Merge pull request #310 from poissonconsulting/dev

More housekeeping

DESCRIPTION

@@ -46,8 +46,6 @@ Depends:
 Imports:
     abind,
     chk,
-    doFuture,
-    foreach,
     furrr,
     generics,
     ggplot2,
@@ -70,8 +68,10 @@ Imports:
     VGAM
 Suggests:
     covr,
+    doFuture,
     dplyr,
     fitdistrplus,
+    foreach,
     future,
     glue,
     grDevices,

NAMESPACE

@@ -66,7 +66,6 @@ export(rgompertz)
 export(rlgumbel)
 export(scale_color_ssd)
 export(scale_colour_ssd)
-export(ssd_cfplot)
 export(ssd_data)
 export(ssd_dists)
 export(ssd_dists_all)
@@ -157,7 +156,6 @@ importFrom(lifecycle,deprecate_warn)
 importFrom(lifecycle,expect_deprecated)
 importFrom(parallel,nextRNGStream)
 importFrom(parallel,nextRNGSubStream)
-importFrom(plyr,llply)
 importFrom(plyr,summarise)
 importFrom(purrr,transpose)
 importFrom(scales,comma)

R/censor.R

@@ -45,7 +45,7 @@ censoring_text <- function(x) {
 #' fits <- ssd_fit_dists(ssddata::ccme_boron)
 #' is_censored(fits)
 is_censored <- function(x) {
-  deprecate_soft("0.3.7", "is_censored()", "ssd_is_censored()")
+  lifecycle::deprecate_warn("0.3.7", "is_censored()", "ssd_is_censored()")
   chk_s3_class(x, "fitdists")
   ssd_is_censored(x)
 }

R/data.R

@@ -12,60 +12,6 @@
 #    See the License for the specific language governing permissions and
 #    limitations under the License.
 
-#' CCME Species Sensitivity Data
-#'
-#' Species Sensitivity Data from
-#' the Canadian Council of Ministers of the Environment.
-#' The taxonomic groups are Amphibian, Fish, Invertebrate and Plant.
-#' Plants includes freshwater algae.
-#' Please use `[ssddata::ccme_data]` instead.
-#'
-#' Additional information on each of the chemicals is available from the
-#' CCME website.
-#' \describe{
-#'   \item{Boron}{<http://ceqg-rcqe.ccme.ca/download/en/324/>}
-#'   \item{Cadmium}{<http://ceqg-rcqe.ccme.ca/download/en/148/>}
-#'   \item{Chloride}{<http://ceqg-rcqe.ccme.ca/download/en/337/>}
-#'   \item{Endosulfan}{<http://ceqg-rcqe.ccme.ca/download/en/327/>}
-#'   \item{Glyphosate}{<http://ceqg-rcqe.ccme.ca/download/en/182/>}
-#'   \item{Uranium}{<http://ceqg-rcqe.ccme.ca/download/en/328/>}
-#'   \item{Silver}{<http://ceqg-rcqe.ccme.ca/download/en/355/>}
-#' }
-#'
-#' \describe{
-#'   \item{Chemical}{The chemical (chr).}
-#'   \item{Species}{The species binomial name (chr).}
-#'   \item{Conc}{The chemical concentration (dbl).}
-#'   \item{Group}{The taxonomic group (fctr).}
-#'   \item{Units}{The units (chr).}
-#' }
-#' @examples
-#' head(ccme_data)
-"ccme_data"
-
-#' CCME Species Sensitivity Data for Boron
-#'
-#' Species Sensitivity Data from
-#' the Canadian Council of Ministers of the Environment.
-#' Please use `[ssddata::ccme_data]` instead.
-#'
-#' Additional information is available from <http://ceqg-rcqe.ccme.ca/download/en/324/>.
-#'
-#' The columns are as follows
-#'
-#' \describe{
-#'   \item{Chemical}{The chemical (chr).}
-#'   \item{Species}{The species binomial name (chr).}
-#'   \item{Concentration}{The chemical concentration (dbl).}
-#'   \item{Units}{The units (chr).}
-#'   \item{Group}{The taxonomic group (fctr).}
-#' }
-#' @seealso [`ccme_data()`]
-#' @family boron
-#' @examples
-#' head(ccme_data)
-"boron_data"
-
 #' Model Averaged Predictions for CCME Boron Data
 #'
 #' A data frame of the predictions based on 1,000 bootstrap iterations.

