Merge pull request #21 from thijsjanzen/master

Fix CRAN issues

.Rbuildignore

@@ -14,3 +14,5 @@
 ^README.md$
 ^CRAN-RELEASE$
 ^\.github$
+^doc$
+^Meta$

.gitignore

@@ -120,3 +120,5 @@ docs/reference/SingleNone.html
 docs/reference/updateHostCount.html
 docs/reference/updateTableState.html
 docs/reference/writeInfected.html
+/doc/
+/Meta/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: nosoi
 Type: Package
 Title: A Forward Agent-Based Transmission Chain Simulator
-Version: 1.1.1
+Version: 1.1.2
 Authors@R: c(person("Sebastian", "Lequime", email = "sebastian.lequime@gmail.com",
                   role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3140-0651")),
                   person("Paul", "Bastide", email = "paul.bastide@umontpellier.fr",
@@ -11,13 +11,15 @@ Authors@R: c(person("Sebastian", "Lequime", email = "sebastian.lequime@gmail.com
                   person("Philippe", "Lemey", email = "philippe.lemey@kuleuven.be",
                   role = "aut", comment = c(ORCID = "0000-0003-2826-5353")),
                   person("Guy", "Baele", email = "guy.baele@kuleuven.be",
-                  role = "aut", comment = c(ORCID = "0000-0002-1915-7732")))
+                  role = "aut", comment = c(ORCID = "0000-0002-1915-7732")),
+                  person("Thijs", "Janzen", email = "t.janzen@rug.nl",
+                  role = "ctb", comment = c(ORCID = "0000-0002-4162-1140")))
 Description: The aim of 'nosoi' (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. Methods in Ecology and Evolution 11:1002-1007). It is named after the daimones of plague, sickness and disease that escaped Pandora's jar in the Greek mythology. 'nosoi' is able to take into account the influence of multiple variable on the transmission process (e.g. dual-host systems (such as arboviruses), within-host viral dynamics, transportation, population structure), alone or taken together, to create complex but relatively intuitive epidemiological simulations.
 URL: https://github.com/slequime/nosoi
 Language: en-US
 License: GPL-3
 Encoding: UTF-8
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 biocViews:
 Depends: 
     data.table (>= 1.12.0),

NEWS.md

@@ -1,3 +1,6 @@
+# nosoi 1.1.2
+* Minor fixes and corrections (documentation, vignettes)
+
 # nosoi 1.1.1
 * `tidyverse` no longer in 'Suggests'.
 * Updating website

R/nosoiSim.R

@@ -114,7 +114,7 @@ nosoiSim <- function(type="single", popStructure="none", ...){
 #' @description
 #' Creates a \code{nosoiSim} object.
 #'
-#' @param pres.time current time of the simulation
+#' @param total.time total time of the simulation
 #' @param type population structure (one of "single or "dual)
 #' @param pop.A an object of class \code{nosoiSimOne} for population A
 #' @param pop.B an object of class \code{nosoiSimOne} for population B
@@ -139,7 +139,6 @@ nosoiSimConstructor <- function(total.time,
   class(res) <- "nosoiSim"
 
   return(res)
-
 }
 
 ##

R/nosoi_sanityChecks-Messages.R

@@ -15,7 +15,7 @@
 CoreSanityChecks <- function(length.sim, max.infected, init.individuals) {
   if (is.na(length.sim) || length.sim <= 1) stop("You must specify a length (in time units) for your simulation (bigger than 1).")
   if (is.na(max.infected) || max.infected <= 1) stop("You must specify a maximum number of infected hosts (bigger than 1).")
-  if (is.na(init.individuals) || init.individuals < 1 || !init.individuals%%1==0) stop("The transmission chain should be started by 1 or more (integer) individuals.")
+  if (is.na(init.individuals) || init.individuals < 1 || !init.individuals %%1 == 0) stop("The transmission chain should be started by 1 or more (integer) individuals.")
 }
 
