# Quantities for R – Ready for a CRAN release

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This is the fourth blog post on
`quantities`

, an
R-Consortium funded project for quantity calculus with R. It is aimed at
providing integration of the ‘units’ and ‘errors’ packages for a
complete quantity calculus system for R vectors, matrices and arrays,
with automatic propagation, conversion, derivation and simplification of
magnitudes and uncertainties. This article summarises the latest
enhancements and investigates how to fit linear regressions with
quantities. In previous articles, we discussed a first working
prototype,
units and errors
parsing,
and data wrangling operations with
quantities.

## Latest enhancements

In the following, we briefly describe some important enhancements made
to the `units`

, `errors`

and `quantities`

packages. Also, we would like
to note that, thanks to Katharine Mullen’s careful review, packages
`units`

, `errors`

and `constants`

are now listed in the ChemPhys CRAN
Task View.

### Mixed units

Apart from various minor improvements and bug fixes, the most notable
new feature is the **support for mixed units**, that will be released on
CRAN, foreseeably, within a month.

One of the most prominent design decisions made in the `units`

package
(which applies to `errors`

and `quantities`

as well), following R’s
philosophy, is that `units`

objects are fundamentally vectors. This
means that a `units`

(`errors`

, `quantities`

) object represents one or
more measurement values of the same quantity, with the same unit (for
instance, repeated measurements of the same quantity). Thus, different
quantities, with different units, must belong to different objects.

However, Bill Denney raised an interesting use case (#134, #145) in which different quantities need to be manipulated in a single data structure. Very briefly, he receives heterogeneous measurements of different analytes from clinical studies as follows:

(analytes <- data.frame( analyte=c("glucose", "insulin", "glucagon"), original_unit=c("mg/dL", "IU/L", "mmol/L"), original_value=c(1, 2, 3), new_unit=c("mmol/L", "mg/dL", "mg/L"), stringsAsFactors=FALSE )) ## analyte original_unit original_value new_unit ## 1 glucose mg/dL 1 mmol/L ## 2 insulin IU/L 2 mg/dL ## 3 glucagon mmol/L 3 mg/L

To be able to convert these values to the new units, first we need to
define some conversion constants between grams and IUs (which stands for
*International Unit*) or moles *of a particular substance* (note:
numbers may be wrong):

# some adjustments (analytes <- within(analytes, { for (i in seq_along(analyte)) { original_unit[i] <- gsub("(mol|IU)", paste0("\\1_", analyte[i]), original_unit[i]) new_unit[i] <- gsub("(mol|IU)", paste0("\\1_", analyte[i]), new_unit[i]) } i <- NULL })) ## analyte original_unit original_value new_unit ## 1 glucose mg/dL 1 mmol_glucose/L ## 2 insulin IU_insulin/L 2 mg/dL ## 3 glucagon mmol_glucagon/L 3 mg/L library(units) ## udunits system database from /usr/share/udunits install_conversion_constant("mol_glucose", "g", 180.156) install_conversion_constant("g", "IU_insulin", 25113.32) install_conversion_constant("mol_glucagon", "g", 3482.80)

Then, the development version of `units`

provides a new method called
`mixed_units()`

intended for this use case:

(analytes <- within(analytes, { original_value <- mixed_units(original_value, original_unit) new_value <- set_units(original_value, new_unit) original_unit <- new_unit <- NULL })) ## analyte original_value new_value ## 1 glucose 1 [mg/dL] 0.05550745 [mmol_glucose/L] ## 2 insulin 2 [IU_insulin/L] 0.007963901 [mg/dL] ## 3 glucagon 3 [mmol_glucagon/L] 10448.4 [mg/L]

Mixed units are basically lists with a custom class, and each element of
the list is a `units`

object:

analytes$original_value ## Mixed units: IU_insulin/L (1), mg/dL (1), mmol_glucagon/L (1) ## 1 [mg/dL], 2 [IU_insulin/L], 3 [mmol_glucagon/L] class(analytes$original_value) ## [1] "mixed_units" unclass(analytes$original_value) ## [[1]] ## 1 [mg/dL] ## ## [[2]] ## 2 [IU_insulin/L] ## ## [[3]] ## 3 [mmol_glucagon/L] class(analytes$original_value[[1]]) ## [1] "units"

