@@ -68,13 +68,13 @@ Citation
Dougherty M, McKay K (2022).
nybem: NY Bight Ecological Model .
-R package version 0.1.3, https://github.com/MVR-GIS/nybem .
+R package version 0.1.4, https://github.com/MVR-GIS/nybem .
@Manual{,
title = {nybem: NY Bight Ecological Model},
author = {Michael Dougherty and Kyle McKay},
year = {2022},
- note = {R package version 0.1.3},
+ note = {R package version 0.1.4},
url = {https://github.com/MVR-GIS/nybem},
}
diff --git a/docs/index.html b/docs/index.html
index 7de7892..d64f905 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -30,7 +30,7 @@
nybem
- 0.1.3
+ 0.1.4
@@ -78,7 +78,7 @@
+
Bug Reports
If you find any bugs using nybem, please open an issue .
diff --git a/docs/news/index.html b/docs/news/index.html
index ba95f28..f1f5ba7 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -10,7 +10,7 @@
nybem
-
0.1.3
+
0.1.4
@@ -51,13 +51,16 @@
-
nybem v0.1.1 (Release date: 2022-02-20)
+
nybem v0.1.4 (Release date: 2022-05-05)
+
Major Changes
+
Added package documentation in preparation for USACE ECO-PCX model review.
+Added nybem_submodels containing the ecological models for the New Jersey Back Bay study.
+Bug Fixes
+Removed ecorest specific functions
+nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/reference/HSIplotter.html b/docs/reference/HSIplotter.html
index 3aee9a1..09f5715 100644
--- a/docs/reference/HSIplotter.html
+++ b/docs/reference/HSIplotter.html
@@ -12,7 +12,7 @@
nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/reference/SIcalc.html b/docs/reference/SIcalc.html
index 1137c40..7571e06 100644
--- a/docs/reference/SIcalc.html
+++ b/docs/reference/SIcalc.html
@@ -16,7 +16,7 @@
nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/reference/are_colors.html b/docs/reference/are_colors.html
index 72d04f4..dfc70c9 100644
--- a/docs/reference/are_colors.html
+++ b/docs/reference/are_colors.html
@@ -12,7 +12,7 @@
nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/reference/has_colortable.html b/docs/reference/has_colortable.html
index 1ced035..30e57bb 100644
--- a/docs/reference/has_colortable.html
+++ b/docs/reference/has_colortable.html
@@ -10,7 +10,7 @@
nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/reference/ifelse.html b/docs/reference/ifelse.html
index d8c0310..6244f7d 100644
--- a/docs/reference/ifelse.html
+++ b/docs/reference/ifelse.html
@@ -14,7 +14,7 @@
nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 2c3ea44..67ee5d1 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -10,7 +10,7 @@
nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/reference/is_RasterLayer.html b/docs/reference/is_RasterLayer.html
index 37b35b0..2159fbd 100644
--- a/docs/reference/is_RasterLayer.html
+++ b/docs/reference/is_RasterLayer.html
@@ -10,7 +10,7 @@
nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/reference/is_cat_raster.html b/docs/reference/is_cat_raster.html
index fd90ef1..7951933 100644
--- a/docs/reference/is_cat_raster.html
+++ b/docs/reference/is_cat_raster.html
@@ -10,7 +10,7 @@
nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/reference/nybem_submodels.html b/docs/reference/nybem_submodels.html
index 43ab733..d2cf811 100644
--- a/docs/reference/nybem_submodels.html
+++ b/docs/reference/nybem_submodels.html
@@ -10,7 +10,7 @@
nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/reference/raster_fig.html b/docs/reference/raster_fig.html
index 9934338..50b2b9d 100644
--- a/docs/reference/raster_fig.html
+++ b/docs/reference/raster_fig.html
@@ -10,7 +10,7 @@
nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/reference/set_habitat_zone.html b/docs/reference/set_habitat_zone.html
index aa2c370..fe4f30a 100644
--- a/docs/reference/set_habitat_zone.html
+++ b/docs/reference/set_habitat_zone.html
@@ -12,7 +12,7 @@
nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/reference/set_salinity_zone.html b/docs/reference/set_salinity_zone.html
index 58eb9c9..d3968c6 100644
--- a/docs/reference/set_salinity_zone.html
+++ b/docs/reference/set_salinity_zone.html
@@ -12,7 +12,7 @@
nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/reference/set_tidal_zone.html b/docs/reference/set_tidal_zone.html
index bd9aede..b0b1ea0 100644
--- a/docs/reference/set_tidal_zone.html
+++ b/docs/reference/set_tidal_zone.html
@@ -10,7 +10,7 @@
nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/reference/write_cat_tif.html b/docs/reference/write_cat_tif.html
index 2c9a5df..ee18818 100644
--- a/docs/reference/write_cat_tif.html
+++ b/docs/reference/write_cat_tif.html
@@ -14,7 +14,7 @@
nybem
- 0.1.3
+ 0.1.4
diff --git a/docs/search.json b/docs/search.json
index 35acfa8..514294a 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -1 +1 @@
-[{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"getting-started","dir":"Articles","previous_headings":"","what":"Getting Started","title":"Using `nybem`","text":"install nybem package, install GitHub using remotes package:","code":"remotes::install_github(repo = \"MVR-GIS/nybem\")"},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"load-required-packages","dir":"Articles","previous_headings":"","what":"Load Required Packages","title":"Using `nybem`","text":"","code":"library(nybem) ## ## Attaching package: 'nybem' ## The following object is masked from 'package:base': ## ## ifelse library(raster) ## Warning: package 'raster' was built under R version 4.1.3 ## Loading required package: sp ## Warning: package 'sp' was built under R version 4.1.3"},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"list-the-nybem-models","dir":"Articles","previous_headings":"","what":"List the NYBEM Models","title":"Using `nybem`","text":"nybem package contains models created ecological modeling section NTBEM feasibility study. Notice nybem::nybem_submodels list contains pair data frames submodel study. pair dataframes named submodel represents (.e., NYBEM.fresh.tid = Freshwater Tidal Zone habitat model). first data frame contains habitat variables matching suitability index values, second data frame (*_labels) contains labels used plotting.","code":"# Load the model data nybem_submodels <- nybem::nybem_submodels # View the available submodels names(nybem_submodels) ## [1] \"NYBEM.fresh.tid\" \"NYBEM.fresh.tid_labels\" ## [3] \"NYBEM.est.int\" \"NYBEM.est.int_labels\" ## [5] \"NYBEM.est.sub.hard\" \"NYBEM.est.sub.hard_labels\" ## [7] \"NYBEM.est.sub.soft.sav\" \"NYBEM.est.sub.soft.sav_labels\" ## [9] \"NYBEM.est.sub.soft.clam\" \"NYBEM.est.sub.soft.clam_labels\" ## [11] \"NYBEM.mar.int\" \"NYBEM.mar.int_labels\" ## [13] \"NYBEM.mar.sub\" \"NYBEM.mar.sub_labels\" ## [15] \"NYBEM.mar.deep\" \"NYBEM.mar.deep_labels\""},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"view-the-suitability-index-data-frame","dir":"Articles","previous_headings":"","what":"View the Suitability Index data frame","title":"Using `nybem`","text":"","code":"# View the Freshwater Tidal model # View table of habitat variables and their suitability index values nybem_submodels$NYBEM.fresh.tid ## salinity.per salinity.SIV veg.cover.per veg.cover.SIV deposition ## 1 0 0 50 0.0 0 ## 2 20 1 57 0.5 1 ## 3 100 1 100 1.0 NA ## deposition.SIV ## 1 1 ## 2 0 ## 3 NA"},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"view-the-suitability-index-model-labels","dir":"Articles","previous_headings":"","what":"View the Suitability Index model labels","title":"Using `nybem`","text":"","code":"nybem_submodels$NYBEM.fresh.tid_labels ## model label variable ## 1 Freshwater, Tidal Salinity duration (% time > 0.5 psu) salinity ## 2 Freshwater, Tidal Vegetation Cover (%) veg.cover ## 3 Freshwater, Tidal Relative Depth deposition"},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"plot-the-suitability-index-values","dir":"Articles","previous_headings":"","what":"Plot the Suitability Index Values","title":"Using `nybem`","text":"","code":"# Freshwater, Tidal nybem::HSIplotter(nybem_submodels$NYBEM.fresh.tid, xlab = nybem_submodels$NYBEM.fresh.tid_labels$label, ylab = nybem_submodels$NYBEM.fresh.tid_labels$variable)"},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"create-site-observations","dir":"Articles","previous_headings":"","what":"Create Site Observations","title":"Using `nybem`","text":"","code":"# Single numeric site observations salinity <- 40 veg.cover <- 100 deposition <- 0 obs_1 <- list(salinity, veg.cover, deposition) obs_1 ## [[1]] ## [1] 40 ## ## [[2]] ## [1] 100 ## ## [[3]] ## [1] 0 # Raster site observations salinity_ras <- raster::raster(ncol = 2, nrow = 2, vals = rep_len(40, 4)) veg.cover_ras <- raster::raster(ncol = 2, nrow = 2, vals = rep_len(100, 4)) deposition_ras <- raster::raster(ncol = 2, nrow = 2, vals = rep_len(0, 4)) obs_2 <- list(salinity_ras, veg.cover_ras, deposition_ras) obs_2 ## [[1]] ## class : RasterLayer ## dimensions : 2, 2, 4 (nrow, ncol, ncell) ## resolution : 180, 90 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## crs : +proj=longlat +datum=WGS84 +no_defs ## source : memory ## names : layer ## values : 40, 40 (min, max) ## ## ## [[2]] ## class : RasterLayer ## dimensions : 2, 2, 4 (nrow, ncol, ncell) ## resolution : 180, 90 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## crs : +proj=longlat +datum=WGS84 +no_defs ## source : memory ## names : layer ## values : 100, 100 (min, max) ## ## ## [[3]] ## class : RasterLayer ## dimensions : 2, 2, 4 (nrow, ncol, ncell) ## resolution : 180, 90 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## crs : +proj=longlat +datum=WGS84 +no_defs ## source : memory ## names : layer ## values : 0, 0 (min, max)"},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"calculate-suitability-index-values","dir":"Articles","previous_headings":"","what":"Calculate Suitability Index Values","title":"Using `nybem`","text":"","code":"# Suitability Index value for single numeric site observations siv_fresh.tid_obs_1 <- nybem::SIcalc(SI = nybem_submodels$NYBEM.fresh.tid, input_proj = obs_1) siv_fresh.tid_obs_1 ## [[1]] ## [1] 1 ## ## [[2]] ## [1] 1 ## ## [[3]] ## [1] 1 # Suitability Index value for raster site observations siv_fresh.tid_obs_2 <- nybem::SIcalc(SI = nybem_submodels$NYBEM.fresh.tid, input_proj = obs_2) siv_fresh.tid_obs_2 ## [[1]] ## class : RasterLayer ## dimensions : 2, 2, 4 (nrow, ncol, ncell) ## resolution : 180, 90 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## crs : +proj=longlat +datum=WGS84 +no_defs ## source : memory ## names : layer ## values : 1, 1 (min, max) ## ## ## [[2]] ## class : RasterLayer ## dimensions : 2, 2, 4 (nrow, ncol, ncell) ## resolution : 180, 90 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## crs : +proj=longlat +datum=WGS84 +no_defs ## source : memory ## names : layer ## values : 1, 1 (min, max) ## ## ## [[3]] ## class : RasterLayer ## dimensions : 2, 2, 4 (nrow, ncol, ncell) ## resolution : 180, 90 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## crs : +proj=longlat +datum=WGS84 +no_defs ## source : memory ## names : layer ## values : 1, 1 (min, max)"},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"calculate-habitat-suitability-index","dir":"Articles","previous_headings":"","what":"Calculate Habitat Suitability Index","title":"Using `nybem`","text":"","code":"# Calculate HSI for single numeric site observations hsi_fresh.tid_obs_1 <- nybem::HSIcalc(si_list = siv_fresh.tid_obs_1) hsi_fresh.tid_obs_1 ## [1] 1 # Calculate HSI for raster site observations hsi_fresh.tid_obs_2 <- nybem::HSIcalc(si_list = siv_fresh.tid_obs_2) hsi_fresh.tid_obs_2 ## class : RasterLayer ## dimensions : 2, 2, 4 (nrow, ncol, ncell) ## resolution : 180, 90 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## crs : +proj=longlat +datum=WGS84 +no_defs ## source : memory ## names : layer ## values : 1, 1 (min, max)"},{"path":"https://github.com/MVR-GIS/nybem/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Michael Dougherty. Author, maintainer. Kyle McKay. Author.","code":""},{"path":"https://github.com/MVR-GIS/nybem/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Dougherty M, McKay K (2022). nybem: NY Bight Ecological Model. R package version 0.1.3, https://github.com/MVR-GIS/nybem.","code":"@Manual{, title = {nybem: NY Bight Ecological Model}, author = {Michael Dougherty and Kyle McKay}, year = {2022}, note = {R package version 0.1.3}, url = {https://github.com/MVR-GIS/nybem}, }"},{"path":[]},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement Michael.P.Dougherty@usace.army.mil. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"nybem","dir":"","previous_headings":"","what":"NY Bight Ecological Model","title":"NY Bight Ecological Model","text":"R package performing coastal habitat modeling.","code":""},{"path":[]},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"description","dir":"","previous_headings":"","what":"Description","title":"NY Bight Ecological Model","text":"package contains collection functions modeling coastal habitat ongoing USACE studies New Jersey Back Bays (NJBB) NY/NJ Harbor Tributaries Study (HATS).","code":""},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"funding","dir":"","previous_headings":"","what":"Funding","title":"NY Bight Ecological Model","text":"Funding development maintenance nybem provided following US Army Corps Engineers (USACE) programs: NY/NJ Harbor Tributaries Study (HATS) New Jersey Back Bays (NJBB)","code":""},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"latest-updates","dir":"","previous_headings":"","what":"Latest Updates","title":"NY Bight Ecological Model","text":"Check NEWS details latest updates.","code":""},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"authors","dir":"","previous_headings":"","what":"Authors","title":"NY Bight Ecological Model","text":"Michael Dougherty, Geographer, Rock Island District, U.S. Army Corps Engineers https://orcid.org/0000-0002-1465-5927 Kyle McKay, Research Civil Engineer, Engineer Research Development Center, Environmental Laboratory, U.S. Army Corps Engineers https://orcid.org/0000-0003-2703-3841","code":""},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"install","dir":"","previous_headings":"","what":"Install","title":"NY Bight Ecological Model","text":"install nybem package, install GitHub using remotes package:","code":"remotes::install_github(repo = \"MVR-GIS/nybem\")"},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"bug-reports","dir":"","previous_headings":"","what":"Bug Reports","title":"NY Bight Ecological Model","text":"find bugs using nybem, please open issue.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/are_colors.html","id":null,"dir":"Reference","previous_headings":"","what":"Are Colors? — are_colors","title":"Are Colors? — are_colors","text":"Determines input vector valid colors according grDevices::col2rgb function.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/are_colors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Are Colors? — are_colors","text":"","code":"are_colors(color_vector)"},{"path":"https://github.com/MVR-GIS/nybem/reference/are_colors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Are Colors? — are_colors","text":"color_vector vector; vector color values.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/are_colors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Are Colors? — are_colors","text":"logical vector.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/are_colors.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Are Colors? — are_colors","text":"Follows advice ","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/has_colortable.html","id":null,"dir":"Reference","previous_headings":"","what":"Has Colortable? — has_colortable","title":"Has Colortable? — has_colortable","text":"Determines RasterLayer valid colortable defined.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/has_colortable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Has Colortable? — has_colortable","text":"","code":"has_colortable(raster)"},{"path":"https://github.com/MVR-GIS/nybem/reference/has_colortable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Has Colortable? — has_colortable","text":"raster RasterLayer; raster tested.