Basic Usage

Introduction

This vignette describes the simple workflow of fitting model to first records data. We’ll go over two examples: fitting the Solow & Costello (2004), and fitting the modified sampling-proxy model.

Solow and Costello (2004) model:

For the most basic demonstration, let’s look at the data provided in Solow and Costello (2004) which describes discoveries of introduced species in the San Francisco estuary (California, USA) between the years 1850–1995 (Cohen, 1995). The data in this case are simply first records of aliens:

data("sfestuary")
print(sfestuary)
#>   [1] 0 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 2 0 1 5 1 0 0 1 1 0 0 0 0 0 0 0 0
#>  [38] 0 0 1 1 0 2 2 2 1 1 1 0 0 2 0 0 3 0 1 1 2 0 0 0 1 1 0 0 0 0 0 0 2 0 0 0 0
#>  [75] 0 0 1 0 1 1 1 1 0 0 1 1 2 4 0 0 0 0 2 0 4 2 1 1 1 0 3 0 1 1 4 0 1 1 0 0 1
#> [112] 2 4 0 1 1 0 1 1 1 2 3 4 1 0 3 5 4 5 1 0 4 2 0 1 4 1 1 2 0 1 7 4 0 0

We’ll plot it in a cumulative form, replicating the plot from Solow and Costello (2004):

library(alien)
library(ggplot2)

years <- seq_along(sfestuary) + 1850 # set starting year for the figure

ggplot()+
  aes(x = years, y = cumsum(sfestuary))+
  geom_line() + 
  coord_cartesian(ylim = c(0,150))+
  scale_x_continuous(breaks = seq(1860, 1980, 20)) + 
  scale_y_continuous(breaks = seq(0, 150, 50)) + 
  ylab("Cumulative discoveries") + theme(axis.title.x = element_blank())

model <- snc(y = sfestuary, control = list(maxit = 1e4))
#> ! no data supplied, using time as independent variable

names(model)
#> [1] "records"        "convergence"    "log-likelihood" "coefficients"  
#> [5] "type"           "fitted.values"  "predict"

model$records
#>   [1] 0 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 2 0 1 5 1 0 0 1 1 0 0 0 0 0 0 0 0
#>  [38] 0 0 1 1 0 2 2 2 1 1 1 0 0 2 0 0 3 0 1 1 2 0 0 0 1 1 0 0 0 0 0 0 2 0 0 0 0
#>  [75] 0 0 1 0 1 1 1 1 0 0 1 1 2 4 0 0 0 0 2 0 4 2 1 1 1 0 3 0 1 1 4 0 1 1 0 0 1
#> [112] 2 4 0 1 1 0 1 1 1 2 3 4 1 0 3 5 4 5 1 0 4 2 0 1 4 1 1 2 0 1 7 4 0 0

model$convergence
#> [1] 0

model$`log-likelihood`
#> [1] 118.7776

model$coefficients
#>             Estimate      Std.Err
#> beta0    -1.12739745     1.835403
#> beta1     0.01401579     1.835403
#> gamma0 -185.89484996 15630.676343
#> gamma1  -79.80040427  7235.922667
#> gamma2   76.23985293  6339.859143

head(model$predict, 4) 
#>        mean     lower_95    higher_95
#> 1 0.3284464 2.464968e-04 4.376407e+02
#> 2 0.3330822 6.848124e-06 1.620061e+04
#> 3 0.3377835 1.902532e-07 5.997150e+05
#> 4 0.3425512 5.285577e-09 2.220028e+07

plot_snc(model, cumulative = T) +
  coord_cartesian(ylim = c(0,150))+
  scale_y_continuous(breaks = seq(0, 150, 50)) + 
  ylab("Cumulative discoveries") + 
  xlab("Years since first record in data")

Constant detection model

We can use the function to specify model parameters for either the introduction or detection. Such changes are also possible without supplementation of external data, by constraining either or both of the introduction and detection processes. Next, we’ll set detection to be constant with time:

constant_detection <- snc(sfestuary, pi = ~ 1, growth = FALSE)
#> ! No formula defined for mu, using time as independent variable

Here, the model constrain the \({\gamma_1}\) to 0 by containing pi to an intercept-only model, and constrain \({\gamma_2}\) to 0 by setting growth to FALSE.

