Merge pull request #317 from poissonconsulting/dev

.covrignore

@@ -1,3 +1 @@
-R/deprecated.R
-R/zzz.R
-R/release.R
+R/devtools-helpers.R

NAMESPACE

@@ -71,8 +71,19 @@ export(ssd_data)
 export(ssd_dists)
 export(ssd_dists_all)
 export(ssd_dists_bcanz)
+export(ssd_eburrIII3)
 export(ssd_ecd)
 export(ssd_ecd_data)
+export(ssd_egamma)
+export(ssd_egompertz)
+export(ssd_einvpareto)
+export(ssd_elgumbel)
+export(ssd_ellogis)
+export(ssd_ellogis_llogis)
+export(ssd_elnorm)
+export(ssd_elnorm_lnorm)
+export(ssd_emulti)
+export(ssd_eweibull)
 export(ssd_exposure)
 export(ssd_fit_bcanz)
 export(ssd_fit_burrlioz)

R/burrrIII3.R

@@ -46,6 +46,15 @@ ssd_rburrIII3 <- function(n, shape1 = 1, shape2 = 1, scale = 1, chk = TRUE) {
   rdist("burrIII3", n = n, shape1 = shape1, shape2 = shape2, scale = scale, chk = chk)
 }
 
+#' @describeIn ssd_e Default Parameter Values for BurrIII Distribution
+#' @export
+#' @examples
+#'
+#' ssd_eburrIII3()
+ssd_eburrIII3 <- function() {
+  c(shape1 = 1, shape2 = 1, scale = 1)
+}
+
 sburrIII3 <- function(data, pars = NULL) {
   if (!is.null(pars)) {
     return(pars)

R/censor.R

@@ -32,7 +32,8 @@ censoring_text <- function(x) {
 }
 
 #' Is Censored
-#'
+#' `r lifecycle::badge('deprecated')`
+#' 
 #' Deprecated for [`ssd_is_censored()`].
 #'
 #' @param x A fitdists object.

R/gamma.R

@@ -46,6 +46,15 @@ ssd_rgamma <- function(n, shape = 1, scale = 1, chk = TRUE) {
   rdist("gamma", n = n, shape = shape, scale = scale, chk = chk)
 }
 
+#' @describeIn ssd_e Default Parameter Values for Gamma Distribution
+#' @export
+#' @examples
+#'
+#' ssd_egamma()
+ssd_egamma <- function() {
+  c(shape = 1, scale = 1)
+}
+
 sgamma <- function(data, pars = NULL) {
   if (!is.null(pars)) {
     return(pars)

R/ggplot.R

@@ -48,10 +48,9 @@ scale_color_ssd <- function(...) {
 }
 
 #' Species Sensitivity Data Points
-#'
+#' 
 #' Uses the empirical cumulative distribution to create scatterplot of points `x`.
 #'
-#' `geom_ssd()` has been deprecated for `geom_ssdpoint()`.
 #' @inheritParams ggplot2::layer
 #' @inheritParams ggplot2::geom_point
 #' @seealso [`ssd_plot_cdf()`]
@@ -181,10 +180,13 @@ geom_xribbon <- function(mapping = NULL,
   )
 }
 
-#' @describeIn geom_ssdpoint Species Sensitivity Data Points
-#'
-#' Uses the empirical cumulative distribution to create scatterplot of points `x`.
+#' Species Sensitivity Data Points
 #' `r lifecycle::badge('deprecated')`
+#' 
+#' `geom_ssd()` has been deprecated for `geom_ssdpoint()`.
+#' 
+#' @inheritParams ggplot2::layer
+#' @inheritParams ggplot2::geom_point
 #' @export
 #' @examples
 #' \dontrun{
@@ -209,9 +211,9 @@ geom_ssd <- function(mapping = NULL,
 }
 
 #' Plot Species Sensitivity Data
+#' `r lifecycle::badge('deprecated')`
 #'
 #' Uses the empirical cumulative density/distribution to visualize species sensitivity data.
-#' `r lifecycle::badge('deprecated')`
 #'
 #' @inheritParams ggplot2::layer
 #' @inheritParams ggplot2::geom_point

R/gompertz.R

@@ -13,7 +13,6 @@
 #    limitations under the License.
 
