Type: Package
Title: Mass Balance Reconstruction
Version: 0.0.1
Author: Hung Nguyen
Maintainer: Hung Nguyen <ntthung@gmail.com>
Description: Mass-balance-adjusted Regression algorithm for streamflow reconstruction at sub-annual resolution (e.g., seasonal or monthly). The algorithm implements a penalty term to minimize the differences between the total sub-annual flows and the annual flow. The method is described in Nguyen et al (2020) <doi:10.1002/essoar.10504791.1>.
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2.0)]
Encoding: UTF-8
LazyData: true
Depends: R (≥ 3.5)
Imports: data.table, dplR, MASS, Matrix, Rfast, stats
RoxygenNote: 7.1.1
URL: https://github.com/ntthung/mbr
BugReports: https://github.com/ntthung/mbr/issues
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-02-12 12:06:00 UTC; ntthu
Repository: CRAN
Date/Publication: 2021-02-16 09:10:02 UTC

mbr: Mass Balance Reconstruction

Description

Mass-balance-adjusted Regression algorithm for streamflow reconstruction at sub-annual resolution (e.g., seasonal or monthly). The algorithm implements a penalty term to minimize the differences between the total sub-annual flows and the annual flow. The method is described in Nguyen et al (2020) <DOI:10.1002/essoar.10504791.1>.

See Also

Useful links:

Kling-Gupta Efficiency

Description

Kling-Gupta Efficiency

Usage

KGE(yhat, y)

Arguments

yhat

Model outputs

y

Observations

Value

KGE value

Examples

KGE(rnorm(100), rnorm(100))

Nash-Sutcliffe Efficiency

Description

Nash-Sutcliffe Efficiency

Usage

NSE(yhat, y)

Arguments

yhat

Model outputs

y

Observations

Value

NSE value

Examples

NSE(rnorm(100), rnorm(100))

Reduction of Error

Description

Reduction of Error

Usage

RE(yhat, y, yc_bar)

Arguments

yhat

Model outputs in the validation set

y

Observations in the validation set

yc_bar

Mean observations in the calibration set

Value

RE value

Examples

x <- rnorm(100)
y <- rnorm(100)
yc_bar <- mean(x[1:50])
RE(x[51:100], y[51:100], yc_bar)

Back-transformation

Description

Transform the reconstructed values back to the flow space and convert to data.table

Usage

back_trans(hat, years, mus, sigmas, log.trans, N, season.names)

Arguments

hat

A vector of estimated flow in the transformed space.

years

A vector of all years in the study period

mus

A vector of means, one for each target.

sigmas

A vector of the standard deviations, one for each target.

log.trans

A vector containing the indices of the columns to be log-transformed.

N

The number of targets (number of seasons plus one for the annual reconstruction).

season.names

A character vector containing the names of the seasons

Value

A data.table with three columns: Q (the back-transformed streamflow), season, and year.

Reconstruction metrics

Description

Calculate reconstruction metrics from the instrumental period

Usage

calculate_metrics(sim, obs, z, norm.fun = mean)

Arguments

sim

A vector of reconstruction output for instrumental period

obs

A vector of all observations

z

A vector of left out indices in cross validation

norm.fun

The function (unquoted name) used to calculate the normalizing constant. Default is mean(), but other functions such as sd() can also be used. THe function must take a vector as input and return a scalar as output, and must have an argument na.rm = TRUE.

Value

A named vector of performance metrics

Examples

calculate_metrics(rnorm(100), rnorm(100), z = 1:10)
calculate_metrics(rnorm(100), rnorm(100), z = 1:10, norm.fun = sd)

Scale columns of a matrix

Description

Same as base::scale() but much faster.

Usage

colScale(x, add_attr = TRUE)

Arguments

x

A matrix.

add_attr

If TRUE, the column means and standard deviations are returned as attributes. This is consistent with base::scale().

Value

The scaled matrix.

Reference

This function was adopted from John Muschelli's code on StackOverflow, but I changed the underlying functions to calculate mean and standard deviation from matrixStats to Rfast, which is much faster.

Unscale columns of a matrix

Description

Backtransform a matrix that was scaled before.

