version 0.3.0

cran · Jan 23, 2023 · f9d562a · f9d562a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: GillespieSSA2
 Title: Gillespie's Stochastic Simulation Algorithm for Impatient People
-Version: 0.2.10
+Version: 0.3.0
 Authors@R: 
     c(person(given = "Robrecht",
              family = "Cannoodt",
@@ -19,10 +19,11 @@ Description: A fast, scalable, and versatile framework for
     'GillespieSSA' package originally written by Mario Pineda-Krch.
     Benefits of this package include major speed improvements (>100x),
     easier to understand documentation, and many unit tests that try to
-    ensure the package works as intended. Cannoodt and Saelens et al. (2020) 
-    <doi:10.1101/2020.02.06.936971>.
+    ensure the package works as intended. Cannoodt and Saelens et al. (2021) 
+    <doi:10.1038/s41467-021-24152-2>.
 License: GPL (>= 3)
-URL: https://github.com/rcannood/GillespieSSA2
+URL: https://rcannood.github.io/GillespieSSA2/,
+        https://github.com/rcannood/GillespieSSA2
 BugReports: https://github.com/rcannood/GillespieSSA2/issues
 Depends: R (>= 3.3)
 Imports: assertthat, dplyr, dynutils, Matrix, methods, purrr, Rcpp (>=
@@ -32,11 +33,11 @@ Suggests: covr, ggplot2, GillespieSSA, knitr, rmarkdown, testthat (>=
 LinkingTo: Rcpp
 VignetteBuilder: knitr
 Encoding: UTF-8
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.2
 NeedsCompilation: yes
-Packaged: 2022-09-23 04:47:00 UTC; rcannood
+Packaged: 2023-01-23 11:54:50 UTC; rcannood
 Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>),
   Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>)
 Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
 Repository: CRAN
-Date/Publication: 2022-09-23 05:10:02 UTC
+Date/Publication: 2023-01-23 19:20:02 UTC
diff --git a/MD5 b/MD5
@@ -1,8 +1,8 @@
-8f41f7ed7564072d184398b8df01e33f *DESCRIPTION
+f5b91b1afcb0b78ae9ce0e7e0211df0e *DESCRIPTION
 824738d9e64b71dcdc15f3dd4cc9f7d1 *NAMESPACE
-cdab9254174b7ab070aae254d47255da *NEWS.md
+1e3e6a778c631805a00b4a95bee91489 *NEWS.md
 8fcca8419edb8e5f6f05edb5a9ab164a *R/RcppExports.R
-f6176e06683b11288eceee32f584ece1 *R/compile_reactions.R
+0ed41f9926ca751fccec5c436dcd684b *R/compile_reactions.R
 8187cadc939326b491c14d43b5db902a *R/ode_em.R
 ca7f7bed69c58ffba28e99dad5f38116 *R/package.R
 29c88d8ada2ce642e79c72cd95c598d2 *R/port_reactions.R
@@ -14,42 +14,43 @@ b7b8f91d2169ae81380dc6a6688cb423 *R/ssa_exact.R
 6beb908b6b6ab7e726e4bacd15e24912 *R/ssa_plot.R
 c3d7b66d3367069b461cf25f600ce460 *R/ssa_simulation.R
 66591901b38888eb1284b979e2529d42 *R/zzz.R
-479d3620835fc9428dee21a939f69557 *README.md
-57fe49e601422a308c7278572afd7958 *build/partial.rdb
-c84c168dedf5b1c8faf9a649b97eb3fa *build/vignette.rds
-b9802047792b5effc3164ec8de783e78 *inst/CITATION
+e4bbcec29a5058f41f9fbcbb0cef3300 *README.md
+5090baddae7c87baed092cb997ee3904 *build/partial.rdb
