How to smooth data of increasing noise - r

Question

Chemist here (so not very good with statistical analysis) and novice in R:
I have various sets of data where the yield of a reaction is monitored with time such as:
The data:
df <- structure(list(time = c(15, 30, 45, 60, 75, 90, 105, 120, 135,
150, 165, 180, 195, 210, 225, 240, 255, 270, 285, 300, 315, 330,
345, 360, 375, 390, 405, 420, 435, 450, 465, 480, 495, 510, 525,
540, 555, 570, 585, 600, 615, 630, 645, 660, 675, 690, 705, 720,
735, 750, 765, 780, 795, 810, 825, 840, 855, 870, 885, 900, 915,
930, 945, 960, 975, 990, 1005, 1020, 1035, 1050, 1065, 1080,
1095, 1110, 1125, 1140, 1155, 1170, 1185, 1200, 1215, 1230, 1245,
1260, 1275, 1290, 1305, 1320, 1335, 1350, 1365, 1380, 1395, 1410,
1425, 1440, 1455, 1470, 1485, 1500, 1515, 1530, 1545, 1560, 1575,
1590, 1605, 1620, 1635, 1650, 1665, 1680, 1695, 1710, 1725, 1740,
1755, 1770, 1785, 1800, 1815, 1830, 1845, 1860, 1875, 1890, 1905,
1920, 1935, 1950, 1965, 1980, 1995, 2010, 2025, 2040, 2055, 2070,
2085, 2100, 2115, 2130), yield = c(9.3411, 9.32582, 10.5475,
13.5358, 17.3376, 16.7444, 20.7234, 19.8374, 24.327, 27.4162,
27.38, 31.3926, 29.3289, 32.2556, 33.0025, 35.3358, 35.8986,
40.1859, 40.3886, 42.2828, 41.23, 43.8108, 43.9391, 43.9543,
48.0524, 47.8295, 48.674, 48.2456, 50.2641, 50.7147, 49.6828,
52.8877, 51.7906, 57.2553, 53.6175, 57.0186, 57.6598, 56.4049,
57.1446, 58.5464, 60.7213, 61.0584, 57.7481, 59.9151, 64.475,
61.2322, 63.5167, 64.6289, 64.4245, 62.0048, 65.5821, 65.8275,
65.7584, 68.0523, 65.4874, 68.401, 68.1503, 67.8713, 69.5478,
69.9774, 73.4199, 66.7266, 70.4732, 67.5119, 69.6107, 70.4911,
72.7592, 69.3821, 72.049, 70.2548, 71.6336, 70.6215, 70.8611,
72.0337, 72.2842, 76.0792, 75.2526, 72.7016, 73.6547, 75.6202,
76.5013, 74.2459, 76.033, 78.4803, 76.3058, 73.837, 74.795, 76.2126,
75.1816, 75.3594, 79.9158, 77.8157, 77.8152, 75.3712, 78.3249,
79.1198, 77.6184, 78.1244, 78.1741, 77.9305, 79.7576, 78.0261,
79.8136, 75.5314, 80.2177, 79.786, 81.078, 78.4183, 80.8013,
79.3855, 81.5268, 78.416, 78.9021, 79.9394, 80.8221, 81.241,
80.6111, 79.7504, 81.6001, 80.7021, 81.1008, 82.843, 82.2716,
83.024, 81.0381, 80.0248, 85.1418, 83.1229, 83.3334, 83.2149,
84.836, 79.5156, 81.909, 81.1477, 85.1715, 83.7502, 83.8336,
83.7595, 86.0062, 84.9572, 86.6709, 84.4124)), .Names = c("time",
"yield"), row.names = c(NA, -142L), class = "data.frame")
What i want to do to the data:
I need to smooth the data in order to plot the 1st derivative. In the paper the author mentioned that one can fit a high order polynomial and use that to do the processing which i think is wrong since we dont really know the true relationship between time and yield for the data and is definitely not polyonymic. I tried regardless and the plot of the derivative did not make any chemical sense as expected. Next i looked into loess using: loes<-loess(Yield~Time,data=df,span=0.9) which gave a much better fit. However, the best results so far was using :
spl <- smooth.spline(df$Time, y=df$Yield,cv=TRUE)
colnames(predspl)<-c('Time','Yield')
pred.der<-as.data.frame(predict(spl, deriv=1))
colnames(pred.der)<-c('Time', 'Yield')
which gave the best fit especially in the initial data points (by visual inspection).
The problem i have:
The issue however is that the derivative looks really good only up to t=500s and then it starts wiggling more and more towards the end. This shouldnt happen from a chemistry point of view and it is just a result of overfitting towards the end of the data due to the increase of the noise. I know this since for some experiments that i have performed 3 times and averaged the data (so the noise decreased) the wiggling is much smaller in the plot of the derivative.
What i have tried so far:
I tried different values of spar which although it smoothens correctly the later data it causes a poor fit in the initial data (which are the most important). I also tried to reduce the number of knots but i got a similar result with the one from changing the spar value. What i think i need is to have a larger amount of knots in the begining which will smoothly decrease to a small number of knots towards the end to avoid that overfitting.
The question:
Is my reasoning correct here? Does anyone know how can i have the above effect in order to get a smooth derivative without any wiggling? Do i need to try a different fit other than the spline maybe? I have attached a pic in the end where you can see the derivative from the smooth.spline vs time and a black line (drawn by hand) of what it should look like. Thank you for your help in advance.

Answer 1

I think you're on the right track on having more closely spaced knots for the spline at the start of the curve. You can specify knot locations for smooth.spline using all.knots (at least on R >= 3.4.3; I skimmed the release notes for R, but couldn't pinpoint the version where this became available).
Below is an example, and the resulting, smoother fit for the derivative after some manual work of trying out different knot positions:
with(df, {
kn <- c(0, c(50, 100, 200, 350, 500, 1500) / max(time), 1)
s <- smooth.spline(time, yield, cv = T)
s2 <- smooth.spline(time, yield, all.knots = kn)
ds <- predict(s, d = 1)
ds2 <- predict(s2, d = 1)
np <- list(mfrow = c(2, 1), mar = c(4, 4, 1, 2))
withr::with_par(np, {
plot(time, yield)
lines(s)
lines(s2, lty = 2, col = 'red')
plot(ds, type = 'l', ylim = c(0, 0.15))
lines(ds2, lty = 2, col = 'red')
})
})
You can probably fine tune the locations further, but I wouldn't be too concerned about it. The primary fits are already near enough indistinguishable, and I'd say you're asking quite a lot from these data in terms of identifying details about the derivative (this should be evident if you plot(time[-1], diff(yield) / diff(time)) which gives you an impression about the level of information your data carry about the derivative).
Created on 2018-02-15 by the reprex package (v0.2.0).