Release 1.5

Release 1.5

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: ospsuite.utils
 Title: Utility Functions for Open Systems Pharmacology R Packages
-Version: 1.4.0
+Version: 1.5.0
 Authors@R: c(
     person("Open-Systems-Pharmacology Community", role = c("cph", "fnd")),
     person("Michael", "Sevestre", , "michael@design2code.ca", role = c("aut", "cre")),

NAMESPACE

@@ -11,6 +11,7 @@ export(enumPut)
 export(enumRemove)
 export(enumValues)
 export(flattenList)
+export(foldSafe)
 export(formatNumerics)
 export(getEnumKey)
 export(getOSPSuiteUtilsSetting)
@@ -25,6 +26,7 @@ export(isIncluded)
 export(isOfLength)
 export(isOfType)
 export(isSameLength)
+export(logSafe)
 export(messages)
 export(objectCount)
 export(ospsuiteUtilsSettingNames)

NEWS.md

@@ -1,4 +1,21 @@
-# ospsuite.utils 1.4.0
+# ospsuite.utils 1.5.0
+
+NEW FUNCTIONS
+
+* `logSafe()` to compute logarithm of values that could be close to 0 or slightly 
+negative.
+
+* `foldSafe()` to compute `x / y` when `x` or `y` could be negative or zero. All values below a 
+certain threshold `epsilon` are substituted by `epsilon`. NOTE: not suited for 
+calculating fold differences of negative numbers.
+
+BUG FIXES
+
+* The print function of the `Printable` class now converts values using the `format` 
+function before printing. E.g., numerical value "0.99999999" will be displayed as "1".
+https://github.com/Open-Systems-Pharmacology/OSPSuite.RUtils/issues/120
+
+# ospsuite.utils 1.4.23
 
 NEW FUNCTIONS
 

R/ospsuite.utils-env.R

@@ -18,6 +18,9 @@ ospsuiteUtilsEnv$suiteName <- "Open Systems Pharmacology"
 # default values for the `formatNumerics()` helper function
 ospsuiteUtilsEnv$formatNumericsDigits <- 2L
 
+# Small value added to zero when calculating log
+ospsuiteUtilsEnv$LOG_SAFE_EPSILON <- 1e-20
+
 #' Names of the settings stored in `ospsuiteEnv`. Can be used with
 #' `getOSPSuiteUtilsSetting()`
 #'

R/printable.R

@@ -37,8 +37,8 @@ Printable <- R6::R6Class(
         entries <- c("  ", entries)
       }
 
-      entries <- c(entries, value)
-      entries <- c(entries, "\n")
+      value <- format(value)
+      entries <- c(entries, value, "\n")
       cat(entries, sep = " ")
       invisible(self)
     },

R/utilities-validation.R

@@ -11,7 +11,7 @@
 .isBaseType <- function(x) {
   baseTypes <- c("character", "logical", "integer", "double")
 
-  if (typeof(x) %in% baseTypes) {
+  if (any(baseTypes == typeof(x))) {
     return(TRUE)
   }
 

R/utilities.R

@@ -61,13 +61,13 @@ flattenList <- function(x, type) {
 
   if (is.list(x)) {
     x <- switch(type,
-      "character" = purrr::flatten_chr(x),
+      "character" = purrr::list_c(x, ptype = "c"),
       "numeric" = ,
       "real" = ,
-      "double" = purrr::flatten_dbl(x),
-      "integer" = purrr::flatten_int(x),
-      "logical" = purrr::flatten_lgl(x),
-      purrr::flatten(x)
+      "double" = purrr::list_c(x, ptype = 1.0),
+      "integer" = purrr::list_c(x, ptype = 1),
+      "logical" = purrr::list_c(x, ptype = TRUE),
+      purrr::list_flatten(x)
     )
   }
 
