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dlizcano · May 21, 2024 · 0df8d52 · 0df8d52
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diff --git a/R/search_mammalcol.R b/R/search_mammalcol.R
@@ -27,6 +27,10 @@
 #' @export
 search_mammalcol <- function(splist, max_distance = 0.2) {
   # Defensive function here, check for user input errors
+  if (missing(splist)) {
+    stop("Argument splist was not defined")
+  }
+
   if (is.factor(splist)) {
     splist <- as.character(splist)
   }

diff --git a/README.Rmd b/README.Rmd
@@ -254,10 +254,14 @@ sp_by_depto <- function(states, type = c("any", "only", "all"), taxa = NULL) {
 [![R-CMD-check](https://github.com/dlizcano/mammalcol/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dlizcano/mammalcol/actions/workflows/R-CMD-check.yaml)
 [![Codecov test coverage](https://codecov.io/gh/dlizcano/mammalcol/branch/main/graph/badge.svg)](https://app.codecov.io/gh/dlizcano/mammalcol?branch=main)
 [![CRAN status](https://www.r-pkg.org/badges/version/mammalcol)](https://CRAN.R-project.org/package=mammalcol)
+[![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
+[![size](https://img.shields.io/github/languages/code-size/dlizcano/mammalcol.svg)](https://github.com/dlizcano/mammalcol)
 <!-- badges: end -->
 
 The goal of mammalcol is to allow easy access to the List of Mammal Species of Colombia.
 
+Researchers can explore Colombia's amazing variety of mammals using the mammalcol R package. This package includes information on 548 mammal species, making Colombia one of the world leaders in mammal diversity. The data comes from the latest "Checklist of the mammals (Mammalia) of Colombia" by [Ramírez-Chaves et al (2021)](https://doi.org/10.47603/mano.v7n2.253). But It's important to remember that how scientists classify mammals keeps changing constantly, so the information in this package has been updated with the checklist [Mamíferos de Colombia](https://doi.org/10.15472/kl1whs), which is published and updated regularly by the Colombian Mammal Society. 
+
 ## Installation
 
 You can install the development version of mammalcol from [GitHub](https://github.com/dlizcano/mammalcol) with:

diff --git a/README.md b/README.md
@@ -10,11 +10,24 @@
 coverage](https://codecov.io/gh/dlizcano/mammalcol/branch/main/graph/badge.svg)](https://app.codecov.io/gh/dlizcano/mammalcol?branch=main)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/mammalcol)](https://CRAN.R-project.org/package=mammalcol)
+[![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
+[![size](https://img.shields.io/github/languages/code-size/dlizcano/mammalcol.svg)](https://github.com/dlizcano/mammalcol)
 <!-- badges: end -->
 
 The goal of mammalcol is to allow easy access to the List of Mammal
 Species of Colombia.
 
+Researchers can explore Colombia’s amazing variety of mammals using the
+mammalcol R package. This package includes information on 548 mammal
+species, making Colombia one of the world leaders in mammal diversity.
+The data comes from the latest “Checklist of the mammals (Mammalia) of
+Colombia” by [Ramírez-Chaves et al
+(2021)](https://doi.org/10.47603/mano.v7n2.253). But It’s important to
+remember that how scientists classify mammals keeps changing constantly,
+so the information in this package has been updated with the checklist
+[Mamíferos de Colombia](https://doi.org/10.15472/kl1whs), which is
+published and updated regularly by the Colombian Mammal Society.
+
 ## Installation
 
 You can install the development version of mammalcol from
@@ -25,6 +38,19 @@ You can install the development version of mammalcol from
 devtools::install_github("dlizcano/mammalcol")
 ```
 
+## load library
+
+``` r
+
+library(mammalcol)
+#> This is mammalcol 0.2.3
+#> 
+#> Attaching package: 'mammalcol'
+#> The following objects are masked _by_ '.GlobalEnv':
+#> 
+#>     mammalmap, search_mammalcol, sp_by_depto
+```
+
 ## Example
 
 ### Search database
@@ -68,7 +94,7 @@ search_mammalcol(splist)
 #>                                                                                                                                                                           distribution
 #> 1                                                                                                                                                          Antioquia | Chocó | Córdoba
 #> 2                                              Antioquia | Cauca | Cundinamarca | Huila | Meta | Nariño | Quindío | Risaralda | Tolima | Valle del Cauca | Caldas | Caquetá | Putumayo
-#> 3 Antioquia | Amazonas | Arauca | Caquetá | Cauca | Cesar | Córdoba | Guainia | La Guajira | Meta | Magdalena | Vaupés | Vichada | Guaviare | Casanare | Norte de Santander | Putumayo
+#> 3 Antioquia | Amazonas | Arauca | Caquetá | Cauca | Cesar | Córdoba | Guainía | La Guajira | Meta | Magdalena | Vaupés | Vichada | Guaviare | Casanare | Norte de Santander | Putumayo
 #> 4                                                                                                              Cauca | Huila | Nariño | Risaralda | Quindío | Tolima | Valle del Cauca
 #>                                                         source endemic
 #> 1 Proceedings of the United States National Museum 103:465-496      No
@@ -129,7 +155,7 @@ search_mammalcol(splist)
 #> 2     1       EN A2cd B1ab (i; ii; iii; iv; v) \r\n
 #> 3     1 EN A2cd+ B1ab (i,ii,iii)+ B2ab (i, ii, iii)
 #>                                                                                                                                                                           distribution
-#> 1 Antioquia | Amazonas | Arauca | Caquetá | Cauca | Cesar | Córdoba | Guainia | La Guajira | Meta | Magdalena | Vaupés | Vichada | Guaviare | Casanare | Norte de Santander | Putumayo
+#> 1 Antioquia | Amazonas | Arauca | Caquetá | Cauca | Cesar | Córdoba | Guainía | La Guajira | Meta | Magdalena | Vaupés | Vichada | Guaviare | Casanare | Norte de Santander | Putumayo
 #> 2                                                                                                              Cauca | Huila | Nariño | Risaralda | Quindío | Tolima | Valle del Cauca
 #> 3                                                                                                                                                          Antioquia | Chocó | Córdoba
 #>                                                         source endemic
@@ -265,7 +291,7 @@ head(occ.any)
 #> 3                                                                             Norte de Santander
 #> 4                                                                 Magdalena | Norte de Santander
 #> 5 Amazonas | Caquetá | Casanare | Huila | Meta | Putumayo | Vaupés | Guaviare | Arauca | Guainía
-#> 6                Cundinamarca | Norte de Santander | Santander | Guania | Meta | Arauca | Tolima
+#> 6               Cundinamarca | Norte de Santander | Santander | Guainía | Meta | Arauca | Tolima
 ```
 
