564 3.584976e+00 0.693614451 1 0.4049377
------------------------------------------------------------------
[1] "GUM.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) Inf 0 Inf NA NA NA
log(Age.weeks.) 8.857942e-42 0 Inf 1.416408e-08 1 9.999050e-01
log(Nochicks) 3.385759e-14 0 Inf 6.454343e-08 1 9.997973e-01
log(Proportion.of.morbidity..per.100.) 4.137498e-27 0 Inf 1.065041e-07 1 9.997396e-01
log(Cumulative.mortality + 1) 1.362195e-05 0 Inf 3.302771e-10 1 9.999855e-01
log(Days.onset) 7.571979e-09 0 Inf 6.169043e-09 1 9.999373e-01
log(Ratio.of.weight.standard.weight) 3.210328e+164 0 Inf 2.648104e+01 1 2.661377e-07
Helminth.Y.NTRUE 8.458762e-42 0 Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 1.396332e+158 0 Inf 4.325238e+02 1 4.587521e-96
RESPIRATORY.SIGNSTRUE 2.683382e-186 0 Inf 2.551632e+01 1 4.386575e-07
DIARRHOEATRUE 4.121315e+62 0 Inf 1.653831e+01 1 4.767712e-05
JOINT.FOOT.PROBLEMSTRUE 4.074419e+11 0 Inf 3.047241e-09 1 9.999560e-01
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 1.989178e-143 0 Inf 1.378809e+01 1 2.046293e-04
ANAEMIATRUE 2.041693e-186 0 Inf 1.102493e-07 1 9.997351e-01
REDUCTION.IN.FEED.CONSUMPTION....TRUE 6.141244e-102 0 Inf 2.146307e+01 1 3.607097e-06
------------------------------------------------------------------
[1] "E.COLI.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 1.032591e-181 0 Inf NA NA NA
log(Age.weeks.) 5.088892e-08 0 Inf 2.817582e-10 1 0.9999866
log(Nochicks) 1.731853e+12 0 Inf 5.328018e-10 1 0.9999816
log(Proportion.of.morbidity..per.100.) 1.296314e+08 0 Inf 4.959666e-09 1 0.9999438
log(Cumulative.mortality + 1) 4.164011e+22 0 Inf 2.328188e-09 1 0.9999615
log(Days.onset) 1.692531e+20 0 Inf 6.309822e-09 1 0.9999366
log(Ratio.of.weight.standard.weight) 6.013016e+24 0 Inf 1.181996e-09 1 0.9999726
Helminth.Y.NTRUE 7.129848e+38 0 Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 1.352272e-32 0 Inf 3.298668e-10 1 0.9999855
RESPIRATORY.SIGNSTRUE 2.459315e-18 0 Inf 7.281842e-10 1 0.9999785
DIARRHOEATRUE 2.729847e-18 0 Inf 3.464380e-10 1 0.9999851
JOINT.FOOT.PROBLEMSTRUE 1.898251e+25 0 Inf 3.070175e-10 1 0.9999860
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 9.069479e-04 0 Inf 4.572005e-10 1 0.9999829
ANAEMIATRUE 5.047674e-55 0 Inf 4.358777e-09 1 0.9999473
REDUCTION.IN.FEED.CONSUMPTION....TRUE 3.046477e-02 0 Inf 2.136934e-09 1 0.9999631
------------------------------------------------------------------With some log transformations:
> sel <- c(1, 3, 6)
> for(i in seq_along(xs)) {
+ print(xs[i])
+ print(make_table(glm(formula(paste(xs[i], "~", paste(c(ys[sel], yslog[-sel], additional_variables), collapse = " + "))), binomial, data2)))
+ cat("------------------------------------------------------------------\n")
+ }
[1] "AVI.FINAL..PCR.CULTURE."
