Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Error when writing equations in matrix form #14

Open
juanrocha opened this issue Sep 23, 2023 · 0 comments
Open

Error when writing equations in matrix form #14

juanrocha opened this issue Sep 23, 2023 · 0 comments

Comments

@juanrocha
Copy link

Thanks for developing and maintaining the package!

I run into the following error when trying to plot a phase diagram on a 2-dim system. The function is:

## Pollution model:
pollution <- function(t, y, params){
  with(as.list(c(y, params)), {
    x = numeric(length = n)
    x = y
    pollutant <- u - s*x + v * (x^alpha/(z^alpha + x^alpha))
    outflow <-  (A_ij * delta_ij) %*% x
    inflow <-  t(A_ij * delta_ij) %*% x

    dx <- pollutant + (inflow - outflow)
    
    return(list(c(dx)))
  })
}

With the following parameters:

n <- 1 # number of systems
delta_ij <- matrix(runif(n^2, min = 0.02, max = 0.05), ncol = n)
A_ij <- matrix(rbinom(n^2, 1, prob = 0.3), n, n)

## Parameters: 
params <- list(
    n = n,                             # number of systems (e.g. lakes)
    u = rep(0.5, n),             # pollution load from humans
    s = rep(2.5, n),             # internal loss rate (sedimentation)
    v = rep(10, n),              # max level of internal nutrient release
    z = rep(2.2, n),             # threshold
    alpha = 4 ,                    # sharpness of the shift
    delta_ij = delta_ij,        # matrix of difussion terms
    A_ij = A_ij                     # adjacency matrix
)

phaseR works on the one-dimensional case, eg:

fld <- flowField(pollution, xlim = c(0,5), ylim = c(-2,7), parameters = params,
          system = "one.dim", add = FALSE)
nll <- nullclines(pollution, xlim = c(0,5), ylim = c(-2,7), parameters = params,
          system = "one.dim", add = TRUE)
trj <- trajectory(pollution, y0 = c(-0.5, 1, 3, 5), tlim = c(0,5), parameters = params,
          system = "one.dim", add = TRUE)

But as soon as I change n = 2 I get the following error:

fld <- flowField(pollution, xlim = c(0,5), ylim = c(-2,7), system = "two.dim", add = FALSE, parameters = params)

Error in (A_ij * delta_ij) %*% x : non-conformable arguments

I don't quite understand the origin of the error. The system works with n = 1, 2, or 100s when doing numerical simulations with deSolve, but for some reason fails on the two-dimensional case in phaseR.

If I rewrite the function in a non-matrix form such as:

pollution2 <- function(t,y,params){
    with(as.list(c(y, params)), {
    x = numeric(length = n)
    x = y
    dx <- u[1] - s[1]*x[1] + v[1] * (x[1]^alpha/(z[1]^alpha + x[1]^alpha)) + (A_ij[2,1] * delta_ij[2,1]) %*% x[1] - (A_ij[1,2] * delta_ij[1,2]) %*% x[2]
    
    dy <- u[2] - s[2]*x[2] + v[2] * (x[2]^alpha/(z[2]^alpha + x[2]^alpha)) + (A_ij[1,2] * delta_ij[1,2]) %*% x[2] - (A_ij[1,2] * delta_ij[1,2]) %*% x[1]
    
    return(list(c(dx, dy)))
  })
}

Trying to get the flow field throughs a different error:

fld <- flowField(pollution2, xlim = c(0,5), ylim = c(-2,7), system = "two.dim", add = FALSE, parameters = params)

Error in if (any(dx[i, j] != 0, dy[i, j] != 0)) { : missing value where TRUE/FALSE needed

Which seems similar to issue #13
Any help is greatly appreciated!

