Resolving symmetry in gnls model - r

I'm trying to fit a logistic growth model in R, using gnls in the nlme package.
I have previously successfully fit a model:
mod1 <- gnls(Weight ~ I(A/(1+exp(b + v0*Age + v1*Sum.T))),
data = df,
start = c(A= 13.157132, b= 3, v0= 0.16, v1= -0.0059),
na.action=na.omit)
However, I now wish to constrain b so that it is not fitted by the model, so have tried fitting a second model:
mod2 <- gnls(Weight ~ I(A/(1+exp(log((A/1.022)-1) + v0*Age + v1*Sum.T))),
data = df,
start = c(A= 13.157132, v0= 0.16, v1= -0.0059),
na.action=na.omit)
This model returned the error:
Error in gnls(Weight ~ A/(1 + exp(log((A/1.022) - 1) + v0 * Age + :
approximate covariance matrix for parameter estimates not of full rank
Warning messages:
1: In log((A/1.022) - 1) : NaNs produced
Searching the error suggests that the problem is caused by symmetry in the model, and solutions to specific questions involve adapting the formula with different parameters. Unfortunately, my statistical knowledge is not good enough to a) fully understand the problem or b) adapt the formula myself.
As for the warning messages (there were 15 in all, all the same) I can't see why they arise because this section of the model works alone (with example numbers).
Any help with any of these queries would be greatly appreciated.

It may be informative for users to know that I finally solved this with what turned out to be a simple solution (with help from a friend).
Since exp(a+b) = exp(a)*exp(b), the equation can be rewritten:
Weight ~ I(A/(1+((A/1.022)-1) * exp(v0*Age + v1*Sum.T))
Which fits without any problems. In general, writing the equation in a different form would seem to be the answer.

Related

Time-dependent covariates- is there something wrong with this code? (R program)

I am checking a few of my Cox multivariate regression analyses' proportional hazard assumptions using time-dependent co-variates, using the survival package. The question is looking at survival in groups with different ADAMTS13 levels (a type of enzyme).
Could I check if something is wrong with my code itself? It keeps saying Error in tt(TMAdata$ADAMTS13level.f) : could not find function "tt" . Why?
Notably, ADAMTS13level.f is a factor variable.
cox_multivariate_survival_ADAMTS13 <- coxph(Surv(TMAdata$Daysalive, TMAdata$'Dead=1')
~TMAdata$ADAMTS13level.f
+TMAdata$`Age at diagnosis`
+TMAdata$CCIwithoutage
+TMAdata$Gender.f
+TMAdata$`Peak Creatinine`
+TMAdata$DICorcrit.f,
tt(TMAdata$ADAMTS13level.f),
tt = function(x, t, ...)
{mtrx <- model.matrix(~x)[,-1]
mtrx * log(t)})
Thanks- starting with the fundamentals of my actual code or typos- I have tried different permutations to no avail yet.
#Limey was on the right track!
The time-transformed version of ADAMTS13level.f needs to be added to the model, instead of being separated into a separate argument of coxph(...).
The form of coxph call when testing the time-dependent categorical variables is described in How to use the timeSplitter by Max Gordon.
Other helpful documentation:
coxph - fit proportional hazards regression model
cox_multivariate_survival_ADAMTS13 <-
coxph(
Surv(
Daysalive,
'Dead=1'
) ~
ADAMTS13level.f
+ `Age at diagnosis`
+ CCIwithoutage
+ Gender.f
+ `Peak Creatinine`
+ DICorcrit.f
+ tt(ADAMTS13level.f),
tt = function(x, t, ...) {
mtrx <- model.matrix(~x)[,-1]
mtrx * log(t)
},
data = TMAdata
)
p.s. with the original data, there was also a problem because Daysalive included a zero (0) value, which eventually resulted in an 'infinite predictor' error from coxph, probably because tt transformed the data using a log(t). (https://rdrr.io/github/therneau/survival/src/R/coxph.R)

