Merge pull request #22 from MindTheGap-ERC/dev

Dev
MindTheGap-ERC · Oct 14, 2024 · 286d6bc · 286d6bc
2 parents 1696240 + 5415ccf
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: StratPal
 Title: Stratigraphic Paleobiology Modeling Pipelines
-Version: 0.2.0.9000
+Version: 0.2.0.9001
 Authors@R: 
     person("Niklas", "Hohmann", , "N.H.Hohmann@uu.nl", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1559-1838"))

diff --git a/R/apply_niche.R b/R/apply_niche.R
@@ -81,7 +81,7 @@ apply_niche.pre_paleoTS = function(x, niche_def, gc){
   thin_vals = change_in_niche(x$t)
   for (i in seq_along(thin_vals)){
     r = prob_remove(x$vals[[i]], prob = thin_vals[i])
-    x$vals[[i]] = x$vals[[i]][as.logical(r)]
+    x$vals[[i]] = r
   }
   return(x)
 }
diff --git a/R/apply_taphonomy.R b/R/apply_taphonomy.R
@@ -50,7 +50,7 @@ apply_taphonomy.pre_paleoTS = function(x, pres_potential, ctc){
   }
   for (i in seq_along(thin_vals)){
     r = prob_remove(x$vals[[i]], prob = thin_vals[i])
-    x$vals[[i]] = x$vals[[i]][as.logical(r)]
+    x$vals[[i]] = r
   }
   return(x)
 }
diff --git a/R/ornstein_uhlenbeck_sl.R b/R/ornstein_uhlenbeck_sl.R
@@ -9,7 +9,7 @@ ornstein_uhlenbeck_sl = function(t, mu = 0, theta = 1, sigma = 1, y0 = 0, intrap
   #' @param theta number, mean reversion speed
   #' @param sigma positive number, strength of randomness
   #' @param y0 number, initial value (value of process at the first entry of t)
-  #' @param intrapop_var intrapopulation variance, determines how many specimens from the same population vary
+  #' @param intrapop_var intrapopulation variance, determines how much specimens from the same population vary
   #' @param n_per_sample integer, number of specimens sampled per population/sampling locality
   #'
   #' @description

diff --git a/R/random_walk_sl.R b/R/random_walk_sl.R
@@ -7,7 +7,7 @@ random_walk_sl = function(t, sigma = 1, mu = 0, y0 = 0, intrapop_var = 1, n_per_
   #' @param sigma positive number, variance parameter
   #' @param mu number, directionality parameter
   #' @param y0 number, starting value (value of the random walk at the first entry of `t`)
-  #' @param intrapop_var intrapopulation variance, determines how many specimens from the same population vary
+  #' @param intrapop_var intrapopulation variance, determines how much specimens from the same population vary
   #' @param n_per_sample integer, number of specimens sampled per population/sampling locality
   #'
   #' @description

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -12,6 +12,7 @@ Jere
 Joël
 Koelewijn
 Lande
+Lidgard
 Lipps
 MFSTFR
 Maruyama
@@ -34,7 +35,6 @@ Taphonomy
 Uhlenbeck
 Zenodo
 al
-approxfun
 artefactual
 automata
 cff
@@ -54,6 +54,7 @@ heterodistant
 hohmann
 https
 interpopulation
+intrapopulation
 io
 ith
 kyr
@@ -65,6 +66,7 @@ ornstein
 paleoTS
 paleobiology
 paleontological
+pnas
 pre
 sedimentological
 siliciclastic
@@ -76,5 +78,6 @@ taphonomic
 taphonomy
 timelist
 uhlenbeck
+un
 uu
 vectorized
diff --git a/man/ornstein_uhlenbeck_sl.Rd b/man/ornstein_uhlenbeck_sl.Rd
diff --git a/man/random_walk_sl.Rd b/man/random_walk_sl.Rd
diff --git a/vignettes/event_data.Rmd b/vignettes/event_data.Rmd
@@ -327,7 +327,7 @@ for details on how to expand on the modeling pipelines described here, or explor
 
 -   Hohmann, Niklas; Koelewijn, Joël R.; Burgess, Peter; Jarochowska, Emilia. 2024. "Identification of the mode of evolution in incomplete carbonate successions." BMC Ecology and Evolution 24, 113. <https://doi.org/10.1186/s12862-024-02287-2>.
 
