ssd_xxmulti_fitdists() functions to accept object of class fitdists.ssd_xxmulti(..., lnorm.weight = 0) (instead of 1) to avoid incorrect values with do.call("ssd_xxmulti", c(..., estimates(fits)) if fits does not include the log-normal distribution.ssdtools v2.0.0, which now includes David Fox and Rebecca Fisher as co-authors, is the second major release of ssdtools.
The following changes are major in the sense that they could alter previous hazard concentrations or break code.
The following arguments were added to ssd_hc() and ssd_hp()
multi_est = TRUE to calculate model averaged estimates treating the distributions as constituting a single mixture distribution (previously it was effectively FALSE).method_ci = "weighted_samples" to specify whether to use "weighted_samples", "weighted_arithmetic", "multi_free" or "multi_fixed" methods to generate confidence intervals (previously it was effectively "weighted_arithmetic").In addition the data frame returned by ssd_hc() and predict() now includes a column proportion with values between 0 and 1 as opposed to a column percentage with between 0 and 100.
Finally, with censored data confidence intervals can now only be estimated by non-parametric bootstrapping as the methods of parametrically bootstrapping censored data require review.
The remaining changes are minor.
The following arguments of ssd_fit_dists() were changed to reduce the chances of the lnorm_lnorm bimodal distribution being dropped from the default set:
min_pmix = ssd_min_pmix(nrow(data)) so that by default min_pmix is 0.1 or 3/nrow(data) if greater.at_boundary_ok = TRUE.computable = TRUE.These changes also allowed the min_pboot = 0.95 argument to be changed from 0.80 for all bootstrapping functions.
It is worth noting that the second two changes also reduce the chances of the BurrIII distribution being dropped.
In addition rescale = TRUE now divides by the geometric mean of the minimum and maximum positive finite values as opposed to dividing by the geometric mean of the maximum finite value to improve the chances of convergence although ssd_fit_bcanz() no longer rescales by default.
Other minor modifications to the model fitting functions include
estimates.fitdists() now includes weights in returned parameters as well as an all_estimates = FALSE argument to allow parameter values for all implemented distributions to be included.delta = 7 instead of delta = 9.21 to ensure weight of included models at least 0.01.lnorm and gompertz initial values are offset from their maximum likelihood estimates to avoid errors in optim().The following functions and arguments were also added:
ssd_hp_bcanz() and ssd_hp.fitburrlioz() to get hazard proportions.ssd_pmulti(), ssd_qmulti() and ssd_rmulti() for combined mixture distributions.ssd_exx() functions to get default parameter estimates for distributions.ssd_censor_data() to censor data.npars = c(2L, 5L) argument to ssd_dists_bcanz() to specify the number of parameters.dists = ssd_dists_bcanz() to ssd_fit_bcanz() to allow other packages to modify.samples = FALSE to ssd_hc() and ssd_hp() include bootstrap samples as list of numeric vector(s).save_to = NULL to ssd_hc() and ssd_hp() to specify a directory in which to save the bootstrap datasets as csv files and parameter estimates as .rds files.ssd_hc() and ssd_hp() now return data frame with parametric column.ssd_hp() now return data frame with wt column.The following functions and arguments were deprecated:
ssd_wqg_bc() and ssd_wqg_burrlioz() were deprecated.percent = 5 in ssd_hc() and predict() was soft-deprecated for proportion = 0.05.is_censored() is now defunct.Perhaps the biggest plotting change is that ssd_plot_cdf() now plots the average SSD together with the individual distributions if average = NA.
In addition, the following functions and arguments were added.
scale_fill_ssd() for color-blind fill scale.ssd_label_comma() for formatting of x-axis labels.trans = "log10" and add_x = 0 to ssd_plot() and ssd_plot_data() to control x-axis scale.big.mark = "," for x-axis labels and suffix = "%" for y-axis labels to all plotting functions.and the following functions deprecated
comma_signif() was soft-deprecated.is_censored(), plot.fitdists(), ssd_plot_cf() geom_ssd() and stat_ssd() are now defunct.The following data sets were removed
ccme_data and ccme_boron (available in ssddata package).pearson1000 data set.size = 0.5 with linewidth = 0.5 in geom_hcintersect() and geom_xribbon().aes_string() with aes() in examples (and internally).tidyverse package.ssd_hp() to be percent affected rather than percent protected.delta = 7 argument to ssd_plot_cdf().ssdtools version 1.0.0 is the first major release of ssdtools with some important improvements and breaking changes.