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/has_colortable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Has Colortable? — has_colortable","text":"Returns TRUE raster valid colortable.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIcalc.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Habitat Suitability Index (HSI) — HSIcalc","title":"Calculate Habitat Suitability Index (HSI) — HSIcalc","text":"Calculates habitat suitability index input suitability indices using specified method.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIcalc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Habitat Suitability Index (HSI) — HSIcalc","text":"","code":"HSIcalc(si_list, method = \"mean\")"},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIcalc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Habitat Suitability Index (HSI) — HSIcalc","text":"si_list list; list suitability indices. method character; method calculating suitability index. Must one \"mean\",","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIcalc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Habitat Suitability Index (HSI) — HSIcalc","text":"HSI object matching data format input suitability indices.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIcalc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Habitat Suitability Index (HSI) — HSIcalc","text":"","code":"# Build manual model # Number of trees > 51cm diameter per 0.4 ha plot tree.num <- c(0, 2, 4, NA) # parameter breakpoints tree.num.SIV <- c(0.1, 1, 1, NA) # parameter suitability indices tree_num <- data.frame(tree.num, tree.num.SIV) # Mean diameter of overstory trees avg.dbh <- c(0, 5, 20, NA) # parameter breakpoints avg.dbh.SIV <- c(0, 0, 1, NA) # parameter suitability indices tree_diameter <- data.frame(avg.dbh, avg.dbh.SIV) # Percent canopy cover of overstory trees can.cov <- c(0, 20, 60, 100) # parameter breakpoints can.cov.SIV <- c(0, 0, 1, 1) # parameter suitability indices canopy_cov <- data.frame(can.cov, can.cov.SIV) barredowl <- data.frame(tree_num, tree_diameter, canopy_cov) bo_test1 <- list(2, 5, 20) # Barredowl si values bo_si_1 <- nybem::SIcalc(barredowl, bo_test1) # Calculate HSI bo_hsi <- HSIcalc(si_list = bo_si_1)"},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIplotter.html","id":null,"dir":"Reference","previous_headings":"","what":"Plots habitat suitability index curves — HSIplotter","title":"Plots habitat suitability index curves — HSIplotter","text":"Plots habitat suitability index curves metrics model.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIplotter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plots habitat suitability index curves — HSIplotter","text":"","code":"HSIplotter(SI, xlab = NA, ylab = NA, ncol = 2)"},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIplotter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plots habitat suitability index curves — HSIplotter","text":"SI data frame; data frame suitability curves ordered parameter breakpoints associated suitability indices parameter appropriate column names. xlab character; vector x-axis label values SI. Defaults SI variable name. ylab character; vector y-axis label values SI. Defaults \"Suitability Index\". ncol numeric; Number columns plot.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIplotter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plots habitat suitability index curves — HSIplotter","text":"multipanel figure displaying suitability curves.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIplotter.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Plots habitat suitability index curves — HSIplotter","text":"US Fish Wildlife Service. (1980). Habitat basis environmental assessment. Ecological Services Manual, 101. US Fish Wildlife Service. (1980). Habitat Evaluation Procedures (HEP). Ecological Services Manual, 102. US Fish Wildlife Service. (1981). Standards Development Habitat Suitability Index Models. Ecological Services Manual, 103.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIplotter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plots habitat suitability index curves — HSIplotter","text":"","code":"# Get barredowl HSI model record from the `ecorest`package (example of # continuous metrics) barredowl_ecorest <- ecorest::HSImodels$barredowl # Create the plot HSIplotter(barredowl_ecorest) # Get americancoot HSI model record from the `ecorest`package (example of # continuous and categorical metrics) americancoot_ecorest <- ecorest::HSImodels$americancoot # Create the plot HSIplotter(americancoot_ecorest)"},{"path":"https://github.com/MVR-GIS/nybem/reference/ifelse.html","id":null,"dir":"Reference","previous_headings":"","what":"Raster Con Function — ifelse","title":"Raster Con Function — ifelse","text":"function designed behave similar ESRI Spatial Analyst Con function. purpose function provide R raster safe ifelse function.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/ifelse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Raster Con Function — ifelse","text":"","code":"ifelse(condition, true_value, false_value)"},{"path":"https://github.com/MVR-GIS/nybem/reference/ifelse.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Raster Con Function — ifelse","text":"condition raster numeric; expression results boolean, matching type condition. true_value raster, constant; Input true raster constant value. false_value raster, constant; Input false raster constant value.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/ifelse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Raster Con Function — ifelse","text":"true false value matching data type condition.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/ifelse.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Raster Con Function — ifelse","text":"function proposed Spacedman gis.stackexchange way back 2013, equivalent arcpy \"Con\" QGIS /R raster-package?","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/is_cat_raster.html","id":null,"dir":"Reference","previous_headings":"","what":"Is Catagorical Raster? — is_cat_raster","title":"Is Catagorical Raster? — is_cat_raster","text":"Catagorical Raster?","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/is_cat_raster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Is Catagorical Raster? — is_cat_raster","text":"","code":"is_cat_raster(ras)"},{"path":"https://github.com/MVR-GIS/nybem/reference/is_cat_raster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Is Catagorical Raster? — is_cat_raster","text":"ras raster; raster layer test.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/is_cat_raster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Is Catagorical Raster? — is_cat_raster","text":"logical; TRUE class type raster::RasterLayer factor.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/is_RasterLayer.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if RasterLayer — is_RasterLayer","title":"Test if RasterLayer — is_RasterLayer","text":"Used test object class raster::RasterLayer.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/is_RasterLayer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if RasterLayer — is_RasterLayer","text":"","code":"is_RasterLayer(x)"},{"path":"https://github.com/MVR-GIS/nybem/reference/is_RasterLayer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if RasterLayer — is_RasterLayer","text":"x object whose class tested.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/is_RasterLayer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test if RasterLayer — is_RasterLayer","text":"logical; TRUE class type raster::RasterLayer","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/nybem_submodels.html","id":null,"dir":"Reference","previous_headings":"","what":"NYBEM Submodels — nybem_submodels","title":"NYBEM Submodels — nybem_submodels","text":"list submodels used NYBEM feasibility study.