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A reproducible manuscript workflow with a Quarto template

Scientists and resource managers increasingly use Markdown-based tools to create reproducible reports and manuscripts. These workflows allow people to use standardized methods that are more reproducible, efficient, and transparent than other standard office tools. We present a Quarto template and demonstrate how this template may be used for a journal, the Journal of Fish and Wildlife Management , in our article. This template may also be readily adapted to other journals that use Microsoft Word-based workflows and for other product types such as annual reports. We also provide a high-level overview of Quarto and other Markdown-based workflows as part of the document. Lastly, we provide examples of some features of the Quarto publishing system that may be helpful for authors when customizing Quarto templates for specific journal formatting requirements and other product types.

Journal of Fish and Wildlife Management↗

Continuous stream discharge, salinity, and associated data collected in the lower St. Johns River and its tributaries, Florida, 2017

The U.S. Army Corps of Engineers, Jacksonville District, plans to deepen the St. Johns River channel in Jacksonville, Florida, from 40 to 47 feet along 13 miles of the river channel, beginning at the mouth of the river at the Atlantic Ocean, to accommodate larger, fully loaded cargo vessels. The U.S. Geological Survey, in cooperation with the U.S. Army Corps of Engineers, (1) installed continuous data collection stations to monitor discharge, salinity, and associated parameters at 23 sites prior to the commencement of dredging and (2) monitored stage and discharge at 13 sites and water temperature, specific conductance, and salinity at 16 sites; all parameters were monitored at some sites. This is the second annual report by the U.S. Geological Survey on data collection for the Jacksonville Harbor deepening and contains information pertinent to the data collection sites during the 2017 water year, from October 2016 to September 2017. One data collection site on the St. Johns River below Shands Bridge was added to the network during this timeframe after the previously monitored location was damaged by Hurricane Matthew. Discharge and salinity varied widely during the data collection period, reflecting the effects of Hurricane Matthew in October 2016 and Hurricane Irma in September 2017. The annual mean discharge at Trout River was greatest among the tributaries, followed by annual mean discharges at Durbin Creek, Ortega River, Julington Creek, Pottsburg Creek, Clapboard Creek, Cedar River, Broward River, and Dunn Creek. Among the tributary sites, annual mean salinity was highest at the site closest to the Atlantic Ocean, Clapboard Creek, and lowest at the site farthest from the ocean, Durbin Creek. Annual mean salinity data from the main-stem sites on the St. Johns River indicate that salinity decreased with distance upstream from the ocean, which is expected. Relative to salinity for the 2016 water year, annual mean salinity in the tributaries was higher for the 2017 water year at four monitoring locations, lower at four monitoring locations, and the same at one location. Of the three sites where salinity was calculated on the main stem in the 2016 water year, salinity was higher at one monitoring location in the 2017 water year and lower at two locations.

Florida↗

Water resources data for Wyoming, water year 1972; part 1, surface water records

Surface-water records for the 1972 water year for Wyoming, including records of streamflow or reservoir storage at gaging stations, partial-record stations, and miscellaneous sites, are given in this report. The locations of the gaging stations and partial-record stations are shown in figures 1 and 2. Records for a few pertinent gaging stations in bordering States also are included. These data represent that portion of the National Water Data System collected by the U.S. Geological Survey and cooperating State and Federal agencies in Wyoming. The records were collected and computed by the Water Resources Division of the U.S. Geological Survey under the direction of Robert L. Cushman, district chief. Wyoming district personnel who contributed significantly to the collection and preparation of data included in this report were: S.A. Druse, D. J. O'Connell, G. S. Craig, Jr., G. W. Armentrout, Jr., H. W. Lowham, B. H. Ringen, P. B. McCollam, C. F. Obert, W. R. Glass, T.W. Custis, R. L. Muench, J. 0. Ragsdale, M. D. Stevens, J. M. Johnson, and J. L. Lynch. Through September 30, 1960, the records of discharge and stage of streams and canals, and contents and stage of lakes or reservoirs, were published in an annual series of U.S. Geological Survey water-supply papers entitled "Surface Water Supply of the United States." Beginning with the 1961 water year, surface-water records have been released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these reports is limited; they are designed primarily for rapid release of data shortly after the end of the water year to meet local needs. Records of discharge and reservoir storage for 1961-65 have been published in a Geological Survey water-supply paper series entitled "Surface Water Supply of the United States 1961-65." Records of discharge and reservoir storage for 1966-70 also will be published in a Geological Survey water-supply paper series entitled "Surface Water Supply of the United States 1966-70."

