** modEvA** is an R package for

The ** modEvA** package works within the free and open-source R statistical software, so you first need to

`monospaced`

font are the commands that you need to type (or copy and paste) into the R console (and then press the `'`

, `"`

) **Install modEvA** by pasting the command below in the R console (when connected to the internet):

`install.packages("modEvA", repos = "http://R-Forge.R-project.org")`

This should work if you have the **latest version of R**; otherwise, it may either fail (producing a message like “*package ‘modEvA’ is not available for your R version*”) or show a warning and install an older version of *modEvA*. To **check the version that you have actually installed**, type `citation(package="modEvA")`

. To install the latest version of the package, you can either upgrade R *or* download the compressed *modEvA* package **source files** to your disk – .*zip* for Windows or .*tar.gz* for Linux and Mac, available at the package development page or at this Dropbox folder and then install the package locally, e.g. with R menu “*Packages - Install packages from local zip files*” (Windows), or “*Packages & Data - Package installer, Packages repository - Local source package*” (Mac), or “*Tools - Install packages - Install from: Package Archive File*” (RStudio).

You only need to install the package once (unless a new version becomes available), but you need to **load it every time you open a new R session** in which you intend to use *modEvA* (no need for an internet connection anymore), by pasting the following command in R:

`library(modEvA)`

Load the *rotif.mods* sample dataset that comes with the *modEvA* package, to use as an example:

`data(rotif.mods)`

You can **get more information on this dataset** (the following command should open an R Documentation window):

`help(rotif.mods)`

You can see that *rotif.mods* is a list containing two elements: a list of *models* and a dataframe with their *predictions*. Let’s leave the predictions alone for now, and work on the model objects. Let’s start by checking out their names:

`names(rotif.mods$models)`

```
## [1] "Abrigh" "Afissa" "Apriod" "Bangul" "Bcalyc" "Bplica" "Bquadr"
## [8] "Burceo" "Cgibba" "Edilat" "Flongi" "Kcochl" "Kquadr" "Ktropi"
## [15] "Lbulla" "Lclost" "Lhamat" "Lluna" "Llunar" "Lovali" "Lpatel"
## [22] "Lquadr" "Mventr" "Ppatul" "Pquadr" "Pvulga" "Specti" "Tpatin"
## [29] "Tsimil" "Ttetra"
```

These names correspond to species codes, and each object in this list is a GLM of the presence-absence of the corresponding species. Now let’s **assign the first model to an individual object**, and use it **to try out modEvA functions**. The following alternate commands should both create a model object named “mod” from the 1st model in the

```
mod <- rotif.mods$models[[1]]
mod <- rotif.mods$models[["Abrigh"]]
```

In most *modEvA* functions, instead of a model object, you can provide observed and predicted values that you’ve obtained elswehere. Let’s extract such values from this model, to be able to use them in examples as well:

`mydata <- data.frame(observed = mod$y, predicted = mod$fitted.values)`

Let’s now try *modEvA* functions on this model’s predictions (or you can use any other GLM object or observed-predicted values that you may have). Let’s start with function ** plotGLM**, which shows

`plotGLM(model = mod, xlab = "Logit (Y)", ylab = "Predicted probability", main = "Model plot")`

**Instead of the model object**, you can provide your

`plotGLM(obs = mydata[ , "observed"], pred = mydata[ , "predicted"], xlab = "Logit (Y)", ylab = "Predicted probability", main = "Model plot")`

Let’s now **calculate the area under the ROC curve (AUC)** for this model. The *AUC* function produces the plot displayed below and also some text results, which will appear in your R console but will not be shown here. Again, as in most *modEvA* functions, you can provide *obs = mydata[ , “observed”], pred = mydata[ , “predicted”]* instead of *model = mod*:

`AUC(model = mod)`

Now **calculate some threshold-based evaluation measures** for this model, using the species’ prevalence (proportion of presences) as the threshold value above which to consider that the model predicts the species to be present. Only the plot is shown here, but additional text results should appear in your R console as well:

```
par(mar = c(5.6, 4.1, 2, 2.1)) # changes figure margins
threshMeasures(model = mod, thresh = "preval", ylim = c(0, 1), main = "Threshold measures")
```

Note that the *thresh*old value used above was *preval*ence, which is adequate when your predicted values are of probability. If, however, you are **evaluating favourability predictions** (see e.g. this other tutorial on favourability modelling),

`help(threshMeasures)`

). Let’s `optiThresh(model = mod, pch = 20)`

You can also calculate the **optimal threshold balancing two complementary evaluation measures**:

`optiPair(model = mod, measures = c("Sensitivity", "Specificity"), main = "Optimal balance")`

You can try the command above with other pairs of related *measures*, such as `c("Omission", "Commission")`

, `c("PPI", "PAI")`

, etc..