Still, `units`

objects cannot be concatenated into mixed lists unless
explicitly enabled by the user, thus maintaining backwards
compatibility:

c(as_units("m"), as_units("s")) # error, cannot convert, cannot mix ## Error in c.units(as_units("m"), as_units("s")): units are not convertible, and cannot be mixed; try setting units_options(allow_mixed = TRUE)? c(as_units("m"), as_units("s"), allow_mixed=TRUE) ## Mixed units: m (1), s (1) ## 1 [m], 1 [s]

This behaviour can be controlled also by the global option `allow_mixed`

(see `help(units_options)`

). Finally, note that mixed units with
non-heterogeneous units are not simplified either unless explicitly
requested:

(x <- mixed_units(1:3, c("m", "s", "m"))) ## Mixed units: m (2), s (1) ## 1 [m], 2 [s], 3 [m] as_units(x) # error, cannot convert, cannot mix ## Error in c.units(structure(1L, units = structure(list(numerator = "m", : units are not convertible, and cannot be mixed; try setting units_options(allow_mixed = TRUE)? x[c(1, 3)] ## Mixed units: m (2) ## 1 [m], 3 [m] as_units(x[c(1, 3)]) ## Units: [m] ## [1] 1 3

Compatibility with this feature has been also added to the `quantities`

package. Specifically, lists of mixed units can contain either `units`

or `quantities`

objects, and additional methods have been defined to
deal with them transparently.

library(quantities) ## Loading required package: errors c(set_quantities(1, m, 0.1), set_quantities(2, s, 0.3), allow_mixed=TRUE) ## Mixed units: m (1), s (1) ## 1.0(1) [m], 2.0(3) [s] (x <- mixed_units(set_errors(1:2, c(0.1, 0.3)), c("m", "km"))) ## Mixed units: km (1), m (1) ## 1.0(1) [m], 2.0(3) [km] as_units(x) ## Units: [m] ## Errors: 0.1 300.0 ## [1] 1 2000 # etc.

Of course, parsers also aware of this new feature (see also the new vignette on parsing quantities):

parse_quantities(c("1.02(5) g", "2.51(0.01) V", "(3.23 +/- 0.12) m")) ## Mixed units: g (1), m (1), V (1) ## 1.02(5) [g], 2.51(1) [V], 3.2(1) [m]

We kindly invite the community to try out this new feature (currently on GitHub only) and report any issue or proposal for improvement.

### Support for correlations

Version 0.3.0 of `errors`

hit CRAN a month ago with a very important
feature that was missing before: **support for correlations between
quantities**.

Due to the design of these packages, as discussed before, the advantage
of having separate vectorised variables to operate freely with them
without having to build an expression (as in the `propagate`

package,
for example) makes it harder to store pairwise correlations and operate
with them. This has been finally resolved in this version thanks to an
internal hash table, which automatically cleans up dangling correlations
when the associated objects are garbage-collected.

The manual page `help("errors-package")`

provides a nice introductory
example on how to set up correlations and how these are propagated (see
`help("correl")`

for more detailed information):

library(errors) # Simultaneous measurements of voltage, intensity and phase GUM.H.2 ## V I phi ## 1 5.007 0.019663 1.0456 ## 2 4.994 0.019639 1.0438 ## 3 5.005 0.019640 1.0468 ## 4 4.990 0.019685 1.0428 ## 5 4.999 0.019678 1.0433 # Obtain mean values and uncertainty from measured values V <- mean(set_errors(GUM.H.2$V)) I <- mean(set_errors(GUM.H.2$I)) phi <- mean(set_errors(GUM.H.2$phi)) # Set correlations between variables correl(V, I) <- with(GUM.H.2, cor(V, I)) correl(V, phi) <- with(GUM.H.2, cor(V, phi)) correl(I, phi) <- with(GUM.H.2, cor(I, phi)) # Computation of resistance, reactance and impedance values (R <- (V / I) * cos(phi)) ## 127.73(7) (X <- (V / I) * sin(phi)) ## 219.8(3) (Z <- (V / I)) ## 254.3(2) # Correlations between derived quantities correl(R, X) ## [1] -0.5884298 correl(R, Z) ## [1] -0.4852592 correl(X, Z) ## [1] 0.9925116