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 2.354353e-02 3.829504e-08 1.015430e+03 NA NA NA
Age.weeks. 1.060136e+00 7.711264e-01 1.577791e+00 0.12567638 1 0.7229577296
Proportion.of.morbidity..per.100. 1.102408e+00 1.028889e+00 1.274521e+00 10.67013902 1 0.0010887893
Ratio.of.weight.standard.weight 1.052066e+07 1.251858e+02 2.191656e+17 12.55459237 1 0.0003952338
log(Nochicks) 1.314016e-01 2.704017e-03 1.238656e+00 3.01991684 1 0.0822476835
log(Cumulative.mortality + 1) 3.061200e-01 3.993897e-02 1.295956e+00 2.49881928 1 0.1139316860
log(Days.onset) 2.292386e+00 2.986653e-01 2.713462e+01 0.63400800 1 0.4258889530
Helminth.Y.NTRUE 4.120533e+02 1.391553e+00 2.738877e+07 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 2.879480e+00 8.830685e-02 2.808980e+02 0.33656095 1 0.5618210645
RESPIRATORY.SIGNSTRUE 7.429863e-01 6.511000e-03 3.536827e+01 0.02067881 1 0.8856573989
DIARRHOEATRUE 7.871736e-01 2.776392e-02 1.689506e+01 0.02684947 1 0.8698428777
JOINT.FOOT.PROBLEMSTRUE 1.371051e-02 4.593389e-06 3.597524e+00 2.28985306 1 0.1302222511
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 6.804240e+03 8.252056e+00 8.158705e+08 7.80878535 1 0.0051992840
ANAEMIATRUE 3.133004e-03 1.946369e-06 1.417010e-01 11.37122915 1 0.0007459050
REDUCTION.IN.FEED.CONSUMPTION....TRUE 2.186428e+00 8.474283e-02 1.828084e+02 0.20019067 1 0.6545669886
------------------------------------------------------------------
[1] "ORT.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 3.776685e-103 0 Inf NA NA NA
Age.weeks. 7.096303e+03 0 Inf 8.387562e-09 1 0.9999269268
Proportion.of.morbidity..per.100. 1.188130e+00 NA 9.820896e+186 4.749756e-11 1 0.9999945011
Ratio.of.weight.standard.weight 3.632195e+34 0 Inf 6.347318e-10 1 0.9999798982
log(Nochicks) 1.039521e+06 0 Inf 1.076919e-09 1 0.9999738163
log(Cumulative.mortality + 1) 3.798195e-13 0 Inf 5.094010e-10 1 0.9999819918
log(Days.onset) 4.706614e+08 NA Inf 7.389112e-11 1 0.9999931414
Helminth.Y.NTRUE 2.216769e+19 0 Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 2.877071e+44 0 Inf 1.469929e+01 1 0.0001260937
RESPIRATORY.SIGNSTRUE 1.319561e-29 NA Inf 4.717138e-09 1 0.9999452002
DIARRHOEATRUE 5.960870e+02 0 Inf 9.925394e-11 1 0.9999920510
JOINT.FOOT.PROBLEMSTRUE 3.332596e+20 0 Inf 4.643779e-10 1 0.9999828060
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 1.129372e-32 0 Inf 2.571924e-09 1 0.9999595360
ANAEMIATRUE 1.068927e-27 0 Inf 2.627591e-10 1 0.9999870664
REDUCTION.IN.FEED.CONSUMPTION....TRUE 6.467126e-05 0 Inf 1.360601e-10 1 0.9999906931
------------------------------------------------------------------
[1] "PM.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 3.835050e-251 0.000000e+00 Inf NA NA NA
Age.weeks. 2.658377e-01 2.220289e-262 1.976043e+251 3.210698e-10 1 0.9999857
Proportion.of.morbidity..per.100. 4.871756e-01 7.631128e-110 4.526131e+104 1.087772e-09 1 0.9999737
Ratio.of.weight.standard.weight 6.745215e+53 0.000000e+00 Inf 3.964913e-09 1 0.9999498
log(Nochicks) 3.210488e+22 0.000000e+00 Inf 1.917191e-09 1 0.9999651
log(Cumulative.mortality + 1) 1.469715e+25 0.000000e+00 Inf 1.313912e-08 1 0.9999085