We can examine the likelihoods of the new model:

constant_detection$`log-likelihood`
#> [1] 122.5792

Constant introduction model

We can also constrain the introduction rate, as we did with the detection probability:]

constant_introduction <- snc(sfestuary, mu = ~1)
#> ! No formula defined for pi, using time as independent variable

Checking the likelihood of this model shows that there is weak statistical support for the introduction to be constant in this example:

constant_introduction$`log-likelihood`
#> [1] 138.9964

Sampling-Proxy Model

Now we’ll look at a more elaborated model, which uses external data to control for changes in sampling intensity (Buba et al, 2024). We’ll demonstrate that using data used in Belmaker et al (2009) which describe discoveries of native and alien species in the Mediterranean Sea between the years 1927–2017 (Golani, 2021). We will the medfish data included in the alien package:

data("medfish")
head(medfish)
#>   year time natives aliens
#> 1 1927    0      52      5
#> 2 1930    3       0      1
#> 3 1931    4      12      0
#> 4 1934    7      18      0
#> 5 1935    8      17      1
#> 6 1937   10       1      1

The data has several columns: 1. year - The year of the observations. 2. time - how much time has passed from the first observation in the data until this point. 3. natives - how many natives were newly described in this year. 4. alien - how many aliens were newly described in this year.

ggplot2::ggplot(medfish)+
  ggplot2::aes(x = year) + 
  ggplot2::geom_point(ggplot2::aes(y = cumsum(natives)), shape = 21, size = 2, fill = "#377EB8") +
  ggplot2::geom_point(ggplot2::aes(y = cumsum(aliens)), shape = 21,  size = 2, fill = "#E41A1C")

Model fitting

Here, for demonstration sake only, we will use the trend in native species discovery as a proxy for the sampling throughout the time series time span. Note that using native discoveries as a proxy for sampling has several limitations as described in Buba et al (2024). We will begin by adding a column to the data where we scale the native species discoveries:

medfish_for_model <- dplyr::mutate(medfish, natives_scaled = scale(natives))

Now, we can use these scaled values in our model:

sampling_proxy_model <- snc(aliens, pi = ~ natives_scaled, data = medfish_for_model, control = list(maxit = 1000))
#> ! No formula defined for mu, using time as independent variable

In case we want to supply variables to \(\mu\), the introduction rate, this can be done by the argument mu of the snc function, in the same manner.

References

Belmaker, J., Brokovich, E., China, V., Golani, D., and Kiflawi, M. 2009. Estimating the rate of biological introductions: Lessepsian fishes in the Mediterranean. Ecology, 90(4), 1134–1141. https://esajournals.onlinelibrary.wiley.com/doi/10.1890/07-1904.1

Buba, Y., Kiflwai, M., McGeoch, M. A., Belmaker, J. (2024) Evaluating models for estimating introduction rates of alien species from discovery records. https://doi.org/10.1111/geb.13859

Cohen, A. N., and J. T. Carlton. 1995. Nonindigenous aquatic species in a United States estuary: a case study of the biological invasions of the San Francisco Bay and Delta. U.S. Fish and Wildlife Service, Washington, D.C., USA. https://repository.library.noaa.gov/view/noaa/40918

Golani, D. 2021. An updated Checklist of the Mediterranean fishes of Israel, with illustrations of recently recorded species and delineation of Lessepsian migrants. Zootaxa, 4956, 1-108. https://www.mapress.com/zt/article/view/zootaxa.4956.1.1

Solow, A. R., & Costello, C. J. (2004). Estimating the rate of species introductions from the discovery record. Ecology, 85(7), 1822–1825. https://doi.org/10.1890/03-3102