Package 'WoodSimulatR'

Means and standard deviations of grade determining properties (GDPs) from literature

Description

Means and standard deviations of grade determining properties (GDPs) from literature

Usage

gdp_data

Format

species

Wood species as a four letter code according to EN 13556. Currently, this is always "PCAB" for Norway spruce (Picea abies).

loadtype

Kind of destructive testing applied to the material – "t" for material tested in tension, "be" for material tested in bending.

project

Research project from which the data originated; "null" if unknown or not applicable.

country

Country from which the material originated, as a two letter country code.

share

Number of pieces on which the values are based.

f_mean, f_sd

Mean and standard deviation of strength, in N/mm².

E_mean, E_sd

Mean and standard deviation of the static modulus of elasticity, in N/mm².

rho_mean, rho_sd

Mean and standard deviation of density, in kg/m³.

literature

Reference to the literature source; "null" if not published yet.

subsample

For distinguishing multiple rows with the same species, loadtype and country – if there are no duplicates, it is the same as country; if there are duplicates, it is country plus a suffixed number separated by "_".

Details

For simulation of an entire dataset with different subsamples with different characteristics (see simulate_dataset), it may be useful to be able to refer to existing results from literature as a basis.

In the dataset gdp_data, means and standard deviations for a number of such subsamples have been collected.

The GDP values collected in gdp_data were selected from publications which aimed at representative sampling within the respective countries. All the same, care must be taken when using these values, due to the natural high variability of timber properties.

Source

The values have been extracted from the following publications:

Ranta-Maunus, Alpo, Julia K. Denzler, and Peter Stapel. 2011. Strength of European Timber. Part 2. Properties of Spruce and Pine Tested in Gradewood Project. VTT.

Rohanová, Alena, and Erika Nunez. 2014. "Prediction Models of Slovakian Structural Timber." Wood Research 59 (5): 757–69.

Stapel, Peter, and Jan-Willem G. van de Kuilen. 2014. “Efficiency of Visual Strength Grading of Timber with Respect to Origin, Species, Cross Section, and Grading Rules: A Critical Evaluation of the Common Standards.” Holzforschung 68 (2): 203–16.

---

Retrieve descriptive data for samples from literature

Description

In the WoodSimulatR package, means and standard deviations of grade determining properties (GDPs) for a number of Norway spruce (Picea abies) samples from literature are stored for use in simulate_dataset. They are indexed by a two-letter country code (and a suffixed number if disambiguation is required).

Usage

get_subsample_definitions(country = NULL, loadtype = "t", species = "PCAB")

Arguments

country	Can be either the number of desired samples, or a named vector of relative subsample sizes where the names can be abbreviations of country names. Alternatively, country can also be a character vector of country abbreviations.
loadtype	Can be either "be" for "bending edgewise" or "t" for "tension".
species	A species code according to EN 13556:2003. Currently, only 'PCAB' (Picea abies = Norway spruce) is supported.

Details

The direct descriptive data can also be directly accessed (gdp_data). The present function is meant to prepare the data as input to the subsets argument of simulate_dataset. It allows picking multiple samples from the same country (disambiguating by creating appropriately named entries in the column subsample) and creating random sample data (uniformly distributed within the range of values given in the full dataset gdp_data for the respective loadtype and species) for sample names not found in this dataset.

The dataset gdp_data contains a column share which gives the number of pieces in the original sample. Unless relative subsample sizes are explicitly asked for by providing a named numeric vector for the argument country, the present function always resets share to 1, prompting simulate_dataset to create (approximately) equal-sized subsamples.

The GDPs depend on the type of destructive testing done (loadtype) – therefore, giving the proper loadtype is required for realistic values.

If country is NULL (or omitted), the full dataset gdp_data for the respective loadtype (and species) is returned.

For sample names not contained in the internal list, a warning is issued and random sample data is returned (uniformly distributed within the range of values given in the full table for the respective loadtype and species).

If country is just a number (and not a named vector), also random sample data is returned; the different "countries" are then named "C1", "C2" and so on.

Value

A data frame with country and subsample names, relative subsample sizes and some meta-information like project and literature references, as well as mean strength and standard deviation of strength, static modulus of elasticity and density.