R/fit.R

@@ -137,16 +137,6 @@ ssd_fit_dists <- function(
   chk_not_any_na(dists)
   chk_unique(dists)
 
-  if ("llog" %in% dists) {
-    deprecate_stop("0.1.0", "dllog()", "dllogis()",
-      details = "The 'llog' distribution has been deprecated for the identical 'llogis' distribution."
-    )
-  }
-  if ("burrIII2" %in% dists) {
-    deprecate_stop("0.1.2", "xburrIII2()",
-      details = "The 'burrIII2' distribution has been deprecated for the identical 'llogis' distribution."
-    )
-  }
   chk_subset(dists, ssd_dists_all())
 
   chk_whole_number(nrow)

R/ggplot.R

@@ -200,7 +200,7 @@ geom_ssd <- function(mapping = NULL,
                      na.rm = FALSE,
                      show.legend = NA,
                      inherit.aes = TRUE) {
-  lifecycle::deprecate_soft("0.3.5", "geom_ssd()", "geom_ssdpoint()")
+  lifecycle::deprecate_warn("0.3.5", "geom_ssd()", "geom_ssdpoint()")
 
   geom_ssdpoint(
     mapping = mapping, data = data, stat = stat,
@@ -232,7 +232,7 @@ stat_ssd <- function(mapping = NULL,
                      na.rm = FALSE,
                      show.legend = NA,
                      inherit.aes = TRUE) {
-  lifecycle::deprecate_soft("0.3.5", "stat_ssd()")
+  lifecycle::deprecate_warn("0.3.5", "stat_ssd()")
 
   layer(
     stat = StatSsdpoint, data = data, mapping = mapping, geom = geom,

R/ggproto.R

@@ -102,7 +102,7 @@ GeomXribbon <- ggproto(
     ids <- cumsum(missing_pos) + 1
     ids[missing_pos] <- NA
 
-    positions <- summarise(data,
+    positions <- plyr::summarise(data,
       y = c(y, rev(y)), x = c(xmax, rev(xmin)), id = c(ids, rev(ids))
     )
     munched <- coord_munch(coord, positions, panel_params)

R/gompertz.R

@@ -21,7 +21,7 @@
 #' @return A numeric vector.
 #' @export
 dgompertz <- function(x, llocation = 0, lshape = 0, log = FALSE) {
-  lifecycle::deprecate_soft("1.0.0", "dgompertz()")
+  lifecycle::deprecate_warn("1.0.0", "dgompertz()")
   ddist("gompertz", x,
     location = exp(llocation), shape = exp(lshape),
     log = log
@@ -44,7 +44,7 @@ ssd_pgompertz <- function(q, location = 1, shape = 1, lower.tail = TRUE, log.p =
 #' `r lifecycle::badge("deprecated")`
 #' @export
 pgompertz <- function(q, llocation = 0, lshape = 0, lower.tail = TRUE, log.p = FALSE) {
-  lifecycle::deprecate_soft("1.0.0", "pgompertz()", "ssd_pgompertz()")
+  lifecycle::deprecate_warn("1.0.0", "pgompertz()", "ssd_pgompertz()")
   ssd_pgompertz(q,
     location = exp(llocation), shape = exp(lshape),
     lower.tail = lower.tail, log.p = log.p
@@ -67,7 +67,7 @@ ssd_qgompertz <- function(p, location = 1, shape = 1, lower.tail = TRUE, log.p =
 #' `r lifecycle::badge("deprecated")`
 #' @export
 qgompertz <- function(p, llocation = 0, lshape = 0, lower.tail = TRUE, log.p = FALSE) {
-  lifecycle::deprecate_soft("1.0.0", "qgompertz()", "ssd_qgompertz()")
+  lifecycle::deprecate_warn("1.0.0", "qgompertz()", "ssd_qgompertz()")
   ssd_qgompertz(
     p = p, location = exp(llocation), shape = exp(lshape),
     lower.tail = lower.tail, log.p = log.p
@@ -88,7 +88,7 @@ ssd_rgompertz <- function(n, location = 1, shape = 1, chk = TRUE) {
 #' `r lifecycle::badge("deprecated")`
 #' @export
 rgompertz <- function(n, llocation = 0, lshape = 0) {
-  lifecycle::deprecate_soft("1.0.0", "rgompertz()", "ssd_rgompertz()")
+  lifecycle::deprecate_warn("1.0.0", "rgompertz()", "ssd_rgompertz()")
   ssd_rgompertz(n = n, location = exp(llocation), shape = exp(lshape))
 }
 

