Removed non-ASCII characters as per message from CRAN

R/cdb_check_species.R

@@ -20,7 +20,7 @@
 #'
 #' @author Danny Buss <dlb50@@cam.ac.uk>
 #' @author Owen R. Jones <jones@@biology.sdu.dk>
-#' @author Rob Salguero-Gómez <rob.salguero@@zoo.ox.ac.uk>
+#' @author Rob Salguero-Gomez <rob.salguero@@zoo.ox.ac.uk>
 #' @author Patrick Barks <patrick.barks@@gmail.com>
 #'
 #' @family data checking

R/cdb_metadata.R

@@ -7,7 +7,7 @@
 #'
 #' @return Tibble with all metadata columns of \code{cdb}
 #'
-#' @author Gesa Römer <gesa.roemer@@gmail.com>
+#' @author Gesa Romer <gesa.roemer@@gmail.com>
 #'
 #' @family data acquisition
 #'

R/mpm_elementwise_apply.R

@@ -154,4 +154,4 @@ mpm_elementwise_apply <- function(x, fun, na_handling = "stop", ...) {
       matC = summaryC,
       matrixClass = x[[1]]@matrixClass
   )
-}
+}

R/mpm_median.R

@@ -125,4 +125,4 @@ mpm_median <- function(x, na.rm = FALSE) {
       matC = medianC,
       matrixClass = x[[1]]@matrixClass
   )
-}
+}

README.Rmd

@@ -21,7 +21,7 @@ knitr::opts_chunk$set(
 | Project | Main branch | Devel branch  |
 |---------|:------------|:--------------|
 | [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html)  | [![R-CMD-check](https://github.com/jonesor/Rcompadre/actions/workflows/main_check.yaml/badge.svg)](https://github.com/jonesor/Rcompadre/actions/workflows/main_check.yaml) | [![R-CMD-check](https://github.com/jonesor/Rcompadre/actions/workflows/devel_build_check.yaml/badge.svg)](https://github.com/jonesor/Rcompadre/actions/workflows/devel_build_check.yaml) |
-| [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) | [![codecov](https://codecov.io/gh/jonesor/Rcompadre/branch/main/graph/badge.svg?token=S9G2a5K9k9)](https://app.codecov.io/gh/jonesor/Rcompadre)     |     |
+| [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) | [![codecov](https://codecov.io/gh/jonesor/Rcompadre/branch/main/graph/badge.svg?token=S9G2a5K9k9)](https://app.codecov.io/gh/jonesor/Rcompadre)     |     |
 | ![](http://cranlogs.r-pkg.org/badges/grand-total/Rcompadre) |[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/Rcompadre)](https://cran.r-project.org/package=Rcompadre)|
 | ![](http://cranlogs.r-pkg.org/badges/Rcompadre)|  |     |
 
@@ -136,7 +136,7 @@ See the Changelog for more details.
 
 ## Citation
 
-Jones, Owen R., Patrick Barks, Iain M. Stott, Tamora D. James, Sam C. Levin, William K. Petry, Pol Capdevila, et al. 2022. “Rcompadre and Rage -- Two R Packages to Facilitate the Use of the COMPADRE and COMADRE Databases and Calculation of Life History Traits from Matrix Population Models.” _Methods in Ecology and Evolution_. doi: [10.1111/2041-210X.13792](https://doi.org/10.1111/2041-210X.13792).
+Jones, Owen R., Patrick Barks, Iain M. Stott, Tamora D. James, Sam C. Levin, William K. Petry, Pol Capdevila, et al. 2022. "Rcompadre and Rage -- Two R Packages to Facilitate the Use of the COMPADRE and COMADRE Databases and Calculation of Life History Traits from Matrix Population Models." _Methods in Ecology and Evolution_. doi: [10.1111/2041-210X.13792](https://doi.org/10.1111/2041-210X.13792).
 
