Fix some warnings/notes on devtools:::check().

.Rbuildignore

@@ -1,2 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^.travis.yml$
+LICENSE.md
+README_assets

DESCRIPTION

@@ -1,11 +1,13 @@
 Package: DNAr
 Type: Package
 Title: Simulates chemical reaction networks constructed with DNA
-Version: 0.9.6
+Version: 0.9.7
 Authors@R: c(person("Daniel", "Kneipp", email = "danielv@dcc.ufmg.br",
-                    role = c("aut", "cre")),
+                    role = c("aut")),
              person("Marcos", "Guterres", email = "mguterres@yahoo.com",
-                    role = c("aut")))
+                    role = c("aut")),
+             person("Renan", "Marks", email = "renan.marks@ufms.br",
+                    role = c("cre")))
 Description: With this package you can simulate CRNs implemented with 
     DNA. Currently there is only one approach for CRN construction with 
     DNA, but the plan is to expand this to other approachs using the CRN 
@@ -23,9 +25,8 @@ Imports:
     reshape2 (>= 1.4.2),
     RColorBrewer (>= 1.1.2),
     assertthat (>= 0.2.0),
-    magrittr (>= 1.5),
     Rdpack (>= 0.4.20)
-RoxygenNote: 6.0.1
+RoxygenNote: 7.3.3
 RdMacros: Rdpack
 Roxygen: list(markdown = TRUE)
 Suggests: testthat

NAMESPACE

@@ -25,6 +25,7 @@ export(save_dsd_script)
 export(save_reactions_txt)
 export(update_crn_4domain)
 export(update_neuron_input_hje)
+importFrom(Rdpack,reprompt)
 importFrom(utils,capture.output)
 importFrom(utils,read.csv)
 importFrom(utils,write.csv)

R/4domain_reactor.R

@@ -29,6 +29,8 @@
 #' \code{TRUE} if the reaction is supported, or \code{FALSE}
 #' otherwise.
 #'
+#' @param reaction   A string containing the text representing the reaction.
+#'
 #' @examples
 #' DNAr:::check_reaction_4domain('A + B -> C')   # Should return TRUE
 #' DNAr:::check_reaction_4domain('2A -> B')      # Should return TRUE
@@ -46,14 +48,22 @@ check_reaction_4domain <- function(reaction) {
 #' The parameters of this function follows the same
 #' semantics of \code{\link{react_4domain}()}.
 #'
+#' @param reactions  A vector with the reactions of the CRN.
+#' @param ki         A vector defining the constant rate of each reaction
+#'                   in \code{reactions}, in order.
+#' @param qmax       Maximum rate constant for the auxiliary reactions.
+#' @param cmax       Maximum initial concentration for the auxiliary species.
+#'
 #' @return \code{NULL} if no buffer modules were added. Otherwise
 #' it returns a list with:
-#'   - `lambda_1`      = lambda^{-1} value;
+#'   - `lambda_1`      = lambda^\{-1\} value;
 #'   - `new_species`   = vector with the new species added;
 #'   - `new_cis`       = vector with the initial concentrations;
 #'   - `new_reactions` = vector with the new reactions;
 #'   - `new_ks`        = constant rate of the new reactions.
 #'
+#' @importFrom Rdpack reprompt
+#'
 #' @references
 #'   - `[1]` \insertRef{soloveichik2010dna}{DNAr}
 get_buff_modules <- function(reactions, ki, qmax, cmax) {

R/analysis.R

@@ -108,6 +108,20 @@ compare_behaviors_nrmse <- function(bhv_sim, bhv_obs, ignore_time_column = T) {
 #' this functions returns the concentration of each species
 #' at a specific point in time within the derivative.
 #'
+#' @param species    A vector with the species of the reaction. The order of
+#'                   this vector is important because it will define the
+#'                   column order of the returned behavior.
+#' @param ci         A vector specifying the initial concentrations of the
+#'                   \code{species} specified, in order.
+#' @param reactions  A vector with the reactions of the CRN. If a reaction has
+#'                   has only reactants that are non in `species`, this
+#'                   reaction will be treated as `0 -> products`. Furthermore,
+#'                   this function treats a reaction `non_registered_species
+#'                   + registered_species -> products` equally to
+#'                   `registered_species -> products`, ignoring the species non
+#'                   registered on the `species` vector.
+#' @param ki         A vector defining the constant rate of each reaction
+#'                   in \code{reactions}, in order.
 #' @param behavior     The data returned by \code{\link{react}()}.
 #' @param time_points  A vector of indexes (representing multiple points in
 #'                     time) used for access lines of `behavior`.

