Hello !

I want to start to work(to play first :)) with Rpath, and I have 2 issues: 1)I try to install Rpath: `> library(devtools)

devtools::install_github('slucey/RpathDev/Rpath', build_vignettes = TRUE) Downloading GitHub repo slucey/RpathDev@master from URL https://api.github.com/repos/slucey/RpathDev/zipball/master Error in download(dest, src, auth) : Not Found (HTTP 404).`

2) If I have this data in EwE: Group name: turbot1, turbot2,turbot3,turbo4,turbot5,turbot6,turbot7,turbot8,turbot9(leading) Age: 0,12,24,36,48,60,72,84,96 Biomass: 11.10,39.06,91.12,144.71,134.56,92.86,55.00,30.54,32.40 Z: 3,0.8,0.1,0.5,0.7,0.8,0.8,0.8,0.8 Consumption/biomass: 13.00,5.50,3.58,2.81,2.38,2.10,1.92,1.79,1.64, how do I write/change the R script : ` groups <- c('Seabirds', 'Whales', 'Seals', 'JuvRoundfish1', 'AduRoundfish1', 'JuvRoundfish2', 'AduRoundfish2', 'JuvFlatfish1', 'AduFlatfish1', 'JuvFlatfish2', 'AduFlatfish2', 'OtherGroundfish', 'Foragefish1', 'Foragefish2', 'OtherForagefish', 'Megabenthos', 'Shellfish', 'Macrobenthos', 'Zooplankton', 'Phytoplankton', 'Detritus', 'Discards', 'Trawlers', 'Midwater', 'Dredgers') stgroups <- c(rep(NA, 3), rep('Roundfish1', 2), rep('Roundfish2', 2), rep('Flatfish1', 2), rep('Flatfish2', 2), rep(NA, 14))

types <- c(rep(0, 19), 1, rep(2, 2), rep(3, 3))

-------------------------------------------------------------------------------

Create Model File

REco.params <- create.rpath.param(group = groups, type = types, stgroup = stgroups, nstanzas = rep(2,4))

Fill appropriate columns

Model

biomass <- c(0.0149, 0.454, NA, NA, 1.39, NA, 5.553, NA, 5.766, NA, 0.739, 7.4, 5.1, 4.7, 5.1, NA, 7, 17.4, 23, 10, rep(NA, 5))

pb <- c(0.098, 0.031, 0.100, 2.026, 0.42, 2.1, 0.425, 1.5, 0.26, 1.1, 0.18, 0.6, 0.61, 0.65, 1.5, 0.9, 1.3, 7, 39, 240, rep(NA, 5))

qb <- c(76.750, 6.976, 34.455, NA, 2.19, NA, 3.78, NA, 1.44, NA, 1.69, 1.764, 3.52, 5.65, 3.6, 2.984, rep (NA, 9))

REco.params$model[, Biomass := biomass] REco.params$model[, PB := pb] REco.params$model[, QB := qb] `

Thank you very much in advance ! George

Dear George,

Sorry for the tardy response. I was at sea with temperamental internet access. The issue with connecting is because the RpathDev repository does not sit on the "Master" branch. Rather it sits on a branch names "Public". It was a naming convention that simplified things for me but has created a lot of confusion from users like yourself trying to download it. To download the code add the follow argument to the install_github command: ref = 'Public'. Please note that some people have been having issues with the vignettes due to issues with their pandoc library.

The second issue looks like you are trying to add a multistanza group. You would add them similar to the way that the juvenile and adult groups are added below. However, you should only add the biomass and consumption for the leading stanza and allow the function rpath.stanzas() calculate the trailing biomasses and consumptions.

Let me know if you have any further questions.

Sean

Sean M. Lucey Fisheries Biologist U. S. Dept. of Commerce/NOAA/NMFS Northeast Fisheries Science Center 166 Water Street, Woods Hole, MA 02543 508-495-2011 (voice) 508-495-2232 (fax)

On Tue, May 10, 2016 at 4:27 AM, GeoTuxMan notifications@github.com wrote:

Hello !