 ## Contributions
 

README.md

@@ -9,7 +9,7 @@
 | Project                                                                                                                                                                                                | Main branch                                                                                                                                                                | Devel branch                                                                                                                                                                             |
 |--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html)                                                                                | [![R-CMD-check](https://github.com/jonesor/Rcompadre/actions/workflows/main_check.yaml/badge.svg)](https://github.com/jonesor/Rcompadre/actions/workflows/main_check.yaml) | [![R-CMD-check](https://github.com/jonesor/Rcompadre/actions/workflows/devel_build_check.yaml/badge.svg)](https://github.com/jonesor/Rcompadre/actions/workflows/devel_build_check.yaml) |
-| [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) | [![codecov](https://codecov.io/gh/jonesor/Rcompadre/branch/main/graph/badge.svg?token=S9G2a5K9k9)](https://app.codecov.io/gh/jonesor/Rcompadre)                            |                                                                                                                                                                                          |
+| [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) | [![codecov](https://codecov.io/gh/jonesor/Rcompadre/branch/main/graph/badge.svg?token=S9G2a5K9k9)](https://app.codecov.io/gh/jonesor/Rcompadre)                            |                                                                                                                                                                                          |
 | ![](http://cranlogs.r-pkg.org/badges/grand-total/Rcompadre)                                                                                                                                            | [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/Rcompadre)](https://cran.r-project.org/package=Rcompadre)                                                       |                                                                                                                                                                                          |
 | ![](http://cranlogs.r-pkg.org/badges/Rcompadre)                                                                                                                                                        |                                                                                                                                                                            |                                                                                                                                                                                          |
 
@@ -91,18 +91,18 @@ filter(compadre, SpeciesAccepted == "Echinacea angustifolia")
 
 #### Example analysis: calculating population growth rates
 
-First we’ll use the function `cdb_flag()` to add columns to the database
+First we'll use the function `cdb_flag()` to add columns to the database
 flagging potential issues with the projection matrices, such as missing
-values, or matrices that don’t meet assumptions like ergodicity,
+values, or matrices that don't meet assumptions like ergodicity,
 irreducibility, or primitivity.
 
 ``` r
 compadre_flags <- cdb_flag(compadre)
 ```
 
-We’ll only be able to calculate population growth rates from matrices
-that don’t contain missing values, and we only want to use matrices that
-meet the assumption of ergodicity, so we’ll subset the database
+We'll only be able to calculate population growth rates from matrices
+that don't contain missing values, and we only want to use matrices that
+meet the assumption of ergodicity, so we'll subset the database
 accordingly.
 
 ``` r
@@ -112,7 +112,7 @@ compadre_sub <- subset(
 )
 ```
 
-Finally, we’ll use the `eigs()` function from the
+Finally, we'll use the `eigs()` function from the
 [popdemo](https://CRAN.R-project.org/package=popdemo) package to
 calculate the population growth rate for every matrix in `compadre_sub`.
 
@@ -142,10 +142,10 @@ See the Changelog for more details.
 ## Citation
 
 Jones, Owen R., Patrick Barks, Iain M. Stott, Tamora D. James, Sam C.
-Levin, William K. Petry, Pol Capdevila, et al. 2022. “Rcompadre and Rage
-– Two R Packages to Facilitate the Use of the COMPADRE and COMADRE
+Levin, William K. Petry, Pol Capdevila, et al. 2022. "Rcompadre and Rage
+- Two R Packages to Facilitate the Use of the COMPADRE and COMADRE
 Databases and Calculation of Life History Traits from Matrix Population
-Models.” *Methods in Ecology and Evolution*. doi:
+Models." *Methods in Ecology and Evolution*. doi:
 [10.1111/2041-210X.13792](https://doi.org/10.1111/2041-210X.13792).
 
 ## Contributions
@@ -161,7 +161,7 @@ There are numerous ways of contributing.
     issue](https://github.com/jonesor/Rcompadre/issues).
 