An important change to the functionality of ssd_fit_dists() was to switch from model fitting using fitdistrplus to TMB which has resulted in improved handling of censored data.
Although it was hoped that model fitting would be faster this is currently not the case.
As a result of the change the fitdists objects returned by ssd_fit_dists() from previous versions of ssdtools are not compatible with the major release and should be regenerated.
As a result of an international collaboration British Columbia and Canada and Australia and New Zealand selected a set of recommended distributions for model averaging and settings when generating final guidelines.
The distributions are
> ssd_dists_bcanz()
[1] "gamma" "lgumbel" "llogis" "lnorm" "lnorm_lnorm" "weibull"
The ssd_fit_bcanz() and ssd_hc_bcanz() functions were added to the package to facilitate the fitting of these distributions and estimation of hazard concentrations using the recommended settings.
In the previous version of ssdtools a distribution was considered to have converged if the following condition was met
stats::optim() returns a code of 0 (indicating successful completion).In the new version an additional two conditions must also be met
at_boundary_ok = TRUE or the user can specify different boundary values - see below)computable = FALSE)Censoring can now be specified by providing a data set with one or more rows that have
It is currently not possible to fit distributions to data sets that have
Rows that have a zero or missing value for the left column and an infinite or missing value for the right column (fully censored) are uninformative and will result in an error.
For uncensored data, Akaike Weights are calculated using AICc (which corrects for small sample size). In the case of censored data, Akaike Weights are calculated using AIC (as the sample size cannot be estimated) but only if all the distributions have the same number of parameters (to ensure the weights are valid).
Weighting must be positive with values <= 1000.
Previously the density functions for the available distributions were exported as R functions to make them accessible to fitdistrplus.
This meant that ssdtools had to be loaded to fit distributions.
The density functions are now defined in C++ as TMB templates and are no longer exported.
The distribution, quantile and random generation functions are more generally useful and are still exported but are now prefixed by ssd_ to prevent clashes with existing functions in other packages.
Thus for example plnorm(), qlnorm() and rlnorm() have been renamed ssd_plnorm(), ssd_qlnorm() and ssd_rlnorm().
The following distributions were added (or in the case of burrIII3 readded) to the new version
burrIII3 - burrIII three parameter distributioninvpareto - inverse pareto (with bias correction in scale order statistic)lnorm_lnorm log-normal/log-normal mixture distributionllogis_llogis log-logistic/log-logistic mixture distributionThe following arguments were added to ssd_fit_dists()
rescale (by default FALSE) to specify whether to rescale concentrations values by dividing by the largest (finite) value. This alters the parameter estimates, which can help some distributions converge, but not the estimates of the hazard concentrations/protections.reweight (by default FALSE) to specify whether to reweight data points by dividing by the largest weight.at_boundary_ok (by default FALSE) to specifying whether a distribution with one or more parameters at a boundary has converged.min_pmix (by default 0) to specify the boundary for the minimum proportion for a mixture distribution.range_shape1 (by default c(0.05, 20)) to specify the lower and upper boundaries for the shape1 parameter of the burrIII3 distribution.range_shape2 (by default the same as range_shape2) to specify the lower and upper boundaries for the shape2 parameter of the burrIII3 distribution.control (by default an empty list) to pass a list of control parameters to stats::optim().It also worth noting that the default value of
computable argument was switched from FALSE to TRUE to enforce stricter requirements on convergence (see above).The following were added to handle multiple distributions
ssd_dists() to specify subsets of the available distributions.delta argument (by default 7) to the subset() generic to only keep those distributions within the specified AIC(c) difference of the best supported distribution.The function ssd_fit_burrlioz() was added to approximate the behaviour of Burrlioz.
