Generate reports for central place foraging species tracked in OPP
opp_reports_cpf.RdThis function passes a table of parameters to an RMarkdown template to generate summary reports on tracking data analysis.
Arguments
- analysis_table
Data frame that provides all values needed for the RMarkdown template, see details. Defaults to the cpf_report_params data object that is contained within OPPTools.
- login
Stored Movebank login credentials if provided, otherwise function will prompt users to enter credentials.
- output_dir
Name of of the directory where reports should be saved.
Details
Still need to write this up, once function is complete.
The example below will only work if the user has permissions for all the projects listed in cpf_report_params
Examples
print(cpf_report_params)
#> mb_project_num report_title
#> 1 1279263376 Cassin's auklet - Triangle Island, BC
#> 2 1912080185 Cassin's auklet - Frederick Island, BC
#> 3 1247096889 Tufted puffin - Triangle Island, BC
#> 4 1895716931 Ancient murrelet - George Island, BC
#> 5 1897273090 Ancient murrelet - Ramsay Island, BC
#> 6 1903294479 Rhinocerous auklet - Lucy Island, BC
#> 7 1904543040 Rhinocerous auklet - Pine Island, BC
#> 8 1904565280 Rhinocerous auklet - Protection Island, WA
#> 9 1903075528 Rhinocerous auklet - SGang Gwaay, BC
#> 10 1901463730 Rhinocerous auklet - Triangle Island, BC
#> 11 1953033045 Leach's storm-petrel - Copper Islands, BC
#> 12 1952967863 Leach's storm-petrel - Gillam Islands, BC
#> 13 1953016048 Leach's storm-petrel - Hippa Island, BC
#> 14 1948459965 Leach's storm-petrel - Storm Islands, BC
#> 15 1953094560 Fork-tailed storm-petrel - Hippa Island, BC
#> 16 1953062177 Fork-tailed storm-petrel - Copper Islands, BC
#> 17 1953086120 Fork-tailed storm-petrel - Gillam Islands, BC
#> file_name spp breeding_pairs minDist
#> 1 CAAU - Triangle Island Cassin's auklet 550000 1.5
#> 2 CAAU - Frederick Island Cassin's auklet NA 1.5
#> 3 TUPU - Triangle Island Tufted puffin NA 1.0
#> 4 ANMU - George Island Ancient murrelet 17000 1.5
#> 5 ANMU - Ramsay Island Ancient murrelet 18000 1.0
#> 6 RHAU - Lucy Island Rhinocerous auklet 25000 2.5
#> 7 RHAU - Pine Island Rhinocerous auklet 140000 1.5
#> 8 RHAU - Protection Island Rhinocerous auklet 34000 0.5
#> 9 RHAU - SGang Gwaay Rhinocerous auklet NA 2.5
#> 10 RHAU - Triangle Island Rhinocerous auklet 42000 3.5
#> 11 LHSP - Copper Islands Leach's storm-petrel NA 5.0
#> 12 LHSP - Gillam Islands Leach's storm-petrel NA 5.0
#> 13 LHSP - Hippa Island Leach's storm-petrel NA 5.0
#> 14 LHSP - Storm Islands Leach's storm-petrel NA 5.0
#> 15 FTSP - Hippa Island Fork-tailed storm petrel NA 5.0
#> 16 FTSP - Copper Islands Fork-tailed storm petrel NA 5.0
#> 17 FTSP - Gillam Islands Fork-tailed storm petrel NA 5.0
#> maxDist minDur gapTime gapDist interpolateGaps timestep gridRes gridExtend
#> 1 20 1 1 12 FALSE 5 min 1 30
#> 2 10 1 1 12 FALSE 5 min 1 30
#> 3 10 1 1 18 FALSE 5 min 1 30
#> 4 20 1 3 19 FALSE 20 min 1 30
#> 5 20 1 3 19 FALSE 20 min 1 30
#> 6 20 1 1 12 FALSE 5 min 1 30
#> 7 10 1 1 12 FALSE 5 min 1 30
#> 8 10 1 1 12 FALSE 5 min 1 30
#> 9 10 1 1 12 FALSE 5 min 1 30
#> 10 10 1 1 12 FALSE 5 min 1 30
#> 11 60 12 6 5 FALSE 60 min 5 500
#> 12 60 12 6 5 FALSE 60 min 5 500
#> 13 60 12 6 5 FALSE 60 min 5 500
#> 14 60 12 6 5 FALSE 60 min 5 500
#> 15 60 12 6 5 FALSE 60 min 2 300
#> 16 60 12 6 5 FALSE 60 min 2 300
#> 17 60 12 6 5 FALSE 60 min 2 300
#> speed mapZoom includeBB
#> 1 50 6.5 1
#> 2 50 6.5 1
#> 3 70 6.5 0
#> 4 75 6.5 1
#> 5 75 6.5 1
#> 6 50 6.5 1
#> 7 50 6.5 0
#> 8 50 6.5 1
#> 9 50 6.5 1
#> 10 50 6.5 1
#> 11 50 4.0 1
#> 12 50 4.5 1
#> 13 50 4.5 1
#> 14 50 4.0 0
#> 15 50 4.0 1
#> 16 50 6.0 0
#> 17 50 7.5 0
opp_reports_cpf()
#> username:
#> password:
#> Warning: path[1]="inst/rmarkdown/templates/opp-cpf-report/skeleton/skeleton.Rmd": No such file or directory
#> Error in abs_path(input): The file 'inst/rmarkdown/templates/opp-cpf-report/skeleton/skeleton.Rmd' does not exist.