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/nybem_submodels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"NYBEM Submodels — nybem_submodels","text":"","code":"nybem_submodels"},{"path":"https://github.com/MVR-GIS/nybem/reference/nybem_submodels.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"NYBEM Submodels — nybem_submodels","text":"list following named submodels: NYBEM.fresh.tid - Freshwater, Tidal Zone model. NYBEM.fresh.tid_labels - Freshwater, Tidal Zone labels. NYBEM.est.int - Estuarine, Intertidal Zone model. NYBEM.est.int_labels - Estuarine, Intertidal Zone labels. NYBEM.est.sub.hard - Estuarine, Subtidal Zone, Hard Bottom model. NYBEM.est.sub.hard_labels - Estuarine, Subtidal Zone, Hard Bottom labels. NYBEM.est.sub.soft.sav - Estuarine, Subtidal Zone, Soft Bottom, Submersed Aquatic Vegetation model. NYBEM.est.sub.soft.sav_labels - Estuarine, Subtidal Zone, Soft Bottom, Submersed Aquatic Vegetation labels. NYBEM.est.sub.soft.clam - Estuarine, Subtidal Zone, Soft Bottom, Hard Clam model. NYBEM.est.sub.soft.clam_labels - Estuarine, Subtidal Zone, Soft Bottom, Hard Clam labels. NYBEM.mar.int - Marine, Intertidal Zone model. NYBEM.mar.int_labels - Marine, Intertidal Zone labels. NYBEM.mar.sub - Marine, Subtidal Zone model. NYBEM.mar.sub_labels - Marine, Subtidal Zone labels. NYBEM.mar.deep - Marine, Deepwater Zone model. NYBEM.mar.deep_labels - Marine, Deepwater Zone labels.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/raster_fig.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a Raster Figure — raster_fig","title":"Create a Raster Figure — raster_fig","text":"Creates raster figure cropped specified extent","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/raster_fig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a Raster Figure — raster_fig","text":"","code":"raster_fig(ras, extent, title = \"Title\")"},{"path":"https://github.com/MVR-GIS/nybem/reference/raster_fig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a Raster Figure — raster_fig","text":"ras raster::RasterLayer; raster object. extent raster::Extent; extent object used crop raster. title character; title raster legend.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/raster_fig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a Raster Figure — raster_fig","text":"tmap object","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_habitat_zone.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Habitat Zone — set_habitat_zone","title":"Set Habitat Zone — set_habitat_zone","text":"Creates habitat zone raster input tidal zone salinity zones rasters.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_habitat_zone.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Habitat Zone — set_habitat_zone","text":"","code":"set_habitat_zone(tidal_zone, salinity_zone)"},{"path":"https://github.com/MVR-GIS/nybem/reference/set_habitat_zone.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Habitat Zone — set_habitat_zone","text":"tidal_zone raster; tidal zone raster. salinity_zone raster; salinity zone raster.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_habitat_zone.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Habitat Zone — set_habitat_zone","text":"categorical habitat zone RasterLayer : Upland Marine-Deep Marine-Subtidal Marine-Intertidal Estuarine-Subtidal Estuarine-Intertidal Freshwater","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_salinity_zone.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Salinity Zone — set_salinity_zone","title":"Set Salinity Zone — set_salinity_zone","text":"Creates Salinity Zone raster input salinity raster applying input threshold parameters.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_salinity_zone.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Salinity Zone — set_salinity_zone","text":"","code":"set_salinity_zone(salinity, estuarine_marine_break, fresh_estuarine_break)"},{"path":"https://github.com/MVR-GIS/nybem/reference/set_salinity_zone.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Salinity Zone — set_salinity_zone","text":"salinity raster; raster salinity measurements estimates. estuarine_marine_break numeric; salinity threshold estuarine marine zones. fresh_estuarine_break numeric; salinity threshold fresh estuarine zones.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_salinity_zone.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Salinity Zone — set_salinity_zone","text":"categorical salinity zone RasterLayer : Marine Estuarine Fresh","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_tidal_zone.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a Tidal Zone Raster — set_tidal_zone","title":"Create a Tidal Zone Raster — set_tidal_zone","text":"Creates tidal zone raster input rasters.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_tidal_zone.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a Tidal Zone Raster — set_tidal_zone","text":"","code":"set_tidal_zone(bed_elevation, MLLW, MHHW)"},{"path":"https://github.com/MVR-GIS/nybem/reference/set_tidal_zone.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a Tidal Zone Raster — set_tidal_zone","text":"bed_elevation RasterLayer; bed elevation raster. MLLW RasterLayer; Mean Higher High Water (MHHW) raster. MHHW RasterLayer; Mean Lower Low Water (MLLW) raster.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_tidal_zone.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a Tidal Zone Raster — set_tidal_zone","text":"tidal zone categorical RasterLayer : Deep Subtidal Intertidal Upland","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_tidal_zone.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a Tidal Zone Raster — set_tidal_zone","text":"z-values input rasters must expressed vertical datum (.e., National Tidal Datum Epoch, NAVD88).","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/SIcalc.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Suitability Indices — SIcalc","title":"Calculate Suitability Indices — SIcalc","text":"SIcalc computes suitability indices given set suitability curves project-specific inputs. Suitability indices may computed based either linear interpolation (continuous variables) lookup method (categorical variables).","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/SIcalc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Suitability Indices — SIcalc","text":"","code":"SIcalc(SI, input_proj)"},{"path":"https://github.com/MVR-GIS/nybem/reference/SIcalc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Suitability Indices — SIcalc","text":"SI data frame matrix; matrix suitability curves ordered parameter breakpoints associated suitability indices parameter. input_proj list; list numeric categorical vectors application-specific input parameters associated suitability curve data SI.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/SIcalc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Suitability Indices — SIcalc","text":"vector suitability index values match given user inputs. Values returned equal extreme range inputs outside model range.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/SIcalc.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Suitability Indices — SIcalc","text":"SI parameter must contain set column pairs. column pairs consist ","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/SIcalc.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate Suitability Indices — SIcalc","text":"US Fish Wildlife Service. (1980). Habitat basis environmental assessment. Ecological Services Manual, 101. US Fish Wildlife Service. (1980). Habitat Evaluation Procedures (HEP). Ecological Services Manual, 102. US Fish Wildlife Service. (1981). Standards Development Habitat Suitability Index Models. Ecological Services Manual, 103.