From 85272dcaedb10915149db82db4785a5706797033 Mon Sep 17 00:00:00 2001 From: Yohann Chauvier-Mendes <43674773+8Ginette8@users.noreply.github.com> Date: Thu, 14 Nov 2024 16:28:24 +0100 Subject: [PATCH 01/12] Update README.md --- README.md | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index f95702a..9404c27 100644 --- a/README.md +++ b/README.md @@ -44,7 +44,7 @@ _(source: globe image from the Noun Project adapted by LenaCassie-Studio)_ - *make_ecoregion()*: A function to create custom ecoregions based on environmental layers. - - *evaluateRM()*: polygon evaluation pipeline, currently under development. + - *evaluateRM()*: evaluation function to validate the species ranges with data provided by the users. Cross-validation process under development. ## Installation @@ -65,12 +65,12 @@ Let's download worldwide the records of *Panthera tigris* only based on true obs ``` r # Download -obs_pt = get_gbif(sp_name="Panthera tigris", - basis=c("OBSERVATION","HUMAN_OBSERVATION","MACHINE_OBSERVATION")) +obs_pt = get_gbif(sp_name = "Panthera tigris", + basis = c("OBSERVATION","HUMAN_OBSERVATION","MACHINE_OBSERVATION")) # Plot species records countries = vect(ne_countries(type = "countries",returnclass = "sf")) -plot(countries,col="#bcbddc") +plot(countries,col = "#bcbddc") points(obs_pt[,c("decimalLongitude","decimalLatitude")],pch=20,col="#99340470",cex=1.5) ``` @@ -89,16 +89,16 @@ Let's now extract the terrestrial ecoregions of the world (Nature Conservancy) a eco_terra = read_bioreg(bioreg_name = "eco_terra", save_dir = NULL) # Range -range_tiger = get_range(occ_coord=obs_pt, - bioreg=eco_terra, - bioreg_name="ECO_NAME") +range_tiger = get_range(occ_coord = obs_pt, + bioreg = eco_terra, + bioreg_name = "ECO_NAME") ``` Let's plot the result now: ``` r -plot(countries,col="#bcbddc") -plot(range_tiger,col="#238b45",add=TRUE,axes=FALSE,legend=FALSE) +plot(countries,col = "#bcbddc") +plot(range_tiger,col = "#238b45",add = TRUE,axes = FALSE,legend = FALSE) ``` ![image](https://user-images.githubusercontent.com/43674773/203769654-0f5d7182-2b96-43bb-ac5c-306b777be268.png) @@ -133,10 +133,10 @@ my_eco = make_ecoregion(rst,200) # Create the range map based on our custom ecoregion # (always set 'EcoRegion' as a name when using a make_ecoregion() output): -range_arcto = get_range(occ_coord=obs_arcto, - bioreg=my_eco, - bioreg_name="EcoRegion", - res=20, +range_arcto = get_range(occ_coord = obs_arcto, + bioreg = my_eco, + bioreg_name = "EcoRegion", + res = 20, degrees_outlier = 5, clustered_points_outlier = 2, buffer_width_point = 4, @@ -149,9 +149,9 @@ Here we adapted the extra-parameters to the extent of the study area, e.g., (i) ``` r # Plot plot(rst[[1]]) -plot(shp_lonlat,add=TRUE) -plot(range_arcto,add=TRUE,col="darkgreen",axes=FALSE,legend=FALSE) -points(obs_arcto[,c("decimalLongitude","decimalLatitude")],pch=20,col="#99340470",cex=1) +plot(shp_lonlat,add = TRUE) +plot(range_arcto,add = TRUE,col = "darkgreen",axes = FALSE,legend = FALSE) +points(obs_arcto[,c("decimalLongitude","decimalLatitude")],pch = 20,col = "#99340470",cex=1) ``` @@ -163,8 +163,8 @@ Let's reapply the same process as for Panthera tigris, but with the marine speci ⚠️Notes that the download takes here longer unless the parameter *occ_samp* is used. Altough giving **less precise observational distribution**, *occ_samp* allows to extract a **subsample of *n* GBIF observations** per created tiles over the study area: ``` r -obs_dd = get_gbif("Delphinus delphis",occ_samp=1000) # Here the example is a sample of 1000 observations per geographic tile -get_status("Delphinus delphis",all=TRUE) # Here the list is longer because 'all=TRUE' includes every names (even doubtful) +obs_dd = get_gbif("Delphinus delphis",occ_samp = 1000) # Here the example is a sample of 1000 observations per geographic tile +get_status("Delphinus delphis",all = TRUE) # Here the list is longer because 'all=TRUE' includes every names (even doubtful) ``` Let's now generate three range maps of *Delphinus delphis* using the *eco.marine* as ecoregion shapefile: @@ -183,8 +183,8 @@ The three results are pretty similar because most of the observations are near t ``` r plot(countries,col="#bcbddc") -plot(range_dd3,col="#238b45",add=TRUE,axes=FALSE,legend=FALSE) -points(obs_dd[,c("decimalLongitude","decimalLatitude")],pch=20,col="#99340470",cex=1) +plot(range_dd3,col = "#238b45",add = TRUE,axes = FALSE,legend = FALSE) +points(obs_dd[,c("decimalLongitude","decimalLatitude")],pch = 20,col = "#99340470",cex = 1) ``` From ede918200b96f06a346c25d453edf8f9bf9b189d Mon Sep 17 00:00:00 2001 From: Yohann Chauvier-Mendes <43674773+8Ginette8@users.noreply.github.com> Date: Thu, 14 Nov 2024 16:29:31 +0100 Subject: [PATCH 02/12] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9404c27..e6d2540 100644 --- a/README.md +++ b/README.md @@ -44,7 +44,7 @@ _(source: globe image from the Noun Project adapted by LenaCassie-Studio)_ - *make_ecoregion()*: A function to create custom ecoregions based on environmental layers. - - *evaluateRM()*: evaluation function to validate the species ranges with data provided by the users. Cross-validation process under development. + - *evaluateRM()*: evaluation function to validate the species ranges with distribution information provided by the user. Cross-validation process under development. ## Installation From 6b6fd4d1949cd75676f6c9cdaceb97a737466bc6 Mon Sep 17 00:00:00 2001 From: Yohann Chauvier-Mendes <43674773+8Ginette8@users.noreply.github.com> Date: Thu, 14 Nov 2024 23:42:52 +0100 Subject: [PATCH 03/12] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e6d2540..f99d668 100644 --- a/README.md +++ b/README.md @@ -44,7 +44,7 @@ _(source: globe image from the Noun Project adapted by LenaCassie-Studio)_ - *make_ecoregion()*: A function to create custom ecoregions based on environmental layers. - - *evaluateRM()*: evaluation function to validate the species ranges with distribution information provided by the user. Cross-validation process under development. + - *evaluate_range()*: evaluation function to validate the species ranges with distribution information provided by the user. Cross-validation process under development. ## Installation From fb3db2bd2c283ab81095c7208fc0650078a7f4c8 Mon Sep 17 00:00:00 2001 From: Yohann Chauvier-Mendes <43674773+8Ginette8@users.noreply.github.com> Date: Thu, 14 Nov 2024 23:44:51 +0100 Subject: [PATCH 04/12] Update README.md --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index f99d668..c60f724 100644 --- a/README.md +++ b/README.md @@ -28,8 +28,7 @@ _(source: globe image from the Noun Project adapted by LenaCassie-Studio)_ - *read_bioreg()*: download and read available ecoregion files from different available URL sources. See also associated calls *bioreg_list*, *get_bioreg()* and *check_and_get_bioreg()*. - *get_status()*: Generates, based on a given species name, its IUCN red list status and a list of all scientific names - (accepted, synonyms) found in the GBIF backbone taxonomy to download the data. Children and related - doubtful names not used to download the data may also be extracted. + (accepted, synonyms) found in the GBIF backbone taxonomy. Children and related doubtful names not used to download the data may also be extracted. - *obs_filter()*: *obs_filter()* accepts as input a *get_gbif()* output (one or several species) and filter the observations according to a specific given grid resolution (one observation per pixel grid kept). This function allows the user to refine the density of GBIF From 42315e2523d96679c0b43bb4f3322975e23e449d Mon Sep 17 00:00:00 2001 From: Yohann Chauvier-Mendes <43674773+8Ginette8@users.noreply.github.com> Date: Thu, 14 Nov 2024 23:46:14 +0100 