R/hc-burrlioz.R

@@ -98,7 +98,7 @@
 #' @export
 ssd_hc_burrlioz <- function(x, percent = 5, ci = FALSE, level = 0.95, nboot = 1000,
                             min_pboot = 0.99, parametric = FALSE) {
-  lifecycle::deprecate_soft("0.3.5", "ssd_hc_burrlioz()", "ssd_hc()")
+  lifecycle::deprecate_warn("0.3.5", "ssd_hc_burrlioz()", "ssd_hc()")
   chk_s3_class(x, "fitburrlioz")
 
   ssd_hc(x,

R/hc.R

@@ -20,7 +20,6 @@
 #' hazard concentrations(s).
 #'
 #' @inheritParams params
-#' @param hc A whole numeric vector between 1 and 99 indicating the percent hazard concentrations (deprecated for percent).
 #' @return A tibble of corresponding hazard concentrations.
 #' @seealso [`predict.fitdists()`] and [`ssd_hp()`].
 #' @export
@@ -181,16 +180,12 @@ no_ssd_hc <- function() {
 
 #' @describeIn ssd_hc Hazard Concentrations for Distributional Estimates
 #' @export
-ssd_hc.list <- function(x, percent = 5, hc = 5, ...) {
+ssd_hc.list <- function(x, percent = 5, ...) {
   chk_list(x)
   chk_named(x)
   chk_unique(names(x))
   chk_unused(...)
 
-  if (!missing(hc)) {
-    deprecate_stop("0.1.0", "ssd_hc(hc = )", "ssd_hc(percent = )")
-  }
-
   if (!length(x)) {
     return(no_ssd_hc())
   }
@@ -203,16 +198,13 @@ ssd_hc.list <- function(x, percent = 5, hc = 5, ...) {
 
 #' @describeIn ssd_hc Hazard Concentrations for fitdists Object
 #' @export
-ssd_hc.fitdists <- function(x, percent = 5, hc = 5, ci = FALSE, level = 0.95, nboot = 1000,
+ssd_hc.fitdists <- function(x, percent = 5, ci = FALSE, level = 0.95, nboot = 1000,
                             average = TRUE, delta = 7, min_pboot = 0.99,
                             parametric = TRUE,
                             control = NULL, ...) {
   chk_vector(percent)
   chk_numeric(percent)
   chk_range(percent, c(0, 100))
-  chk_vector(hc)
-  chk_numeric(hc)
-  chk_range(hc, c(0, 100))
   chk_flag(ci)
   chk_number(level)
   chk_range(level)
@@ -227,10 +219,6 @@ ssd_hc.fitdists <- function(x, percent = 5, hc = 5, ci = FALSE, level = 0.95, nb
   chk_null_or(control, vld = vld_list)
   chk_unused(...)
 
-  if (!missing(hc)) {
-    deprecate_stop("0.1.0", "ssd_hc(hc = )", "ssd_hc(percent = )")
-  }
-
   x <- subset(x, delta = delta)
   hc <- .ssd_hc_fitdists(x, percent,
     ci = ci, level = level, nboot = nboot, min_pboot = min_pboot, control = control,

R/lgumbel.R

@@ -21,7 +21,7 @@
 #' @return A numeric vector.
 #' @export
 dlgumbel <- function(x, locationlog = 0, scalelog = 1, log = FALSE) {
-  lifecycle::deprecate_soft("1.0.0", "dlgumbel()")
+  lifecycle::deprecate_warn("1.0.0", "dlgumbel()")
   ddist("gumbel",
     x = x, location = locationlog, scale = scalelog,
     log = log, .lgt = TRUE
@@ -44,7 +44,7 @@ ssd_plgumbel <- function(q, locationlog = 0, scalelog = 1, lower.tail = TRUE, lo
 #' `r lifecycle::badge("deprecated")`
 #' @export
 plgumbel <- function(q, locationlog = 0, scalelog = 1, lower.tail = TRUE, log.p = FALSE) {
-  lifecycle::deprecate_soft("1.0.0", "plgumbel()", "ssd_plgumbel()")
+  lifecycle::deprecate_warn("1.0.0", "plgumbel()", "ssd_plgumbel()")
   ssd_plgumbel(q,
     locationlog = locationlog, scalelog = scalelog,
     lower.tail = lower.tail, log.p = log.p
@@ -67,7 +67,7 @@ ssd_qlgumbel <- function(p, locationlog = 0, scalelog = 1, lower.tail = TRUE, lo
 #' `r lifecycle::badge("deprecated")`
 #' @export
 qlgumbel <- function(p, locationlog = 0, scalelog = 1, lower.tail = TRUE, log.p = FALSE) {
-  lifecycle::deprecate_soft("1.0.0", "qlgumbel()", "ssd_qlgumbel()")
+  lifecycle::deprecate_warn("1.0.0", "qlgumbel()", "ssd_qlgumbel()")
   ssd_qlgumbel(p,
     locationlog = locationlog, scalelog = scalelog,
     lower.tail = lower.tail, log.p = log.p
@@ -88,7 +88,7 @@ ssd_rlgumbel <- function(n, locationlog = 0, scalelog = 1, chk = TRUE) {
 #' `r lifecycle::badge("deprecated")`
 #' @export
 rlgumbel <- function(n, locationlog = 0, scalelog = 1) {
-  lifecycle::deprecate_soft("1.0.0", "rlgumbel()", "ssd_rlgumbel()")
+  lifecycle::deprecate_warn("1.0.0", "rlgumbel()", "ssd_rlgumbel()")
   ssd_rlgumbel(n, locationlog = locationlog, scalelog = scalelog)
 }
 