How to cluster standard errors with small sample corrections in R

I have the following code:
library(lmtest)
library(sandwich)
library(plm)
library(multiwayvcov)
reg <- lm(Y ~ x1 + x1_sq + x2 + x2_sq + x1x2 + d1 + d2 + d3 + d4, df)
coeftest(reg, vcov = vcovHC(reg, type="HC1")
coeftest(reg, vcov = vcovHC(reg, type="sss", cluster="study"))
I want to compare the regression when I use typical heteroskedasticity-robust standard errors and when I cluster the standard errors at the study level with a small sample correction. The regression and first -coeftest- work, but the second spits out a clear error message:
Error in match.arg(type) : 'arg' should be one of “HC3”, “const”, “HC”, “HC0”, “HC1”, “HC2”, “HC4”, “HC4m”, “HC5”
I found the code online where they use -type="sss"- as a small sample correction but it doesn't seem to work here. Is there something I am doing wrong or is one of the above listed in the error message the heteroskedastic-adjusted covariance matrix and the code was maybe updated? Clearly I cannot use -type="sss"-, but I don't know how to incorporate the small sample correction otherwise.
Using -...vcovHC(df, type="sss", cluster="study")- is a dated way to incorporate small sample corrections. Upon understanding differences between the sandwich estimators HC0-HC4, using the code previous to it:
coeftest(reg, vcov = vcovHC(reg, type="HC1")
is appropriate with the corresponding sandwich estimator in the type argument. The issue was with the dated syntax that followed and this is the correct format.

Strange glmulti results: Why are interaction variables from the candidate model dropped/not included?

I have been using glmulti to obtain model averaged estimates and relative importance values for my variables of interest. In running glmulti I specified a candidate model for which all variables and interactions were included based on a priori knowledge (see code below).
After running the glmutli model I studied the results by using the functions summary() and weightable(). There seem to be a number of strange things going on with the results which I do not understand.
First of all, when I run my candidate model with lme4 glmer() function I obtain an AIC value of 2086. In the glmulti output this candidate model (with exactly the same formula) has a lower AIC value (2107), as a result of which it appears at position 8 out of 26 in the list of all potential models (as obtained through the weigtable() function).
What seems to be causing this problem is that the logArea:Habitat interaction is dropped from the candidate model, despite level=2 being specified. The function summary(output_new#objects[[8]]) provides a different formula (without the logArea:Habitat interaction variable) compared to the formula provided through weightable(). This explains why the candidate model AIC value is not the same as obtained through lme4, but I do not understand why the interaction variables logArea:Habitat is missing from the formula. The same is happening for other possible models. It seems that for all models with 2 or more interactions, one interaction is dropped.
Does anyone have an explanation for what is going on? Any help would be much appreciated!
Best,
Robert
Note: I have created a subset of my data (https://drive.google.com/open?id=1rc0Gkp7TPdnhW6Bw87FskL5SSNp21qxl) and simplified the candidate model by removing variables in order to decrease model run time. (The problem remains the same)
newdat <- Data_ommited2[, c("Presabs","logBodymass", "logIsolation", "Matrix", "logArea", "Protection","Migration", "Habitat", "Guild", "Study","Species", "SpeciesStudy")]
glmer.glmulti <- function (formula, data, random, ...) {
glmer(paste(deparse(formula), random), data = data, family=binomial(link="logit"),contrasts=list(Matrix=contr.sum, Habitat=contr.treatment, Protection=contr.treatment, Guild=contr.sum),glmerControl(optimizer="bobyqa", optCtrl = list(maxfun = 100000)))
}
output_new <- glmulti(y = Presabs ~ Matrix + logArea*Protection + logArea*Habitat,
data = sampledata,
random = '+(1|Study)+(1|Species)+(1|SpeciesStudy)',
family = binomial,
method = 'h',
level=2,
marginality=TRUE,
crit = 'aic',
fitfunc = glmer.glmulti,
confsetsize = 26)
print(output_new)
summary(output_new)
weightable(output_new)
I found a post (https://stats.stackexchange.com/questions/341356/glmulti-package-in-r-reporting-incorrect-aicc-values) of someone who encountered the same problem and it appears that the problem was caused by this line of code:
glmer.glmulti <- function (formula, data, random, ...) {
glmer(paste(deparse(formula), random), data = data, family=binomial(link="logit"))
}
By changing this part of the code into the following the problem was solved:
glmer.glmulti<-function(formula,data,random,...) {
newf <- formula
newf[[3]] <- substitute(f+r,
list(f=newf[[3]],
r=reformulate(random)[[2]]))
glmer(newf,data=data,
family=binomial(link="logit"))
}

Extracting path coefficients of piecewise SEM (structural equation model)