log(Days.onset) 1.240454e-12 0.000000e+00 Inf 5.050906e-10 1 0.9999821
Helminth.Y.NTRUE 1.437932e+74 0.000000e+00 Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 4.232523e+36 0.000000e+00 Inf 4.086970e-09 1 0.9999490
RESPIRATORY.SIGNSTRUE 2.678016e-07 0.000000e+00 Inf 5.473666e-11 1 0.9999941
DIARRHOEATRUE 3.353105e-08 0.000000e+00 Inf 2.142198e-11 1 0.9999963
JOINT.FOOT.PROBLEMSTRUE 2.005463e-49 0.000000e+00 Inf 3.190836e-09 1 0.9999549
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 2.773955e-08 0.000000e+00 Inf 7.815704e-11 1 0.9999929
ANAEMIATRUE 3.931628e+34 0.000000e+00 Inf 6.942778e-09 1 0.9999335
REDUCTION.IN.FEED.CONSUMPTION....TRUE 7.355702e+02 0.000000e+00 Inf 6.133760e-12 1 0.9999980
------------------------------------------------------------------
[1] "MG.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 1.749025e-03 1.019402e-07 8.449584 NA NA NA
Age.weeks. 9.444862e-01 7.226840e-01 1.194739 0.22839472 1 0.63271668
Proportion.of.morbidity..per.100. 1.014626e+00 9.805975e-01 1.052003 0.73731133 1 0.39052352
Ratio.of.weight.standard.weight 1.147992e+02 1.740870e+00 57285.209703 5.08256191 1 0.02416763
log(Nochicks) 8.163815e-01 1.960235e-01 3.051974 0.09415411 1 0.75896104
log(Cumulative.mortality + 1) 7.639400e-01 2.061321e-01 2.598142 0.19017139 1 0.66277401
log(Days.onset) 4.823463e+00 7.266514e-01 64.520006 2.56336067 1 0.10936588
Helminth.Y.NTRUE 6.204470e+00 5.496617e-01 116.700117 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 1.169797e+01 5.254886e-01 833.232845 2.33143784 1 0.12678472
RESPIRATORY.SIGNSTRUE 9.458703e-02 3.482179e-03 1.167916 3.35179614 1 0.06713173
DIARRHOEATRUE 2.357754e-01 1.044306e-02 2.713836 1.26693216 1 0.26034299
JOINT.FOOT.PROBLEMSTRUE 1.273618e+01 5.828248e-01 731.352358 2.56207319 1 0.10945496
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 2.935882e-02 1.721125e-05 3.212085 1.91538397 1 0.16636642
ANAEMIATRUE 1.304030e+00 1.151561e-01 12.447430 0.05339846 1 0.81725183
REDUCTION.IN.FEED.CONSUMPTION....TRUE 7.191569e+00 4.031946e-01 442.027513 1.63285001 1 0.20130931
------------------------------------------------------------------
[1] "IBV.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 6.8702271 0.0002679733 7.175393e+05 NA NA NA
Age.weeks. 0.7039792 0.4191540826 9.825689e-01 4.3510203751 1 0.03698678
Proportion.of.morbidity..per.100. 1.0312653 0.9977751943 1.075590e+00 3.3286513780 1 0.06808268
Ratio.of.weight.standard.weight 30.0249316 0.3854392975 1.156585e+04 2.2354235002 1 0.13487966
log(Nochicks) 0.3849146 0.0523087738 1.906209e+00 1.3541512526 1 0.24455370
log(Cumulative.mortality + 1) 0.7108609 0.1683472277 2.393150e+00 0.2942077105 1 0.58753666
log(Days.onset) 1.9169209 0.3958206009 1.123301e+01 0.6600000233 1 0.41655994
Helminth.Y.NTRUE 25.9797193 1.0279677247 3.349539e+03 NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 0.1705528 0.0040644289 3.042557e+00 1.3862310601 1 0.23904262
RESPIRATORY.SIGNSTRUE 0.3669792 0.0312000070 4.230606e+00 0.6919696714 1 0.40549523
DIARRHOEATRUE 0.1991193 0.0097276777 2.124882e+00 1.7296126753 1 0.18846037