R/crn_reactor.R

@@ -22,6 +22,11 @@
 #' This matrix  has #lines = #reactions and #columns = #species and it
 #' represents the stoichiometry of each species at each reaction.
 #'
+#' @param species    A vector with the species of the reaction. The order of
+#'                   this vector is important because it will define the
+#'                   column order of the returned behavior.
+#' @param reactions  A vector with the reactions of the CRN.
+#'
 #' @return A list with the named indexes `prod` (stoichiometry matrix of the
 #'         products), `react` (stoichiometry matrix of reactants) and `M`
 #'         (the M matrix generate from the difference of theses two matrices).

R/dsd.R

@@ -913,12 +913,12 @@ get_dsd_def_str <- function(key, val) {
 #'
 #' If a reaction has 2 reactants and 1 product,
 #' will be in the position 3,2. The formation reactions are in the
-#' line 1, and the degradation reactions are in the column 1 ([[,1]]).
+#' line 1, and the degradation reactions are in the column 1 (\[\[,1\]\]).
 #'
-#' The position [[1,1]] is filled with `NA` because it represents an
+#' The position \[\[1,1\]\] is filled with `NA` because it represents an
 #' invalid reaction (`0 -> 0`).
 #'
-#' @return  The matrix of functions which can be accesses with [[i,j]]
+#' @return  The matrix of functions which can be accesses with \[\[i,j\]\]
 dsd_4d_modules <- function() {
     # Matrix with the module functions. The higher the row,the  higher
     # the number of products, The columns has the same relation with
@@ -1135,6 +1135,26 @@ dsd_4d_module_str <- function(reaction, species_domains, k_idx) {
 #' the name of the file that will be exported and should be specified with
 #' an extension, since there is no standard extension for DSD scripts.
 #'
+#' @param species      A vector with the species of the reaction. The order of
+#'                     this vector is important because it will define the
+#'                     column order of the returned behavior. The species names
+#'                     `L[0-9]*`, `H[0-9]*`, `W[0-9]*`, `O[0-9]*`,
+#'                     `T[0-9]*`, `G[0-9]*`, `LS[0-9]*`, `HS[0-9]*`,
+#'                     `WS[0-9]*` are not supported. For more information
+#'                     about this, see the Section of **Known limitations**.
+#' @param ci           A vector specifying the initial concentrations of the
+#'                     \code{species} specified, in order.
+#' @param reactions    A vector with the reactions of the CRN^*.
+#' @param ki           A vector defining the constant rate of each reaction
+#'                     in \code{reactions}, in order.
+#' @param qmax         Maximum rate constant for the auxiliary reactions.
+#' @param cmax         Maximum initial concentration for the auxiliary species.
+#' @param alpha,beta   Rescaling parameters.
+#' @param t            A vector specifying the time interval. Each value
+#'                     would be a specific time point.
+#' @param filename     The name of the file that will be exported and should be specified with
+#' an extension, since there is no standard extension for DSD scripts.
+#'
 #' @export
 save_dsd_script <- function(
     species,

R/io.R

@@ -48,7 +48,7 @@ fte_theme <- function() {
 
         # Format the grid
         ggplot2::theme(panel.grid.major = ggplot2::element_line(
-            color = color.grid.major, size = .25
+            color = color.grid.major, linewidth = .25
         )) +
         ggplot2::theme(panel.grid.minor = ggplot2::element_blank()) +
         ggplot2::theme(axis.ticks = ggplot2::element_blank()) +

