add seminar embed; update site

nicholasjclark · Jan 16, 2024 · d4e89f2 · d4e89f2
1 parent 524c348
commit d4e89f2
Show file tree

Hide file tree

Showing 43 changed files with 197 additions and 43 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -220,11 +220,13 @@ importFrom(stats,predict)
 importFrom(stats,printCoefmat)
 importFrom(stats,qbinom)
 importFrom(stats,qcauchy)
+importFrom(stats,qlogis)
 importFrom(stats,qnorm)
 importFrom(stats,qqline)
 importFrom(stats,qqnorm)
 importFrom(stats,quantile)
 importFrom(stats,rbeta)
+importFrom(stats,rbinom)
 importFrom(stats,reformulate)
 importFrom(stats,rgamma)
 importFrom(stats,rlnorm)

diff --git a/R/families.R b/R/families.R
@@ -26,7 +26,7 @@
 #'   \item \code{nmix} for count data with imperfect detection modeled via a
 #'   State-Space N-Mixture model. The latent states are Poisson (with log link), capturing the 'true' latent
 #'   abundance, while the observation process is Binomial to account for imperfect detection. The
-#'   observation formula in these models is used to set up a linear predictor for the detection
+#'   observation \code{formula} in these models is used to set up a linear predictor for the detection
 #'   probability (with logit link). See the example below for a more detailed worked explanation
 #'   of the `nmix()` family
 #'   }
@@ -174,7 +174,7 @@ student_t = function(link = 'identity'){
 #' det_plot <- plot(conditional_effects(mod,
 #'                                      type = 'detection',
 #'                                      effects = 'rainfall'),
-#'                  plot = FALSE
+#'                  plot = FALSE)
 #' det_plot[[1]] +
 #'   ylab('Pr(detection)')
 #'

diff --git a/R/mvgam.R b/R/mvgam.R
@@ -35,7 +35,7 @@
 #'@param trend_knots As for `knots` above, this is an optional \code{list} of knot values for smooth
 #'functions within the `trend_formula`
 #'@param data A \code{dataframe} or \code{list} containing the model response variable and covariates
-#'required by the GAM \code{formula}. Should include columns:
+#'required by the GAM \code{formula} and optional \code{trend_formula}. Should include columns:
 #'`series` (a \code{factor} index of the series IDs;the number of levels should be identical
 #'to the number of unique series labels (i.e. `n_series = length(levels(data$series))`))
 #'`time` (\code{numeric} or \code{integer} index of the time point for each observation).

diff --git a/README.Rmd b/README.Rmd
@@ -33,7 +33,7 @@ A series of [vignettes cover data formatting, forecasting and several extended c
 
 ## Installation
 Install from `GitHub` using:
-`devtools::install_github("nicholasjclark/mvgam")`. Note that to condition models with MCMC sampling, either `JAGS` (along with packages `rjags` and `runjags`) or `Stan` must be installed (along with either `rstan` and/or `cmdstanr`). Please refer to installation links for `JAGS` [here](https://sourceforge.net/projects/mcmc-jags/files/){target="_blank"}, for `Stan` with `rstan` [here](https://mc-stan.org/users/interfaces/rstan){target="_blank"}, or for `Stan` with `cmdstandr` [here](https://mc-stan.org/cmdstanr/){target="_blank"}. You will need a fairly recent version of `Stan` to ensure all syntax is recognized. If you see warnings such as `variable "array" does not exist`, this is usually a sign that you need to update `Stan`. We highly recommend you use `Cmdstan` through the `cmdstanr` interface. This is because `Cmdstan` is easier to install, is more up to date with new features, and uses less memory than `Rstan`. See [this documentation from the `Cmdstan` team for more information](http://mc-stan.org/cmdstanr/articles/cmdstanr.html#comparison-with-rstan){target="_blank"}. 
+`devtools::install_github("nicholasjclark/mvgam")`. Note that to condition models on observed data, either `JAGS` (along with packages `rjags` and `runjags`) or `Stan` must be installed (along with either `rstan` and/or `cmdstanr`). Please refer to installation links for `JAGS` [here](https://sourceforge.net/projects/mcmc-jags/files/){target="_blank"}, for `Stan` with `rstan` [here](https://mc-stan.org/users/interfaces/rstan){target="_blank"}, or for `Stan` with `cmdstandr` [here](https://mc-stan.org/cmdstanr/){target="_blank"}. You will need a fairly recent version of `Stan` to ensure all syntax is recognized. If you see warnings such as `variable "array" does not exist`, this is usually a sign that you need to update `Stan`. We highly recommend you use `Cmdstan` through the `cmdstanr` interface. This is because `Cmdstan` is easier to install, is more up to date with new features, and uses less memory than `Rstan`. See [this documentation from the `Cmdstan` team for more information](http://mc-stan.org/cmdstanr/articles/cmdstanr.html#comparison-with-rstan){target="_blank"}. 
 