Below my session info if useful:

session_info()
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.2 (2022-10-31)
 os       macOS Ventura 13.5.2
 system   x86_64, darwin17.0
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Stockholm
 date     2023-09-23
 rstudio  2023.06.0+421 Mountain Hydrangea (desktop)
 pandoc   2.14.2 @ /usr/local/bin/pandoc

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────
 package        * version date (UTC) lib source
 assertthat       0.2.1   2019-03-21 [1] CRAN (R 4.2.0)
 backports        1.4.1   2021-12-13 [1] CRAN (R 4.2.0)
 broom            1.0.2   2022-12-15 [1] CRAN (R 4.2.2)
 cachem           1.0.7   2023-02-24 [1] CRAN (R 4.2.0)
 callr            3.7.3   2022-11-02 [1] CRAN (R 4.2.0)
 cellranger       1.1.0   2016-07-27 [1] CRAN (R 4.2.0)
 cli              3.6.1   2023-03-23 [1] CRAN (R 4.2.0)
 coda             0.19-4  2020-09-30 [1] CRAN (R 4.2.0)
 colorspace       2.1-0   2023-01-23 [1] CRAN (R 4.2.0)
 crayon           1.5.2   2022-09-29 [1] CRAN (R 4.2.0)
 DBI              1.1.3   2022-06-18 [1] CRAN (R 4.2.0)
 dbplyr           2.2.1   2022-06-27 [1] CRAN (R 4.2.0)
 deSolve        * 1.34    2022-10-22 [1] CRAN (R 4.2.0)
 devtools       * 2.4.5   2022-10-11 [1] CRAN (R 4.2.0)
 digest           0.6.33  2023-07-07 [1] CRAN (R 4.2.0)
 dplyr          * 1.1.1   2023-03-22 [1] CRAN (R 4.2.0)
 ellipsis         0.3.2   2021-04-29 [1] CRAN (R 4.2.0)
 fansi            1.0.4   2023-01-22 [1] CRAN (R 4.2.0)
 fastmap          1.1.1   2023-02-24 [1] CRAN (R 4.2.0)
 forcats        * 0.5.2   2022-08-19 [1] CRAN (R 4.2.0)
 fs               1.6.3   2023-07-20 [1] CRAN (R 4.2.0)
 gargle           1.2.1   2022-09-08 [1] CRAN (R 4.2.0)
 generics         0.1.3   2022-07-05 [1] CRAN (R 4.2.0)
 ggplot2        * 3.4.2   2023-04-03 [1] CRAN (R 4.2.0)
 glue             1.6.2   2022-02-24 [1] CRAN (R 4.2.0)
 googledrive      2.0.0   2021-07-08 [1] CRAN (R 4.2.0)
 googlesheets4    1.0.1   2022-08-13 [1] CRAN (R 4.2.0)
 gtable           0.3.3   2023-03-21 [1] CRAN (R 4.2.0)
 haven            2.5.1   2022-08-22 [1] CRAN (R 4.2.0)
 hms              1.1.2   2022-08-19 [1] CRAN (R 4.2.0)
 htmltools        0.5.5   2023-03-23 [1] CRAN (R 4.2.0)
 htmlwidgets      1.6.0   2022-12-15 [1] CRAN (R 4.2.2)
 httpuv           1.6.9   2023-02-14 [1] CRAN (R 4.2.0)
 httr             1.4.5   2023-02-24 [1] CRAN (R 4.2.0)
 igraph           1.3.5   2022-09-22 [1] CRAN (R 4.2.0)
 jsonlite         1.8.7   2023-06-29 [1] CRAN (R 4.2.0)
 knitr            1.43    2023-05-25 [1] CRAN (R 4.2.0)
 later            1.3.0   2021-08-18 [1] CRAN (R 4.2.0)
 lattice          0.20-45 2021-09-22 [1] CRAN (R 4.2.2)
 lifecycle        1.0.3   2022-10-07 [1] CRAN (R 4.2.0)
 lubridate        1.9.2   2023-02-10 [1] CRAN (R 4.2.0)
