major upgrade #45

KevinSee · 2023-11-29T23:16:30Z

Lots of updates from Kevin See and Mike Ackerman. Some may not be backwards compatible

…Nodes

pulled in updates from Mike Ackerman

…lder MRR files. Matches update on main and develop branches

… since A0 is now _U and B0 is now _D. Dropped the need for %<>%

Updated vignettes

added underscores to _U and _D in extractSites()

…to npt_dev_ks

latest updates - no conflicts

Merge all the updates from Mike Ackerman and Kevin See

…e possible need for an API key now

…e that requires an API key)

…lar site for a particular calendar year

…d in more recent versions of PITcleanr

… the package

…m more flexible in how things are configured

…apture histories

…to_keep_obs not completely filled in.

…und existing sites)

…e Chinook from the upper lemhi screw trap.

…it was causing error when buffer_dist = 0.

…alled (particularly important for nhdplusTools)

… an error around buffer distances given as unit objects.

mackerman44 and others added 30 commits August 10, 2023 08:23

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

d9b49ae

updated buildConfig() documentation

cc5b3e1

adding addParentChildNodes_LGR() until we can merge w/ addParentChild…

cff065c

…Nodes

updated example in addParentChildNodes()

86fa032

adding estimateSpawnLoc_LGR() from RK

c19a45a

renamed estimateSpawnLoc()

c8882a6

updated estimateSpawnLoc name in NAMESPACE

5409b8e

roxygenized estimateSpawnLoc()

d155af3

Merge pull request #30 from mackerman44/npt_develop

8ffd316

pulled in updates from Mike Ackerman

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

b5dbe8d

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

2ad8b6e

updated documentation of buildConfig()

56b9291

needed to add a match.arg()

5b31014

fixed minor suffix issues in addParentChildNodes.R

6aaf57a

removing addParentChildNodes_LGR()

c6e8f97

renamed to estimateSpawnLoc()

1a7406a

adding underscores in estNodeEff()

23dceb3

updated defineRepGrps() to use _D instead of _B0

1e6d2a1

updated queryMRRDataFile function to better handle some issues with o…

df834c8

…lder MRR files. Matches update on main and develop branches

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

2f71019

cleaned up some redundant code

9d044f2

added underscores to _U and _D in extractSites()

6ca4d58

replaced grepl with str_detect. changed order that nodes were sorted,…

7511779

… since A0 is now _U and B0 is now _D. Dropped the need for %<>%

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

7cf6fb0

Merge pull request #36 from KevinSee/npt_dev_ks

a5c3372

Updated vignettes

Merge pull request #37 from KevinSee/npt_dev_ma

b0e61cb

added underscores to _U and _D in extractSites()

errant string_detect() in addParentChildNodes

be8aac2

corrected string_detect to str_detect

264b395

Merge branch 'npt_dev_ks' of https://github.com/KevinSee/PITcleanr in…

3e1a251

…to npt_dev_ks

Merge pull request #38 from KevinSee/npt_dev_ks

947bee7

latest updates - no conflicts

KevinSee and others added 29 commits September 21, 2023 16:03

corrected a line indent

21373b6

fixed several other indents

64193d2

Merge pull request #42 from KevinSee/npt_develop

827c589

Merge all the updates from Mike Ackerman and Kevin See

deleted a commented out section of code

9a00784

updated a comment in a test script

6a04386

updated request url: http to https

e4f8725

renamed tag_code argument to ptagis_tag_code to avoid confusion

378ed66

updated to use queryTagMeta to get mark information. This includes th…

2d68094

…e possible need for an API key now

made it optional to include mark information in capture history (sinc…

731e63b

…e that requires an API key)

added a function to query data about test tag detections at a particu…

ef5db17

…lar site for a particular calendar year

deleted a number of old legacy functions that have all been supercede…

d0c8198

…d in more recent versions of PITcleanr

updated several vignettes to point to updated data files contained in…

0d19cd7

… the package

added a function to build a standard capture history

e551110

updated help file which propogated to other help files

883cb02

updated 2 functions related to building capture histories to make the…

f72706c

…m more flexible in how things are configured

updated main vignette to explain how PITcleanr can be used to build c…

438879e

…apture histories

updated buildCapHist to deal with situations when user_keep_obs or au…

8b214e9

…to_keep_obs not completely filled in.

added an arguement to allow for more downstream flowlines (buffer aro…

fab3d07

…und existing sites)

added data for example of smolts from LEMTRP

fd951cc

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

da262a6

updated compressDART to use configuration argument

4c296e2

added to the CJS vignette

d665fe4

started a test script to prep data for and run a CJS model of juvenil…

fef5ceb

…e Chinook from the upper lemhi screw trap.

added an if{} else {} for whether buffer_dist == 0 or not. Otherwise …

b64798c

…it was causing error when buffer_dist = 0.

updated where some prepped data files are saved

7b54e50

updated required package versions based on what I currently have inst…

85e703f

…alled (particularly important for nhdplusTools)

minor code formatting

f05d048

updated queryFlowlines to deal with an if statement that was throwing…

1e5af5e

… an error around buffer distances given as unit objects.

reorganized presentation of CJS model results

fa4dc81

KevinSee merged commit 3fac5bd into main Nov 29, 2023
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major upgrade #45

major upgrade #45

KevinSee commented Nov 29, 2023

major upgrade #45

major upgrade #45

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KevinSee commented Nov 29, 2023