 ## Citing mvgam and related software
 When using any software please make sure to appropriately acknowledge the hard work that developers and maintainers put into making these packages available. Citations are currently the best way to formally acknowledge this work, so we highly encourage you to cite any packages that you rely on for your research.

diff --git a/README.md b/README.md
@@ -38,7 +38,7 @@ been compiled:
 
 Install from `GitHub` using:
 `devtools::install_github("nicholasjclark/mvgam")`. Note that to
-condition models with MCMC sampling, either `JAGS` (along with packages
+condition models on observed data, either `JAGS` (along with packages
 `rjags` and `runjags`) or `Stan` must be installed (along with either
 `rstan` and/or `cmdstanr`). Please refer to installation links for
 `JAGS` <a href="https://sourceforge.net/projects/mcmc-jags/files/"
@@ -317,29 +317,29 @@ summary(lynx_mvgam)
 #> 
 #> 
 #> GAM coefficient (beta) estimates:
-#>               2.5%    50% 97.5% Rhat n_eff
-#> (Intercept)   6.10  6.600 7.000 1.00   355
-#> s(season).1  -0.59  0.046 0.710 1.00  1022
-#> s(season).2  -0.26  0.770 1.800 1.00   443
-#> s(season).3  -0.12  1.100 2.400 1.00   399
-#> s(season).4  -0.51  0.410 1.300 1.00   890
-#> s(season).5  -1.20 -0.130 0.950 1.01   503
-#> s(season).6  -1.00 -0.011 1.100 1.01   699
-#> s(season).7  -0.71  0.340 1.400 1.00   711
-#> s(season).8  -0.92  0.180 1.800 1.00   371
-#> s(season).9  -1.10 -0.290 0.710 1.00   476
-#> s(season).10 -1.30 -0.660 0.027 1.00   595
+#>                2.5%     50%  97.5% Rhat n_eff
+#> (Intercept)   6.200  6.6000  7.000    1  1020
+#> s(season).1  -0.590  0.0500  0.700    1  1094
+#> s(season).2  -0.240  0.8100  1.800    1   417
+#> s(season).3  -0.057  1.2000  2.500    1   365
+#> s(season).4  -0.510  0.4200  1.400    1   951
+#> s(season).5  -1.200 -0.1400  1.000    1   538
+#> s(season).6  -1.100  0.0074  1.100    1   632
+#> s(season).7  -0.790  0.3800  1.400    1   847
+#> s(season).8  -1.000  0.2900  1.800    1   413
+#> s(season).9  -1.100 -0.2700  0.670    1   574
+#> s(season).10 -1.400 -0.6900 -0.025    1   641
 #> 
 #> Approximate significance of GAM observation smooths:
-#>            edf Chi.sq p-value
-#> s(season) 5.08  17751    0.25
+#>           edf Chi.sq p-value
+#> s(season)   5  17851    0.28
 #> 
 #> Latent trend AR parameter estimates:
 #>           2.5%   50% 97.5% Rhat n_eff
-#> ar1[1]    0.74  1.10 1.400    1   635
-#> ar2[1]   -0.84 -0.40 0.062    1  1514
-#> ar3[1]   -0.47 -0.13 0.290    1   540
-#> sigma[1]  0.40  0.50 0.640    1  1154
+#> ar1[1]    0.74  1.10 1.400    1   695
+#> ar2[1]   -0.82 -0.41 0.045    1  1630
+#> ar3[1]   -0.47 -0.12 0.280    1   453
+#> sigma[1]  0.40  0.50 0.630    1  1101
 #> 
 #> Stan MCMC diagnostics:
 #> n_eff / iter looks reasonable for all parameters
@@ -348,7 +348,7 @@ summary(lynx_mvgam)
 #> 0 of 2000 iterations saturated the maximum tree depth of 12 (0%)
 #> E-FMI indicated no pathological behavior
 #> 
-#> Samples were drawn using NUTS(diag_e) at Mon Jan 15 8:57:57 AM 2024.
+#> Samples were drawn using NUTS(diag_e) at Tue Jan 16 8:42:08 PM 2024.
 #> For each parameter, n_eff is a crude measure of effective sample size,
 #> and Rhat is the potential scale reduction factor on split MCMC chains
 #> (at convergence, Rhat = 1)
@@ -470,7 +470,7 @@ plot(lynx_mvgam, type = 'forecast', newdata = lynx_test)
 <img src="man/figures/README-unnamed-chunk-21-1.png" width="60%" style="display: block; margin: auto;" />
 