In a similar way, correlations transparently work with `quantities`

objects. For example, let us suppose that we measured the position of a
particle at several time instants:

library(quantities) x <- set_quantities(1:5, m, 0.05) t <- set_quantities(1:5, s, 0.05)

Each measurement has some uncertainty (the same for all values here for simplicity). Now we can compute the distance covered in each interval, and then the instantaneous velocity, which is constant here:

dx <- diff(x) dt <- diff(t) (v <- dx/dt) ## Units: [m/s] ## Errors: 0.1 0.1 0.1 0.1 ## [1] 1 1 1 1

Obviously, there should be a strong correlation between the instantaneous velocity and the distance covered for each interval. And here it is:

correl(dx, v) ## [1] 0.7071068 0.7071068 0.7071068 0.7071068

## Fitting linear models with quantities

A linear regression models the relationship between a dependent variable
and one or more explanatory variables. These variables are usually
quantities, some measurements with some unit and uncertainty associated.
Therefore, the output from a linear regression (coefficients, fitted
values, predictions…) are quantities as well. However, functions such as
`lm`

are not compatible with `quantities`

. This section describes
current issues and discusses several approaches to overcome them, along
with their benefits, advantages and limitations.

### Current issues

Let us generate some artificial data with the classical formula for uniformly accelerated movement, \(s(t) = s_0 + v_0t + \frac{1}{2}at^2\):

library(quantities) set.seed(1234) t <- seq(1, 10, 0.1) s <- 3 + 2*t + t^2 # some noise added df <- data.frame( t = set_quantities(t + rnorm(length(t), 0, 0.01), s, 0.01), s = set_quantities(s + rnorm(length(t), 0, 1), m, 1) ) plot(df)

Then, we try to adjust a linear model using `lm`

:

fit <- lm(s ~ poly(t, 2), df) # error Ops.units ## Error in Ops.units(X, Y, ...): power operation only allowed with length-one numeric power

First issue: it seems that `poly`

computes powers in a vectorised way
(i.e., `t^0L:degree`

), which is not currently supported in `units`

,
because it would generate *different* units for each value. Now that
mixed units are supported, this could be a way to circumvent this, but
it is not clear whether the resulting list of mixed units may create
more problems. This is something that we should explore anyway.

Let us try this time by explicitly defining the powers:

(fit <- lm(s ~ t + I(t^2), df)) ## Warning: In 'Ops' : non-'errors' operand automatically coerced to an ## 'errors' object with no uncertainty ## ## Call: ## lm(formula = s ~ t + I(t^2), data = df) ## ## Coefficients: ## (Intercept) t I(t^2) ## 3.373 1.910 1.006

Now it works. We obtain the (unitless, errorless) coefficients, and these are other parameters and summaries:

coef(fit) # plain numeric, as show above ## (Intercept) t I(t^2) ## 3.373459 1.909901 1.006140 residuals(fit)[1:5] # wrong uncertainty, copied from 's' ## Units: [m] ## Errors: 1 1 1 1 1 ## 1 2 3 4 5 ## 0.01289180 1.41273622 0.68031389 -0.65668199 0.07589058 fitted(fit)[1:5] # wrong uncertainty ## Units: [m] ## Errors: 0 0 0 0 0 ## 1 2 3 4 5 ## 6.242304 6.703228 7.161199 7.451099 8.039660 predict(fit, data.frame(t=11:15)) # plain numeric ## 1 2 3 4 5 ## 146.1253 171.1765 198.2399 227.3156 258.4035 summary(fit) # error Ops.units ## Error in Ops.units(mean(f)^2, var(f)): both operands of the expression should be "units" objects

In summary, we do not get the benefit of obtaining coefficients, fitted values, predictions… with the right units and uncertainty, and the whole object is a mess due to diverse incompatibilities.

### Wrapping linear models

There are several possible ways to overcome the issues above. The most
direct one would be to wrap the `lm`

call, so that `quantities`

are
dropped before calling `lm`

, and the resulting object is modified to set
up the proper `quantities`

*a posteriori*. However, in this way, some
`lm`

methods may work while some others may still be broken.