 #' @title Checks if a function is properly formatted
@@ -29,7 +29,6 @@ CoreSanityChecks <- function(length.sim, max.infected, init.individuals) {
 #' @param timeDep is the function differential according to absolute time? (TRUE/FALSE)
 #' @param diff is the function differential according to state/env.variable? (TRUE/FALSE)
 #' @param hostCount is the function differential according to host count? (TRUE/FALSE)
-#' @param structure is the function to be used in a structured population? (TRUE/FALSE)
 #' @param continuous is the function to be used in a continuous space? (TRUE/FALSE)
 #' @param stateNames name of the states (vector) in case of discrete structure.
 #'
@@ -49,15 +48,15 @@ FunctionSanityChecks <- function(pFunc, name, param.pFunc, timeDep, diff, hostCo
       || (diff == TRUE && timeDep == FALSE && hostCount == FALSE && length(formalArgs(pFunc)) > 2)
       || (diff == TRUE && timeDep == FALSE && hostCount == TRUE && length(formalArgs(pFunc)) > 3)
       || (diff == FALSE && timeDep == TRUE && length(formalArgs(pFunc)) > 2)
-      || (diff == TRUE && timeDep==TRUE && hostCount == FALSE && length(formalArgs(pFunc)) > 3)
-      || (diff == TRUE && timeDep==TRUE && hostCount == TRUE && length(formalArgs(pFunc)) > 4)) {
+      || (diff == TRUE && timeDep == TRUE && hostCount == FALSE && length(formalArgs(pFunc)) > 3)
+      || (diff == TRUE && timeDep == TRUE && hostCount == TRUE && length(formalArgs(pFunc)) > 4)) {
     if (!is.list(param.pFunc) && is.na(param.pFunc)) {
       stop("There is a probleme with your function ", name, ": you should provide a parameter list named param.", name, ".")
     }
 
     if (is.list(param.pFunc)) {
       pFunc.param <- formalArgs(pFunc)[-1]
-      if(! all(names(param.pFunc) %in% pFunc.param)) stop("Parameter name in param.", name, " should match the name used in ", name, ".")
+      if(!all(names(param.pFunc) %in% pFunc.param)) stop("Parameter name in param.", name, " should match the name used in ", name, ".")
     }
   }
 
@@ -111,7 +110,7 @@ MatrixSanityChecks <- function(structure.matrix, init.structure, none.at.start=N
 ##
 
 RasterSanityChecks <- function(structure.raster, init.structure, none.at.start=NULL) {
-  if(!class(structure.raster) == "RasterLayer") stop("structure.raster must be a raster (class RasterLayer).")
+  if(!inherits(structure.raster, "RasterLayer")) stop("structure.raster must be a raster (class RasterLayer).")
 
   if(is.null(none.at.start)){
     start.env <- raster::extract(structure.raster,cbind(init.structure[1],init.structure[2]))

R/nosoi_tablesManagment.R

@@ -9,7 +9,6 @@
 #' @param hosts.ID unique ID for the new host
 #' @param infected.by unique ID of host that transmits to the new one
 #' @param infected.in state in which the host was infected
-#' @param current.in state in which the host currently is
 #' @param time.is time in the simulation, when the infection takes place
 #' @param ParamHost list of individual based parameters.
 #' @param current.environmental.value current environmental value
@@ -22,10 +21,14 @@
 #' @keywords internal
 
 newLine <- function(hosts.ID,
-                    infected.by, infected.in,
+                    infected.by,
+                    infected.in,
                     time.is,
-                    ParamHost, current.environmental.value = NULL, current.cell.number.raster = NULL,
-                    current.count.A = integer(0), current.count.B = integer(0)) {
+                    ParamHost,
+                    current.environmental.value = NULL,
+                    current.cell.number.raster = NULL,
+                    current.count.A = integer(0),
+                    current.count.B = integer(0)) {
 
   if (length(infected.in) == 1) {
     if (is.na(infected.in)) infected.in <- NULL

R/nosoi_utilityFunctions.R

@@ -15,8 +15,8 @@
 #'
 #' @return list of parsed quantities:
 #' \itemize{
-#'  \item{"vect"}{Vectorized version of the function.}
-#'  \item{"vectArgs"}{Vector of arguments for the vectorized function.}
+#'  \item "vect" Vectorized version of the function.
+#'  \item "vectArgs" Vector of arguments for the vectorized function.
 #' }
 #'
 #' @keywords internal