Usage

colUnscale(x, cm, csd)

Arguments

x

A matrix.

cm

A vector of column means

csd

A vector of column standard deviations

Value

The unscaled matrix

Cross-validation

Description

Cross-validation

Usage

cv_mb(
  instQ,
  pc.list,
  cv.folds,
  start.year,
  lambda = 1,
  log.trans = NULL,
  force.standardize = FALSE,
  return.type = c("fval", "metrics", "metric means", "Q")
)

Arguments

instQ

Instrumental data, in the same order as pc.list. The "season" column must be a factor.

pc.list

List of PC matrices

cv.folds

A list containing the cross validation folds

start.year

The first year of record

lambda

The penalty weight

log.trans

A vector containing indices of the targets to be log-transformed. If no transformation is needed, provide NULL.

force.standardize

If TRUE, all observations are standardized. See Details.

return.type

The type of results to be returned. Several types are possible to suit multiple use cases.

fval

Only the objective function value (penalized least squares) is returned; this is useful for the outer optimization for site selection.

metrics

all performance metrics are returned.

⁠metric means⁠

the Tukey's biweight robust mean of each metric is returned.

Q

The predicted flow in each cross-validation run is returned. This is the most basic output, so that you can use it to calculate other metrics that are not provided by the package.

Value

A data.table containing cross-validation results (metrics, fval, or metric means) for each target.

Examples

cvFolds <- make_Z(1922:2003, nRuns = 50, frac = 0.25, contiguous = TRUE)
cv <- cv_mb(p1Seasonal, pc3seasons, cvFolds, 1750, log.trans = 1:3, return.type = 'metrics')

Least square with mass balance penalty

Description

Least square with mass balance penalty

Usage

lsq_mb(hat, obs, lambda, mus, sigmas, log.seasons, log.ann, N, sInd)

Arguments

hat

A vector of estimated flow in the transformed space.

obs

A vector of observed flow in the transformed space.

lambda

Penalty weight.

mus

A vector of means, one for each target.

sigmas

A vector of the standard deviations, one for each target.

log.seasons

A vector containing the indices of the seasons that are log-transformed.

log.ann

TRUE if the annual reconstruction is log-transformed.

N

The number of targets (number of seasons plus one for the annual reconstruction).

sInd

Indices of the seasons, i.e, 1...N-1

Value

Objective function value: least squares plus a penalty term.

Make cross-validation folds.

Description

Make a list of cross-validation folds. Each element of the list is a vector of the cross-validation points for one cross-validation run.

Usage

make_Z(obs, nRuns = 30, frac = 0.1, contiguous = TRUE)

Arguments

obs

Vector of observations.

nRuns

Number of repetitions.

frac

Fraction of left-out points. For leave-one-out, use frac = 1, otherwise use any value less than 1. Default is 0.1 (leave-10%-out).

contiguous

Logical. If TRUE, the default, the left-out points are made in contiguous blocks; otherwise, they are scattered randomly.

Value

A list of cross-validation folds

Examples

Z <- make_Z(p1Seasonal$Qa, nRuns = 30, frac = 0.25, contiguous = TRUE)

Fit parameters with mass balance criterion

Description

Fit parameters with mass balance criterion

Usage

mb_fit(X, Y, lambda, mus, sigmas, log.seasons, log.ann, N, sInd)

Arguments

X

Inputs, must have columns of 1 added

Y

Observed Dry, Wet, and Annual log-transformed flows

lambda

Penalty weight.

mus

A vector of means, one for each target.

sigmas

A vector of the standard deviations, one for each target.

log.seasons

A vector containing the indices of the seasons that are log-transformed.

log.ann

TRUE if the annual reconstruction is log-transformed.

N

The number of targets (number of seasons plus one for the annual reconstruction).

sInd

Indices of the seasons, i.e, 1...N-1

Value

A one-column matrix of beta value

Mass-balance-adjusted reconstruction

Description

Mass-balance-adjusted reconstruction

Usage

mb_reconstruction(
  instQ,
  pc.list,
  start.year,
  lambda = 1,
  log.trans = NULL,
  force.standardize = FALSE
)

Arguments

instQ

Instrumental data, in the same order as pc.list. The "season" column must be a factor.

pc.list

List of PC matrices. The first element is for the first season, second element for second season, and so on. The last element is for the annual reconstruction.

start.year

The first year of record

lambda

The penalty weight

log.trans

A vector containing indices of the targets to be log-transformed. If no transformation is needed, provide NULL.

force.standardize

If TRUE, all observations are standardized. See Details.