+9828b259bd842cddd67e9761b5d6c75a *build/vignette.rds
+ecb8ffdc199e5746c40aa89c230e8392 *inst/CITATION
+e9ceee3ba1b05393de18fcb29fd2641f *inst/REFERENCES.bib
 6259d0e8d0745ae7b3f91fa929136220 *inst/doc/an_introduction.R
 eb938dd5bf4359137d770768c897dc3c *inst/doc/an_introduction.Rmd
-8b559f741849b52fa845421f6e5cfce9 *inst/doc/an_introduction.html
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 3f33398e5a745c5868294073192ded1c *inst/doc/converting_from_GillespieSSA.R
 47746770110cc68b84b66f35fae83c1a *inst/doc/converting_from_GillespieSSA.Rmd
-5f2e6ceef5ed0207e6294a403d14f92e *inst/doc/converting_from_GillespieSSA.html
+06d931fa3c1e7ae93b28b05a1ca42971 *inst/doc/converting_from_GillespieSSA.html
 ea28ca14a02f3042f16a7ec1c9ffd3d7 *inst/doc/decaying_dimer.R
-6f47b4e254ec886cea970c410da995f3 *inst/doc/decaying_dimer.Rmd
-59b561a34f14c4d76ef299345e410f21 *inst/doc/decaying_dimer.html
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 e4fad73432106caa5cc6cee9cc6d0119 *inst/doc/epi_chain.R
-a7cd8a2160162c9a6b066c0a692e1a03 *inst/doc/epi_chain.Rmd
-58c6983388b58f17b904a5596b025d7e *inst/doc/epi_chain.html
+c3d18bcf07a9c49f57ccf7353bb0a2fa *inst/doc/epi_chain.Rmd
+ad0b95cd51c26d1feb1d3eb84feb874e *inst/doc/epi_chain.html
 df35701ec3d5431e46380cb634f5285e *inst/doc/linear_chain.R
-d241625929888c6741be09391f7a13c2 *inst/doc/linear_chain.Rmd
-73651c1f119506af149b19148d68e90a *inst/doc/linear_chain.html
+af349ed16a74ef418faa92bbdb498625 *inst/doc/linear_chain.Rmd
+26509b2070048ee008fb57f113bd91f9 *inst/doc/linear_chain.html
 731cb4f07f219d66c90e6513c8b2e303 *inst/doc/logistic_growth.R
-4b965e551fa7ccde34c25ba7068bfbdc *inst/doc/logistic_growth.Rmd
-f9467b02c32a93112677f88e7e4f3dac *inst/doc/logistic_growth.html
+493793d47eb8247d39df273be706eccb *inst/doc/logistic_growth.Rmd
+dffef6c0776034f6f27f4d688d347e57 *inst/doc/logistic_growth.html
 72d80133111eaf60d5e7cd959263eba7 *inst/doc/lotka_predator_prey.R
-9326f9bfc31d687d3be5c322cebec6f6 *inst/doc/lotka_predator_prey.Rmd
-35138cad9823b64a7dbdd38fc72c5695 *inst/doc/lotka_predator_prey.html
+db3edc8b691fdb9f8db8bdad5a6cdb94 *inst/doc/lotka_predator_prey.Rmd
+2b9a16ee0c744a7e328b30eb19fd10c5 *inst/doc/lotka_predator_prey.html
 982d701ae77f8067874109debaa33ecc *inst/doc/radioactive_decay.R
-1f81b1df3982b49719d59f1f528df279 *inst/doc/radioactive_decay.Rmd
-6cf32a38a88d61214b7875b302c1baf6 *inst/doc/radioactive_decay.html
+06f03813daab33cb5be1be20f3ae72c7 *inst/doc/radioactive_decay.Rmd
+67e3928ce7b468d2b3cec787d64072a8 *inst/doc/radioactive_decay.html
 bf14a1fdda72e32ea87067d94e7e0a69 *inst/doc/rm_predator_prey.R
-6117cd70a102e574eb32c91b68c51008 *inst/doc/rm_predator_prey.Rmd
-17cfb003b7f01e03f06087951bd92e01 *inst/doc/rm_predator_prey.html
+b205f1267c3e46ef29ac3577c510f064 *inst/doc/rm_predator_prey.Rmd
+4771057a985b3ff10193c35144828304 *inst/doc/rm_predator_prey.html