Notes

The GDP values collected in gdp_data were selected from publications which aimed at representative sampling within the respective countries. All the same, care must be taken when using these values, due to the natural high variability of timber properties.

Examples

# get all subsample data for loadtype bending, or tension
get_subsample_definitions()
get_subsample_definitions(loadtype='be')

# get six random samples, explicitly state loadtype tension
get_subsample_definitions(country=6, loadtype='t')

# get subsample data for the German tension sample in different ways
get_subsample_definitions(country='de', loadtype='t')
get_subsample_definitions(country=c(de=1), loadtype='t')
get_subsample_definitions(country=c(de=6), loadtype='t')

# bending samples from Sweden (both samples), Poland, and France, equally
# weighted
get_subsample_definitions(c('se', 'se_1', 'pl', 'fr'))
get_subsample_definitions(c(se=1, se_1=1, pl=1, fr=1))
get_subsample_definitions(c(se=5, se_1=5, pl=5, fr=5))

# four tension samples from Romania, two from Ukraine and one from Slovakia,
# weighted so that each country contributes equally
get_subsample_definitions(c(ro=1, ro=1, ro=1, ro=1, ua=2, ua=2, sk=4), loadtype='t')

# non-existant subsample names get replaced by random values (which are based
# on the range of stored values for the respective loadtype)
get_subsample_definitions(c('xx', 'yy', 'zz'))
get_subsample_definitions(c('xx', 'yy', 'zz'), loadtype='t')

# subsample names are case-sensitive!
get_subsample_definitions(c('at', 'aT', 'At', 'AT'), loadtype='t')

---

Return labels for given transforms

Description

The function simbase_covar allows the specification of a transform for one or more variables. The present function creates short names for such transforms for use in labelling (by default, the labelling is done by simbase_labeler).

Usage

get_transform_names(
  transforms,
  prefer_primitive = c("if_shorter", "never", "always")
)

Arguments

transforms	A named list of objects of class trans or class transform (see function trans_new in package scales)
prefer_primitive	If "never", the function always returns the value of the field name (except if this is missing). If "always", the name of the called function is returned unless it cannot be identified (in many cases, the transform will not be primitive). If "if_shorter", the shorter option of the two above is returned if both can be retrieved.

Details

The label of a transform could be the value of the field name from each object of class trans (or transform), but also the name of the transform function itself, if it is a primitive function or just calls one function.

Each object of class trans (or transform) should have a field name which can be returned by the present function.

The function examines the field transform. If this field contains a primitive function (see is_primitive), or if there is just one function call in the body of this transform function, we can also return the name of this called function.

If there is no field name and no single function is called from the function defined in the field transform, a generic function name "f." is returned.

Value

A named vector of transforms names.

Examples

get_transform_names(list(a = scales::log_trans(), b = scales::boxcox_trans(0)));
get_transform_names(list(x = list(name = 'a very long name', transform = log, inverse = exp)))

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Predefined simbases in WoodSimulatR

Description

Predefined simbases in WoodSimulatR

Usage

ws_t
 ws_t_tr
 ws_t_te
 ws_t_logf
 ws_t_tr_logf
 ws_t_te_logf
 ws_be
 ws_be_tr
 ws_be_te
 ws_be_logf
 ws_be_tr_logf
 ws_be_te_logf

Format

For statistical simulation of datasets in WoodSimulatR, one needs a simbase_covar object. WoodSimulatR contains a set of such predefined simbases for Norway spruce (Picea abies) grown in Austria.

The names of the simbases follow the following schema – the different parts are separated by "_":

• "ws" – abbreviation of "WoodSimulatR simbase"

• loadtype – can either be "t" for material tested in tension, or "be" for material tested in bending

• subsample – empty for the full dataset, "tr" for the part of the dataset that was used for training, "te" for the part that was used for testing. The latter two can be used to more closely simulate independent training and test samples

• transformation – empty for no transformation, "logf" if the strength has been log-transformed prior to calculation of the simbase – see also the argument transforms in simbase_covar.

The simbases contain the basis for simulating the following variables:

f

Bending or tension strength, in N/mm².

E

Static modulus of elasticity in bending or tension, in N/mm².

rho

Density of a small clear sample, in kg/m³.

E_dyn

Dynamic modulus of elasticity of the timber after drying to a moisture content of about 12%, in N/mm².