Subject: [PATCH 05/12] Update README.md --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index c60f724..9a05a4c 100644 --- a/README.md +++ b/README.md @@ -27,21 +27,21 @@ _(source: globe image from the Noun Project adapted by LenaCassie-Studio)_ - *read_bioreg()*: download and read available ecoregion files from different available URL sources. See also associated calls *bioreg_list*, *get_bioreg()* and *check_and_get_bioreg()*. - - *get_status()*: Generates, based on a given species name, its IUCN red list status and a list of all scientific names + - *get_status()*: generates, based on a given species name, its IUCN red list status and a list of all scientific names (accepted, synonyms) found in the GBIF backbone taxonomy. Children and related doubtful names not used to download the data may also be extracted. - *obs_filter()*: *obs_filter()* accepts as input a *get_gbif()* output (one or several species) and filter the observations according to a specific given grid resolution (one observation per pixel grid kept). This function allows the user to refine the density of GBIF observations according to a defined analysis/study's resolution. - - *make_tiles()*: May be used to generate a set of *SpatialExtent* and geometry arguments POLYGON() based on a given + - *make_tiles()*: may be used to generate a set of *SpatialExtent* and geometry arguments POLYGON() based on a given geographic extent. This function is meant to help users who want to use the *rgbif* R package and its parameter *geometry* that uses a POLYGON() argument. - - *get_doi()*: A small wrapper of *derived_dataset()* in *rgbif* that simplifies the obtention of a general DOI + - *get_doi()*: a small wrapper of *derived_dataset()* in *rgbif* that simplifies the obtention of a general DOI for a set of several gbif species datasets. - - *make_ecoregion()*: A function to create custom ecoregions based on environmental layers. + - *make_ecoregion()*: a function to create custom ecoregions based on environmental layers. - *evaluate_range()*: evaluation function to validate the species ranges with distribution information provided by the user. Cross-validation process under development. From 7a0e8b22ecb7b2c77658cd213acaaf776578f22b Mon Sep 17 00:00:00 2001 From: Yohann Chauvier-Mendes <43674773+8Ginette8@users.noreply.github.com> Date: Thu, 14 Nov 2024 23:49:33 +0100 Subject: [PATCH 06/12] Update README.md --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 9a05a4c..e276472 100644 --- a/README.md +++ b/README.md @@ -203,6 +203,8 @@ Chauvier, Y., Thuiller, W., Brun, P., Lavergne, S., Descombes, P., Karger, D. N. Lyu, L., Leugger, F., Hagen, O., Fopp, F., Boschman, L. M., Strijk, J. S., ... & Pellissier, L. (2022). An integrated high‐resolution mapping shows congruent biodiversity patterns of Fagales and Pinales. New Phytologist, 235(2), doi: 10.1111/nph.18158 +Pinkert, S., Sica, Y. V., Winner, K., & Jetz, W. (2023). The potential of ecoregional range maps for boosting taxonomic coverage in ecology and conservation. Ecography, 12, e06794. doi: 10.1111/ecog.06794 + Chamberlain, S., Oldoni, D., & Waller, J. (2022). rgbif: interface to the global biodiversity information facility API. doi: 10.5281/zenodo.6023735 Zizka, A., Silvestro, D., Andermann, T., Azevedo, J., Duarte Ritter, C., Edler, D., ... & Antonelli, A. (2019). CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases. Methods in Ecology and Evolution, 10(5), 744-751. doi: 10.1111/2041-210X.13152 From 7adfa2b427a60fc67b6e35bbe36815cedf3ee796 Mon Sep 17 00:00:00 2001 From: Yohann Chauvier-Mendes <43674773+8Ginette8@users.noreply.github.com> Date: Thu, 14 Nov 2024 23:50:57 +0100 Subject: [PATCH 07/12] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e276472..3134be6 100644 --- a/README.md +++ b/README.md @@ -201,9 +201,9 @@ Oskar Hagen, Lisa Vaterlaus, Camille