R/plot-cf.R

@@ -29,7 +29,7 @@ ssd_plot_cf <- function(data, left = "Conc") {
     err("Package 'fitdistrplus' is required to produce Cullen and Frey plots.")
   }
 
-  deprecate_soft("0.3.5", "ssd_plot_cf()", "fitdistrplus::descdist()",
+  lifecycle::deprecate_warn("0.3.5", "ssd_plot_cf()", "fitdistrplus::descdist()",
     details = "Please use fitdistrplus::descdist(data$Conc, boot = 100L)."
   )
 
@@ -40,10 +40,3 @@ ssd_plot_cf <- function(data, left = "Conc") {
   fitdistrplus::descdist(data[[left]], boot = 100L)
   invisible()
 }
-
-#' @describeIn ssd_plot_cf Defunct Cullen and Frey Plot
-#' @export
-ssd_cfplot <- function(data, left = "Conc") {
-  deprecate_stop("0.1.0", "ssd_cfplot()", "ssd_plot_cf()")
-  ssd_plot_cf(data, left)
-}

R/plot.R

@@ -17,6 +17,6 @@ graphics::plot
 
 #' @export
 plot.fitdists <- function(x, ...) {
-  lifecycle::deprecate_warn("0.3.4", "plot.fitdists()", "autoplot.fitdists()")
+  lifecycle::deprecate_stop("0.3.4", "plot.fitdists()", "autoplot.fitdists()")
   autoplot(x)
 }

R/ssdtools-package.R

@@ -16,3 +16,29 @@
 "_PACKAGE"
 
 utils::globalVariables("where")
+
+## usethis namespace: start
+#' @import chk ggplot2
+#' @importFrom abind abind
+#' @importFrom furrr future_map furrr_options
+#' @importFrom generics augment glance tidy
+#' @importFrom ggplot2 autoplot sym
+#' @importFrom goftest ad.test cvm.test
+#' @importFrom graphics par plot title
+#' @importFrom grid gList gpar grobName gTree polygonGrob segmentsGrob
+#' @importFrom lifecycle expect_deprecated deprecate_soft deprecate_stop deprecate_warn
+#' @importFrom parallel nextRNGStream nextRNGSubStream
+#' @importFrom plyr summarise
+#' @importFrom purrr transpose
+#' @importFrom Rcpp sourceCpp
+#' @importFrom scales comma manual_pal percent trans_breaks
+#' @importFrom ssddata gm_mean
+#' @importFrom stats coef complete.cases ks.test logLik nobs optim plogis predict qlogis runif sd setNames weighted.mean
+#' @importFrom stringr str_order
+#' @importFrom tibble as_tibble tibble
+#' @importFrom TMB MakeADFun sdreport
+#' @importFrom universals estimates npars
+#' @importFrom utils capture.output
+#' @importFrom VGAM gompertz vglm
+## usethis namespace: end
+NULL

R/tidy.R

@@ -23,7 +23,7 @@ generics::tidy
   est <- unname(x[, 1])
   names(est) <- rownames(x)
   est <- est[!grepl("^log(it){0,1}_", names(est))]
-  est[str_order(names(est))]
+  est[stringr::str_order(names(est))]
 }
 
 #' @export
@@ -44,7 +44,7 @@ tidy.tmbfit <- function(x, all = FALSE, ...) {
   if (!all) {
     x <- x[!grepl("^log(it){0,1}_", x$term), ]
   }
-  x <- x[str_order(x$term), ]
+  x <- x[stringr::str_order(x$term), ]
   x
 }