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/SIcalc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Suitability Indices — SIcalc","text":"","code":"# Build manual model # Number of trees > 51cm diameter per 0.4 ha plot tree.num <- c(0, 2, 4, NA) # parameter breakpoints tree.num.SIV <- c(0.1, 1, 1, NA) # parameter suitability indices tree_num <- data.frame(tree.num, tree.num.SIV) # Mean diameter of overstory trees avg.dbh <- c(0, 5, 20, NA) # parameter breakpoints avg.dbh.SIV <- c(0, 0, 1, NA) # parameter suitability indices tree_diameter <- data.frame(avg.dbh, avg.dbh.SIV) # Percent canopy cover of overstory trees can.cov <- c(0, 20, 60, 100) # parameter breakpoints can.cov.SIV <- c(0, 0, 1, 1) # parameter suitability indices canopy_cov <- data.frame(can.cov, can.cov.SIV) barredowl <- data.frame(tree_num, tree_diameter, canopy_cov) bo_test1 <- list(2, 5, 20) # Barredowl si values bo_si_1 <- nybem::SIcalc(barredowl, bo_test1)"},{"path":"https://github.com/MVR-GIS/nybem/reference/write_cat_tif.html","id":null,"dir":"Reference","previous_headings":"","what":"Write Catagorical Raster TIFF file — write_cat_tif","title":"Write Catagorical Raster TIFF file — write_cat_tif","text":"Writes catagorical raster file .tiff format correct raster attribute table information read ESRI ArcGIS products.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/write_cat_tif.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write Catagorical Raster TIFF file — write_cat_tif","text":"","code":"write_cat_tif(cat_raster, out_dir, out_name)"},{"path":"https://github.com/MVR-GIS/nybem/reference/write_cat_tif.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write Catagorical Raster TIFF file — write_cat_tif","text":"cat_raster raster::Raster*; catagorical raster. out_dir character; path folder. out_name character; file name.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/write_cat_tif.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Write Catagorical Raster TIFF file — write_cat_tif","text":"function used side-effect writing catagorical raster file.","code":""},{"path":[]},{"path":[]},{"path":[]}]
+[{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"getting-started","dir":"Articles","previous_headings":"","what":"Getting Started","title":"Using `nybem`","text":"install nybem package, install GitHub using remotes package:","code":"remotes::install_github(repo = \"MVR-GIS/nybem\")"},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"load-required-packages","dir":"Articles","previous_headings":"","what":"Load Required Packages","title":"Using `nybem`","text":"","code":"library(nybem) ## ## Attaching package: 'nybem' ## The following object is masked from 'package:base': ## ## ifelse library(raster) ## Warning: package 'raster' was built under R version 4.1.3 ## Loading required package: sp ## Warning: package 'sp' was built under R version 4.1.3"},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"list-the-nybem-models","dir":"Articles","previous_headings":"","what":"List the NYBEM Models","title":"Using `nybem`","text":"nybem package contains models created ecological modeling section NTBEM feasibility study. Notice nybem::nybem_submodels list contains pair data frames submodel study. pair dataframes named submodel represents (.e., NYBEM.fresh.tid = Freshwater Tidal Zone habitat model). first data frame contains habitat variables matching suitability index values, second data frame (*_labels) contains labels used plotting.","code":"# Load the model data nybem_submodels <- nybem::nybem_submodels # View the available submodels names(nybem_submodels) ## [1] \"NYBEM.fresh.tid\" \"NYBEM.fresh.tid_labels\" ## [3] \"NYBEM.est.int\" \"NYBEM.est.int_labels\" ## [5] \"NYBEM.est.sub.hard\" \"NYBEM.est.sub.hard_labels\" ## [7] \"NYBEM.est.sub.soft.sav\" \"NYBEM.est.sub.soft.sav_labels\" ## [9] \"NYBEM.est.sub.soft.clam\" \"NYBEM.est.sub.soft.clam_labels\" ## [11] \"NYBEM.mar.int\" \"NYBEM.mar.int_labels\" ## [13] \"NYBEM.mar.sub\" \"NYBEM.mar.sub_labels\" ## [15] \"NYBEM.mar.deep\" \"NYBEM.mar.deep_labels\""},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"view-the-suitability-index-data-frame","dir":"Articles","previous_headings":"","what":"View the Suitability Index data frame","title":"Using `nybem`","text":"","code":"# View the Freshwater Tidal model # View table of habitat variables and their suitability index values nybem_submodels$NYBEM.fresh.tid ## salinity.per salinity.SIV veg.cover.per veg.cover.SIV deposition ## 1 0 0 50 0.0 0 ## 2 20 1 57 0.5 1 ## 3 100 1 100 1.0 NA ## deposition.SIV ## 1 1 ## 2 0 ## 3 NA"},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"view-the-suitability-index-model-labels","dir":"Articles","previous_headings":"","what":"View the Suitability Index model labels","title":"Using `nybem`","text":"","code":"nybem_submodels$NYBEM.fresh.tid_labels ## model label variable ## 1 Freshwater, Tidal Salinity duration (% time > 0.5 psu) salinity ## 2 Freshwater, Tidal Vegetation Cover (%) veg.cover ## 3 Freshwater, Tidal Relative Depth deposition"},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"plot-the-suitability-index-values","dir":"Articles","previous_headings":"","what":"Plot the Suitability Index Values","title":"Using `nybem`","text":"","code":"# Freshwater, Tidal nybem::HSIplotter(nybem_submodels$NYBEM.fresh.tid, xlab = nybem_submodels$NYBEM.fresh.tid_labels$label, ylab = nybem_submodels$NYBEM.fresh.tid_labels$variable)"},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"create-site-observations","dir":"Articles","previous_headings":"","what":"Create Site Observations","title":"Using `nybem`","text":"","code":"# Single numeric site observations salinity <- 40 veg.cover <- 100 deposition <- 0 obs_1 <- list(salinity, veg.cover, deposition) obs_1 ## [[1]] ## [1] 40 ## ## [[2]] ## [1] 100 ## ## [[3]] ## [1] 0 # Raster site observations salinity_ras <- raster::raster(ncol = 2, nrow = 2, vals = rep_len(40, 4)) veg.cover_ras <- raster::raster(ncol = 2, nrow = 2, vals = rep_len(100, 4)) deposition_ras <- raster::raster(ncol = 2, nrow = 2, vals = rep_len(0, 4)) obs_2 <- list(salinity_ras, veg.cover_ras, deposition_ras) obs_2 ## [[1]] ## class : RasterLayer ## dimensions : 2, 2, 4 (nrow, ncol, ncell) ## resolution : 180, 90 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## crs : +proj=longlat +datum=WGS84 +no_defs ## source : memory ## names : layer ## values : 40, 40 (min, max) ## ## ## [[2]] ## class : RasterLayer ## dimensions : 2, 2, 4 (nrow, ncol, ncell) ## resolution : 180, 90 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## crs : +proj=longlat +datum=WGS84 +no_defs ## source : memory ## names : layer ## values : 100, 100 (min, max) ## ## ## [[3]] ## class : RasterLayer ## dimensions : 2, 2, 4 (nrow, ncol, ncell) ## resolution : 180, 90 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## crs : +proj=longlat +datum=WGS84 +no_defs ## source : memory ## names : layer ## values : 0, 0 (min, max)"},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"calculate-suitability-index-values","dir":"Articles","previous_headings":"","what":"Calculate Suitability Index Values","title":"Using `nybem`","text":"","code":"# Suitability Index value for single numeric site observations siv_fresh.tid_obs_1 <- nybem::SIcalc(SI = nybem_submodels$NYBEM.fresh.tid, input_proj = obs_1) siv_fresh.tid_obs_1 ## [[1]] ## [1] 1 ## ## [[2]] ## [1] 1 ## ## [[3]] ## [1] 1 # Suitability Index value for raster site observations siv_fresh.tid_obs_2 <- nybem::SIcalc(SI = nybem_submodels$NYBEM.fresh.tid, input_proj = obs_2) siv_fresh.tid_obs_2 ## [[1]] ## class : RasterLayer ## dimensions : 2, 2, 4 (nrow, ncol, ncell) ## resolution : 180, 90 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## crs : +proj=longlat +datum=WGS84 +no_defs ## source : memory ## names : layer ## values : 1, 1 (min, max) ## ## ## [[2]] ## class : RasterLayer ## dimensions : 2, 2, 4 (nrow, ncol, ncell) ## resolution : 180, 90 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## crs : +proj=longlat +datum=WGS84 +no_defs ## source : memory ## names : layer ## values : 1, 1 (min, max) ## ## ## [[3]] ## class : RasterLayer ## dimensions : 2, 2, 4 (nrow, ncol, ncell) ## resolution : 180, 90 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## crs : +proj=longlat +datum=WGS84 +no_defs ## source : memory ## names : layer ## values : 1, 1 (min, max)"},{"path":"https://github.com/MVR-GIS/nybem/articles/Using_nybem.html","id":"calculate-habitat-suitability-index","dir":"Articles","previous_headings":"","what":"Calculate Habitat Suitability Index","title":"Using `nybem`","text":"","code":"# Calculate HSI for single numeric site observations hsi_fresh.tid_obs_1 <- nybem::HSIcalc(si_list = siv_fresh.tid_obs_1) hsi_fresh.tid_obs_1 ## [1] 1 # Calculate HSI for raster site observations hsi_fresh.tid_obs_2 <- nybem::HSIcalc(si_list = siv_fresh.tid_obs_2) hsi_fresh.tid_obs_2 ## class : RasterLayer ## dimensions : 2, 2, 4 (nrow, ncol, ncell) ## resolution : 180, 90 (x, y) ## extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax) ## crs : +proj=longlat +datum=WGS84 +no_defs ## source : memory ## names : layer ## values : 1, 1 (min, max)"},{"path":"https://github.com/MVR-GIS/nybem/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Michael Dougherty. Author, maintainer. Kyle McKay. Author.","code":""},{"path":"https://github.com/MVR-GIS/nybem/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Dougherty M, McKay K (2022). nybem: NY Bight Ecological Model. R package version 0.1.4, https://github.com/MVR-GIS/nybem.","code":"@Manual{, title = {nybem: NY Bight Ecological Model}, author = {Michael Dougherty and Kyle McKay}, year = {2022}, note = {R package version 0.1.4}, url = {https://github.com/MVR-GIS/nybem}, }"},{"path":[]},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement Michael.P.Dougherty@usace.army.mil. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://github.com/MVR-GIS/nybem/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"nybem","dir":"","previous_headings":"","what":"NY Bight Ecological Model","title":"NY Bight Ecological Model","text":"R package performing coastal habitat modeling.","code":""},{"path":[]},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"description","dir":"","previous_headings":"","what":"Description","title":"NY Bight Ecological Model","text":"package contains collection functions modeling coastal habitat ongoing USACE studies New Jersey Back Bays (NJBB) NY/NJ Harbor Tributaries Study (HATS).","code":""},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"funding","dir":"","previous_headings":"","what":"Funding","title":"NY Bight Ecological Model","text":"Funding development maintenance nybem provided following US Army Corps Engineers (USACE) programs: NY/NJ Harbor Tributaries Study (HATS) New Jersey Back Bays (NJBB)","code":""},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"latest-updates","dir":"","previous_headings":"","what":"Latest Updates","title":"NY Bight Ecological Model","text":"Check NEWS details latest updates.","code":""},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"authors","dir":"","previous_headings":"","what":"Authors","title":"NY Bight Ecological Model","text":"Michael Dougherty, Geographer, Rock Island District, U.S. Army Corps Engineers https://orcid.org/0000-0002-1465-5927 Kyle McKay, Research Civil Engineer, Engineer Research Development Center, Environmental Laboratory, U.S. Army Corps Engineers https://orcid.org/0000-0003-2703-3841","code":""},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"install","dir":"","previous_headings":"","what":"Install","title":"NY Bight Ecological Model","text":"install nybem package, install GitHub using remotes package:","code":"remotes::install_github(repo = \"MVR-GIS/nybem\")"},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"documentation","dir":"","previous_headings":"","what":"Documentation","title":"NY Bight Ecological Model","text":"Read documentation.","code":""},{"path":"https://github.com/MVR-GIS/nybem/index.html","id":"bug-reports","dir":"","previous_headings":"","what":"Bug Reports","title":"NY Bight Ecological Model","text":"find bugs using nybem, please open issue.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/are_colors.html","id":null,"dir":"Reference","previous_headings":"","what":"Are Colors? — are_colors","title":"Are Colors? — are_colors","text":"Determines input vector valid colors according grDevices::col2rgb function.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/are_colors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Are Colors? — are_colors","text":"","code":"are_colors(color_vector)"},{"path":"https://github.com/MVR-GIS/nybem/reference/are_colors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Are Colors? — are_colors","text":"color_vector vector; vector color values.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/are_colors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Are Colors? — are_colors","text":"logical vector.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/are_colors.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Are Colors? — are_colors","text":"Follows advice ","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/has_colortable.html","id":null,"dir":"Reference","previous_headings":"","what":"Has Colortable? — has_colortable","title":"Has Colortable? — has_colortable","text":"Determines RasterLayer valid colortable defined.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/has_colortable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Has Colortable? — has_colortable","text":"","code":"has_colortable(raster)"},{"path":"https://github.com/MVR-GIS/nybem/reference/has_colortable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Has Colortable? — has_colortable","text":"raster RasterLayer; raster tested.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/has_colortable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Has Colortable? — has_colortable","text":"Returns TRUE raster valid colortable.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIcalc.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Habitat Suitability Index (HSI) — HSIcalc","title":"Calculate Habitat Suitability Index (HSI) — HSIcalc","text":"Calculates habitat suitability index input suitability indices using specified method.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIcalc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Habitat Suitability Index (HSI) — HSIcalc","text":"","code":"HSIcalc(si_list, method = \"mean\")"},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIcalc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Habitat Suitability Index (HSI) — HSIcalc","text":"si_list list; list suitability indices. method character; method calculating suitability index. Must one \"mean\",","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIcalc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Habitat Suitability Index (HSI) — HSIcalc","text":"HSI object matching data format input suitability indices.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIcalc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Habitat Suitability Index (HSI) — HSIcalc","text":"","code":"# Build manual model # Number of trees > 51cm diameter per 0.4 ha plot tree.num <- c(0, 2, 4, NA) # parameter breakpoints tree.num.SIV <- c(0.1, 1, 1, NA) # parameter suitability indices tree_num <- data.frame(tree.num, tree.num.SIV) # Mean diameter of overstory trees avg.dbh <- c(0, 5, 20, NA) # parameter breakpoints avg.dbh.SIV <- c(0, 0, 1, NA) # parameter suitability indices tree_diameter <- data.frame(avg.dbh, avg.dbh.SIV) # Percent canopy cover of overstory trees can.cov <- c(0, 20, 60, 100) # parameter breakpoints can.cov.SIV <- c(0, 0, 1, 1) # parameter suitability indices canopy_cov <- data.frame(can.cov, can.cov.SIV) barredowl <- data.frame(tree_num, tree_diameter, canopy_cov) bo_test1 <- list(2, 5, 20) # Barredowl si values bo_si_1 <- nybem::SIcalc(barredowl, bo_test1) # Calculate HSI bo_hsi <- HSIcalc(si_list = bo_si_1)"},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIplotter.html","id":null,"dir":"Reference","previous_headings":"","what":"Plots habitat suitability index curves — HSIplotter","title":"Plots habitat suitability index curves — HSIplotter","text":"Plots habitat suitability index curves metrics model.