 6273d82ad27b9c6b81720a65c12680da *inst/doc/sir.R
-e7391b08c6fab835d293a636a3690c89 *inst/doc/sir.Rmd
-8a02528c77784cb5bdb928b9b35ee607 *inst/doc/sir.html
+6019e10b7401171ea419cb73ef122358 *inst/doc/sir.Rmd
+37ad68c09bcba1e91d17f1e057239a16 *inst/doc/sir.html
 1d412520a0f0af2c8d4943ea186d2be5 *man/GillespieSSA2.Rd
-fac9373cca89eee02113c13c7955aa37 *man/compile_reactions.Rd
+c527a114f82a847f0e1d7338e9049848 *man/compile_reactions.Rd
 fd4c47d761c9f639c188d297da449d64 *man/figures/dependencies.png
 47b54f1c878c06fc218c268b82d13ef4 *man/ode_em.Rd
 c96b29826ec798db4de2bbb74affcea1 *man/plot_ssa.Rd
@@ -74,7 +75,7 @@ bde4cd198553f4f2f2bb64ade0b2f79e *src/utils.h
 1f805c4be7c74e9df39994f09c36fa25 *tests/testthat.R
 b42108b1f1173cd9d808546e2add30a1 *tests/testthat/helper-test_propensity.R
 3f38c64eff5561aafca0ad2172b8874e *tests/testthat/helper-test_ssa_step.R
-9598bac6aa535675370ee8e7fabeb5fe *tests/testthat/test-compile_reactions.R
+70fbaee4190043af5443297db532a120 *tests/testthat/test-compile_reactions.R
 abb0748b010db2641b963047e151e6dc *tests/testthat/test-ode_em.R
 ed1ac27aaa28558d05f8ba4ee2327c4e *tests/testthat/test-reaction.R
 a941cab6602f231a3f2a9d5077f81265 *tests/testthat/test-ssa.R
@@ -83,11 +84,11 @@ a941cab6602f231a3f2a9d5077f81265 *tests/testthat/test-ssa.R
 95e9d9020887f6a76fcf9cf6471f3667 *tests/testthat/test-ssa_exact.R
 eb938dd5bf4359137d770768c897dc3c *vignettes/an_introduction.Rmd
 47746770110cc68b84b66f35fae83c1a *vignettes/converting_from_GillespieSSA.Rmd
-6f47b4e254ec886cea970c410da995f3 *vignettes/decaying_dimer.Rmd
-a7cd8a2160162c9a6b066c0a692e1a03 *vignettes/epi_chain.Rmd
-d241625929888c6741be09391f7a13c2 *vignettes/linear_chain.Rmd
-4b965e551fa7ccde34c25ba7068bfbdc *vignettes/logistic_growth.Rmd
-9326f9bfc31d687d3be5c322cebec6f6 *vignettes/lotka_predator_prey.Rmd
-1f81b1df3982b49719d59f1f528df279 *vignettes/radioactive_decay.Rmd
-6117cd70a102e574eb32c91b68c51008 *vignettes/rm_predator_prey.Rmd
-e7391b08c6fab835d293a636a3690c89 *vignettes/sir.Rmd
+3329ff40ef14aa33e12a9ed366628147 *vignettes/decaying_dimer.Rmd
+c3d18bcf07a9c49f57ccf7353bb0a2fa *vignettes/epi_chain.Rmd
+af349ed16a74ef418faa92bbdb498625 *vignettes/linear_chain.Rmd
+493793d47eb8247d39df273be706eccb *vignettes/logistic_growth.Rmd
+db3edc8b691fdb9f8db8bdad5a6cdb94 *vignettes/lotka_predator_prey.Rmd
+06f03813daab33cb5be1be20f3ae72c7 *vignettes/radioactive_decay.Rmd
+b205f1267c3e46ef29ac3577c510f064 *vignettes/rm_predator_prey.Rmd
+6019e10b7401171ea419cb73ef122358 *vignettes/sir.Rmd
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+# GillespieSSA2 0.3.0
+
+* MINOR CHANGE: Add `debug` parameter to print out propensity functions before compiling.
+
+* MINOR CHANGE: Add spaces between terms in the reaction propensity C++ code to 
+  avoid pasting together important key words (e.g. `if` and `else`).
+
 # GillespieSSA2 0.2.10
 
