From d10e9f24ae9865834f881d9bcff6ff7d2af12beb Mon Sep 17 00:00:00 2001 From: d2gex <34709566+d2gex@users.noreply.github.com> Date: Fri, 5 Apr 2024 15:52:16 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20d2gex/LH?= =?UTF-8?q?Tpicker@0860b2bffd4dfb1c8df5fbc67443954ba9a43380=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- pkgdown.yml | 2 +- reference/TaxonUpdatedLHTGetter.html | 176 +++++++++++++++++++++++++++ reference/index.html | 10 +- search.json | 2 +- sitemap.xml | 6 +- 5 files changed, 186 insertions(+), 10 deletions(-) create mode 100644 reference/TaxonUpdatedLHTGetter.html diff --git a/pkgdown.yml b/pkgdown.yml index 51647cb..cef3d7b 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: tutorial: tutorial.html -last_built: 2024-04-05T15:47Z +last_built: 2024-04-05T15:52Z urls: reference: https://d2gex.github.io/LHTpicker/reference article: https://d2gex.github.io/LHTpicker/articles diff --git a/reference/TaxonUpdatedLHTGetter.html b/reference/TaxonUpdatedLHTGetter.html new file mode 100644 index 0000000..e92f8dd --- /dev/null +++ b/reference/TaxonUpdatedLHTGetter.html @@ -0,0 +1,176 @@ + +Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter • LHTpicker + Skip to contents + + +
+
+
+

Single Taxon LHT Predictor class

+ +
TaxonUpdatedLHTGetter.Rd
+
+ +
+

Class that given some LHTs will fetch their predicted version according to FishLife covariance

+
+ + +
+

Value

+ + +

matrix-form LHT values to be passed on to FishLife

+
+
+

Super class

+

LHTpicker::MixinUtilities -> TaxonUpdatedLHTGetter

+
+
+

Public fields

+

common_columns_ds
+

common columns across the underlying data structure of FishLife. Taxa's LHT +could end up having additional fields that the overall covariance matrix does not support.

+ + +

+
+
+

Methods

+ +
+

Public methods

+ +

Inherited methods

+

Method new()

+ +
+

Usage

+

TaxonUpdatedLHTGetter$new(
+  master_db,
+  estimated_lhts,
+  estimated_lht_cov,
+  new_lhts,
+  func_domains
+)

+
+ +
+

Arguments

+

master_db
+

Fishlife database

+ + +
estimated_lhts
+

taxon's LHT numeric vector as fetched from Fishlife.

+ + +
new_lhts
+

predicting LHT list which names must conform to FishLife's expectations

+ + +
func_domains
+

list of transforming function which names must conform to FishLife's expectations

+ + +
estimated_lht_conv
+

taxon's covariance matrix as fetched from Fishlife

+ + +

+
+ +

+

Method generate_new_lht_matrix()

+

Generate the new LHT matrix in shape and mathematical domain expected by Fishlife

+

Usage

+

TaxonUpdatedLHTGetter$generate_new_lht_matrix()

+
+ + +

+

Method predict()

+

Generate a matrix with the new predicted LHTs given some initial values, both in log and log-converted space

+

Usage

+

TaxonUpdatedLHTGetter$predict()

+
+ + +

+

Method clone()

+

The objects of this class are cloneable with this method.

+

Usage

+

TaxonUpdatedLHTGetter$clone(deep = FALSE)

+
+ +
+

Arguments

+

deep
+

Whether to make a deep clone.

+ + +

+
+ +
+ +
+ +
+ + +
+ + + + + + + diff --git a/reference/index.html b/reference/index.html index 8551050..8bd315f 100644 --- a/reference/index.html +++ b/reference/index.html @@ -73,11 +73,6 @@

All functionsTaxonLHTPredictor - -
Single Taxon LHT Predictor class
-
- TaxonPredictedLHTGetter
Single Taxon LHT GRABBER class
@@ -88,6 +83,11 @@