JOINT.FOOT.PROBLEMSTRUE 0.7516794 0.0059542206 3.346740e+01 0.0207234319 1 0.88553493
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 2.7475493 0.0235171292 2.470669e+02 0.2107007543 1 0.64621871
ANAEMIATRUE 0.9674701 0.0689884644 1.116484e+01 0.0007256858 1 0.97850874
REDUCTION.IN.FEED.CONSUMPTION....TRUE 0.5909126 0.0508477817 7.048174e+00 0.1906020583 1 0.66241600
------------------------------------------------------------------
[1] "GUM.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 5.012423e+28 0.000000e+00 Inf NA NA NA
Age.weeks. 8.762438e-06 1.072523e-264 7.758836e+258 1.769892e-08 1 9.998939e-01
Proportion.of.morbidity..per.100. 2.392902e-01 2.020601e-24 1.976095e+23 7.151383e-08 1 9.997866e-01
Ratio.of.weight.standard.weight 9.271375e+162 0.000000e+00 Inf 2.303838e+01 1 1.587993e-06
log(Nochicks) 3.301427e-05 0.000000e+00 Inf 3.045618e-09 1 9.999560e-01
log(Cumulative.mortality + 1) 9.443703e+00 0.000000e+00 Inf 2.196363e-10 1 9.999882e-01
log(Days.onset) 5.691377e-08 0.000000e+00 Inf 1.622774e-09 1 9.999679e-01
Helminth.Y.NTRUE 1.029271e-24 0.000000e+00 Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 2.039573e+106 0.000000e+00 Inf 5.177852e-08 1 9.998184e-01
RESPIRATORY.SIGNSTRUE 7.092675e-120 0.000000e+00 Inf 2.498670e+01 1 5.772718e-07
DIARRHOEATRUE 5.630361e+52 0.000000e+00 Inf 1.595424e+01 1 6.489227e-05
JOINT.FOOT.PROBLEMSTRUE 2.612124e+03 0.000000e+00 Inf 4.575238e-10 1 9.999829e-01
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 2.551396e-132 0.000000e+00 Inf 4.514931e-07 1 9.994639e-01
ANAEMIATRUE 2.090099e-109 0.000000e+00 Inf 9.171905e-09 1 9.999236e-01
REDUCTION.IN.FEED.CONSUMPTION....TRUE 2.938439e-80 0.000000e+00 Inf 2.210738e+01 1 2.578170e-06
------------------------------------------------------------------
[1] "E.COLI.FINAL"
Estimate 2.5 % 97.5 % LR Chisq Df Pr(>Chisq)
(Intercept) 7.372734e-226 0.000000e+00 Inf NA NA NA
Age.weeks. 8.684346e-01 0.000000e+00 Inf 2.218998e-10 1 0.9999881
Proportion.of.morbidity..per.100. 1.796725e+00 1.274884e-50 4.314867e+48 8.869727e-10 1 0.9999762
Ratio.of.weight.standard.weight 6.475344e+39 0.000000e+00 Inf 9.078991e-10 1 0.9999760
log(Nochicks) 2.684610e+09 0.000000e+00 Inf 2.804743e-10 1 0.9999866
log(Cumulative.mortality + 1) 2.402869e+27 0.000000e+00 Inf 6.944137e-09 1 0.9999335
log(Days.onset) 1.816518e+18 0.000000e+00 Inf 3.061058e-09 1 0.9999559
Helminth.Y.NTRUE 4.268023e+54 0.000000e+00 Inf NA 0 NA
Nematodes.y.nTRUE NA NA NA NA 0 NA
Cestodes.Y.NTRUE 5.589092e-16 0.000000e+00 Inf 2.477507e-10 1 0.9999874
RESPIRATORY.SIGNSTRUE 3.746167e-29 0.000000e+00 NA 9.768950e-10 1 0.9999751
DIARRHOEATRUE 4.288378e-22 0.000000e+00 Inf 8.810144e-10 1 0.9999763
JOINT.FOOT.PROBLEMSTRUE 8.845324e+33 0.000000e+00 Inf 9.318603e-09 1 0.9999230
ABNORMAL.EGGSTRUE NA NA NA NA 0 NA
NERVOUS.SIGNSTRUE 1.229151e+06 0.000000e+00 Inf 2.826206e-10 1 0.9999866
ANAEMIATRUE 9.052763e-50 0.000000e+00 Inf 2.944696e-09 1 0.9999567
REDUCTION.IN.FEED.CONSUMPTION....TRUE 4.591750e+09 0.000000e+00 Inf 3.109153e-10 1 0.9999859
------------------------------------------------------------------