I am trying to convert Absorbance (Abs) values to Concentration (ng/mL), based on an established linear model & standard curve. I planned to do this by using the predict() function. I am having trouble getting predict() to return the desired results. Here is a sample of my code:
Standards<-data.frame(ng_mL=c(0,0.4,1,4),
Abs550nm=c(1.7535,1.5896,1.4285,0.9362))
LM.2<-lm(log(Standards[['Abs550nm']])~Standards[['ng_mL']])
Abs<-c(1.7812,1.7309,1.3537,1.6757,1.7409,1.7875,1.7533,1.8169,1.753,1.6721,1.7036,1.6707,
0.3903,0.3362,0.2886,0.281,0.3596,0.4122,0.218,0.2331,1.3292,1.2734)
predict(object=LM.2,
newdata=data.frame(Concentration=Abs[1]))#using Abs[1] as an example, but I eventually want predictions for all values in Abs
Running that last lines gives this output:
> predict(object=LM.2,
+ newdata=data.frame(Concentration=Abs[1]))
1 2 3 4
0.5338437 0.4731341 0.3820697 -0.0732525
Warning message:
'newdata' had 1 row but variables found have 4 rows
This does not seem to be the output I want. I am trying to get a single predicted Concentration value for each Absorbance (Abs) entry. It would be nice to be able to predict all of the entries at once and add them to an existing data frame, but I can't even get it to give me a single value correctly. I've read many threads on here, webpages found on Google, and all of the help files, and for the life of me I cannot understand what is going on with this function. Any help would be appreciated, thanks.
You must have a variable in newdata that has the same name as that used in the model formula used to fit the model initially.
You have two errors:
You don't use a variable in newdata with the same name as the covariate used to fit the model, and
You make the problem much more difficult to resolve because you abuse the formula interface.
Don't fit your model like this:
mod <- lm(log(Standards[['Abs550nm']])~Standards[['ng_mL']])
fit your model like this
mod <- lm(log(Abs550nm) ~ ng_mL, data = standards)
Isn't that some much more readable?
To predict you would need a data frame with a variable ng_mL:
predict(mod, newdata = data.frame(ng_mL = c(0.5, 1.2)))
Now you may have a third error. You appear to be trying to predict with new values of Absorbance, but the way you fitted the model, Absorbance is the response variable. You would need to supply new values for ng_mL.
The behaviour you are seeing is what happens when R can't find a correctly-named variable in newdata; it returns the fitted values from the model or the predictions at the observed data.
This makes me think you have the formula back to front. Did you mean:
mod2 <- lm(ng_mL ~ log(Abs550nm), data = standards)
?? In which case, you'd need
predict(mod2, newdata = data.frame(Abs550nm = c(1.7812,1.7309)))
say. Note you don't need to include the log() bit in the name. R recognises that as a function and applies to the variable Abs550nm for you.
If the model really is log(Abs550nm) ~ ng_mL and you want to find values of ng_mL for new values of Abs550nm you'll need to invert the fitted model in some way.
Related
I'm trying to create a GAM model using environmental variables and mean abundance data.
the data im using is:
and the code I'm using to create the model is so:
imod2 <- gam(mean ~ s(BO_chlomean, bs="cr"), data = envgroup2, family = poisson, method="REML", na.action = na.fail, select=T)
(ideally I want to add the other 2 variables but one thing at a time.)
however when I run the code I get:
Error in if (abs(old.score - score) > score.scale * conv.tol) { :
missing value where TRUE/FALSE needed
I also get 50 or more warnings, consisting of:
1: In dpois(y, y, log = TRUE) : non-integer x = 0.200000
i'm very new to R and finding to hard to understand. any help to sort this issue would be amazing
You're asking gam() to fit a model assuming an integer response and passing it a real-valued (decimal) variable.
If you have replicate counts and averaged them to get the mean variable, then don't do the averaging. Include all rows of data and deal with the clustering by subject with a random effect term.
If you got mean by scaling by an effort variable, you should fit the model with the original count/integer values and add offset(log(effort_var)) to the formula where effort_var is the variable you divided the original response by to get mean.
Working in R to develop regression models, I have something akin to this:
c_lm = lm(trainingset$dependent ~ trainingset$independent)
c_pred = predict(c_lm,testset$independent))
and every single time, I get a mysterious error from R:
Warning message:
'newdata' had 34 rows but variables found have 142 rows
which essentially translates into R not being able to find the independent column of the testset data.frame. This is simply because the exact name from the right-hand side of the formula in lm must be there in predict. To fix it, I can do this:
tempset = trainingset
c_lm = lm(trainingset$dependent ~ tempset$independent)
tempset = testset
c_pred = predict(c_lm,tempset$independent))
or some similar variation, but this is really sloppy, in my opinion.
Is there another way to clean up the translation between the two so that the independent variables' data frame does not have to have the exact same name in predict as it does in lm?