 2.  You can copy or fork the repository, make your own code edits and
-    then send us a pull request. [Here’s how to do
+    then send us a pull request. [Here's how to do
     that](https://jarv.is/notes/how-to-pull-request-fork-github/).
 
 3.  You can get to know us and join as a collaborator on the main

cran-comments.md

@@ -42,4 +42,4 @@
 ❯ checking HTML version of manual ... NOTE
   Skipping checking HTML validation: no command 'tidy' found
 
-0 errors ✔ | 0 warnings ✔ | 1 note ✖
+0 errors ✔ | 0 warnings ✔ | 1 note ✖

data-raw/ConvertASCII.R

@@ -0,0 +1,66 @@
+library(Rcompadre)
+
+#COMPADRE  -----
+# Create a copy of Compadre to store the corrected version
+Compadre2 <- Compadre
+
+# Loop through all columns in Compadre
+for (col_name in names(Compadre)) {
+  # Check if the column is of character type (since non-ASCII makes sense only for character columns)
+  if (is.character(Compadre[[col_name]])) {
+    # Find non-ASCII characters in the current column
+    nonASCII <- tools::showNonASCII(Compadre[[col_name]])
+
+    # If there are non-ASCII characters, replace them with ASCII equivalents
+    if (length(nonASCII) > 0) {
+      Compadre2[[col_name]] <- stringi::stri_trans_general(Compadre[[col_name]], "latin-ascii")
+    }
+  }
+}
+
+#COMADRE -----
+# Create a copy of Comadre to store the corrected version
+Comadre2 <- Comadre
+
+# Loop through all columns in Comadre
+for (col_name in names(Comadre)) {
+  # Check if the column is of character type (since non-ASCII makes sense only for character columns)
+  if (is.character(Comadre[[col_name]])) {
+    # Find non-ASCII characters in the current column
+    nonASCII <- tools::showNonASCII(Comadre[[col_name]])
+
+    # If there are non-ASCII characters, replace them with ASCII equivalents
+    if (length(nonASCII) > 0) {
+      Comadre2[[col_name]] <- stringi::stri_trans_general(Comadre[[col_name]], "latin-ascii")
+    }
+  }
+}
+
+#COMPADRE LEGACY -----
+# Create a copy of Comadre to store the corrected version
+CompadreLegacy2 <- CompadreLegacy
+
+# Loop through all columns in Comadre
+for (col_name in names(CompadreLegacy)) {
+  # Check if the column is of character type (since non-ASCII makes sense only for character columns)
+  if (is.character(CompadreLegacy[[col_name]])) {
+    # Find non-ASCII characters in the current column
+    nonASCII <- tools::showNonASCII(CompadreLegacy[[col_name]])
+
+    # If there are non-ASCII characters, replace them with ASCII equivalents
+    if (length(nonASCII) > 0) {
+      CompadreLegacy2[[col_name]] <- stringi::stri_trans_general(CompadreLegacy[[col_name]], "latin-ascii")
+    }
+  }
+}
+
+
+Compadre <- Compadre2
+Comadre <- Comadre2
+CompadreLegacy <- CompadreLegacy2
+
+usethis::use_data(Comadre,
+                  Compadre,
+                  CompadreLegacy,
+                  overwrite = TRUE
+)

vignettes/a01_GettingStarted.Rmd

@@ -197,6 +197,6 @@ hist(lambdaVals, main = "Lambda values")
 
 Caswell, H. (2001). Matrix Population Models: Construction, Analysis, and Interpretation. 2nd edition. Sinauer Associates, Sunderland, MA. ISBN-10: 0878930965
 