All functionsTaxonUpdatedLHTGetter + +
Single Taxon LHT Predictor class
+

+ UpdatedLHTGenerator
Multiple Updated LHT Generator class
diff --git a/search.json b/search.json index 70a98ae..31fceb4 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/articles/tutorial.html","id":"inputted-taxa-details","dir":"Articles","previous_headings":"1. Fetch wanted LHTs from FishLife","what":"1.1 Inputted taxa details","title":"Tutorial: Use Cases","text":"csv file taxon names wanted LHTs required shown ","code":"taxon_lhts_to_fetch <- readRDS(\"vignettes/data/wanted_taxon_details.rds\") head(taxon_lhts_to_fetch) #> taxon Linf Winf K L50 M Amat Amax Temperature #> 1 Trisopterus luscus NA NA NA NA NA NA NA NA #> 2 Pollachius pollachius NA NA NA NA NA NA NA NA"},{"path":"https://d2gex.github.io/LHTpicker/articles/tutorial.html","id":"fetching-predicted-lhts","dir":"Articles","previous_headings":"1. Fetch wanted LHTs from FishLife","what":"1.2 Fetching predicted LHTs","title":"Tutorial: Use Cases","text":"","code":"p_lht_picker <- PredictedLHTPicker$new(FishLife::FishBase_and_Morphometrics, fishlife_context$lht_names, fishlife_context$backtransform_function_list, taxon_lhts_to_fetch) predicted_lht_df <- p_lht_picker$pick_and_backtransform() head(predicted_lht_df) #> taxon Linf Winf K L50 M #> 1 Trisopterus luscus 43.86770 833.9878 0.3737931 19.52203 0.5981946 #> 2 Pollachius pollachius 87.30785 5819.9735 0.1867131 34.71789 0.3085845 #> Amat Amax Temperature #> 1 1.400562 6.458926 17.36961 #> 2 3.456610 12.138258 12.11773"},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/articles/tutorial.html","id":"inputted-predicting-taxa-details","dir":"Articles","previous_headings":"2 Fetch updated LHTs given new data","what":"2.1 Inputted predicting taxa details","title":"Tutorial: Use Cases","text":"csv file taxon names wanted--update LHTs required shown ","code":"taxon_lhts_to_update <- readRDS(\"vignettes/data/wanted_update_taxon_details.rds\") head(taxon_lhts_to_update) #> taxon Linf Winf K L50 M Amat Amax Temperature #> 1 Trisopterus luscus 42.41 921 0.210 19.45 0.254 NA 9 14.3 #> 2 Pollachius pollachius 102.14 12045 0.193 41.60 0.284 NA 8 14.3"},{"path":"https://d2gex.github.io/LHTpicker/articles/tutorial.html","id":"fetching-updated-lhts","dir":"Articles","previous_headings":"2 Fetch updated LHTs given new data","what":"2.2 Fetching updated LHTs","title":"Tutorial: Use Cases","text":"","code":"u_lht_picker <- UpdatedLHTPicker$new( FishLife::FishBase_and_Morphometrics, taxon_lhts_to_update, fishlife_context$updated_prefix, fishlife_context$transform_function_list, fishlife_context$backtransform_function_list, fishlife_context$lht_names ) updated_lht_df <- u_lht_picker$pick_and_backtransform() head(updated_lht_df) #> taxon Linf Winf K L50 M Amat Amax Temperature #> 1 Trisopterus luscus 42.41 921 0.210 19.45 0.254 NA 9 14.3 #> 2 Pollachius pollachius 102.14 12045 0.193 41.60 0.284 NA 8 14.3 #> updated_Linf updated_Winf updated_K updated_M updated_L50 updated_Amax #> 1 44.24669 846.1382 0.3422767 0.5655704 19.91196 7.024725 #> 2 95.11434 8399.8020 0.1878959 0.2989860 36.52335 11.118416 #> updated_Amat updated_Temperature #> 1 1.445218 16.72769 #> 2 3.418150 13.05402"},{"path":"https://d2gex.github.io/LHTpicker/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Dan G. Author, maintainer.","code":""},{"path":"https://d2gex.github.io/LHTpicker/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"G D (2024). LHTpicker: Fishlife LHT picker. R package version 1.0, https://d2gex.github.io/LHTpicker/.","code":"@Manual{, title = {LHTpicker: Fishlife LHT picker}, author = {Dan G}, year = {2024}, note = {R package version 1.0}, url = {https://d2gex.github.io/LHTpicker/}, }"},{"path":"https://d2gex.github.io/LHTpicker/index.html","id":"lhtpicker","dir":"","previous_headings":"","what":"Fishlife LHT picker","title":"Fishlife LHT picker","text":"thin wrapper FishLife library helps abstract underlying data structure final user, easing fetching update local LHTs. following processes integrated: Fetch predicted LHTs ‘’ FishLife individual taxon. Provide predicting LHTs fetch updated predicted values FishLife individual taxon. processes, 1 2 can accomplished streamline fashion multiple taxa via csv file. Please look tutorial understand works.","code":""},{"path":"https://d2gex.github.io/LHTpicker/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Fishlife LHT picker","text":"R package can installed devtools follows:","code":"devtools::install_github(\"https://github.com/d2gex/LHTpicker\", dep=TRUE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":null,"dir":"Reference","previous_headings":"","what":"Fishlife Context class — FishlifeLHTNameSpace","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"Class allows transition user-defined LHT names specifically used Fishlife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"updated_prefix string added obtained LHT FishLife lht_names User-defined list LHT names associated expected FishLife names transform_function_list Forward function conversion required user-defined parameter. backtransform_function_list Backward function conversion required obtained LHT value.","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"FishlifeLHTNameSpace$new() FishlifeLHTNameSpace$clone()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"Initialise Fishlife Context class","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"","code":"FishlifeLHTNameSpace$new( updated_prefix = \"updated\", lht_names = list(Linf = \"log(length_infinity)\", Winf = \"log(weight_infinity)\", K = \"log(growth_coefficient)\", M = \"log(natural_mortality)\", L50 = \"log(length_maturity)\", Amax = \"log(age_max)\", Amat = \"log(age_maturity)\", Temperature = \"temperature\"), transform_function_list = list(`log(length_infinity)` = log, `log(weight_infinity)` = log, `log(growth_coefficient)` = log, `log(natural_mortality)` = log, `log(length_maturity)` = log, `log(age_max)` = log, `log(age_maturity)` = log, temperature = base::identity), backtransform_function_list = list(`log(length_infinity)` = exp, `log(weight_infinity)` = exp, `log(growth_coefficient)` = exp, `log(natural_mortality)` = exp, `log(length_maturity)` = exp, `log(age_max)` = exp, `log(age_maturity)` = exp, temperature = base::identity) )"},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"","code":"FishlifeLHTNameSpace$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":null,"dir":"Reference","previous_headings":"","what":"Mixin Utility class — MixinUtilities","title":"Mixin Utility class — MixinUtilities","text":"class holds util methods used across classes R package","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Mixin Utility class — MixinUtilities","text":"MixinUtilities$create_empty_dataframe() MixinUtilities$list_of_vectors_to_dataframe() MixinUtilities$apply_func_to_df() MixinUtilities$clone()","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mixin Utility class — MixinUtilities","text":"","code":"MixinUtilities$create_empty_dataframe(col_names)"},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Mixin Utility class — MixinUtilities","text":"","code":"MixinUtilities$list_of_vectors_to_dataframe(lht_list)"},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Mixin Utility class — MixinUtilities","text":"","code":"MixinUtilities$apply_func_to_df(data, func_space)"},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Mixin Utility class — MixinUtilities","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Mixin Utility class — MixinUtilities","text":"","code":"MixinUtilities$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mixin Utility class — MixinUtilities","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":null,"dir":"Reference","previous_headings":"","what":"Multiple Taxon Collector class — PredictedLHTPicker","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"Fetch, transform build predicted LHT dataframe multiple species obtained FishLife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"dataframe keeps LHT values per taxon subset matrix LHT values","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"LHTpicker::MixinUtilities -> PredictedLHTPicker","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"LHTpicker::MixinUtilities$apply_func_to_df() LHTpicker::MixinUtilities$create_empty_dataframe() LHTpicker::MixinUtilities$list_of_vectors_to_dataframe()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"PredictedLHTPicker$new() PredictedLHTPicker$pick_and_backtransform() PredictedLHTPicker$clone()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"Initialise PredictedLHTPicker","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"","code":"PredictedLHTPicker$new( master_db, lht_names, backtransform_function_list, wanted_lht_df )"},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"master_db Fishlife database lht_names list user-defined LHT names associated FishLife's counterparts backtransform_function_list list backward-transformation functions applied obtained LHT FishLife wanted_lht_df dataframe holding wanted taxa details rows LHT columns","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"method-pick-and-backtransform-","dir":"Reference","previous_headings":"","what":"Method pick_and_backtransform()","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"Pick backtransform LHT values per taxon beed obtained Fishlife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"","code":"PredictedLHTPicker$pick_and_backtransform()"},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"","code":"PredictedLHTPicker$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":null,"dir":"Reference","previous_headings":"","what":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"Class extracts transform predicted values LHTs multiple species obtained FishLife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"dataframe keeps original updated LHT values per taxon updated dataframe results original updated LHT values","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"LHTpicker::MixinUtilities -> TaxaUpdateExtractor","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"LHTpicker::MixinUtilities$apply_func_to_df() LHTpicker::MixinUtilities$create_empty_dataframe() LHTpicker::MixinUtilities$list_of_vectors_to_dataframe()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"TaxaUpdateExtractor$new() TaxaUpdateExtractor$extract_and_backtransform() TaxaUpdateExtractor$clone()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"Initialise TaxaPredictionExtractor","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"","code":"TaxaUpdateExtractor$new( update_prefix, lht_names, backtransform_function_list, predicting_lht_df, updated_lht_list )"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"update_prefix string added prefix column names keeping obtained new LHT values lht_names list user-defined LHT names associated FishLife's counterparts backtransform_function_list list backward-transformation functions applied obtained LHT FishLife predicting_lht_df dataframe keeping original inputted LHTs per taxon updated_lht_list list updated LHTs per taxon obtained Fishlife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"method-extract-and-backtransform-","dir":"Reference","previous_headings":"","what":"Method extract_and_backtransform()","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"Extract backtransform updated LHT values per taxon beed obtained Fishlife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"","code":"TaxaUpdateExtractor$extract_and_backtransform()"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"","code":"TaxaUpdateExtractor$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":null,"dir":"Reference","previous_headings":"","what":"Single Taxon LHT Predictor class — TaxonLHTPredictor","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"Class given LHTs fetch predicted version according FishLife covariance","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"matrix-form LHT values passed FishLife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"LHTpicker::MixinUtilities -> TaxonLHTPredictor","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"common_columns_ds common columns across underlying data structure FishLife. Taxa's LHT end additional fields overall covariance matrix support.