E_dyn_u

Dynamic modulus of elasticity of the timber in the green state, with moisture contents mostly above fibre saturation point, in N/mm².

ip_rho

An "indicating property" (IP) for density, established by measuring the weight of each board and dividing by its volume, in kg/m³.

ip_f

An "indicating property" (IP) for strength, established by linear regression on E_dyn, ip_rho and a knot parameter called "total knot area ratio" (tKAR), in N/mm².

Source

The simbases were created based on data from the research project SiOSiP of Holzforschung Austria. "SiOSiP" is short for "simulation-based optimization of sawn timber production" and ran from 2014 to 2017.

---

Calculate reference data for simulating values based on a covariance matrix approach

Description

Given the covariance matrix and the means of a set of variables, we can simulate not only the distribution of the variables, but also their correlations. The present function calculates the basic values required for the simulation and returns them packed into an object of class simbase_covar.

Usage

simbase_covar(
  data,
  variables = NULL,
  transforms = list(),
  label = simbase_labeler,
  ...
)

Arguments

data	The dataset for the calculation of the reference data for simulation; for grouped datasets (see group_by), the reference data is calculated for each group separately (see also simbase_list).
variables	Character vector containing the names in data which should be included in the simulation. If missing, all numeric variables in data are used.
transforms	A named list of objects of class trans or class transform (see function trans_new in package scales); the name of each list entry must correspond to a variable name in variables.
label	Either a string describing the data and the simulation approach, or a labelling function which returns a label string and takes as input the data, a string giving the class of the simbase object (here "simbase_covar") and the transforms list.
...	Arguments to be passed on to simbase_list (if it is called).

Details

If some of the variables are non-normally distributed, a transform may improve the prediction. The transforms are passed to the function as a named list, where the name of a list entry must correspond to the name of the variable in the data which is to be transformed.

Predefined transforms can be found in the package scales, where they are used for axis transformations as a preparation for plotting. The package scales also contains a function trans_new which can be used to define new transforms.

In the context of destructively measured sawn timber properties, the type of destructive test applied is of interest. If the dataset data contains a variable loadtype which consistently throughout the dataset has either the value "t" (i.e. all sawn timber has been tested in tension) or the value "be" (i.e. all sawn timber has been tested in bending, edgewise), then the returned object also has a field loadtype with that value.

One can also calculate a simbase under the assumption that the correlations are different for different subgroups of the data. This is done by grouping the dataset data prior to passing it to the function, using group_by. In this case, several objects of class simbase_covar are created and joined together in a tibble – see also simbase_list.

Value

An S3 object of class simbase_list if data is grouped, and an object of class simbase_covar otherwise.

Examples

# obtain a dataset for demonstration
dataset <- simulate_dataset();

# calculate a simbase without transforms
simbase_covar(dataset, c('f', 'E', 'rho', 'E_dyn'));

# calculate a simbase with log-transformed f
simbase_covar(dataset, c('f', 'E', 'rho', 'E_dyn'), list(f = scales::log_trans()));

# if we group the dataset, we get a simbase_list object
simbase_covar(dplyr::group_by(dataset, country), c('f', 'E', 'rho', 'E_dyn'));

---

Default labelling function for simbase objects

Description

Each simbase object should have a label which can be used for differentiating different simulations. This function tries to simplify the label generation.

Usage

simbase_labeler(data, simbase_class, transforms)

Arguments

data	The dataset for the calculation of the basic simulation data.
simbase_class	The class of the simbase object for which the label is to be generated. Currently, only "simbase_covar" is supported.
transforms	The transforms applied to variables in the dataset. Must be objects of class trans or class transform (see function trans_new in package scales).

Details

Primarily, this function is intended to be called as a default from simbase_covar. It can also serve as a template for creating custom labelling functions.

Value

A string for labelling a simbase object.

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Wrapper for the simbase_* functions for grouped data

Description

If a function of the simbase_* family encounters grouped data (as caused by group_by), it should invoke simbase_list to create a collection of separate simbases for each group.

Usage

simbase_list(data, simbase_constructor, ..., suffix = "_lst")

Arguments

data	A grouped dataset (see group_by)
simbase_constructor	A function which returns a simbase_* object, like simbase_covar
...	Further arguments passed to the simbase_* function.
suffix	Suffix to be added to the individual simbase labels if they are all the same (see details).