R/neuron_hjelmfelt.R

@@ -15,7 +15,6 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-
 #' Get a neuron based on Hjelmfelt A. et al. `[1]` approach
 #'
 #' This function returns a neuron based on the model described by
@@ -27,6 +26,8 @@
 #'
 #' @return  A CRN representing the neuron.
 #'
+#' @importFrom Rdpack reprompt
+#'
 #' @export
 #'
 #' @references
@@ -195,7 +196,8 @@ update_neuron_input_hje <- function(neuron, bindings) {
 #'
 #' @param gate_name               String specifying the gate name. Used for
 #'                                identification purpose.
-#' @param input_neuron_name       A list of string. Each string specifies
+#' @param input_neuron_names      A list of string. Each string specifies a
+#'                                neuron name.
 #' @param output_neuron_name      A string being the output neuron name
 #' @param input_neuron_cis        A vector of number representing the
 #'                                initial concentration of each neuron
@@ -853,7 +855,7 @@ get_neuron_majority_gate <- function(
     })
 
     # Get the gate
-    gate <- DNAr:::get_neuron_generic_gate_hje(
+    gate <- get_neuron_generic_gate_hje(
         gate_name = gate_name,
         input_neuron_names = input_names,
         output_neuron_name = output_name,

R/parser.R

@@ -20,6 +20,8 @@
 #'
 #' Given a reaction like 'A + B -> C', this function
 #' returns 'A + B '.
+#'
+#' @param react_str  A string representing the reaction
 get_first_part <- function(react_str) {
     return(sub('->.*', '', react_str))
 }
@@ -28,6 +30,8 @@ get_first_part <- function(react_str) {
 #'
 #' Given a reaction like 'A + B -> C', this function
 #' returns ' C'.
+#'
+#' @param react_str  A string representing the reaction
 get_second_part <- function(react_str) {
     return(sub('.*->', '', react_str))
 }
@@ -37,6 +41,8 @@ get_second_part <- function(react_str) {
 #' Given a reaction, this functions checks if it is
 #' a bimolecular reaction.
 #'
+#' @param react_str  A string representing the reaction
+#'
 #' @examples
 #' DNAr:::is_bimolecular('2A -> B')     # Should return TRUE
 #' DNAr:::is_bimolecular('A + B -> C')  # Should return TRUE
@@ -51,6 +57,8 @@ is_bimolecular <- function(react_str) {
 #' Given a reaction, this functions checks if it is
 #' a unimolecular reaction.
 #'
+#' @param react_str  A string representing the reaction
+#'
 #' @examples
 #' DNAr:::is_bimolecular('2A -> B')     # Should return FALSE
 #' DNAr:::is_bimolecular('A + B -> C')  # Should return FALSE
@@ -95,6 +103,8 @@ is_formation <- function(react_str) {
 #' \code{\link{get_second_part}()} and then use this function with the second
 #' part as the parameter.
 #'
+#' @param react_part  A string containing part of the reaction
+#'
 #' @examples
 #' sp <- DNAr:::get_second_part('A -> 0')
 #' DNAr:::isempty_part(sp)  # Should return TRUE
@@ -108,6 +118,9 @@ isempty_part <- function(react_part) {
 #' With the reaction part 'A + B ', for instance, and \code{one_species}
 #' begin equal to 'A', this function would return 1. On the case of '2A ' it
 #' would return 2.
+#'
+#' @param one_species A string containing a species from reaction_part.
+#' @param reaction_part  Left or right part of a reaction.
 get_onespecies_count <- function(one_species, reaction_part) {
     m <- gregexpr(
         paste('\\b[1-9]*', one_species, '\\b', sep = ''),
@@ -132,6 +145,9 @@ get_onespecies_count <- function(one_species, reaction_part) {
 #' and right part of a reaction to get the stoichiometry of a species
 #' in a reaction.
 #'
+#' @param one_species A string containing a species from reaction.
+#' @param reaction  A string representing the reaction.
+#'
 #' @return A list with \code{left_sto} being the stoichiometry of a
 #' species in the left side of a reaction, and \code{right_sto} being
 #' the same but for the right side of the reaction.
@@ -157,6 +173,8 @@ get_stoichiometry_onespecies <- function(one_species, reaction) {
 #' This function is used when you want to know the count of molecules
 #' in part of a reaction.
 #'
+#' @param reaction_part  Left or right part of a reaction.