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"LHTpicker::MixinUtilities$apply_func_to_df() LHTpicker::MixinUtilities$create_empty_dataframe() LHTpicker::MixinUtilities$list_of_vectors_to_dataframe()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"TaxonLHTPredictor$new() TaxonLHTPredictor$generate_new_lht_matrix() TaxonLHTPredictor$predict() TaxonLHTPredictor$clone()","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"","code":"TaxonLHTPredictor$new( master_db, estimated_lhts, estimated_lht_cov, new_lhts, func_domains )"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"master_db Fishlife database estimated_lhts taxon's LHT numeric vector fetched Fishlife. new_lhts predicting LHT list names must conform FishLife's expectations func_domains list transforming function names must conform FishLife's expectations estimated_lht_conv taxon's covariance matrix fetched Fishlife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":"method-generate-new-lht-matrix-","dir":"Reference","previous_headings":"","what":"Method generate_new_lht_matrix()","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"Generate new LHT matrix shape mathematical domain expected Fishlife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"","code":"TaxonLHTPredictor$generate_new_lht_matrix()"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":"method-predict-","dir":"Reference","previous_headings":"","what":"Method predict()","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"Generate matrix new predicted LHTs given initial values, log log-converted space","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"","code":"TaxonLHTPredictor$predict()"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"","code":"TaxonLHTPredictor$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Single Taxon LHT Predictor class — TaxonLHTPredictor","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":null,"dir":"Reference","previous_headings":"","what":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"Abstracts away underlying FishLife dynamics grab predicted LHT details given taxon","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"list three elements: ) database unique identifier sought taxon b) predicted stored LHTs taxon c) convariance matrix parameters associated sought taxon","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"TaxonPredictedLHTGetter$new() TaxonPredictedLHTGetter$extract() TaxonPredictedLHTGetter$clone()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"Initialise Taxon LHT Grabber class","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"","code":"TaxonPredictedLHTGetter$new(master_db, taxon)"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"master_db Fishlife database taxon string holding taxon name","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"method-extract-","dir":"Reference","previous_headings":"","what":"Method extract()","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"Fetch sought taxon details","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"","code":"TaxonPredictedLHTGetter$extract()"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"","code":"TaxonPredictedLHTGetter$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":null,"dir":"Reference","previous_headings":"","what":"Single Taxon Update Extractor class — TaxonUpdateExtractor","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"Class extracts transform predicted values LHTs single species obtained FishLife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"dataframe backtransformed LHT values","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"TaxonUpdateExtractor$new() TaxonUpdateExtractor$extract_and_backtransform() TaxonUpdateExtractor$clone()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"Initialise TaxonPredictionExtractor","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"","code":"TaxonUpdateExtractor$new( update_prefix, lht_names, backtransform_function_list, predicted_results )"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"update_prefix string added prefix column names keeping obtained new LHT values lht_names list user-defined LHT names associated FishLife's counterparts backtransform_function_list list backward-transformation functions applied obtained LHT FishLife predicted_results matrix predicted results FishLife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"method-extract-and-backtransform-","dir":"Reference","previous_headings":"","what":"Method extract_and_backtransform()","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"Extract backtransform updated LHT values FishLife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"","code":"TaxonUpdateExtractor$extract_and_backtransform()"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"","code":"TaxonUpdateExtractor$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":null,"dir":"Reference","previous_headings":"","what":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"Allows streamline-generation updated LHTs given new data.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"list LHT matrices, name list corresponds single taxon unnamed list LHT values per taxon renamed list lht names conform Fishlife's expected patterns list LHT values (another list) taxon","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"UpdatedLHTGenerator$new() UpdatedLHTGenerator$update() UpdatedLHTGenerator$clone()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"Initialise Updated LHT Generator class","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"","code":"UpdatedLHTGenerator$new( master_db, predicting_lht_df, transform_function_list, lht_names )"},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"master_db Fishlife database predicting_lht_df dataframe providing taxon details predicting LHT values transform_function_list list transforming function names must conform FishLife's expectations lht_names list user-defined LHT names associated FishLife's counterparts","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"method-update-","dir":"Reference","previous_headings":"","what":"Method update()","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"Update given LHTs per taxon according new predicted value yielded FishLfe","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"","code":"UpdatedLHTGenerator$update()"},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"","code":"UpdatedLHTGenerator$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTPicker.html","id":null,"dir":"Reference","previous_headings":"","what":"Taxa's updated LHT picker — UpdatedLHTPicker","title":"Taxa's updated LHT picker — UpdatedLHTPicker","text":"Fetch, transform build dataframe updated LHT values per taxon obtained FishLife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTPicker.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Taxa's updated LHT picker — UpdatedLHTPicker","text":"dataframe predicting updated LHTs. latter prefixed keyword.","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTPicker.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Taxa's updated LHT picker — UpdatedLHTPicker","text":"UpdatedLHTPicker$new() UpdatedLHTPicker$pick_and_backtransform() UpdatedLHTPicker$clone()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTPicker.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Taxa's updated LHT picker — UpdatedLHTPicker","text":"Initialise UpdatedLHTPicker class","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTPicker.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Taxa's updated LHT picker — UpdatedLHTPicker","text":"","code":"UpdatedLHTPicker$new( master_db, predicting_lht_df, updated_prefix, transform_function_list, backtransform_function_list, lht_names = NULL )"},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTPicker.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Taxa's updated LHT picker — UpdatedLHTPicker","text":"master_db Fishlife database predicting_lht_df dataframe keeping original inputted LHTs per taxon transform_function_list list transforming function names must conform FishLife's expectations backtransform_function_list list backward-transformation functions applied obtained LHT FishLife lht_names list user-defined LHT names associated FishLife's counterparts update_prefix string added prefix column names keeping obtained new LHT values","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTPicker.html","id":"method-pick-and-backtransform-","dir":"Reference","previous_headings":"","what":"Method pick_and_backtransform()","title":"Taxa's updated LHT picker — UpdatedLHTPicker","text":"Build dataframe updated LHT wanted taxon ","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTPicker.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Taxa's updated LHT picker — UpdatedLHTPicker","text":"","code":"UpdatedLHTPicker$pick_and_backtransform()"},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTPicker.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Taxa's updated LHT picker — UpdatedLHTPicker","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTPicker.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Taxa's updated LHT picker — UpdatedLHTPicker","text":"","code":"UpdatedLHTPicker$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTPicker.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Taxa's updated LHT picker — UpdatedLHTPicker","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://d2gex.github.io/LHTpicker/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling `rhs(lhs)`.","code":""}] +[{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/articles/tutorial.html","id":"inputted-taxa-details","dir":"Articles","previous_headings":"1. Fetch wanted LHTs from FishLife","what":"1.1 Inputted taxa details","title":"Tutorial: Use Cases","text":"csv file taxon names wanted LHTs required shown ","code":"taxon_lhts_to_fetch <- readRDS(\"vignettes/data/wanted_taxon_details.rds\") head(taxon_lhts_to_fetch) #> taxon Linf Winf K L50 M Amat Amax Temperature #> 1 Trisopterus luscus NA NA NA NA NA NA NA NA #> 2 Pollachius pollachius NA NA NA NA NA NA NA NA"},{"path":"https://d2gex.github.io/LHTpicker/articles/tutorial.html","id":"fetching-predicted-lhts","dir":"Articles","previous_headings":"1. Fetch wanted LHTs from FishLife","what":"1.2 Fetching predicted LHTs","title":"Tutorial: Use Cases","text":"","code":"p_lht_picker <- PredictedLHTPicker$new(FishLife::FishBase_and_Morphometrics, fishlife_context$lht_names, fishlife_context$backtransform_function_list, taxon_lhts_to_fetch) predicted_lht_df <- p_lht_picker$pick_and_backtransform() head(predicted_lht_df) #> taxon Linf Winf K L50 M #> 1 Trisopterus luscus 43.86770 833.9878 0.3737931 19.52203 0.5981946 #> 2 Pollachius pollachius 87.30785 5819.9735 0.1867131 34.71789 0.3085845 #> Amat Amax Temperature #> 1 1.400562 6.458926 17.36961 #> 2 3.456610 12.138258 12.11773"},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/articles/tutorial.html","id":"inputted-predicting-taxa-details","dir":"Articles","previous_headings":"2 Fetch updated LHTs given new data","what":"2.1 Inputted predicting taxa details","title":"Tutorial: Use Cases","text":"csv file taxon names wanted--update LHTs required shown ","code":"taxon_lhts_to_update <- readRDS(\"vignettes/data/wanted_update_taxon_details.rds\") head(taxon_lhts_to_update) #> taxon Linf Winf K L50 M Amat Amax Temperature #> 1 Trisopterus luscus 42.41 921 0.210 19.45 0.254 NA 9 14.3 #> 2 Pollachius pollachius 102.14 12045 0.193 41.60 0.284 NA 8 14.3"},{"path":"https://d2gex.github.io/LHTpicker/articles/tutorial.html","id":"fetching-updated-lhts","dir":"Articles","previous_headings":"2 Fetch updated LHTs given new data","what":"2.2 Fetching updated LHTs","title":"Tutorial: Use Cases","text":"","code":"u_lht_picker <- UpdatedLHTPicker$new( FishLife::FishBase_and_Morphometrics, taxon_lhts_to_update, fishlife_context$updated_prefix, fishlife_context$transform_function_list, fishlife_context$backtransform_function_list, fishlife_context$lht_names ) updated_lht_df <- u_lht_picker$pick_and_backtransform() head(updated_lht_df) #> taxon Linf Winf K L50 M Amat Amax Temperature #> 1 Trisopterus luscus 42.41 921 0.210 19.45 0.254 NA 9 14.3 #> 2 Pollachius pollachius 102.14 12045 0.193 