Albouy, Andrew Brown, Flurin Leugger, Rensk Chauvier, Y., Thuiller, W., Brun, P., Lavergne, S., Descombes, P., Karger, D. N., ... & Zimmermann, N. E. (2021). Influence of climate, soil, and land cover on plant species distribution in the European Alps. Ecological monographs, 91(2), e01433. doi: 10.1002/ecm.1433 -Lyu, L., Leugger, F., Hagen, O., Fopp, F., Boschman, L. M., Strijk, J. S., ... & Pellissier, L. (2022). An integrated high‐resolution mapping shows congruent biodiversity patterns of Fagales and Pinales. New Phytologist, 235(2), doi: 10.1111/nph.18158 +Lyu, L., Leugger, F., Hagen, O., Fopp, F., Boschman, L. M., Strijk, J. S., ... & Pellissier, L. (2022). An integrated high‐resolution mapping shows congruent biodiversity patterns of Fagales and Pinales. New Phytologist, 235(2). doi: 10.1111/nph.18158 -Pinkert, S., Sica, Y. V., Winner, K., & Jetz, W. (2023). The potential of ecoregional range maps for boosting taxonomic coverage in ecology and conservation. Ecography, 12, e06794. doi: 10.1111/ecog.06794 +Pinkert, S., Sica, Y. V., Winner, K., & Jetz, W. (2023). The potential of ecoregional range maps for boosting taxonomic coverage in ecology and conservation. Ecography, 12, e06794. doi: 10.1111/ecog.06794 Chamberlain, S., Oldoni, D., & Waller, J. (2022). rgbif: interface to the global biodiversity information facility API. doi: 10.5281/zenodo.6023735 From 56852e6b852a15b7ab4feb4b3ebc405e02f9af7c Mon Sep 17 00:00:00 2001 From: Yohann Chauvier-Mendes <43674773+8Ginette8@users.noreply.github.com> Date: Thu, 14 Nov 2024 23:51:43 +0100 Subject: [PATCH 08/12] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3134be6..7f0b94e 100644 --- a/README.md +++ b/README.md @@ -203,7 +203,7 @@ Chauvier, Y., Thuiller, W., Brun, P., Lavergne, S., Descombes, P., Karger, D. N. Lyu, L., Leugger, F., Hagen, O., Fopp, F., Boschman, L. M., Strijk, J. S., ... & Pellissier, L. (2022). An integrated high‐resolution mapping shows congruent biodiversity patterns of Fagales and Pinales. New Phytologist, 235(2). doi: 10.1111/nph.18158 -Pinkert, S., Sica, Y. V., Winner, K., & Jetz, W. (2023). The potential of ecoregional range maps for boosting taxonomic coverage in ecology and conservation. Ecography, 12, e06794. doi: 10.1111/ecog.06794 +Pinkert, S., Sica, Y. V., Winner, K., & Jetz, W. (2023). The potential of ecoregional range maps for boosting taxonomic coverage in ecology and conservation. Ecography, 12, e06794. doi: 10.1111/ecog.06794 Chamberlain, S., Oldoni, D., & Waller, J. (2022). rgbif: interface to the global biodiversity information facility API. doi: 10.5281/zenodo.6023735 From eaaea1ef47d1ac9f2cc806efc00fc24fee824353 Mon Sep 17 00:00:00 2001 From: Yohann Chauvier-Mendes <43674773+8Ginette8@users.noreply.github.com> Date: Thu, 14 Nov 2024 23:52:53 +0100 Subject: [PATCH 09/12] Update README.md --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 7f0b94e..f0bbdfa 100644 --- a/README.md +++ b/README.md @@ -203,7 +203,8 @@ Chauvier, Y., Thuiller, W., Brun, P., Lavergne, S., Descombes, P., Karger, D. N. Lyu, L., Leugger, F., Hagen, O., Fopp, F., Boschman, L. M., Strijk, J. S., ... & Pellissier, L. (2022). An integrated high‐resolution mapping shows congruent biodiversity patterns of Fagales and Pinales. New Phytologist, 235(2). doi: 10.1111/nph.18158 -Pinkert, S., Sica, Y. V., Winner, K., & Jetz, W. (2023). The potential of ecoregional range maps for boosting taxonomic coverage in ecology and conservation. Ecography, 12, e06794. doi: 10.1111/ecog.06794 +Pinkert, S., Sica, Y. V., Winner, K., & Jetz, W. (2023). The potential of ecoregional range maps for boosting taxonomic coverage in ecology and conservation. Ecography, 12, e06794. +doi: 10.1111/ecog.06794 Chamberlain, S., Oldoni, D., & Waller, J. (2022). rgbif: interface to the global biodiversity information facility API. doi: 10.5281/zenodo.6023735 From