+#'
 #' @examples
 #' DNAr:::get_stoichiometry_part('A + B ')  # It should return 2
 #' DNAr:::get_stoichiometry_part('2A ')     # It should return 2
@@ -180,6 +198,8 @@ get_stoichiometry_part <- function(reaction_part) {
 #' Use this function to get the stoichiometry of the left and
 #' right part of a reaction.
 #'
+#' @param reaction  A string representing the reaction
+#'
 #' @return a list with left_sto and right_sto being the stoichiometry
 #' of the left and right part respectively.
 #'
@@ -201,6 +221,8 @@ get_stoichiometry_all <- function(reaction) {
 #' Use this function to get rid of the stoichiometry of a
 #' species string.
 #'
+#' @param species A string containing the species from a reaction_part.
+#'
 #' @return The species string without the stoichiometry (number)
 #' specifying the number of molecules
 #'
@@ -260,6 +282,8 @@ get_species <- function(reaction_part) {
 #' This function returns the reactants of a reactions,
 #' removing their stoichiometry.
 #'
+#' @param reaction  A string representing the reaction.
+#'
 #' @examples
 #' DNAr:::get_reactants('A + B -> C')  # Returns c('A', 'B')
 #' DNAr:::get_reactants('2A -> B')     # Returns c('A')
@@ -276,6 +300,8 @@ get_reactants <- function(reaction) {
 #' 'A -> 0', '0' is returned as a species since it is considered
 #' a special species.
 #'
+#' @param reaction  A string representing the reaction.
+#'
 #' @examples
 #' DNAr:::get_products('A + B -> C')   # Returns c('C')
 #' DNAr:::get_products('2A -> B + C')  # Returns c('B', 'C')
@@ -293,6 +319,11 @@ get_products <- function(reaction) {
 #' species indexes in \code{species} that are reactants
 #' in \code{reaction}.
 #'
+#' @param species    A vector with the species of the reaction. The order of
+#'                   this vector is important because it will define the
+#'                   column order of the returned behavior.
+#' @param reaction  A string representing the reaction.
+#'
 #' @return A vector filled with indexes specifying the
 #' species that are in a reaction as a reactant.
 #'
@@ -326,6 +357,23 @@ reactants_in_reaction <- function(species, reaction) {
 #'  - If there is no duplicate of species names on the `species` parameter.
 #' The parameters of this function are the same of \code{\link{react}()}.
 #'
+#' @param species    A vector with the species of the reaction. The order of
+#'                   this vector is important because it will define the
+#'                   column order of the returned behavior.
+#' @param ci         A vector specifying the initial concentrations of the
+#'                   \code{species} specified, in order.
+#' @param reactions  A vector with the reactions of the CRN. If a reaction has
+#'                   has only reactants that are non in `species`, this
+#'                   reaction will be treated as `0 -> products`. Furthermore,
+#'                   this function treats a reaction `non_registered_species
+#'                   + registered_species -> products` equally to
+#'                   `registered_species -> products`, ignoring the species non
+#'                   registered on the `species` vector.
+#' @param ki         A vector defining the constant rate of each reaction
+#'                   in \code{reactions}, in order.
+#' @param t          A vector specifying the time interval. Each value
+#'                   would be a specific time point.
+#'
 #' @return  The reactions after the preprocessing made by
 #'          `\link{check_fix_reaction}()` witch checks the reactions and fix
 #'          them when it is possible.
@@ -334,7 +382,7 @@ check_crn <- function(species, ci, reactions, ki, t) {
     # This is a helper function to check the parameters
     check_var <- function(vec, type_checker, err_msgs) {
         # Check if the vec parameter is if the type vector
-        assertthat::assert_that(is.vector(species), msg = err_msg[[1]])
+        assertthat::assert_that(is.vector(species), msg = err_msgs[[1]])
 
         # Check if all vector elements are of the correct type
         # using the type_checker function