41.60 0.284 NA 8 14.3 #> updated_Linf updated_Winf updated_K updated_M updated_L50 updated_Amax #> 1 44.24669 846.1382 0.3422767 0.5655704 19.91196 7.024725 #> 2 95.11434 8399.8020 0.1878959 0.2989860 36.52335 11.118416 #> updated_Amat updated_Temperature #> 1 1.445218 16.72769 #> 2 3.418150 13.05402"},{"path":"https://d2gex.github.io/LHTpicker/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Dan G. Author, maintainer.","code":""},{"path":"https://d2gex.github.io/LHTpicker/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"G D (2024). LHTpicker: Fishlife LHT picker. R package version 1.0, https://d2gex.github.io/LHTpicker/.","code":"@Manual{, title = {LHTpicker: Fishlife LHT picker}, author = {Dan G}, year = {2024}, note = {R package version 1.0}, url = {https://d2gex.github.io/LHTpicker/}, }"},{"path":"https://d2gex.github.io/LHTpicker/index.html","id":"lhtpicker","dir":"","previous_headings":"","what":"Fishlife LHT picker","title":"Fishlife LHT picker","text":"thin wrapper FishLife library helps abstract underlying data structure final user, easing fetching update local LHTs. following processes integrated: Fetch predicted LHTs ‘’ FishLife individual taxon. Provide predicting LHTs fetch updated predicted values FishLife individual taxon. processes, 1 2 can accomplished streamline fashion multiple taxa via csv file. Please look tutorial understand works.","code":""},{"path":"https://d2gex.github.io/LHTpicker/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Fishlife LHT picker","text":"R package can installed devtools follows:","code":"devtools::install_github(\"https://github.com/d2gex/LHTpicker\", dep=TRUE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":null,"dir":"Reference","previous_headings":"","what":"Fishlife Context class — FishlifeLHTNameSpace","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"Class allows transition user-defined LHT names specifically used Fishlife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"updated_prefix string added obtained LHT FishLife lht_names User-defined list LHT names associated expected FishLife names transform_function_list Forward function conversion required user-defined parameter. backtransform_function_list Backward function conversion required obtained LHT value.","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"FishlifeLHTNameSpace$new() FishlifeLHTNameSpace$clone()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"Initialise Fishlife Context class","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"","code":"FishlifeLHTNameSpace$new( updated_prefix = \"updated\", lht_names = list(Linf = \"log(length_infinity)\", Winf = \"log(weight_infinity)\", K = \"log(growth_coefficient)\", M = \"log(natural_mortality)\", L50 = \"log(length_maturity)\", Amax = \"log(age_max)\", Amat = \"log(age_maturity)\", Temperature = \"temperature\"), transform_function_list = list(`log(length_infinity)` = log, `log(weight_infinity)` = log, `log(growth_coefficient)` = log, `log(natural_mortality)` = log, `log(length_maturity)` = log, `log(age_max)` = log, `log(age_maturity)` = log, temperature = base::identity), backtransform_function_list = list(`log(length_infinity)` = exp, `log(weight_infinity)` = exp, `log(growth_coefficient)` = exp, `log(natural_mortality)` = exp, `log(length_maturity)` = exp, `log(age_max)` = exp, `log(age_maturity)` = exp, temperature = base::identity) )"},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"","code":"FishlifeLHTNameSpace$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/FishlifeLHTNameSpace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fishlife Context class — FishlifeLHTNameSpace","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":null,"dir":"Reference","previous_headings":"","what":"Mixin Utility class — MixinUtilities","title":"Mixin Utility class — MixinUtilities","text":"class holds util methods used across classes R package","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Mixin Utility class — MixinUtilities","text":"MixinUtilities$create_empty_dataframe() MixinUtilities$list_of_vectors_to_dataframe() MixinUtilities$apply_func_to_df() MixinUtilities$clone()","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mixin Utility class — MixinUtilities","text":"","code":"MixinUtilities$create_empty_dataframe(col_names)"},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Mixin Utility class — MixinUtilities","text":"","code":"MixinUtilities$list_of_vectors_to_dataframe(lht_list)"},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Mixin Utility class — MixinUtilities","text":"","code":"MixinUtilities$apply_func_to_df(data, func_space)"},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Mixin Utility class — MixinUtilities","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Mixin Utility class — MixinUtilities","text":"","code":"MixinUtilities$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/MixinUtilities.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mixin Utility class — MixinUtilities","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":null,"dir":"Reference","previous_headings":"","what":"Multiple Taxon Collector class — PredictedLHTPicker","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"Fetch, transform build predicted LHT dataframe multiple species obtained FishLife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"dataframe keeps LHT values per taxon subset matrix LHT values","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"LHTpicker::MixinUtilities -> PredictedLHTPicker","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"LHTpicker::MixinUtilities$apply_func_to_df() LHTpicker::MixinUtilities$create_empty_dataframe() LHTpicker::MixinUtilities$list_of_vectors_to_dataframe()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"PredictedLHTPicker$new() PredictedLHTPicker$pick_and_backtransform() PredictedLHTPicker$clone()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"Initialise PredictedLHTPicker","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"","code":"PredictedLHTPicker$new( master_db, lht_names, backtransform_function_list, wanted_lht_df )"},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"master_db Fishlife database lht_names list user-defined LHT names associated FishLife's counterparts backtransform_function_list list backward-transformation functions applied obtained LHT FishLife wanted_lht_df dataframe holding wanted taxa details rows LHT columns","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"method-pick-and-backtransform-","dir":"Reference","previous_headings":"","what":"Method pick_and_backtransform()","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"Pick backtransform LHT values per taxon beed obtained Fishlife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"","code":"PredictedLHTPicker$pick_and_backtransform()"},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"","code":"PredictedLHTPicker$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/PredictedLHTPicker.