No, No, No, No, No, No! Do not use the formula interface in the way you are doing if you want all the other sugar that comes with model formulas. You wrote:
c_lm = lm(trainingset$dependent ~ trainingset$independent)
You repeat trainingset twice, which is a waste of fingers/time, redundant, and not least causing you the problem that you are hitting. When you now call predict, it will be looking for a variable in testset that has the name trainingset$independent, which of course doesn't exist. Instead, use the data argument in your call to lm(). For example, this fits the same model as your formula but is efficient and also works properly with predict()
c_lm = lm(dependent ~ independent, data = trainingset)
Now when you call predict(c_lm, newdata = testset), you only need to have a data frame with a variable whose name is independent (or whatever you have in the model formula).
An additional reason to write formulas as I show them, is legibility. Getting the object name out of the formula allows you to more easily see what the model is.
I have created a loop to fit a non-linear model to six data points by participants (each participant has 6 data points). The first model is a one parameter model. Here is the code for that model that works great. The time variable is defined. The participant variable is the id variable. The data is in long form (one row for each datapoint of each participant).
Here is the loop code with 1 parameter that works:
1_p_model <- dlply(discounting_long, .(Participant), function(discounting_long) {wrapnls(indiff ~ 1/(1+k*time), data = discounting_long, start = c(k=0))})
However, when I try to fit a two parameter model, I get this error "Error: singular gradient matrix at initial parameter estimates" while still using the wrapnls function. I realize that the model is likely over parameterized, that is why I am trying to use wrapnls instead of just nls (or nlsList). Some in my field insist on seeing both model fits. I thought that the wrapnls model avoids the problem of 0 or near-0 residuals. Here is my code that does not work. The start values and limits are standard in the field for this model.
2_p_model <- dlply(discounting_long, .(Participant), function(discounting_long) {nlxb(indiff ~ 1/(1+k*time^s), data = discounting_long, lower = c (s = 0), start = c(k=0, s=.99), upper = c(s=1))})
I realize that I could use nlxb (which does give me the correct parameter values for each participant) but that function does not give predictive values or residuals of each data point (at least I don't think it does) which I would like to compute AIC values.
I am also open to other solutions for running a loop through the data by participants.
You mention at the end that 'nlxb doesn't give you residuals', but it does. If your result from your call to nlxbis called fit then the residuals are in fit$resid. So you can get the fitted values using just by adding them to the original data. Honestly I don't know why nlxb hasn't been made to work with the predict() function, but at least there's a way to get the predicted values.
Starting from a linear model1 = lm(temp~alt+sdist) i need to develop a prediction model, where new data will come in hand and predictions about temp will be made.
I have tried doing something like this:
model2 = predict.lm(model1, newdata=newdataset)
However, I am not sure this is the right way. What I would like to know here is, if this is the right way to go in order to make prediction about temp. Also I am a bit confused when it comes to the newdataset. Which values should be filled in etc.?
I am putting everything from the comments into this answer.
1) You can use predict rather than predict.lm as predict will know your input is of class lm and do the right thing automatically.
2 The newdataset should be a data.frame with the same variables as your original predictors - in this case alt and sdist.
3) If you are bringing in you data using read.table by default it will create a data.frame. This assumes that the new data has columns named alt and sdist Then you can do:
NewDataSet<-read.table(whatever)
NewPredictions<- predict(model1, newdata=NewDatSet)
4) After you have done this if you want to check the predictions - you can do the following
summary(model1)
This will give you the intercept and the coefficients for alt and sdist
NewDataSet[1,]
This should give you the alt and sdist values for the first row, you can change the 1 in the bracket to be any row you want. Then use the information from summary(model1) to calculate what the predicted value should be using any method that you trust.
Finally use
NewPredictions[1]
to get what predict() gave you for the first row (or change the 1 to any other row)
Hopefully that should all work out.
Working in R to develop regression models, I have something akin to this:
c_lm = lm(trainingset$dependent ~ trainingset$independent)
c_pred = predict(c_lm,testset$independent))
and every single time, I get a mysterious error from R:
Warning message:
'newdata' had 34 rows but variables found have 142 rows
which essentially translates into R not being able to find the independent column of the testset data.frame. This is simply because the exact name from the right-hand side of the formula in lm must be there in predict. To fix it, I can do this:
tempset = trainingset
c_lm = lm(trainingset$dependent ~ tempset$independent)
tempset = testset
c_pred = predict(c_lm,tempset$independent))
or some similar variation, but this is really sloppy, in my opinion.
Is there another way to clean up the translation between the two so that the independent variables' data frame does not have to have the exact same name in predict as it does in lm?
No, No, No, No, No, No! Do not use the formula interface in the way you are doing if you want all the other sugar that comes with model formulas. You wrote:
c_lm = lm(trainingset$dependent ~ trainingset$independent)
You repeat trainingset twice, which is a waste of fingers/time, redundant, and not least causing you the problem that you are hitting. When you now call predict, it will be looking for a variable in testset that has the name trainingset$independent, which of course doesn't exist. Instead, use the data argument in your call to lm(). For example, this fits the same model as your formula but is efficient and also works properly with predict()
c_lm = lm(dependent ~ independent, data = trainingset)
Now when you call predict(c_lm, newdata = testset), you only need to have a data frame with a variable whose name is independent (or whatever you have in the model formula).
An additional reason to write formulas as I show them, is legibility. Getting the object name out of the formula allows you to more easily see what the model is.