--   Holland, Steven M. and Patzkowsky, Mark E. 1999. "Models for simulating the fossil record." Geology. [https://doi.org/10.1130/0091-7613(1999)027%3C0491:MFSTFR%3E2.3.CO;2](https://doi.org/10.1130/0091-7613(1999)027%3C0491:MFSTFR%3E2.3.CO;2){.uri}
+-   Holland, Steven M. and Patzkowsky, Mark E. 1999. "Models for simulating the fossil record." Geology. <https://doi.org/10.1130/0091-7613(1999)027%3C0491:MFSTFR%3E2.3.CO;2>
 
 -   Holland, Steven M. and Patzkowsky, Mark E. 2015. "The stratigraphy of mass extinction." Palaeontology. <https://doi.org/10.1111/pala.12188>.
 

diff --git a/vignettes/paleoTS_functionality.Rmd b/vignettes/paleoTS_functionality.Rmd
@@ -39,7 +39,7 @@ The `paleoTS` package defines its own `paleoTS` format to store time series. It
 
 Functions to model trait evolution on specimen level have the suffix `_sl`, standing for "specimen level". Internally, they are of S3 class `pre_paleoTS`. In addition to the options provided to simulate mean trait values, you can simulate strict stasis using `strict_stasis_sl`. All functions have the same parametrization as the as the other functions for simulating trait evolution, which simulate mean trait evolution. In addition, they take two additional parameters: `intrapop_var` for the variance of the population around the mean trait value, and `n_per_sample` for the number of specimens per sampling location.
 
-`pre_paleoTS` results can be converted to the `paleoTS` format using the function `reduce_to_paleoTS`. After this you can plot them with the standard plotting procedure from paleoTS using `plot` (resp, `plot.paleoTS`). Note that you can not plot `pre_paloeTS` objects directly, only after conversion to `paleoTS`.
+`pre_paleoTS` results can be converted to the `paleoTS` format using the function `reduce_to_paleoTS`. After this you can plot them with the standard plotting procedure from paleoTS using `plot` (resp, `plot.paleoTS`). Note that you can not plot `pre_paloeTS` objects directly, only after conversion to `paleoTS` format.
 
 ```{r fig.alt="plot of strict stasis"}
 library(StratPal)
@@ -62,7 +62,7 @@ adm = tp_to_adm(t = scenarioA$t_myr,               # define age-depth model
                 T_unit = "Myr")    
 set.seed(42)                                      # set seed for reproducibility
 seq(min_time(adm), max_time(adm), by = 0.01) |>   # sample every 0.01 Myr
-  random_walk_sl(n_per_sample = 10) |>            # simulate random walk on specimen level
+  random_walk_sl(n_per_sample = 5) |>            # simulate random walk on specimen level
   time_to_strat(adm) |>                           # transform into stratigraphic domain
   reduce_to_paleoTS() |>                          # transform into paleoTS format
   plot()                                          # plot
@@ -73,7 +73,7 @@ Of course you can also immediately add functions from `paleoTS` to the pipeline,
 ```{r}
 set.seed(42)                                      # set seed for reproducibility
 seq(min_time(adm), max_time(adm), by = 0.01) |>   # sample every 0.01 Myr
-  random_walk_sl(n_per_sample = 10) |>            # simulate random walk on specimen level
+  random_walk_sl(n_per_sample = 5) |>            # simulate random walk on specimen level
   time_to_strat(adm) |>                           # transform into stratigraphic domain
   reduce_to_paleoTS() |>                          # transform into paleoTS format
   fit3models()                                    # fit 3 models to time series