 The argument type = “only” retrieves species present only in that
@@ -298,14 +324,32 @@ head(occ.bats)
 #> 2                                                                                             Arauca | Caldas | Norte de Santander | Tolima | Putumayo | Guaviare | Amazonas | Antioquia | Atlántico | Caquetá | Casanare | Guainía | Meta | Vichada
 #> 3                                                                                                                  Amazonas | Arauca | Boyacá | Casanare | Meta | Vichada | Caquetá | Cundinamarca | Norte de Santander | Putumayo | Guainía | Sucre
 #> 4 Caldas | Cauca | Quindío | Risaralda | Amazonas | Caquetá | Guaviare | Meta | Putumayo | Antioquia | Arauca | Casanare | Chocó | Córdoba | Guainía | Magdalena | Nariño | Norte de Santander | Sucre | Tolima | Valle del Cauca | Vaupés | Vichada
-#> 5              Caldas | Cauca | Cundinamarca | Quindío | Risaralda | Amazonas | Caqueta | Putumayo | Antioquia | Arauca | Casanare | Cesar | Chocó | Guainía | Huila | Magdalena | Nariño | Norte de Santander | Putumayo | Tolima | Valle del Cauca
-#> 6                                                                                                             Cundinamarca | Magdalena | Amazonas | Caquetá | Guaviare | Arauca | Casanare | Chocó | Cordoba | Guainia | Norte de Santander | Tolima
+#> 5              Caldas | Cauca | Cundinamarca | Quindío | Risaralda | Amazonas | Caquetá | Putumayo | Antioquia | Arauca | Casanare | Cesar | Chocó | Guainía | Huila | Magdalena | Nariño | Norte de Santander | Putumayo | Tolima | Valle del Cauca
+#> 6                                                                                                             Cundinamarca | Magdalena | Amazonas | Caquetá | Guaviare | Arauca | Casanare | Chocó | Córdoba | Guainía | Norte de Santander | Tolima
 ```
 
 ### Sugested citation
 
 ``` r
 citation("mammalcol")
+#> To cite mammalcol package in publications use:
+#> 
+#>   Lizcano, DJ. et al., (2024). mammalcol: Access to the List of Mammal
+#>   Species of Colombia. R package version 0.2.2
+#> 
+#> A BibTeX entry for LaTeX users is
+#> 
+#>   @Manual{,
+#>     title = {mammalcol: Access to the List of Mammal Species of Colombia},
+#>     author = {Diego J. Lizcano and Baltazar González and Alejandra Bonilla-Sánchez and Andres F. Suárez-Castro and Camilo A. Calderón-Acevedo},
+#>     year = {2024},
+#>     note = {R data package version 0.2.2},
+#>     url = {https://dlizcano.github.io/mammalcol/},
+#>   }
+#> 
+#> To cite just the original mammalcol dataset, please use: Mammals of
+#> Colombia / Mamíferos de Colombia. SCMas: <doi:10.15472/kl1whs>, but
+#> keep in mind taxonomy is dinamic and have changed.
 ```
 
 Lizcano, DJ. (2024). mammalcol: Access to the List of Mammal Species of

diff --git a/data-raw/convert_tables.R b/data-raw/convert_tables.R
@@ -253,6 +253,9 @@ mammalmap <- function(species, legend=TRUE){
 
 
 
+
+
+
 ### package flow
 # 0. load pakgdown, usethis
 # 1 load data objects

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
Original file line number	Diff line number	Diff line change
Expand Up		@@ -253,6 +253,9 @@ mammalmap <- function(species, legend=TRUE){






		### package flow
		# 0. load pakgdown, usethis
		# 1 load data objects
Expand Down