 #' Gompertz Probability Density
-#'
 #' `r lifecycle::badge("deprecated")`
 #'
 #' @param x A numeric vector of values.
@@ -40,8 +39,9 @@ ssd_pgompertz <- function(q, location = 1, shape = 1, lower.tail = TRUE, log.p =
   )
 }
 
-#' @describeIn ssd_p Cumulative Distribution Function for Gompertz Distribution
+#' Cumulative Distribution Function for Gompertz Distribution
 #' `r lifecycle::badge("deprecated")`
+#' @inheritParams params
 #' @export
 pgompertz <- function(q, llocation = 0, lshape = 0, lower.tail = TRUE, log.p = FALSE) {
   lifecycle::deprecate_warn("1.0.0", "pgompertz()", "ssd_pgompertz()")
@@ -63,8 +63,9 @@ ssd_qgompertz <- function(p, location = 1, shape = 1, lower.tail = TRUE, log.p =
   )
 }
 
-#' @describeIn ssd_q Quantile Function for Gompertz Distribution
+#' Quantile Function for Gompertz Distribution
 #' `r lifecycle::badge("deprecated")`
+#' @inheritParams params
 #' @export
 qgompertz <- function(p, llocation = 0, lshape = 0, lower.tail = TRUE, log.p = FALSE) {
   lifecycle::deprecate_warn("1.0.0", "qgompertz()", "ssd_qgompertz()")
@@ -84,8 +85,18 @@ ssd_rgompertz <- function(n, location = 1, shape = 1, chk = TRUE) {
   rdist("gompertz", n = n, location = location, shape = shape, chk = chk)
 }
 
-#' @describeIn ssd_r Random Generation for Gompertz Distribution
+#' @describeIn ssd_e Default Parameter Values for Gompertz Distribution
+#' @export
+#' @examples
+#'
+#' ssd_egompertz()
+ssd_egompertz <- function() {
+  c(location = 1, shape = 1)
+}
+
+#' Random Generation for Gompertz Distribution
 #' `r lifecycle::badge("deprecated")`
+#' @inheritParams params
 #' @export
 rgompertz <- function(n, llocation = 0, lshape = 0) {
   lifecycle::deprecate_warn("1.0.0", "rgompertz()", "ssd_rgompertz()")

R/hc-burrlioz.R

@@ -85,7 +85,8 @@
 }
 
 #' Hazard Concentrations for Burrlioz Fit
-#'
+#' `r lifecycle::badge('deprecated')`
+#' 
 #' Deprecated for [`ssd_hc()`].
 #'
 #' @inheritParams params

R/invpareto.R

@@ -46,6 +46,15 @@ ssd_rinvpareto <- function(n, shape = 3, scale = 1, chk = TRUE) {
   rdist("invpareto", n = n, shape = shape, scale = scale, chk = chk)
 }
 
+#' @describeIn ssd_e Default Parameter Values for Inverse Pareto Distribution
+#' @export
+#' @examples
+#'
+#' ssd_einvpareto()
+ssd_einvpareto <- function() {
+  c(shape = 3, scale = 1)
+}
+
 sinvpareto <- function(data, pars = NULL) {
   scale <- max(data$right)
   shape <- 1 / mean(log(scale / data$right))

R/lgumbel.R

@@ -13,7 +13,6 @@
 #    limitations under the License.
 
 #' Log-Gumbel (Inverse Weibull) Probability Density
-#'
 #' `r lifecycle::badge("deprecated")`
 #'
 #' @param x A numeric vector of values.
@@ -40,8 +39,18 @@ ssd_plgumbel <- function(q, locationlog = 0, scalelog = 1, lower.tail = TRUE, lo
   )
 }
 
-#' @describeIn ssd_p Cumulative Distribution Function for Log-Gumbel Distribution
+#' @describeIn ssd_e Default Parameter Values for Log-Gumbel Distribution
+#' @export
+#' @examples
+#'
+#' ssd_einvpareto()
+ssd_elgumbel <- function() {
+  list(locationlog = 0, scalelog = 1)
+}
+
+#' Cumulative Distribution Function for Log-Gumbel Distribution
 #' `r lifecycle::badge("deprecated")`
+#' @inheritParams params
 #' @export
 plgumbel <- function(q, locationlog = 0, scalelog = 1, lower.tail = TRUE, log.p = FALSE) {
   lifecycle::deprecate_warn("1.0.0", "plgumbel()", "ssd_plgumbel()")
@@ -63,8 +72,9 @@ ssd_qlgumbel <- function(p, locationlog = 0, scalelog = 1, lower.tail = TRUE, lo
   )
 }
 