b322a84114efc2b6c1e80215f97d8a8f956f8f60 Mon Sep 17 00:00:00 2001 From: Yohann Chauvier-Mendes <43674773+8Ginette8@users.noreply.github.com> Date: Thu, 14 Nov 2024 23:54:54 +0100 Subject: [PATCH 10/12] Update README.md --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index f0bbdfa..f9f3b15 100644 --- a/README.md +++ b/README.md @@ -203,8 +203,7 @@ Chauvier, Y., Thuiller, W., Brun, P., Lavergne, S., Descombes, P., Karger, D. N. Lyu, L., Leugger, F., Hagen, O., Fopp, F., Boschman, L. M., Strijk, J. S., ... & Pellissier, L. (2022). An integrated high‐resolution mapping shows congruent biodiversity patterns of Fagales and Pinales. New Phytologist, 235(2). doi: 10.1111/nph.18158 -Pinkert, S., Sica, Y. V., Winner, K., & Jetz, W. (2023). The potential of ecoregional range maps for boosting taxonomic coverage in ecology and conservation. Ecography, 12, e06794. -doi: 10.1111/ecog.06794 +Pinkert, S., Sica, Y. V., Winner, K., & Jetz, W. (2023). The potential of ecoregional range maps for boosting taxonomic coverage in ecology and conservation. Ecography, 12, e06794. doi: 10.1111/ecog.06794 Chamberlain, S., Oldoni, D., & Waller, J. (2022). rgbif: interface to the global biodiversity information facility API. doi: 10.5281/zenodo.6023735 From bbf78fd3331beb74d5b5aec1c427b1bb06efc7b0 Mon Sep 17 00:00:00 2001 From: Yohann Chauvier-Mendes <43674773+8Ginette8@users.noreply.github.com> Date: Thu, 14 Nov 2024 23:55:52 +0100 Subject: [PATCH 11/12] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index f9f3b15..fccf58f 100644 --- a/README.md +++ b/README.md @@ -203,7 +203,7 @@ Chauvier, Y., Thuiller, W., Brun, P., Lavergne, S., Descombes, P., Karger, D. N. Lyu, L., Leugger, F., Hagen, O., Fopp, F., Boschman, L. M., Strijk, J. S., ... & Pellissier, L. (2022). An integrated high‐resolution mapping shows congruent biodiversity patterns of Fagales and Pinales. New Phytologist, 235(2). doi: 10.1111/nph.18158 -Pinkert, S., Sica, Y. V., Winner, K., & Jetz, W. (2023). The potential of ecoregional range maps for boosting taxonomic coverage in ecology and conservation. Ecography, 12, e06794. doi: 10.1111/ecog.06794 +Pinkert, S., Sica, Y. V., Winner, K., & Jetz, W. (2023). The potential of ecoregional range maps for boosting taxonomic coverage in ecology and conservation. Ecography, 12, e06794. doi: 10.1111/ecog.06794 Chamberlain, S., Oldoni, D., & Waller, J. (2022). rgbif: interface to the global biodiversity information facility API. doi: 10.5281/zenodo.6023735 From 203287e6053c8b66c17e872ddfe62efd9cb8a080 Mon Sep 17 00:00:00 2001 From: Yohann Chauvier-Mendes <43674773+8Ginette8@users.noreply.github.com> Date: Wed, 18 Dec 2024 14:27:49 +0100 Subject: [PATCH 12/12] Update get_status.R --- R/get_status.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/get_status.R b/R/get_status.R index f2b2793..70ac0a8 100644 --- a/R/get_status.R +++ b/R/get_status.R @@ -16,7 +16,7 @@ #' relevant name from the list (higher taxa level than species allowed here). Also, unlike search=TRUE, #' fuzzy search (~approximative name match) is here allowed, and the 'rank', phylum', 'class', order' #' and 'family' parameters are optionally used only if no convincing name match is found. FALSE is -#' particularly useful if the given species name already incluede the author. +#' particularly useful if the given species name already include the author. #' @param rank Character. "SPECIES", "SUBSPECIES" or "VARIETY". If NULL (default), the order of priority #' is (1) species, (2) subspecies and (3) variety unless "subsp." or "var." is found in 'sp_name'. #' @param phylum Character. Optional. What is the species' Phylum? Adds a criteria to deal with alternative @@ -277,4 +277,4 @@ get_status=function(sp_name = NULL, e_output[e_output$scientificName%in%sc_name,"sp_nameMatch"][1] = "INPUT" return(e_output) -} \ No newline at end of file +}