Value

A data.table with the following columns: season, year, Q, and lambda.

Details

If some targets are log transformed and some are not, they will have different scales, which affects the objective function. In this case the observations will be standardized so that they are in the same range. Otherwise, standardization are skipped for speed. However, in some cases you may want to standardize any ways, for example when flows in some months are much larger than in other months. In this case, set force.standardize = TRUE.

Examples

mb_reconstruction(p1Seasonal, pc3seasons, 1750, lambda = 1, log.trans = 1:3)

Normalized root-mean-square error

Description

RMSE is normalized by the normalization constant

Usage

nRMSE(yhat, y, normConst)

Arguments

yhat

Model outputs

y

Observations

normConst

The normalization constant

Value

normalized RMSE value

Examples

x <- rnorm(100)
y <- rnorm(100)
nRMSE(x, y, sd(y))

Objective function from parameters

Description

This is a wrapper for lsq_mb(). It first calculates hat, then calls lsq_mb(). This is used in optim(), so it returns a scalar.

Usage

obj_fun(beta, X, Y, lambda, mus, sigmas, log.seasons, log.ann, N, sInd)

Arguments

beta

Parameters

X

Inputs, must have columns of 1 added

Y

Observed Dry, Wet, and Annual log-transformed flows

lambda

Penalty weight.

mus

A vector of means, one for each target.

sigmas

A vector of the standard deviations, one for each target.

log.seasons

A vector containing the indices of the seasons that are log-transformed.

log.ann

TRUE if the annual reconstruction is log-transformed.

N

The number of targets (number of seasons plus one for the annual reconstruction).

sInd

Indices of the seasons, i.e, 1...N-1

Value

Objective function value

Seasonal streamflow at P.1 station

Description

Streamflow at P.1 station (Chiang Mai, Thailand) for three reconstruction targets: dry season (NJ, Nov-Jun), wet season (JO, Jul-Oct), and water year (WY, Nov-Oct), as used by Nguyen et al (2020).

Usage

p1Seasonal

Format

A data table with 246 rows and 3 variables:

season

a factor with three levels: "NJ", "JO", and "WY"

year

integer, from 1922 to 2003

Qa

Annual flow for each target

Source

https://www.essoar.org/doi/10.1002/essoar.10504791.1

References

Nguyen, H. T. T., Galelli, S., Xu, C., & Buckley, B. (2020). Multi-Proxy, Multi-Season Streamflow Reconstruction with Mass Balance Adjustment. Earth and Space Science Open Archive, 22. https://doi.org/10.1002/essoar.10504791.1

Principal components of tree rings

Description

Principal components of the Southeast Asian Dendrochronology Network, after appropriate sites have been selected for each season.

Usage

pc3seasons

Format

A list with three elements (NJ, JO, and WY), each element is a principal component matrix.

Source

https://www.essoar.org/doi/10.1002/essoar.10504791.1

References

Nguyen, H. T. T., Galelli, S., Xu, C., & Buckley, B. (2020). Multi-Proxy, Multi-Season Streamflow Reconstruction with Mass Balance Adjustment. Earth and Space Science Open Archive, 22. https://doi.org/10.1002/essoar.10504791.1

Prepend a column of ones

Description

Prepend a column of ones

Usage

prepend_ones(x)

Arguments

x

The input matrix

Value

x with a column of ones prepended, which is named 'Int' for 'intercept'

Scale rows of a Matrix

Description

Similar to colScale

Usage

rowScale(x, add_attr = TRUE)

Arguments

x

A matrix.

add_attr

If TRUE, the column means and standard deviations are returned as attributes. This is consistent with base::scale().

Value

The scaled matrix.

Unscale rows of a matrix

Description

Backtransform a matrix that was scaled before.

Usage

rowUnscale(x, rm, rsd)

Arguments

x

A matrix.

rm

A vector of row means

rsd

A vector of row standard deviations

Value

The unscaled matrix