-#' @describeIn ssd_q Quantile Function for Log-Gumbel Distribution
+#' Quantile Function for Log-Gumbel Distribution
 #' `r lifecycle::badge("deprecated")`
+#' @inheritParams params
 #' @export
 qlgumbel <- function(p, locationlog = 0, scalelog = 1, lower.tail = TRUE, log.p = FALSE) {
   lifecycle::deprecate_warn("1.0.0", "qlgumbel()", "ssd_qlgumbel()")
@@ -84,8 +94,18 @@ ssd_rlgumbel <- function(n, locationlog = 0, scalelog = 1, chk = TRUE) {
   rdist("gumbel", n = n, location = locationlog, scale = scalelog, .lgt = TRUE, chk = chk)
 }
 
-#' @describeIn ssd_r Random Generation for log-Gumbel Distribution
+#' @describeIn ssd_e Default Parameter Values for log-Gumbel Distribution
+#' @export
+#' @examples
+#'
+#' ssd_elgumbel()
+ssd_elgumbel <- function() {
+  c(locationlog = 0, scalelog = 1)
+}
+
+#' Random Generation for log-Gumbel Distribution
 #' `r lifecycle::badge("deprecated")`
+#' @inheritParams params
 #' @export
 rlgumbel <- function(n, locationlog = 0, scalelog = 1) {
   lifecycle::deprecate_warn("1.0.0", "rlgumbel()", "ssd_rlgumbel()")

R/llogis-llogis.R

@@ -56,6 +56,16 @@ ssd_rllogis_llogis <- function(n, locationlog1 = 0, scalelog1 = 1,
   )
 }
 
+#' @describeIn ssd_e Default Parameter Values for Log-Logistic/Log-Logistic Mixture Distribution
+#' @export
+#' @examples
+#'
+#' ssd_ellogis_llogis()
+ssd_ellogis_llogis <- function() {
+  c(locationlog1 = 0, scalelog1 = 1, 
+       locationlog2 = 1, scalelog2 = 1, pmix = 0.5)
+}
+
 sllogis_llogis <- function(data, pars = NULL) {
   if (!is.null(pars)) {
     return(pars)

R/llogis.R

@@ -46,6 +46,15 @@ ssd_rllogis <- function(n, locationlog = 0, scalelog = 1, chk = TRUE) {
   rdist("logis", n = n, location = locationlog, scale = scalelog, .lgt = TRUE, chk = chk)
 }
 
+#' @describeIn ssd_e Default Parameter Values for Log-Logistic Distribution
+#' @export
+#' @examples
+#'
+#' ssd_ellogis()
+ssd_ellogis <- function() {
+  c(locationlog = 0, scalelog = 1)
+}
+
 sllogis <- function(data, pars = NULL) {
   if (!is.null(pars)) {
     return(pars)

R/lnorm-lnorm.R

@@ -56,6 +56,16 @@ ssd_rlnorm_lnorm <- function(n, meanlog1 = 0, sdlog1 = 1,
   )
 }
 
+#' @describeIn ssd_e Default Parameter Values for Log-Normal/Log-Normal Mixture Distribution
+#' @export
+#' @examples
+#'
+#' ssd_elnorm_lnorm()
+ssd_elnorm_lnorm <- function() {
+  c(meanlog1 = 0, sdlog1 = 1,
+       meanlog2 = 1, sdlog2 = 1, pmix = 0.5)
+}
+
 slnorm_lnorm <- function(data, pars = NULL) {
   if (!is.null(pars)) {
     return(pars)

R/lnorm.R

@@ -46,6 +46,15 @@ ssd_rlnorm <- function(n, meanlog = 0, sdlog = 1, chk = TRUE) {
   rdist("lnorm", n = n, meanlog = meanlog, sdlog = sdlog, chk = chk)
 }
 
+#' @describeIn ssd_e Default Parameter Values for Log-Normal Distribution
+#' @export
+#' @examples
+#'
+#' ssd_elnorm()
+ssd_elnorm <- function() {
+  c(meanlog = 0, sdlog = 1)
+}
+
 slnorm <- function(data, pars = NULL) {
   if (!is.null(pars)) {
     return(pars)