I want to start to work(to play first :)) with Rpath, and I have 2 issues: 1)I try to install Rpath: `> library(devtools)

devtools::install_github('slucey/RpathDev/Rpath', build_vignettes = TRUE) Downloading GitHub repo slucey/RpathDev@master from URL https://api.github.com/repos/slucey/RpathDev/zipball/master Error in download(dest, src, auth) : Not Found (HTTP 404).`

2) If I have this data in EwE: Group name: turbot1, turbot2,turbot3,turbo4,turbot5,turbot6,turbot7,turbot8,turbot9(leading) Age: 0,12,24,36,48,60,72,84,96 Biomass: 11.10,39.06,91.12,144.71,134.56,92.86,55.00,30.54,32.40 Z: 3,0.8,0.1,0.5,0.7,0.8,0.8,0.8,0.8 Consumption/biomass: 13.00,5.50,3.58,2.81,2.38,2.10,1.92,1.79,1.64, how do I write/change the R script : ` groups <- c('Seabirds', 'Whales', 'Seals', 'JuvRoundfish1', 'AduRoundfish1', 'JuvRoundfish2', 'AduRoundfish2', 'JuvFlatfish1', 'AduFlatfish1', 'JuvFlatfish2', 'AduFlatfish2', 'OtherGroundfish', 'Foragefish1', 'Foragefish2', 'OtherForagefish', 'Megabenthos', 'Shellfish', 'Macrobenthos', 'Zooplankton', 'Phytoplankton', 'Detritus', 'Discards', 'Trawlers', 'Midwater', 'Dredgers') stgroups <- c(rep(NA, 3), rep('Roundfish1', 2), rep('Roundfish2', 2), rep('Flatfish1', 2), rep('Flatfish2', 2), rep(NA, 14))

types <- c(rep(0, 19), 1, rep(2, 2), rep(3, 3))

-------------------------------------------------------------------------------

Create Model File

REco.params <- create.rpath.param(group = groups, type = types, stgroup = stgroups, nstanzas = rep(2,4))

Fill appropriate columns

Model

biomass <- c(0.0149, 0.454, NA, NA, 1.39, NA, 5.553, NA, 5.766, NA, 0.739, 7.4, 5.1, 4.7, 5.1, NA, 7, 17.4, 23, 10, rep(NA, 5))

pb <- c(0.098, 0.031, 0.100, 2.026, 0.42, 2.1, 0.425, 1.5, 0.26, 1.1, 0.18, 0.6, 0.61, 0.65, 1.5, 0.9, 1.3, 7, 39, 240, rep(NA, 5))

qb <- c(76.750, 6.976, 34.455, NA, 2.19, NA, 3.78, NA, 1.44, NA, 1.69, 1.764, 3.52, 5.65, 3.6, 2.984, rep (NA, 9))

REco.params$model[, Biomass := biomass] REco.params$model[, PB := pb] REco.params$model[, QB := qb] `

Thank you very much in advance ! George

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/slucey/RpathDev/issues/1

Dear Sean,

Thanks for your reply, it's really help me. I install RPath; it was need to install Rtools and rmarkdown before. Regarding my R script, I don't have time in this period, to rewrite the script; so we'll discuss later about that.

Cheers ! George

2016-05-16 16:24 GMT+03:00 Sean Lucey notifications@github.com:

Dear George,

Sorry for the tardy response. I was at sea with temperamental internet access. The issue with connecting is because the RpathDev repository does not sit on the "Master" branch. Rather it sits on a branch names "Public". It was a naming convention that simplified things for me but has created a lot of confusion from users like yourself trying to download it. To download the code add the follow argument to the install_github command: ref = 'Public'. Please note that some people have been having issues with the vignettes due to issues with their pandoc library.