@@ -111,3 +111,62 @@ toMissingOfType <- function(x, type) {
 
   return(x)
 }
+
+#' Computes logarithm of a number or of a vector of numbers and handles zeros while
+#' substituting all values below `epsilon` by `epsilon`.
+#'
+#' @param x A numeric or a vector of numerics.
+#' @param base a positive or complex number: the base with respect to which logarithms are computed. Defaults to e = exp(1).
+#' @param epsilon A very small number which is considered as threshold below which
+#' all values are treated as `epsilon`. Allows computation of `log` close to 0.
+#' Default value is `getOSPSuiteUtilsSetting("LOG_SAFE_EPSILON")`.
+#'
+#' @return `log(x, base = base)` for `x > epsilon`, or `log(epsilon, base = base)`,
+#' or `NA_real_` for `NA` elements.
+#' @export
+#'
+#' @examples
+#' inputVector <- c(NA, 1, 5, 0, -1)
+#' logSafe(inputVector)
+logSafe <- function(x, base = exp(1), epsilon = ospsuiteUtilsEnv$LOG_SAFE_EPSILON) {
+  x <- sapply(X = x, function(element) {
+    element <- ospsuite.utils::toMissingOfType(element, type = "double")
+    if (is.na(element)) {
+      return(NA_real_)
+    } else if (element < epsilon) {
+      return(log(epsilon, base = base))
+    } else {
+      return(log(element, base = base))
+    }
+  })
+
+  return(x)
+}
+
+#' Safe fold calculation
+#'
+#' @description
+#' Calculates `x / y` while substituting values below `epsilon` (for x and y) by `epsilon`.
+#' `x` and `y` must be of the same length
+#'
+#'
+#' @param x A numeric or a vector of numerics.
+#' @param y A numeric or a vector of numerics.
+#' @param epsilon A very small number which is considered as threshold below which
+#' all values are treated as `epsilon`. Allows computation of fold changes for values close to 0.
+#' Default value is `getOSPSuiteUtilsSetting("LOG_SAFE_EPSILON")`.
+#'
+#' @return A vector with `x / y`.
+#' @export
+#'
+#' @examples
+#' inputX <- c(NA, 1, 5, 0, -1)
+#' inputY <- c(1, -1, NA, 0, -1)
+#' folds <- foldSafe(inputX, inputY)
+foldSafe <- function(x, y, epsilon = ospsuiteUtilsEnv$LOG_SAFE_EPSILON) {
+  validateIsSameLength(x, y)
+  x[x <= epsilon] <- epsilon
+  y[y <= epsilon] <- epsilon
+
+  return(x / y)
+}

R/validation-type.R

@@ -117,7 +117,7 @@ validateIsInteger <- function(object, nullAllowed = FALSE) {
   }
 
   if (is.list(object)) {
-    object <- unlist(object)
+    object <- unlist(object, use.names = FALSE)
   }
 
   # if it's an actual integer (e.g. 5L)

_pkgdown.yml

@@ -47,6 +47,12 @@ reference:
       - messages
       - objectCount
       - flattenList
+      - logSafe
+      - foldSafe
+
+  - tite: Math helpers
+    contents:
+      - logSafe
 
   - title: Package settings
     contents:

appveyor.yml

@@ -13,12 +13,13 @@ install:
   - git submodule update --init --recursive
 
 environment:
-  app_version: "1.4"
+  app_version: "1.5"
   USE_RTOOLS: true
-  R_VERSION: "4.1.0"
+  R_VERSION: "4.3.1"
   R_ARCH: x64
   KEEP_VIGNETTES: true
   NOT_CRAN: true
+  R_PKGTYPE: binary
 
 version: "$(app_version).{build}"
 
@@ -50,14 +51,10 @@ before_build:
 build_script:
   - travis-tool.sh install_deps
   - travis-tool.sh r_binary_install curl
-  - Rscript -e "install.packages('covr', repos = 'http://cran.us.r-project.org', type = 'source')"
 
 test_script:
   - travis-tool.sh run_tests
 
-on_success:
-  - Rscript -e "covr::codecov()"
-
 after_test:
   - ps: copy ospsuite.utils_*.zip ospsuite.utils.zip