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multiple Taxon Collector class — PredictedLHTPicker","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":null,"dir":"Reference","previous_headings":"","what":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"Class extracts transform predicted values LHTs multiple species obtained FishLife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"dataframe keeps original updated LHT values per taxon updated dataframe results original updated LHT values","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"LHTpicker::MixinUtilities -> TaxaUpdateExtractor","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"LHTpicker::MixinUtilities$apply_func_to_df() LHTpicker::MixinUtilities$create_empty_dataframe() LHTpicker::MixinUtilities$list_of_vectors_to_dataframe()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"TaxaUpdateExtractor$new() TaxaUpdateExtractor$extract_and_backtransform() TaxaUpdateExtractor$clone()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"Initialise TaxaPredictionExtractor","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"","code":"TaxaUpdateExtractor$new( update_prefix, lht_names, backtransform_function_list, predicting_lht_df, updated_lht_list )"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"update_prefix string added prefix column names keeping obtained new LHT values lht_names list user-defined LHT names associated FishLife's counterparts backtransform_function_list list backward-transformation functions applied obtained LHT FishLife predicting_lht_df dataframe keeping original inputted LHTs per taxon updated_lht_list list updated LHTs per taxon obtained Fishlife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"method-extract-and-backtransform-","dir":"Reference","previous_headings":"","what":"Method extract_and_backtransform()","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"Extract backtransform updated LHT values per taxon beed obtained Fishlife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"","code":"TaxaUpdateExtractor$extract_and_backtransform()"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"","code":"TaxaUpdateExtractor$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multiple Taxon Update Extractor class — TaxaUpdateExtractor","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":null,"dir":"Reference","previous_headings":"","what":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"Abstracts away underlying FishLife dynamics grab predicted LHT details given taxon","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"list three elements: ) database unique identifier sought taxon b) predicted stored LHTs taxon c) convariance matrix parameters associated sought taxon","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"TaxonPredictedLHTGetter$new() TaxonPredictedLHTGetter$extract() TaxonPredictedLHTGetter$clone()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"Initialise Taxon LHT Grabber class","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"","code":"TaxonPredictedLHTGetter$new(master_db, taxon)"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"master_db Fishlife database taxon string holding taxon name","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"method-extract-","dir":"Reference","previous_headings":"","what":"Method extract()","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"Fetch sought taxon details","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"","code":"TaxonPredictedLHTGetter$extract()"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"","code":"TaxonPredictedLHTGetter$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Single Taxon LHT GRABBER class — TaxonPredictedLHTGetter","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":null,"dir":"Reference","previous_headings":"","what":"Single Taxon Update Extractor class — TaxonUpdateExtractor","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"Class extracts transform predicted values LHTs single species obtained FishLife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"dataframe backtransformed LHT values","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"TaxonUpdateExtractor$new() TaxonUpdateExtractor$extract_and_backtransform() TaxonUpdateExtractor$clone()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"Initialise TaxonPredictionExtractor","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"","code":"TaxonUpdateExtractor$new( update_prefix, lht_names, backtransform_function_list, predicted_results )"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"update_prefix string added prefix column names keeping obtained new LHT values lht_names list user-defined LHT names associated FishLife's counterparts backtransform_function_list list backward-transformation functions applied obtained LHT FishLife predicted_results matrix predicted results FishLife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"method-extract-and-backtransform-","dir":"Reference","previous_headings":"","what":"Method extract_and_backtransform()","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"Extract backtransform updated LHT values FishLife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"","code":"TaxonUpdateExtractor$extract_and_backtransform()"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"","code":"TaxonUpdateExtractor$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Single Taxon Update Extractor class — TaxonUpdateExtractor","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":null,"dir":"Reference","previous_headings":"","what":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"Class given LHTs fetch predicted version according FishLife covariance","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"matrix-form LHT values passed FishLife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"LHTpicker::MixinUtilities -> TaxonUpdatedLHTGetter","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"common_columns_ds common columns across underlying data structure FishLife. Taxa's LHT end additional fields overall covariance matrix support.