Value

A simbase_list object; this is essentially a tibble with the grouping columns of data and a column .simbase which contains the simbase_* objects.

Technical details

Currently, the "simbase_* family" only consists of simbase_covar (although, in a broader sense, simbase_list can also be thought to be part of this "family"). It is planned to add further simulation types in a later release.

The functions of the simbase_* family support label generation (see e.g. simbase_covar). These functions should generate the label before invoking simbase_list, so that there is a common label for all of the simbases; simbase_list adds a suffix suffix. A warning is issued if the labels of the different simbases are not all equal; no suffix is added in this case.

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Add simulated values to a dataset conditionally, based on a simbase_* object

Description

Add simulated values to a dataset conditionally, based on a simbase_* object

Usage

simulate_conditionally(data, simbase, force_positive = TRUE, ...)

Arguments

data	The dataset where simulated values are added to. The dataset has to contain at least one variable which is also included in the simbase_* object.
simbase	Basic data object for the simulation, as calculated e.g. by simbase_covar or simbase_list.
force_positive	If TRUE, the resulting values are forced to be $\ge 0$.
...	further arguments passed to or from other methods.

Details

Given a simbase_* object, this function adds simulated values to a dataset, conditional on the values of some of the variables already contained in the dataset.

Value

The modified dataset data with simulated values.

Examples

# add simulated tension data based on a simbase stored in WoodSimulatR
dataset <- data.frame(E_dyn = rnorm(n = 100, mean = 12500, sd = 2200));
dataset_t <- simulate_conditionally(dataset, ws_t)

# add simulated bending data
dataset_be <- simulate_conditionally(dataset, ws_be)

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Add simulated values to a dataset conditionally, based on a simbase_list object

Description

Add simulated values to a dataset conditionally, based on a simbase_list object

Usage

## S3 method for class 'simbase_list'
simulate_conditionally(
  data,
  simbase,
  force_positive = TRUE,
  ...,
  error_when_groups_missing = TRUE
)

Arguments

data	The dataset where simulated values are added to.
simbase	Basic data object for the simulation, as calculated by simbase_list.
force_positive	If TRUE, the resulting values are forced to be $\ge 0$.
...	further arguments passed to or from other methods.
error_when_groups_missing	Whether to raise an error if for a certain value combination in the grouping variables no dedicated simbase exists (see details).

Details

Simulating values based on a simbase_list object has some special aspects compared to that of other simbase_* objects, (see simulate_conditionally).

In particular, a simbase_list object stores simbases for specific value combinations within the grouping variables.

These grouping variables must also be present in data.

If there is a value combination in these grouping variables for which no dedicated simbase object exists, this will lead to NA values in the columns to be simulated and either to an error (if error_when_groups_missing = TRUE) or to a warning.

Due to the internal call to nest and subsequent call to unnest, the returned dataset will be ordered according to the grouping variables in the simbase, with any grouping variable combinations missing in the simbase coming last.

Value

The modified dataset data with simulated values.

Examples

# create a simbase_list object for the values of subsets = c('AT', 'DE')
dataset_0 <- simulate_dataset(subsets = c('AT', 'DE'));
simbase <- simbase_covar(dplyr::group_by(dataset_0, country), c('f', 'E', 'E_dyn'));

# simulate on another dataset
dataset <- data.frame(E_dyn = rnorm(n = 100, mean = 12500, sd = 2200), country = 'AT');
dataset_1 <- simulate_conditionally(dataset, simbase);
head(dataset_1);

# warning if for some value of country we don't have an entry in the simbase
dataset$country <- 'CH';
dataset_2 <- simulate_conditionally(dataset, simbase, error_when_groups_missing = FALSE);
head(dataset_2);

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Generate an artificial dataset with correlated variables

Description

Generate an artificial dataset with correlated variables and defined means and standard deviations.