A cleaner approach would be to wrap the `lm`

call to add a custom class
to the hierarchy and save units and errors for later use:

qlm <- function(formula, data, ...) { # get units info, then drop quantities row <- data[1,] for (var in colnames(data)) if (inherits(data[[var]], "quantities")) { data[[var]] <- drop_quantities(data[[var]]) } # fit linear model and add units info for later use fit <- lm(formula, data, ...) fit$units <- lapply(eval(attr(fit$terms, "variables"), row), units) class(fit) <- c("qlm", class(fit)) fit } (fit <- qlm(s ~ t + I(t^2), df)) ## ## Call: ## lm(formula = formula, data = data) ## ## Coefficients: ## (Intercept) t I(t^2) ## 3.373 1.910 1.006 class(fit) ## [1] "qlm" "lm"

Then, this custom class can be used to build specific methods of interest:

coef.qlm <- function(object, ...) { # compute coefficients' units coef.units <- lapply(object$units, as_units) for (i in seq_len(length(coef.units)-1)+1) coef.units[[i]] <- coef.units[[1]]/coef.units[[i]] coef.units <- lapply(coef.units, units) # use units above and vcov diagonal to set quantities coef <- mapply(set_quantities, NextMethod(), coef.units, sqrt(diag(vcov(object))), mode="symbolic", SIMPLIFY=FALSE) # use the rest of the vcov to set correlations p <- combn(names(coef), 2) for (i in seq_len(ncol(p))) covar(coef[[p[1, i]]], coef[[p[2, i]]]) <- vcov(fit)[p[1, i], p[2, i]] coef } coef(fit) ## $`(Intercept)` ## 3.4(5) [m] ## ## $t ## 1.9(2) [m/s] ## ## $`I(t^2)` ## 1.01(2) [m/s^2] fitted.qlm <- function(object, ...) { # set residuals as std. errors of fitted values set_quantities(NextMethod(), object$units[[1]], residuals(object), mode="symbolic") } fitted(fit)[1:5] ## Units: [m] ## Errors: 0.01289180 1.41273622 0.68031389 0.65668199 0.07589058 ## 1 2 3 4 5 ## 6.242304 6.703228 7.161199 7.451099 8.039660 predict.qlm <- function(object, ...) { # set se.fit as std. errors of predictions set_quantities(NextMethod(), object$units[[1]], NextMethod(se.fit=TRUE)$se.fit, mode="symbolic") } predict(fit, data.frame(t=11:15)) ## Units: [m] ## Errors: 0.4570381 0.6507279 0.8804014 1.1448265 1.4434174 ## 1 2 3 4 5 ## 146.1253 171.1765 198.2399 227.3156 258.4035

and so on and so forth.

### Open problems

This analysis is limited to the `lm`

function, but there are others,
both in R base (such as `glm`

) and in other packages, which have
different sets of input parameters and output. Instead of developing
multiple sets of wrappers and methods, it would be desirable to manage
everything through a common wrapper, class and set of methods (see,
e.g., how `ggplot2::geom_smooth`

works). It should be assessed whether
this is possible, at least for a limited, widely-used, group of
functions.

Also, there may be users interested in fitting linear models with units only, or with uncertainty only. As with the rest of the functionalities in these packages, it should be studied how to wisely break down this feature.

## Summary

This article summarises the latest enhancements in the `units`

, `errors`

and `quantities`

packages, and provides some initial prospects on
fitting linear models with quantities. Also, this is the last
deliverable of the R-quantities project, which has reached the following
milestones:

- A first working prototype.
- Support for units and errors parsing.
- An analysis of data wrangling operations with quantities.
- Prospects on fitting linear models with quantities.

And along the way, there have been multiple exciting improvements, both
in `units`

and `errors`

, to support all these features and make
`quantities`

possible, which is ready for an imminent CRAN release. This
project ends, but the r-quantities
GitHub organisation will continue to thrive and to provide the best
tools for quantity calculus to the R community.

## Acknowledgements

This project gratefully acknowledges financial support from the R Consortium. Also I would like to thank Edzer Pebesma for his continued support and collaboration.

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