The second issue looks like you are trying to add a multistanza group. You would add them similar to the way that the juvenile and adult groups are added below. However, you should only add the biomass and consumption for the leading stanza and allow the function rpath.stanzas() calculate the trailing biomasses and consumptions.

Let me know if you have any further questions.

Sean

Sean M. Lucey Fisheries Biologist U. S. Dept. of Commerce/NOAA/NMFS Northeast Fisheries Science Center 166 Water Street, Woods Hole, MA 02543 508-495-2011 (voice) 508-495-2232 (fax)

On Tue, May 10, 2016 at 4:27 AM, GeoTuxMan notifications@github.com wrote:

Hello !

I want to start to work(to play first :)) with Rpath, and I have 2 issues: 1)I try to install Rpath: `> library(devtools)

devtools::install_github('slucey/RpathDev/Rpath', build_vignettes = TRUE) Downloading GitHub repo slucey/RpathDev@master from URL https://api.github.com/repos/slucey/RpathDev/zipball/master Error in download(dest, src, auth) : Not Found (HTTP 404).`

2) If I have this data in EwE: Group name: turbot1, turbot2,turbot3,turbo4,turbot5,turbot6,turbot7,turbot8,turbot9(leading) Age: 0,12,24,36,48,60,72,84,96 Biomass: 11.10,39.06,91.12,144.71,134.56,92.86,55.00,30.54,32.40 Z: 3,0.8,0.1,0.5,0.7,0.8,0.8,0.8,0.8 Consumption/biomass: 13.00,5.50,3.58,2.81,2.38,2.10,1.92,1.79,1.64, how do I write/change the R script : ` groups <- c('Seabirds', 'Whales', 'Seals', 'JuvRoundfish1', 'AduRoundfish1', 'JuvRoundfish2', 'AduRoundfish2', 'JuvFlatfish1', 'AduFlatfish1', 'JuvFlatfish2', 'AduFlatfish2', 'OtherGroundfish', 'Foragefish1', 'Foragefish2', 'OtherForagefish', 'Megabenthos', 'Shellfish', 'Macrobenthos', 'Zooplankton', 'Phytoplankton', 'Detritus', 'Discards', 'Trawlers', 'Midwater', 'Dredgers') stgroups <- c(rep(NA, 3), rep('Roundfish1', 2), rep('Roundfish2', 2), rep('Flatfish1', 2), rep('Flatfish2', 2), rep(NA, 14))

types <- c(rep(0, 19), 1, rep(2, 2), rep(3, 3))

-------------------------------------------------------------------------------

Create Model File

REco.params <- create.rpath.param(group = groups, type = types, stgroup = stgroups, nstanzas = rep(2,4))

Fill appropriate columns

Model

biomass <- c(0.0149, 0.454, NA, NA, 1.39, NA, 5.553, NA, 5.766, NA, 0.739, 7.4, 5.1, 4.7, 5.1, NA, 7, 17.4, 23, 10, rep(NA, 5))

pb <- c(0.098, 0.031, 0.100, 2.026, 0.42, 2.1, 0.425, 1.5, 0.26, 1.1, 0.18, 0.6, 0.61, 0.65, 1.5, 0.9, 1.3, 7, 39, 240, rep(NA, 5))

qb <- c(76.750, 6.976, 34.455, NA, 2.19, NA, 3.78, NA, 1.44, NA, 1.69, 1.764, 3.52, 5.65, 3.6, 2.984, rep (NA, 9))

REco.params$model[, Biomass := biomass] REco.params$model[, PB := pb] REco.params$model[, QB := qb] `

Thank you very much in advance ! George

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/slucey/RpathDev/issues/1

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/slucey/RpathDev/issues/1#issuecomment-219423761

slucey / RpathDev

Error install #1

-------------------------------------------------------------------------------

Create Model File

Fill appropriate columns

Model

-------------------------------------------------------------------------------

Create Model File

Fill appropriate columns

Model

-------------------------------------------------------------------------------

Create Model File

Fill appropriate columns

Model