 * MINOR CHANGE: Turn array of propensity functions into vector of propensity functions.

diff --git a/R/compile_reactions.R b/R/compile_reactions.R
@@ -10,6 +10,7 @@
 #' @param hardcode_params `[logical]` Whether or not to hardcode the values of `params` in the compilation of the propensity functions.
 #'   Setting this to `TRUE` will result in a minor sacrifice in accuracy for a minor increase in performance.
 #' @param fun_by `[integer]` Combine this number of propensity functions into one function.
+#' @param debug `[logical]` Whether to print the resulting C++ code before compiling.
 #'
 #' @return A list of objects solely to be used by [ssa()].
 #'
@@ -66,7 +67,8 @@ compile_reactions <- function(
   params,
   buffer_ids = NULL,
   hardcode_params = FALSE,
-  fun_by = 10000L
+  fun_by = 10000L,
+  debug = FALSE
 ) {
   assert_that(is.list(reactions))
   walk(seq_along(reactions), function(i) {
@@ -108,19 +110,21 @@ compile_reactions <- function(
   # add reaction ids assignments to propensity functions
   propensity_funs <- map_chr(reactions, "propensity")
   for (i in seq_along(propensity_funs)) {
-    propensity_funs[[i]] <- gsub("(.*;)?([^;]*)", paste0("\\1", reaction_ids[[i]], " = \\2"), propensity_funs[[i]])
+    propensity_funs[[i]] <- gsub("(.*; *)?([^;]*)", paste0("\\1", reaction_ids[[i]], " = \\2"), propensity_funs[[i]])
   }
 
   # preprocess propensity functions
   variable_names <- propensity_funs %>% str_extract_all("[A-Za-z_0-9]* *=") %>% map(function(x) str_replace_all(x, "[ =]", ""))
   reaction_ids <- variable_names %>% map_chr(last)
 
   buffer_usages <- map_int(variable_names, length) - 1
-  buffer_size <- sum(buffer_usages)
-
   if (is.null(buffer_ids)) {
-    buffer_ids <- variable_names %>% unlist() %>% discard(~ . %in% reaction_ids)
+    buffer_ids <- variable_names %>%
+      unlist() %>%
+      discard(~ . %in% reaction_ids) %>%
+      unique()
   }
+  buffer_size <- length(buffer_ids)
 
   # split propensity functions into words and non-words
   prop_split <-
@@ -159,7 +163,8 @@ compile_reactions <- function(
 
   # get indices of semi colons
   prop_lines <-
-    paste0(prop_split, collapse = "") %>%
+    paste0(prop_split, collapse = " ") %>%
+    str_replace_all(" *; *", ";") %>%
     str_split(";") %>%
     first() %>%
     discard(~ . == "")
@@ -183,6 +188,9 @@ compile_reactions <- function(
     rcpp_function_code_blocks,
     "}\n"
   )
+  if (debug) {
+    cat(rcpp_codes)
+  }
 
   # create temporary dir for compilation
   tmpdir <- dynutils::safe_tempdir("gillespie")

diff --git a/README.md b/README.md
@@ -16,8 +16,9 @@ Status](https://app.codecov.io/gh/rcannood/GillespieSSA2/branch/master/graph/bad
 
 **GillespieSSA2** is a fast, scalable, and versatile framework for
 simulating large systems with Gillespie’s Stochastic Simulation
-Algorithm (SSA). This package is the spiritual successor to the
-GillespieSSA package originally written by Mario Pineda-Krch.
+Algorithm (SSA) (Cannoodt et al. 2021). This package is the spiritual
+successor to the GillespieSSA package originally written by Mario
+Pineda-Krch (Pineda-Krch 2008).
 