Usage

simulate_dataset(
  n = 5000,
  subsets = 4,
  random_seed = NULL,
  simbase = WoodSimulatR::ws_t_logf,
  loadtype = NULL,
  ...,
  RNGversion = "3.6.0"
)

Arguments

n	Number of rows in the dataset
subsets	Either NULL, or a data.frame describing the subsets (see details) or a character vector or named numeric vector suitable for argument country in get_subsample_definitions.
random_seed	Allows to set an integer seed value for the random number generator to achieve reproducible results (see also set.seed).
simbase	An object of class simbase_covar or simbase_list. In particular, one of the simbases stored in WoodSimulatR may be used – see simbase.
loadtype	For passing on to get_subsample_definitions. A string with either "t" (for material tested in tension) or "be" (for material tested in edgewise bending). Is only used if the simbase doesn't contain a field loadtype or if the loadtype is ambiguous or not equal to "t" or "be".
...	arguments passed on to get_subsample_definitions.
RNGversion	In WoodSimulatR 0.5, the RNGversion had been fixed to RNGversion = "3.5.0", but this setting now causes a warning because the random number generator was changed in R version 3.6.0 (see RNGversion). For perfect reproducibility of results from WoodSimulatR 0.5, one should set RNGversion = "3.5.0".

Details

In the package WoodSimulatR, a number of predefined base values for simulation are stored – see simbase.

Using a character vector for the argument subsets leads to subsets as equal in size as possible.

The argument subsets enables differing means and standard deviations for different subsamples. There are several possible usages:

• If subsets = NULL, the information about means and standard deviations is taken from the simbase. There can still be different means and standard deviations if simbase is an object of class simbase_list.

• If a numeric vector or a character vector, it is used as argument country in an internal call to get_subsample_definitions.

• If a dataset, there are the following requirements:

  • identifier columns: The dataset has to have one or more discrete-valued identifier columns (usually character vectors or factors) which uniquely identify each row. These identifier columns are named "country" and "subsample" in the standard case as yielded by get_subsample_definitions. In the general case, the identifier columns are detected as those columns which are not named share, species, loadtype or literature and which do not end in _mean or _sd. If the argument simbase is of class simbase_list, further restrictions apply (see below).

  • means and standard deviations: For at least one of the variables defined in the simbase, also the mean and the standard deviation need to be given in each row; the column names for this data must be the name of the respective variable(s) from the simbase, suffixed by _mean and _sd, respectively.

  • optional: A column share can be used to create subsamples of different sizes proportional to the values in share.

The argument simbase can be either an object of class simbase_covar or of class simbase_list.

• various predefined simbase_covar objects are available in WoodSimulatR – see simbase.

• for objects of class simbase_list, additional restrictions apply:

  1. the object may only have grouping variable(s) which are also identifier columns according to the subsets definition above – if the subsets argument is not a data frame, the identifier columns are "country" and "subsample".

  2. The value combinations in the identifier columns have to match those which the subsets argument leads to (see also get_subsample_definitions).

Both the means and standard deviations in the subsample definitions (see get_subsample_definitions) as well as the values in the simbase depend on the way the destructive testing of the sawn timber was done. If the simbase has a field loadtype (see also simbase_covar), this value is used in the call to get_subsample_definitions. Otherwise, the loadtype has to be passed directly to the present function unless no call to get_subsample_definitions is necessary (this depends on the value of subsets – see above). If a loadtype has been defined, a variable loadtype is also created in the resulting dataset for reference.

Negative values in any numeric column of the result dataset are forced to zero.

If random_seed is not NULL, reproducibility of results is enforced by using set.seed with arguments kind='Mersenne-Twister' and normal.kind='Inversion', and by calling RNGversion with argument RNGversion.

If random_seed is not NULL, the random number generator is reset at the end of the function using set.seed(NULL) and RNGversion(toString(getRversion())).

Examples

simulate_dataset(n = 10, subsets = 1, random_seed = 1)

# As the loadtype is defined in the simbase, the argument loadtype is ignored
# with a warning
simulate_dataset(n = 10, subsets = 1, random_seed = 1, loadtype = 'be')

# Two subsamples
simulate_dataset(n = 10, subsets = 2, random_seed = 1)

# Two subsamples from pre-defined countries
simulate_dataset(n = 10, subsets = c('at', 'de'), random_seed = 1)

# Two subsamples from pre-defined countries with different sample sizes
simulate_dataset(n = 10, subsets = c(at = 3, de = 2), random_seed = 1)

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