Let’s now assess the **proportion of variation that the model accounts for**. For GLMs there isn’t a single consensual measure for this; *modEvA* can calculate the **explained deviance** (*D-squared*), optionally adjusted for the number of observations and parameters; and some **pseudo R-squared** values (see `help(Dsquared)`

and `help(RsqGLM)`

for further info):

`Dsquared(model = mod)`

`## [1] 0.1114199`

`Dsquared(model = mod, adjust = TRUE)`

`## [1] 0.09264705`

`RsqGLM(model = mod)`

```
## $CoxSnell
## [1] 0.1380008
##
## $Nagelkerke
## [1] 0.187434
##
## $McFadden
## [1] 0.1114199
##
## $Tjur
## [1] 0.1365661
##
## $sqPearson
## [1] 0.134168
```

You can **visualise these R-squared measures** with the *barplot* R function:

`barplot(unlist(RsqGLM(model = mod)), ylim = c(0, 1), las = 2, main = "R-squared values")`

We can also take a look at some model calibration measures, such as **Miller’s calibration statistics** and the **Hosmer-Lemeshow goodness-of-fit**. Note, however, that the former is not useful for evaluating a model on the same data used for building it (the results will always look good); and that the latter can depend strongly on the *bin.method* used for grouping the values. See `help(MillerCalib)`

and `help(HLfit)`

to find out how these measures are calculated and how their results can be interpreted.

`MillerCalib(model = mod)`

```
## $intercept
## [1] 1.799596e-13
##
## $slope
## [1] 1
```

`HLfit(model = mod, bin.method = "quantiles", main = "Hosmer-Lemeshow GOF, quantiles")`

```
## $bins.table
## BinCenter NBin BinObs BinPred BinObsCIlower BinObsCIupper
## 1 0.1194811 29 0.03448276 0.1016246 0.0008726469 0.1776443
## 2 0.1819756 29 0.31034483 0.1789304 0.1528459396 0.5083234
## 3 0.2482370 29 0.17241379 0.2445406 0.0584560830 0.3577476
## 4 0.3084812 29 0.31034483 0.3091572 0.1528459396 0.5083234
## 5 0.3618102 29 0.44827586 0.3607436 0.2644553037 0.6430613
## 6 0.3927488 29 0.41379310 0.3942488 0.2352402098 0.6106372
## 7 0.4383741 29 0.37931034 0.4372018 0.2068686995 0.5773954
## 8 0.5130304 29 0.48275862 0.5063462 0.2944855830 0.6746850
## 9 0.5960986 29 0.58620690 0.5910230 0.3893627914 0.7647598
## 10 0.6933976 29 0.68965517 0.7070658 0.4916766462 0.8471541
## 11 0.9044237 1 1.00000000 0.9044237 0.0250000000 1.0000000
##
## $chi.sq
## [1] 7.278077
##
## $DF
## [1] 9
##
## $p.value
## [1] 0.6081922
```

`HLfit(model = mod, bin.method = "n.bins", main = "Hosmer-Lemeshow GOF, N bins")`

```
## $bins.table
## BinCenter NBin BinObs BinPred BinObsCIlower
## (0.026,0.114] 0.05859488 13 0.0000000 0.06339589 0.00000000
## (0.114,0.202] 0.15729121 40 0.2000000 0.15678701 0.09052241
## (0.202,0.29] 0.24840042 40 0.2000000 0.24634002 0.09052241
## (0.29,0.378] 0.34035838 51 0.4117647 0.33974064 0.27584296
## (0.378,0.466] 0.41206526 59 0.3898305 0.41510104 0.26549147
## (0.466,0.554] 0.51322862 30 0.4666667 0.50772771 0.28341808
## (0.554,0.642] 0.60663508 34 0.5882353 0.60041852 0.40696943
## (0.642,0.729] 0.66899210 12 0.6666667 0.67465548 0.34887551
## (0.729,0.817] 0.78101033 9 0.7777778 0.77077823 0.39990643
## (0.817,0.905] 0.83199370 3 1.0000000 0.85136910 0.29240177
## BinObsCIupper
## (0.026,0.114] 0.2470526
## (0.114,0.202] 0.3564780
## (0.202,0.29] 0.3564780
## (0.29,0.378] 0.5583072
## (0.378,0.466] 0.5256215
## (0.466,0.554] 0.6567448
## (0.554,0.642] 0.7535293
## (0.642,0.729] 0.9007539
## (0.729,0.817] 0.9718550
## (0.817,0.905] 1.0000000
##
## $chi.sq
## [1] 3.995296
##
## $DF
## [1] 8
##
## $p.value
## [1] 0.8575476
```

You can calulate a set of **evaluation measures for several models simultaneously**, if you have them in a list like *rotif.mods$models* (results not shown here):

```
model_eval <- multModEv(models = rotif.mods$models, thresh = "preval", bin.method = "quantiles")
model_eval
```

With the *multModEv* function, if you want to use observed and predicted values rather than a list of model objects, get all your values in a table and call them by their column index numbers – e.g., if your observed data are in columns 2 to 8 and your predicted data are in columns 9 to 15 (note that species must be **in the same order** on both *observed* and *predicted* columns!), you can use this command:

`multModEv(obs.data = mydata[ , 2:8], pred.data = mydata[ , 9:15], thresh = "preval")`

If you’ve successfully executed any of the two commands above, you can save these results to a file on your disk. The following command will save a comma-separated values (CSV) file in your working directory (type `getwd()`

to find out where it is):

`write.csv(model_eval, file = "model_eval.csv", row.names = FALSE)`

Some other potentially useful *modEvA* functions are (still) not covered in this tutorial, but you can find out about them as well:

```
help(evenness)
help(prevalence)
help(OA)
help(MESS)
help(varPart)
```

You can find out additional options and further info on any function with *help(function.name)* (e.g., `help(multModEv)`

).

That’s it! You can e-mail me with any suggestions or concerns, but first remember to check for updates to the package or this tutorial at http://modEvA.r-forge.r-project.org. This tutorial was built with *RStudio* + *rmarkdown* + *knitr*. Thanks!