another round of pre cran corrections

Author: ischlo

DESCRIPTION

@@ -2,18 +2,21 @@ Package: cppSim
 Title: Fast and Memory Efficient Spatial Interaction Models
 Version: 0.2
 Authors@R: 
-    person("Ivann", "Schlosser", , "ivann.schlosser.19@ucl.ac.uk", role = c("aut", "cre"),
+    person(given = "Ivann", family = "Schlosser", email = "ivann.schlosser.19@ucl.ac.uk", role = c("aut", "cre"),
            comment = c(ORCID = "0009-0004-4099-3198"))
+Author: Ivann Schlosser [aut, cre] (<https://orcid.org/0009-0004-4099-3198>)
 Maintainer: Ivann Schlosser <ivann.schlosser.19@ucl.ac.uk>
 Description: Building on top of the 'RcppArmadillo' linear
     algebra functionalities to do fast spatial interaction models in the
     context of urban analytics, geography, transport modelling. It uses
     the Newton root search algorithm to determine the optimal cost
     exponent and can run country level models with thousands of origins
     and destinations. It aims at implementing an easy approach based on
-    matrices. Currently, the simplest form of production, destination and
+    matrices, that can originate from various routing and processing steps earlier in an workflow. 
+    Currently, the simplest form of production, destination and
     doubly constrained models are implemented.
-Date: 2025-04-17
+    Schlosser et al. (2023) <doi:10.48550/arXiv.2309.02112>.
+Date: 2025-08-29
 License: MIT + file LICENSE
 URL: https://ischlo.github.io/cppSim/, https://github.com/ischlo/cppSim
 Depends:

README.Rmd

@@ -75,7 +75,7 @@ model_test <- run_model(
 
 For an example of what can be done with this package, please refer to the publication on active travel spatial interaction models in London for which it was originally developed.
 
-> [Schlosser, I., Maureira, V.M., Milton, R., Arcaute, E., Batty, M., 2023. Active-travel modelling: a methodological approach to networks for walking and cycling commuting analysis.](http://arxiv.org/abs/2309.02112)
+> [Schlosser, I., Maureira, V.M., Milton, R., Arcaute, E., Batty, M., 2023. Active-travel modelling: a methodological approach to networks for walking and cycling commuting analysis.](https://arxiv.org/abs/2309.02112)
 
 The accompanying code for the analysis is provided in the [`ischlo/quant_cycle_walk`](https://github.com/ischlo/quant_cycle_walk) repository.
 
@@ -93,7 +93,7 @@ On the R side, it uses `Rcpp` [@eddelbuettel2011] and `RcppArmadillo` [@eddelbue
 
 ## Performance
 
-Compared to the equivalent functions implemented in pure R, it runs about x10 faster for a $\sim 1000\times 1000$ OD matrix, the speed up is increasingly more significant as matrices get bigger.
+Compared to the equivalent functions implemented in pure R, it runs about x10 faster for a $\sim 1000 \times 1000$ OD matrix, the speed up is increasingly more significant as matrices get bigger.
 
 ```{r performance,eval=TRUE,include=TRUE,echo = FALSE}
 

README.md

@@ -14,6 +14,7 @@ stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://
 ![](https://github.com/ischlo/cppSim/actions/workflows/rhub.yaml/badge.svg)
 
 <!-- ![](https://github.com/ischlo/cppSim/actions/workflows/test-coverage.yaml/badge.svg) -->
+
 <!-- badges: end -->
 
 This aims at providing a set of fast, memory efficient functions to
@@ -82,7 +83,7 @@ for which it was originally developed.
 > [Schlosser, I., Maureira, V.M., Milton, R., Arcaute, E., Batty, M.,
 > 2023. Active-travel modelling: a methodological approach to networks
 > for walking and cycling commuting
-> analysis.](http://arxiv.org/abs/2309.02112)
+> analysis.](https://arxiv.org/abs/2309.02112)
 
 The accompanying code for the analysis is provided in the
 [`ischlo/quant_cycle_walk`](https://github.com/ischlo/quant_cycle_walk)
@@ -108,26 +109,27 @@ On the R side, it uses `Rcpp` \[@eddelbuettel2011\] and `RcppArmadillo`
 ## Performance
 
 Compared to the equivalent functions implemented in pure R, it runs
-about x10 faster for a $\sim 1000\times 1000$ OD matrix, the speed up is
-increasingly more significant as matrices get bigger.
+about x10 faster for a $`\sim 1000 \times 1000`$ OD matrix, the speed up
+is increasingly more significant as matrices get bigger.
 
     [1] "/Users/cenv1069/Library/R/arm64/4.4/library/cppSim/extdata/benchmark_test.rds"
 
 ## Citation
 
     To cite package 'cppSim' in publications use:
 
-      Schlosser I (2024). _cppSim: Fast and Memory Efficient Spatial
-      Interaction Models_. R package version 0.2,
-      https://github.com/ischlo/cppSim, <https://ischlo.github.io/cppSim/>.
+      Schlosser I (2023). _cppSim: Fast and Memory Efficient Spatial
+      Interaction Models_. doi:10.5281/zenodo.14367756
+      <https://doi.org/10.5281/zenodo.14367756>,
+      <https://ischlo.github.io/cppSim/>.
 
     A BibTeX entry for LaTeX users is
 
       @Manual{,
         title = {cppSim: Fast and Memory Efficient Spatial Interaction Models},
         author = {Ivann Schlosser},
-        year = {2024},
-        note = {R package version 0.2, https://github.com/ischlo/cppSim},
+        year = {2023},
+        doi = {10.5281/zenodo.14367756},
         url = {https://ischlo.github.io/cppSim/},
       }
 

vignettes/getting_started_2.Rmd

@@ -50,10 +50,15 @@ dim(flows_test)
 
 ```{r echo=FALSE, fig.show='hold', out.width="45%"}
 
-par(cex = .6)
+oldpar <- par(cex = .6)
+
 plot(density(distance_test), main = "Distribution of distances", xlab = "OD distance (km)")
 plot(density(flows_test), main = "Distribution of flows", xlab = "flow", log = "x")
 
+# Restore
+par(oldpar)
+
+
 ```
 
 # Visualisation