I'm constructing a piecewise structural equation model using the piecewiseSEM package in R (Lefcheck - https://cran.r-project.org/web/packages/piecewiseSEM/vignettes/piecewiseSEM.html)
I already created the model set and I could evaluate the model fit, so the model itself works. Also, the data fits the model (p = 0.528).
But I do not succeed in extracting the path coefficients.
This is the error i get: Error in cbind(Xlarge, Xsmall) : number of rows of matrices must match (see arg 2)
I already tried (but this did not work):
standardising my data because of the warning: Some predictor variables are on very different scales: consider rescaling
adapted my data (threw some NA values away)
This is my modellist:
predatielijst = list(
lmer(plantgrootte ~ gapfraction + olsen_P + (1|plot_ID), data = d),
glmer(piek1 ~ gapfraction + olsen_P + plantgrootte + (1|plot_ID),
family = poisson, data = d),
glmer(predatie ~ piek1 + (1|plot_ID), family = binomial, data = d)
)
with "predatie" being a binary variable (yes or no) and all the rest continuous variables (gapfraction, plantgrootte, olsen_P & piek1)
Thanks in advance!
Try installing the development version:
library(devtools)
install_github("jslefche/piecewiseSEM#2.0")
Replace list with psem and run the coefs or summary function. It will likely get rid of your error. If not, open a bug on Github!
WARNING: this will overwrite your current version from CRAN. You will need to reinstall from CRAN to get version 1.4 back.
try to use lme (out of the nlme library) ilstead of glmer. As far as I understand, the fact that lmer does not provide p-values (while lme does) seems to be the problem here.
Hope this works.

Error with ZIP and ZINB Models upon subseting and factoring data

I am trying to run ZIP and ZINB models to try look at some of the factors which might help explain disease (orf) distribution within 8 geographical regions. The models works fine for some regions and not others. However upon factoring and running the model in R I get error message.
How can I solve this problem or would there be a model that might work better with the subset as the analysis will only make sense when it’s all uniform across all regions.
zinb3 = zeroinfl(Cases2012 ~ Precip+ Altitude +factor(Breed)+ factor(Farming.Practise)+factor(Lambing.Management)+ factor(Thistles) ,data=orf3, dist="negbin",link="logit")
Error in solve.default(as.matrix(fit$hessian)) :
system is computationally singular: reciprocal condition number = 2.99934e-24
Results after fitting zerotrunc & glm as suggested by #Achim Zeileis. How do i interprete zerotruc output given that no p values. Also how can I correct the error with glm?
zerotrunc(Cases2012 ~ Flock2012+Stocking.Density2012+ Precip+ Altitude +factor(Breed)+ factor(Farming.Practise)+factor(Lambing.Management)+ factor(Thistles),data=orf1, subset = Cases2012> 0)
Call:
zerotrunc(formula = Cases2012 ~ Flock2012 + Stocking.Density2012 + Precip + Altitude +
factor(Breed) + factor(Farming.Practise) + factor(Lambing.Management) + factor(Thistles),
data = orf1, subset = Cases2012 > 0)
Coefficients (truncated poisson with log link):
(Intercept) Flock2012 Stocking.Density2012
14.1427130 -0.0001318 -0.0871504
Precip Altitude factor(Breed)2
-0.1467075 -0.0115919 -3.2138767
factor(Farming.Practise)2 factor(Lambing.Management)2 factor(Thistles)3
1.3699477 -2.9790725 2.0403543
factor(Thistles)4
0.8685876
glm(factor(Cases2012 ~ 0) ~ Precip+ Altitude +factor(Breed)+ factor(Farming.Practise)+factor(Lambing.Management)+ factor(Thistles) +Flock2012+Stocking.Density2012 ,data=orf1, family = binomial)
Error in unique.default(x, nmax = nmax) :
unique() applies only to vectors
It's hard to say exactly what is going on based on the information provided. However, I would suspect that the data in some regions does not allow to fit the model specified. For example, there might be some regions where certain factor levels (of Breed or Farming.Practise or Lambin.Management or Thristles) only have zero values (or only non-zero but that is less frequent in practice). Then the coefficient estimates often degenerate so that the associated zero-inflation probability goes to 1 and the count coefficient cannot be estimated.
It's typically easier to separate these effects by using the hurdle rather the zero-inflation model. Then the two parts of the model can also be fitted separately by glm(factor(y > 0) ~ ..., ..., family = binomial) and zerotrunc(y ~ ..., ..., subset = y > 0). The latter function is essentially the same code as pscl uses but has been factored into a standalone function in the package countreg on R-Forge (not yet on CRAN).

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