 GillespieSSA2 has the following added benefits:
 
@@ -59,20 +60,42 @@ The following example models are available:
     `vignette("an_introduction", package="GillespieSSA2")`
 -   Converting from GillespieSSA to GillespieSSA2:  
     `vignette("converting_from_GillespieSSA", package="GillespieSSA2")`
--   Decaying-Dimerization Reaction Set (Gillespie, 2001):  
+-   Decaying-Dimerization Reaction Set:  
     `vignette("decaying_dimer", package="GillespieSSA2")`
--   SIRS metapopulation model (Pineda-Krch, 2008):  
+-   SIRS metapopulation model:  
     `vignette("epi_chain", package="GillespieSSA2")`
--   Linear Chain System (Cao et al., 2004):  
+-   Linear Chain System:  
     `vignette("linear_chain", package="GillespieSSA2")`
--   Pearl-Verhulst Logistic Growth model (Kot, 2001):  
+-   Pearl-Verhulst Logistic Growth model:  
     `vignette("logistic_growth", package="GillespieSSA2")`
--   Lotka Predator-Prey model (Gillespie, 1977; Kot, 2001):  
+-   Lotka Predator-Prey model:  
     `vignette("lotka_predator_prey", package="GillespieSSA2")`
--   Radioactive Decay model (Gillespie, 1977):  
+-   Radioactive Decay model:  
     `vignette("radioactive_decay", package="GillespieSSA2")`
--   Rosenzweig-MacArthur Predator-Prey model (Pineda-Krch et al.,
-    2007):  
+-   Rosenzweig-MacArthur Predator-Prey model:  
     `vignette("rm_predator_prey", package="GillespieSSA2")`
--   Kermack-McKendrick SIR model (Brown & Rothery, 1993):  
+-   Kermack-McKendrick SIR model:  
     `vignette("sir", package="GillespieSSA2")`
+
+## References
+
+<div id="refs" class="references csl-bib-body hanging-indent">
+
+<div id="ref-Cannoodt2021" class="csl-entry">
+
+Cannoodt, Robrecht, Wouter Saelens, Louise Deconinck, and Yvan Saeys.
+2021. “Spearheading Future Omics Analyses Using Dyngen, a Multi-Modal
+Simulator of Single Cells.” *Nature Communications* 12 (1).
+<https://doi.org/10.1038/s41467-021-24152-2>.
+
+</div>
+
+<div id="ref-PinedaKrch2008" class="csl-entry">
+
+Pineda-Krch, Mario. 2008. “GillespieSSA: Implementing the Stochastic
+Simulation Algorithm in r.” *Journal of Statistical Software* 25 (12).
+<https://doi.org/10.18637/jss.v025.i12>.
+
+</div>
+
+</div>
diff --git a/build/partial.rdb b/build/partial.rdb
diff --git a/build/vignette.rds b/build/vignette.rds
diff --git a/inst/CITATION b/inst/CITATION
@@ -8,11 +8,9 @@ citEntry(
     person("Louise", "Deconinck"),
     person("Yvan", "Saeys")
   ),
-  title    = "dyngen: a multi-modal simulator for spearheading new single-cell omics analyses",
-  journal  = "bioRxiv",
-  year     = "2020",
-  month    = "2",
-  doi      = "10.1101/2020.02.06.936971",
-  url      = "https://www.biorxiv.org/content/10.1101/2020.02.06.936971v2",
-  textVersion = "dyngen: a multi-modal simulator for spearheading new single-cell omics analyses. Robrecht Cannoodt, Wouter Saelens, Louise Deconinck, Yvan Saeys. bioRxiv 2020.02.06.936971; doi: https://doi.org/10.1101/2020.02.06.936971."
+  title    = "Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells",
+  journal  = "Nature Communications",
+  year     = "2021",
+  doi      = "10.1038/s41467-021-24152-2",
+  textVersion = "Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells. Robrecht Cannoodt, Wouter Saelens, Louise Deconinck, Yvan Saeys. Nat Commun 12, 3942 (2021); doi: https://doi.org/10.1038/s41467-021-24152-2."
 )