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIplotter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plots habitat suitability index curves — HSIplotter","text":"","code":"HSIplotter(SI, xlab = NA, ylab = NA, ncol = 2)"},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIplotter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plots habitat suitability index curves — HSIplotter","text":"SI data frame; data frame suitability curves ordered parameter breakpoints associated suitability indices parameter appropriate column names. xlab character; vector x-axis label values SI. Defaults SI variable name. ylab character; vector y-axis label values SI. Defaults \"Suitability Index\". ncol numeric; Number columns plot.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIplotter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plots habitat suitability index curves — HSIplotter","text":"multipanel figure displaying suitability curves.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIplotter.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Plots habitat suitability index curves — HSIplotter","text":"US Fish Wildlife Service. (1980). Habitat basis environmental assessment. Ecological Services Manual, 101. US Fish Wildlife Service. (1980). Habitat Evaluation Procedures (HEP). Ecological Services Manual, 102. US Fish Wildlife Service. (1981). Standards Development Habitat Suitability Index Models. Ecological Services Manual, 103.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/HSIplotter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plots habitat suitability index curves — HSIplotter","text":"","code":"# Get barredowl HSI model record from the `ecorest`package (example of # continuous metrics) barredowl_ecorest <- ecorest::HSImodels$barredowl # Create the plot HSIplotter(barredowl_ecorest) # Get americancoot HSI model record from the `ecorest`package (example of # continuous and categorical metrics) americancoot_ecorest <- ecorest::HSImodels$americancoot # Create the plot HSIplotter(americancoot_ecorest)"},{"path":"https://github.com/MVR-GIS/nybem/reference/ifelse.html","id":null,"dir":"Reference","previous_headings":"","what":"Raster Con Function — ifelse","title":"Raster Con Function — ifelse","text":"function designed behave similar ESRI Spatial Analyst Con function. purpose function provide R raster safe ifelse function.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/ifelse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Raster Con Function — ifelse","text":"","code":"ifelse(condition, true_value, false_value)"},{"path":"https://github.com/MVR-GIS/nybem/reference/ifelse.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Raster Con Function — ifelse","text":"condition raster numeric; expression results boolean, matching type condition. true_value raster, constant; Input true raster constant value. false_value raster, constant; Input false raster constant value.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/ifelse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Raster Con Function — ifelse","text":"true false value matching data type condition.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/ifelse.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Raster Con Function — ifelse","text":"function proposed Spacedman gis.stackexchange way back 2013, equivalent arcpy \"Con\" QGIS /R raster-package?","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/is_cat_raster.html","id":null,"dir":"Reference","previous_headings":"","what":"Is Catagorical Raster? — is_cat_raster","title":"Is Catagorical Raster? — is_cat_raster","text":"Catagorical Raster?","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/is_cat_raster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Is Catagorical Raster? — is_cat_raster","text":"","code":"is_cat_raster(ras)"},{"path":"https://github.com/MVR-GIS/nybem/reference/is_cat_raster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Is Catagorical Raster? — is_cat_raster","text":"ras raster; raster layer test.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/is_cat_raster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Is Catagorical Raster? — is_cat_raster","text":"logical; TRUE class type raster::RasterLayer factor.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/is_RasterLayer.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if RasterLayer — is_RasterLayer","title":"Test if RasterLayer — is_RasterLayer","text":"Used test object class raster::RasterLayer.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/is_RasterLayer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if RasterLayer — is_RasterLayer","text":"","code":"is_RasterLayer(x)"},{"path":"https://github.com/MVR-GIS/nybem/reference/is_RasterLayer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if RasterLayer — is_RasterLayer","text":"x object whose class tested.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/is_RasterLayer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test if RasterLayer — is_RasterLayer","text":"logical; TRUE class type raster::RasterLayer","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/nybem_submodels.html","id":null,"dir":"Reference","previous_headings":"","what":"NYBEM Submodels — nybem_submodels","title":"NYBEM Submodels — nybem_submodels","text":"list submodels used NYBEM feasibility study.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/nybem_submodels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"NYBEM Submodels — nybem_submodels","text":"","code":"nybem_submodels"},{"path":"https://github.com/MVR-GIS/nybem/reference/nybem_submodels.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"NYBEM Submodels — nybem_submodels","text":"list following named submodels: NYBEM.fresh.tid - Freshwater, Tidal Zone model. NYBEM.fresh.tid_labels - Freshwater, Tidal Zone labels. NYBEM.est.int - Estuarine, Intertidal Zone model. NYBEM.est.int_labels - Estuarine, Intertidal Zone labels. NYBEM.est.sub.hard - Estuarine, Subtidal Zone, Hard Bottom model. NYBEM.est.sub.hard_labels - Estuarine, Subtidal Zone, Hard Bottom labels. NYBEM.est.sub.soft.sav - Estuarine, Subtidal Zone, Soft Bottom, Submersed Aquatic Vegetation model. NYBEM.est.sub.soft.sav_labels - Estuarine, Subtidal Zone, Soft Bottom, Submersed Aquatic Vegetation labels. NYBEM.est.sub.soft.clam - Estuarine, Subtidal Zone, Soft Bottom, Hard Clam model. NYBEM.est.sub.soft.clam_labels - Estuarine, Subtidal Zone, Soft Bottom, Hard Clam labels. NYBEM.mar.int - Marine, Intertidal Zone model. NYBEM.mar.int_labels - Marine, Intertidal Zone labels. NYBEM.mar.sub - Marine, Subtidal Zone model. NYBEM.mar.sub_labels - Marine, Subtidal Zone labels. NYBEM.mar.deep - Marine, Deepwater Zone model. NYBEM.mar.deep_labels - Marine, Deepwater Zone labels.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/raster_fig.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a Raster Figure — raster_fig","title":"Create a Raster Figure — raster_fig","text":"Creates raster figure cropped specified extent","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/raster_fig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a Raster Figure — raster_fig","text":"","code":"raster_fig(ras, extent, title = \"Title\")"},{"path":"https://github.com/MVR-GIS/nybem/reference/raster_fig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a Raster Figure — raster_fig","text":"ras raster::RasterLayer; raster object. extent raster::Extent; extent object used crop raster. title character; title raster legend.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/raster_fig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a Raster Figure — raster_fig","text":"tmap object","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_habitat_zone.