 magrittr         2.0.3   2022-03-30 [1] CRAN (R 4.2.0)
 memoise          2.0.1   2021-11-26 [1] CRAN (R 4.2.0)
 mime             0.12    2021-09-28 [1] CRAN (R 4.2.0)
 miniUI           0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0)
 modelr           0.1.10  2022-11-11 [1] CRAN (R 4.2.0)
 munsell          0.5.0   2018-06-12 [1] CRAN (R 4.2.0)
 network          1.18.0  2022-10-06 [1] CRAN (R 4.2.0)
 phaseR         * 2.2.1   2022-09-02 [1] CRAN (R 4.2.0)
 pillar           1.9.0   2023-03-22 [1] CRAN (R 4.2.0)
 pkgbuild         1.4.0   2022-11-27 [1] CRAN (R 4.2.0)
 pkgconfig        2.0.3   2019-09-22 [1] CRAN (R 4.2.0)
 pkgload          1.3.2.1 2023-07-08 [1] CRAN (R 4.2.0)
 prettyunits      1.1.1   2020-01-24 [1] CRAN (R 4.2.0)
 processx         3.8.2   2023-06-30 [1] CRAN (R 4.2.0)
 profvis          0.3.7   2020-11-02 [1] CRAN (R 4.2.0)
 promises         1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0)
 ps               1.7.5   2023-04-18 [1] CRAN (R 4.2.0)
 purrr          * 1.0.2   2023-08-10 [1] CRAN (R 4.2.0)
 R6               2.5.1   2021-08-19 [1] CRAN (R 4.2.0)
 Rcpp             1.0.10  2023-01-22 [1] CRAN (R 4.2.0)
 readr          * 2.1.3   2022-10-01 [1] CRAN (R 4.2.0)
 readxl           1.4.1   2022-08-17 [1] CRAN (R 4.2.0)
 remotes          2.4.2.1 2023-07-18 [1] CRAN (R 4.2.0)
 reprex           2.0.2   2022-08-17 [1] CRAN (R 4.2.0)
 rlang            1.1.1   2023-04-28 [1] CRAN (R 4.2.0)
 rstudioapi       0.14    2022-08-22 [1] CRAN (R 4.2.0)
 rvest            1.0.3   2022-08-19 [1] CRAN (R 4.2.0)
 scales           1.2.1   2022-08-20 [1] CRAN (R 4.2.0)
 sessioninfo      1.2.2   2021-12-06 [1] CRAN (R 4.2.0)
 shiny            1.7.4   2022-12-15 [1] CRAN (R 4.2.2)
 statnet.common   4.7.0   2022-09-08 [1] CRAN (R 4.2.0)
 stringi          1.7.12  2023-01-11 [1] CRAN (R 4.2.0)
 stringr        * 1.5.0   2022-12-02 [1] CRAN (R 4.2.0)
 tibble         * 3.2.1   2023-03-20 [1] CRAN (R 4.2.0)
 tidyr          * 1.3.0   2023-01-24 [1] CRAN (R 4.2.0)
 tidyselect       1.2.0   2022-10-10 [1] CRAN (R 4.2.0)
 tidyverse      * 1.3.2   2022-07-18 [1] CRAN (R 4.2.0)
 timechange       0.2.0   2023-01-11 [1] CRAN (R 4.2.0)
 tzdb             0.3.0   2022-03-28 [1] CRAN (R 4.2.0)
 urlchecker       1.0.1   2021-11-30 [1] CRAN (R 4.2.0)
 usethis        * 2.1.6   2022-05-25 [1] CRAN (R 4.2.0)
 utf8             1.2.3   2023-01-31 [1] CRAN (R 4.2.0)
 vctrs            0.6.3   2023-06-14 [1] CRAN (R 4.2.0)
 waydown        * 1.1.0   2021-03-17 [1] CRAN (R 4.2.0)
 withr            2.5.0   2022-03-03 [1] CRAN (R 4.2.0)
 xfun             0.40    2023-08-09 [1] CRAN (R 4.2.0)
 xml2             1.3.5   2023-07-06 [1] CRAN (R 4.2.0)
 xtable           1.8-4   2019-04-21 [1] CRAN (R 4.2.0)

 [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@juanrocha