     #> Out of sample CRPS:
-    #> [1] 2892.767
+    #> [1] 2856.97
 
 And the estimated latent trend component, again using the more flexible
 `plot_mvgam_...()` option to show first derivatives of the estimated
@@ -626,7 +626,7 @@ summary(mod, include_betas = FALSE)
 #> 0 of 2000 iterations saturated the maximum tree depth of 12 (0%)
 #> E-FMI indicated no pathological behavior
 #> 
-#> Samples were drawn using NUTS(diag_e) at Mon Jan 15 8:59:01 AM 2024.
+#> Samples were drawn using NUTS(diag_e) at Tue Jan 16 8:44:20 PM 2024.
 #> For each parameter, n_eff is a crude measure of effective sample size,
 #> and Rhat is the potential scale reduction factor on split MCMC chains
 #> (at convergence, Rhat = 1)

diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/reference/figures/README-unnamed-chunk-13-1.png b/docs/reference/figures/README-unnamed-chunk-13-1.png
diff --git a/docs/reference/figures/README-unnamed-chunk-14-1.png b/docs/reference/figures/README-unnamed-chunk-14-1.png
diff --git a/docs/reference/figures/README-unnamed-chunk-15-1.png b/docs/reference/figures/README-unnamed-chunk-15-1.png
diff --git a/docs/reference/figures/README-unnamed-chunk-16-1.png b/docs/reference/figures/README-unnamed-chunk-16-1.png
diff --git a/docs/reference/figures/README-unnamed-chunk-17-1.png b/docs/reference/figures/README-unnamed-chunk-17-1.png
diff --git a/docs/reference/figures/README-unnamed-chunk-18-1.png b/docs/reference/figures/README-unnamed-chunk-18-1.png
diff --git a/docs/reference/figures/README-unnamed-chunk-19-1.png b/docs/reference/figures/README-unnamed-chunk-19-1.png
diff --git a/docs/reference/figures/README-unnamed-chunk-20-1.png b/docs/reference/figures/README-unnamed-chunk-20-1.png
diff --git a/docs/reference/figures/README-unnamed-chunk-21-1.png b/docs/reference/figures/README-unnamed-chunk-21-1.png
diff --git a/docs/reference/figures/README-unnamed-chunk-22-1.png b/docs/reference/figures/README-unnamed-chunk-22-1.png
diff --git a/docs/reference/figures/README-unnamed-chunk-23-1.png b/docs/reference/figures/README-unnamed-chunk-23-1.png
diff --git a/docs/reference/figures/README-unnamed-chunk-24-1.png b/docs/reference/figures/README-unnamed-chunk-24-1.png
diff --git a/docs/reference/figures/README-unnamed-chunk-8-1.png b/docs/reference/figures/README-unnamed-chunk-8-1.png
diff --git a/docs/reference/get_mvgam_priors.html b/docs/reference/get_mvgam_priors.html
diff --git a/docs/reference/mvgam.html b/docs/reference/mvgam.html