-Salguero‐Gómez, R. , Jones, O. R., Archer, C. R., Buckley, Y. M., Che‐Castaldo, J. , Caswell, H. , Hodgson, D. , Scheuerlein, A. , Conde, D. A., Brinks, E. , Buhr, H. , Farack, C. , Gottschalk, F. , Hartmann, A. , Henning, A. , Hoppe, G. , Römer, G. , Runge, J. , Ruoff, T. , Wille, J. , Zeh, S. , Davison, R. , Vieregg, D. , Baudisch, A. , Altwegg, R. , Colchero, F. , Dong, M. , Kroon, H. , Lebreton, J. , Metcalf, C. J., Neel, M. M., Parker, I. M., Takada, T. , Valverde, T. , Vélez‐Espino, L. A., Wardle, G. M., Franco, M. and Vaupel, J. W. (2015), The COMPADRE Plant Matrix Database: an open online repository for plant demography. J Ecol, 103: 202-218. <\doi:10.1111/1365-2745.12334>
+Salguero-Gomez, R. , Jones, O. R., Archer, C. R., Buckley, Y. M., Che-Castaldo, J. , Caswell, H. , Hodgson, D. , Scheuerlein, A. , Conde, D. A., Brinks, E. , Buhr, H. , Farack, C. , Gottschalk, F. , Hartmann, A. , Henning, A. , Hoppe, G. , Romer, G. , Runge, J. , Ruoff, T. , Wille, J. , Zeh, S. , Davison, R. , Vieregg, D. , Baudisch, A. , Altwegg, R. , Colchero, F. , Dong, M. , Kroon, H. , Lebreton, J. , Metcalf, C. J., Neel, M. M., Parker, I. M., Takada, T. , Valverde, T. , Velez-Espino, L. A., Wardle, G. M., Franco, M. and Vaupel, J. W. (2015), The COMPADRE Plant Matrix Database: an open online repository for plant demography. J Ecol, 103: 202-218. <\doi:10.1111/1365-2745.12334>
 
-Salguero‐Gómez, R. , Jones, O. R., Archer, C. R., Bein, C. , Buhr, H. , Farack, C. , Gottschalk, F. , Hartmann, A. , Henning, A. , Hoppe, G. , Römer, G. , Ruoff, T. , Sommer, V. , Wille, J. , Voigt, J. , Zeh, S. , Vieregg, D. , Buckley, Y. M., Che‐Castaldo, J. , Hodgson, D. , Scheuerlein, A. , Caswell, H. and Vaupel, J. W. (2016), COMADRE: a global data base of animal demography. J Anim Ecol, 85: 371-384. <\doi:10.1111/1365-2656.12482>
+Salguero-Gomez, R. , Jones, O. R., Archer, C. R., Bein, C. , Buhr, H. , Farack, C. , Gottschalk, F. , Hartmann, A. , Henning, A. , Hoppe, G. , Romer, G. , Ruoff, T. , Sommer, V. , Wille, J. , Voigt, J. , Zeh, S. , Vieregg, D. , Buckley, Y. M., Che-Castaldo, J. , Hodgson, D. , Scheuerlein, A. , Caswell, H. and Vaupel, J. W. (2016), COMADRE: a global data base of animal demography. J Anim Ecol, 85: 371-384. <\doi:10.1111/1365-2656.12482>

vignettes/a03_VectorisingRcompadre.Rmd

@@ -28,7 +28,7 @@ knitr::opts_chunk$set(dev = "png", dev.args = list(type = "cairo-png"))
 
 COM(P)ADRE databases contain thousands of matrix population models. If we want to derive traits from a large set of these matrices, we'll need to use either loops or vectorisation.
 
-Vectorising means applying a function to each element of a vector. Here vector is defined broadly — it could be a sequence of character strings, a column of a `data.frame`, a `list` of matrices, etc. Vectorised code generally runs faster than loops, and many R users find that vectorised code is easier to write and understand.
+Vectorising means applying a function to each element of a vector. Here vector is defined broadly - it could be a sequence of character strings, a column of a `data.frame`, a `list` of matrices, etc. Vectorised code generally runs faster than loops, and many R users find that vectorised code is easier to write and understand.
 
 ## Preliminaries