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"LHTpicker::MixinUtilities$apply_func_to_df() LHTpicker::MixinUtilities$create_empty_dataframe() LHTpicker::MixinUtilities$list_of_vectors_to_dataframe()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"TaxonUpdatedLHTGetter$new() TaxonUpdatedLHTGetter$generate_new_lht_matrix() TaxonUpdatedLHTGetter$predict() TaxonUpdatedLHTGetter$clone()","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"","code":"TaxonUpdatedLHTGetter$new( master_db, estimated_lhts, estimated_lht_cov, new_lhts, func_domains )"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"master_db Fishlife database estimated_lhts taxon's LHT numeric vector fetched Fishlife. new_lhts predicting LHT list names must conform FishLife's expectations func_domains list transforming function names must conform FishLife's expectations estimated_lht_conv taxon's covariance matrix fetched Fishlife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":"method-generate-new-lht-matrix-","dir":"Reference","previous_headings":"","what":"Method generate_new_lht_matrix()","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"Generate new LHT matrix shape mathematical domain expected Fishlife","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"","code":"TaxonUpdatedLHTGetter$generate_new_lht_matrix()"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":"method-predict-","dir":"Reference","previous_headings":"","what":"Method predict()","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"Generate matrix new predicted LHTs given initial values, log log-converted space","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"","code":"TaxonUpdatedLHTGetter$predict()"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"","code":"TaxonUpdatedLHTGetter$clone(deep = FALSE)"},{"path":"https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Single Taxon LHT Predictor class — TaxonUpdatedLHTGetter","text":"deep Whether make deep clone.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":null,"dir":"Reference","previous_headings":"","what":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"Allows streamline-generation updated LHTs given new data.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"list LHT matrices, name list corresponds single taxon unnamed list LHT values per taxon renamed list lht names conform Fishlife's expected patterns list LHT values (another list) taxon","code":""},{"path":[]},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"UpdatedLHTGenerator$new() UpdatedLHTGenerator$update() UpdatedLHTGenerator$clone()","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"Initialise Updated LHT Generator class","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"","code":"UpdatedLHTGenerator$new( master_db, predicting_lht_df, transform_function_list, lht_names )"},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"master_db Fishlife database predicting_lht_df dataframe providing taxon details predicting LHT values transform_function_list list transforming function names must conform FishLife's expectations lht_names list user-defined LHT names associated FishLife's counterparts","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"method-update-","dir":"Reference","previous_headings":"","what":"Method update()","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"Update given LHTs per taxon according new predicted value yielded FishLfe","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"","code":"UpdatedLHTGenerator$update()"},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"objects class cloneable method.","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Multiple Updated LHT Generator class — UpdatedLHTGenerator","text":"","code":"UpdatedLHTGenerator$clone(deep = 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)"},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTPicker.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Taxa's updated LHT picker — UpdatedLHTPicker","text":"master_db Fishlife database predicting_lht_df dataframe keeping original inputted LHTs per taxon transform_function_list list transforming function names must conform FishLife's expectations backtransform_function_list list backward-transformation functions applied obtained LHT FishLife lht_names list user-defined LHT names associated FishLife's counterparts update_prefix string added prefix column names keeping obtained new LHT values","code":""},{"path":"https://d2gex.github.io/LHTpicker/reference/UpdatedLHTPicker.html","id":"method-pick-and-backtransform-","dir":"Reference","previous_headings":"","what":"Method pick_and_backtransform()","title":"Taxa's updated LHT picker — UpdatedLHTPicker","text":"Build dataframe updated LHT wanted taxon 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b/sitemap.xml index 9975bf7..192a72b 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -30,15 +30,15 @@ https://d2gex.github.io/LHTpicker/reference/TaxaUpdateExtractor.html - - https://d2gex.github.io/LHTpicker/reference/TaxonLHTPredictor.html - https://d2gex.github.io/LHTpicker/reference/TaxonPredictedLHTGetter.html https://d2gex.github.io/LHTpicker/reference/TaxonUpdateExtractor.html + + https://d2gex.github.io/LHTpicker/reference/TaxonUpdatedLHTGetter.html + https://d2gex.github.io/LHTpicker/reference/UpdatedLHTGenerator.html