Hazard concentration estimation is performed by ssd_hc() (which is wrapped by predict()) and hazard protection estimation by ssd_hp().
By default confidence intervals are estimated by parametric bootstrapping.
To reduce the time required for bootstrapping, parallelization was implemented using the future package.
The following arguments were added to ssd_hc() and ssd_hp()
delta (by default 7) to only keep those distributions within the specified AIC difference of the best supported distribution.min_pboot (by default 0.90) to specify minimum proportion of bootstrap samples that must successfully fit.parametric (by default TRUE) to allow non-parametric bootstrapping.control (by default an empty list) to pass a list of control parameters to stats::optim().and the following columns were added to the output data frame
wt to specify the Akaike weight.method to indicate whether parametric or non-parametric bootstrap was used.nboot to indicate how many bootstrap samples were used.pboot to indicate the proportion of bootstrap samples which fitted.It also worth noting that the
dist column was moved from the last to the first position in the output data frame.Confidence intervals cannot be estimated for interval censored data.
Confidence intervals cannot be estimated for unequally weighted data.
The pvalue argument (by default FALSE) was added to ssd_gof() to specify whether to return p-values for the test statistics as opposed to the test statistics themselves.
There have also been some substantive changes to the plotting functionality.
Added following functions
ssd_plot_data() to plot censored and uncensored data by calling geom_ssdpoint() for the left and for the right column (alpha parameter values should be adjusted accordingly)geom_ssdsegment() to allow plotting of the range of a censored data points using segments.scale_colour_ssd() (and scale_color_ssd()) to provide an 8 color-blind scale.Made the following changes to ssd_plot()
bounds (by default c(left = 1, right = 1)) argument specify how many orders of magnitude to extend the plot beyond the minimum and maximum (non-missing) values.linetype (by default NULL) argument to specify line type.linecolor (by default NULL) argument to specify line color.ylab from "Percent of Species Affected" to "Species Affected".Renamed
GeomSsd to GeomSsdpoint.StatSsd to StatSsdpointSoft-deprecated
geom_ssd() for geom_ssdpoint().stat_ssd().ssd_plot_cf() for fitdistrplus::descdist().ssddataThe dataset boron_data was renamed ccme_boron and moved to the ssddata R package together with the other CCME datasets.
The ssddata package provides a suite of datasets for testing and comparing species sensitivity distribution fitting software.
Added
ssd_data() to return original data for a fitdists object.ssd_ecd_data() to get empirical cumulative density for data.ssd_sort_data() to sort data by empirical cumulative density.npars() now orders by distribution name.Implemented the following generics for fitdists objects
glance() to get the model likelihoods, information-theoretic criteria etc.augment() to return original data set.logLik() to return the log-likelihood.summary.fitdists() to summarize.wt (Akaike weight) column to predict(), ssd_hc() and ssd_hp()ic to predict(), ssd_hc() and ssd_hp() because unused.ssd_fit_dists().actuar package.comma_signif() so that now rounds to 3 significant digits by default and only applies scales::comma() to values >= 1000.... argument to comma_signif().rdist() functions now use length of n if length(n) > 1.slnorm() to get starting values for 'dlnorm' distribution.rllog() that was causing error.ssd_hc() and predict() where ci = TRUE to explicit ssd_hc(ci = FALSE) and predict(ci = FALSE).shape and scale arguments to llog() with lshape and lscale.location and scale arguments to lgumbel() with llocation and lscale.burrIII2).ssd_hp() to calculate hazard percent at specific concentrations.ssd_exposure() to calculate proportion exposed based on distribution of concentrations.predict() and added parallel argument.ssd_fit_dists() now checks if standard errors computable.burrIII3).sdist(x) functionality to set starting values for distributions.ssd_plot_cdf() to plot cumulative distribution function (equivalent to autoplot())nobs() for censored data now returns a missing value.ssd_fit_dists() distributions now ordered alphabetically.ssd_hc() argument hc = 5L for percent = 5L.dllog() etc for dllogis().ssd_cfplot() for ssd_plot_cf().llog distribution with small concentrations.