R/output_treeGenerator.r

@@ -50,9 +50,9 @@
 #' )
 #'
 #' ## Make sure all needed packages are here
-#' if (requireNamespace("ape", quietly = TRUE)
-#'     || requireNamespace("tidytree", quietly = TRUE)
-#'     || requireNamespace("treeio", quietly = TRUE)) {
+#' if (requireNamespace("ape", quietly = TRUE) &&
+#'     requireNamespace("tidytree", quietly = TRUE) &&
+#'     requireNamespace("treeio", quietly = TRUE)) {
 #'   library(ape)
 #'   library(tidytree)
 #'   library(treeio)
@@ -84,7 +84,9 @@
 #' @export getTransmissionTree
 
 getTransmissionTree <- function(nosoiInf) {
-  if (!requireNamespace("ape", quietly = TRUE) || !requireNamespace("tidytree", quietly = TRUE) || !requireNamespace("treeio", quietly = TRUE)) {
+  if (!(requireNamespace("ape", quietly = TRUE) &&
+        requireNamespace("tidytree", quietly = TRUE) &&
+        requireNamespace("treeio", quietly = TRUE))) {
     stop("Packages 'ape', 'tidytree' and 'treeio' are needed for transmission tree generation.",
          call. = FALSE)
   }

R/single-none.R

@@ -61,7 +61,6 @@
 #'test.nosoi
 #'}
 #' @export singleNone
-
 singleNone <- function(length.sim,
                        max.infected,
                        init.individuals,

nosoi.Rproj

@@ -18,3 +18,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

tests/testthat/testSingleNone.R

@@ -28,9 +28,11 @@ test_that("Transmission is coherent with single introduction, constant pExit and
   expect_equal(clusters(g, "weak")$no, 1)
   expect_equal(diameter(g, directed=F, weights=NA), 12)
 
-  dynOld <- getDynamicOld(test.nosoiA)
-  dynNew <- getDynamic(test.nosoiA)
-  expect_equal(dynOld, dynNew)
+  if (requireNamespace("dplyr")) {
+    dynOld <- getDynamicOld(test.nosoiA)
+    dynNew <- getDynamic(test.nosoiA)
+    expect_equal(dynOld, dynNew)
+  }
 
   ## Output
   expect_output(print(test.nosoiA), "a single host with no structure")

vignettes/continuous.Rmd

@@ -54,7 +54,8 @@ test.raster <- focal(focal(test.raster, w=matrix(1, 5, 5), mean), w=matrix(1, 5,
 
 test.raster_df <- as.data.frame(test.raster, xy = TRUE) 
 
-if (!requireNamespace("ggplot2", quietly = TRUE) || !requireNamespace("viridis", quietly = TRUE)) {
+if (!(requireNamespace("ggplot2", quietly = TRUE) && 
+      requireNamespace("viridis", quietly = TRUE))) {
   message("Packages 'ggplot2' and 'viridis' are needed for plotting this figure.")
 } else {
   library(ggplot2)
@@ -189,7 +190,8 @@ move.test2$type = "Not attracted by raster"
 
 move.test.all = rbindlist(list(move.test,move.test2))
 
-if (!requireNamespace("ggplot2", quietly = TRUE) || !requireNamespace("viridis", quietly = TRUE)) {
+if (!(requireNamespace("ggplot2", quietly = TRUE) &&
+      requireNamespace("viridis", quietly = TRUE))) {
   message("Packages 'ggplot2' and 'viridis' are needed for plotting this figure.")
 } else {
   ggplot() +