Code

major upgrade#45

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KevinSee merged 74 commits intomainKevinSee/PITcleanr:mainfrom developKevinSee/PITcleanr:developCopy head branch name to clipboardNov 29, 2023

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Commits

Commits on Aug 10, 2023

• update to buildConfig.R to allow for 3 different sets of array suffixes

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• updated buildConfig() documentation

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• adding addParentChildNodes_LGR() until we can merge w/ addParentChildNodes

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• updated example in addParentChildNodes()

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• adding estimateSpawnLoc_LGR() from RK

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• renamed estimateSpawnLoc()

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• updated estimateSpawnLoc name in NAMESPACE

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• roxygenized estimateSpawnLoc()

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Commits on Aug 14, 2023

• Merge pull request #30 from mackerman44/npt_develop

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Commits on Aug 15, 2023

• changed default array_suffix to "UD" instead of "A0B0"

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• replaced A0 & B0 with U & D in all (3) PITcleanr functions

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• updated documentation of buildConfig()

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• needed to add a match.arg()

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• fixed minor suffix issues in addParentChildNodes.R

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• removing addParentChildNodes_LGR()

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• renamed to estimateSpawnLoc()

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• adding underscores in estNodeEff()

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• updated defineRepGrps() to use _D instead of _B0

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Commits on Aug 16, 2023

• updated queryMRRDataFile function to better handle some issues with older MRR files. Matches update on main and develop branches

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• updated this function to work with PTAGIS's latest API interface

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• cleaned up some redundant code

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Commits on Aug 18, 2023

• added underscores to _U and _D in extractSites()

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• replaced grepl with str_detect. changed order that nodes were sorted, since A0 is now _U and B0 is now _D. Dropped the need for %<>%

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• updated vignettes to refer to "_U" and "_D" instead of "A0" and "B0"

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Commits on Aug 21, 2023

• Merge pull request #36 from KevinSee/npt_dev_ks

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Commits on Aug 28, 2023

• Merge pull request #37 from KevinSee/npt_dev_ma

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• errant string_detect() in addParentChildNodes

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• corrected string_detect to str_detect

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• Merge branch 'npt_dev_ks' of https://github.com/KevinSee/PITcleanr into npt_dev_ks

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• Merge pull request #38 from KevinSee/npt_dev_ks

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Commits on Aug 30, 2023

• added a few details about prepping data for DABOM into the quick_prep vignette

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• deleted the _DABOM_prep vignette, as it's been superceded by other vignettes. Removed it from the .Rbuildignore file as well.

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Commits on Sep 8, 2023

• added the starting date (when tag history began) to the tag summary

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• updated script with latest PITcleanr arguments

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• added start date (when tag history began) to the tag summary

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Commits on Sep 11, 2023

• Merge pull request #39 from KevinSee/npt_dev_ks

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Commits on Sep 16, 2023

• updated all the example datasets, including a script to prepare many of them. Also updated a script to test how to use PITcleanr to prepare data for a DABOM model.

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• deleted more old data

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• Merge branch 'npt_dev_ks' into npt_develop

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Commits on Sep 19, 2023

• added two functions, getNodeInfo and defineCapHistCols

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Commits on Sep 20, 2023

• dropped the "updated_data" folder from several paths

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Commits on Sep 21, 2023

• updated defineCapHistCols to provide better option of using rkm

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• Merge pull request #40 from KevinSee/npt_dev_ma

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• small modifications to test script

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• Merge pull request #41 from KevinSee/npt_dev_ks

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• corrected a line indent

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• fixed several other indents

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• Merge pull request #42 from KevinSee/npt_develop

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Commits on Sep 25, 2023

• deleted a commented out section of code

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Commits on Sep 27, 2023

• updated a comment in a test script

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Commits on Oct 6, 2023

• updated request url: http to https

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• renamed tag_code argument to ptagis_tag_code to avoid confusion

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• updated to use queryTagMeta to get mark information. This includes the possible need for an API key now

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• made it optional to include mark information in capture history (since that requires an API key)

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• added a function to query data about test tag detections at a particular site for a particular calendar year

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Commits on Oct 7, 2023

• deleted a number of old legacy functions that have all been superceded in more recent versions of PITcleanr

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• updated several vignettes to point to updated data files contained in the package

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• added a function to build a standard capture history

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Commits on Oct 10, 2023

• updated help file which propogated to other help files

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• updated 2 functions related to building capture histories to make them more flexible in how things are configured

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• updated main vignette to explain how PITcleanr can be used to build capture histories

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• updated buildCapHist to deal with situations when user_keep_obs or auto_keep_obs not completely filled in.

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Commits on Oct 12, 2023

• added an arguement to allow for more downstream flowlines (buffer around existing sites)

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• added data for example of smolts from LEMTRP

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• started a vignette detailing how to wrangle data for a CJS model

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Commits on Oct 18, 2023

• updated compressDART to use configuration argument

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Commits on Oct 30, 2023

• added to the CJS vignette

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• started a test script to prep data for and run a CJS model of juvenile Chinook from the upper lemhi screw trap.

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• added an if{} else {} for whether buffer_dist == 0 or not. Otherwise it was causing error when buffer_dist = 0.

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Commits on Oct 31, 2023

• updated where some prepped data files are saved

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• updated required package versions based on what I currently have installed (particularly important for nhdplusTools)

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Commits on Nov 1, 2023

• minor code formatting

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Commits on Nov 2, 2023

• updated queryFlowlines to deal with an if statement that was throwing an error around buffer distances given as unit objects.

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Commits on Nov 7, 2023

• reorganized presentation of CJS model results

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