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Habitat Zone — set_habitat_zone","title":"Set Habitat Zone — set_habitat_zone","text":"Creates habitat zone raster input tidal zone salinity zones rasters.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_habitat_zone.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Habitat Zone — set_habitat_zone","text":"","code":"set_habitat_zone(tidal_zone, salinity_zone)"},{"path":"https://github.com/MVR-GIS/nybem/reference/set_habitat_zone.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Habitat Zone — set_habitat_zone","text":"tidal_zone raster; tidal zone raster. salinity_zone raster; salinity zone raster.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_habitat_zone.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Habitat Zone — set_habitat_zone","text":"categorical habitat zone RasterLayer : Upland Marine-Deep Marine-Subtidal Marine-Intertidal Estuarine-Subtidal Estuarine-Intertidal Freshwater","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_salinity_zone.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Salinity Zone — set_salinity_zone","title":"Set Salinity Zone — set_salinity_zone","text":"Creates Salinity Zone raster input salinity raster applying input threshold parameters.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_salinity_zone.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Salinity Zone — set_salinity_zone","text":"","code":"set_salinity_zone(salinity, estuarine_marine_break, fresh_estuarine_break)"},{"path":"https://github.com/MVR-GIS/nybem/reference/set_salinity_zone.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Salinity Zone — set_salinity_zone","text":"salinity raster; raster salinity measurements estimates. estuarine_marine_break numeric; salinity threshold estuarine marine zones. fresh_estuarine_break numeric; salinity threshold fresh estuarine zones.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_salinity_zone.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Salinity Zone — set_salinity_zone","text":"categorical salinity zone RasterLayer : Marine Estuarine Fresh","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_tidal_zone.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a Tidal Zone Raster — set_tidal_zone","title":"Create a Tidal Zone Raster — set_tidal_zone","text":"Creates tidal zone raster input rasters.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_tidal_zone.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a Tidal Zone Raster — set_tidal_zone","text":"","code":"set_tidal_zone(bed_elevation, MLLW, MHHW)"},{"path":"https://github.com/MVR-GIS/nybem/reference/set_tidal_zone.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a Tidal Zone Raster — set_tidal_zone","text":"bed_elevation RasterLayer; bed elevation raster. MLLW RasterLayer; Mean Higher High Water (MHHW) raster. MHHW RasterLayer; Mean Lower Low Water (MLLW) raster.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_tidal_zone.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a Tidal Zone Raster — set_tidal_zone","text":"tidal zone categorical RasterLayer : Deep Subtidal Intertidal Upland","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/set_tidal_zone.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a Tidal Zone Raster — set_tidal_zone","text":"z-values input rasters must expressed vertical datum (.e., National Tidal Datum Epoch, NAVD88).","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/SIcalc.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Suitability Indices — SIcalc","title":"Calculate Suitability Indices — SIcalc","text":"SIcalc computes suitability indices given set suitability curves project-specific inputs. Suitability indices may computed based either linear interpolation (continuous variables) lookup method (categorical variables).","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/SIcalc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Suitability Indices — SIcalc","text":"","code":"SIcalc(SI, input_proj)"},{"path":"https://github.com/MVR-GIS/nybem/reference/SIcalc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Suitability Indices — SIcalc","text":"SI data frame matrix; matrix suitability curves ordered parameter breakpoints associated suitability indices parameter. input_proj list; list numeric categorical vectors application-specific input parameters associated suitability curve data SI.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/SIcalc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Suitability Indices — SIcalc","text":"vector suitability index values match given user inputs. Values returned equal extreme range inputs outside model range.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/SIcalc.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Suitability Indices — SIcalc","text":"SI parameter must contain set column pairs. column pairs consist ","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/SIcalc.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate Suitability Indices — SIcalc","text":"US Fish Wildlife Service. (1980). Habitat basis environmental assessment. Ecological Services Manual, 101. US Fish Wildlife Service. (1980). Habitat Evaluation Procedures (HEP). Ecological Services Manual, 102. US Fish Wildlife Service. (1981). Standards Development Habitat Suitability Index Models. Ecological Services Manual, 103.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/SIcalc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Suitability Indices — SIcalc","text":"","code":"# Build manual model # Number of trees > 51cm diameter per 0.4 ha plot tree.num <- c(0, 2, 4, NA) # parameter breakpoints tree.num.SIV <- c(0.1, 1, 1, NA) # parameter suitability indices tree_num <- data.frame(tree.num, tree.num.SIV) # Mean diameter of overstory trees avg.dbh <- c(0, 5, 20, NA) # parameter breakpoints avg.dbh.SIV <- c(0, 0, 1, NA) # parameter suitability indices tree_diameter <- data.frame(avg.dbh, avg.dbh.SIV) # Percent canopy cover of overstory trees can.cov <- c(0, 20, 60, 100) # parameter breakpoints can.cov.SIV <- c(0, 0, 1, 1) # parameter suitability indices canopy_cov <- data.frame(can.cov, can.cov.SIV) barredowl <- data.frame(tree_num, tree_diameter, canopy_cov) bo_test1 <- list(2, 5, 20) # Barredowl si values bo_si_1 <- nybem::SIcalc(barredowl, bo_test1)"},{"path":"https://github.com/MVR-GIS/nybem/reference/write_cat_tif.html","id":null,"dir":"Reference","previous_headings":"","what":"Write Catagorical Raster TIFF file — write_cat_tif","title":"Write Catagorical Raster TIFF file — write_cat_tif","text":"Writes catagorical raster file .tiff format correct raster attribute table information read ESRI ArcGIS products.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/write_cat_tif.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write Catagorical Raster TIFF file — write_cat_tif","text":"","code":"write_cat_tif(cat_raster, out_dir, out_name)"},{"path":"https://github.com/MVR-GIS/nybem/reference/write_cat_tif.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write Catagorical Raster TIFF file — write_cat_tif","text":"cat_raster raster::Raster*; catagorical raster. out_dir character; path folder. out_name character; file name.","code":""},{"path":"https://github.com/MVR-GIS/nybem/reference/write_cat_tif.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Write Catagorical Raster TIFF file — write_cat_tif","text":"function used side-effect writing catagorical raster file.","code":""},{"path":[]},{"path":"https://github.com/MVR-GIS/nybem/news/index.html","id":"major-changes-0-1-4","dir":"Changelog","previous_headings":"","what":"Major Changes","title":"nybem v0.1.4 (Release date: 2022-05-05)","text":"Added package documentation preparation USACE ECO-PCX model review. Added nybem_submodels containing ecological models New Jersey Back Bay study.","code":""},{"path":"https://github.com/MVR-GIS/nybem/news/index.html","id":"bug-fixes-0-1-4","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"nybem v0.1.4 (Release date: 2022-05-05)","text":"Removed ecorest specific functions","code":""}]