Wyoming↗

A project for monitoring trends in burn severity

Jeff Eidenshink, Brian Schwind, Ken Brewer, Zhi-Liang Zhu, Brad Quayle, and Elected officials and leaders of environmental agencies need information about the effects of large wildfires in order to set policy and make management decisions. Recently, the Wildland Fire Leadership Council (WFLC), which implements and coordinates the National Fire Plan (NFP) and Federal Wildland Fire Management Policies (National Fire Plan 2004), adopted a strategy to monitor the effectiveness of the National Fire Plan and the Healthy Forests Restoration Act (HFRA). One component of this strategy is to assess the environmental impacts of large wildland fires and identify the trends of burn severity on all lands across the United States. To that end, WFLC has sponsored a six-year project, Monitoring Trends in Burn Severity (MTBS), which requires the U.S. Department of Agriculture Forest Service (USDA-FS) and the U.S. Geological Survey (USGS) to map and assess the burn severity for all large current and historical fires. Using Landsat data and the differenced Normalized Burn Ratio (dNBR) algorithm, the USGS Center for Earth Resources Observation and Science (EROS) and USDA-FS Remote Sensing Applications Center will map burn severity of all fires since 1984 greater than 202 ha (500ac) in the east, and 404 ha (1,000 ac) in the west. The number of historical fires from this period combined with current fires occurring during the course of the project will exceed 9,000. The MTBS project will generate burn severity data, maps, and reports, which will be available for use at local, state, and national levels to evaluate trends in burn severity and help develop and assess the effectiveness of land management decisions. Additionally, the information developed will provide a baseline from which to monitor the recovery and health of fire-affected landscapes over time. Spatial and tabular data quantifying burn severity will augment existing information used to estimate risk associated with a range of current and future resource threats. The annual report of 2004 fires has been completed. All data and results will be distributed to the public on a Web site. A Project for Monitoring Trends in Burn Severity

Fire Ecology↗

Water Resources Data: Hawaii and Other Pacific Areas, Water Year 1999. Volume 1. Hawaii

This report includes records on both surface and ground water in the State. Specifically, it contains: (1) Discharge records for 74 stream-gaging stations, 71 miscellaneous streamflow stations, and 88 crest-stage partial-record streamflow stations; (2) water-quality records for 6 streamflow-gaging stations, and 28 partial-record streamflow stations; (3) water-level records for 84 observation wells; (4) water-quality records for 122 observation wells; and (5) accumulated rainfall records for 40 rainfall stations. This series of annual reports for Hawaii began with the 1961 fiscal year (State of Hawaii) with a report that contained only data relating to the quantities of surface water. For the 1964 fiscal year, a similar report was introduced that contained only data relating to water quality. Beginning with the 1975 water year, the report format was changed to include, in one volume, data on quantities of surface water, quality of surface and ground water, and ground-water levels. Beginning with the 1993 water year, accumulated rainfall data were included in the report.

Water Data Report↗

Water resources data for Kansas, water year 1973; Part 1, Surface water records

Surface-water records for the 1973 water year for Kansas, including records of streamflow or reservoir storage at gaging stations and partial-record stations, are given in this report. The locations of the stations are on figures 1 and 2. Records for a few pertinent gaging stations in bordering States also are included. These data represent that part of the National Water Data System collected by the U. S. Geological Survey and cooperating State and Federal agencies in Kansas. The records were collected and computed by the Water Resources Division of the U. S. Geological Survey under the direction of C. W. Lane, district chief. Kansas district personnel who contributed significantly to the collection and preparation of data included in this report were: J. L. Ebling, C. 0. Geiger, K. D. Medina, C. 0. Peek, J. D. Craig, L. L. Jones, J. P. Marshall, W. J. Carswell, D. L. Lacock, G. G. Quy II, J. T. Religa, R. D. Thomas, S. V. Bond, S. T. Green, C. G. Sauer, L. M. Pope, F. D. Toepfer, A. F. Browning, M. L. Penny, M. Pabst, and L. R. Stringer. Through September 30, 1960, the records of discharge and stage of streams and canals and contents and stage of lakes or reservoirs were published in an annual series of U. S. Geological Survey water-supply papers entitled "Surface Water Supply of the United States." Beginning with the 1961 water year, surface-water records have been released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these reports is limited; they are designed primarily for rapid release of data shortly after the end of the water year to meet local needs. The discharge and reservoir storage records for 1961-65 also have been published in a Geological Survey water-supply paper series entitled "Surface Water Supply of the United States 1961-65."

Kansas↗

Water resources data for Wyoming, water year 1972; part 2, water quality records

Water-resources data for the 1972 water year for Wyoming include records of data for the chemical and physical characteristics of surface and ground water. Data on the quality of surface water (chemical, temperature, and sediment) were collected from designated sampling sites at predetermined intervals such as once daily, weekly, monthly or less frequently. At some sites water-temperature data were recorded on charts by recorders. Data are given for 138 sampling stations of which 112 are continuous-record stations and 26 are miscellaneous sites. Chemical analyses also are given for 127 ground-water sites. Locations of surface water-quality stations are shown in figure 1 and locations of ground-water sites are shown in figure 2. These data represent that portion of the National Water Data System collected by the U.S. Geological Suryey and cooperating State and Federal agencies in Wyoming. The records were collected and computed by the Water Resources Division of the U.S. Geological Survey under the direction of Robert L. Cushman, district chief. Wyoming district personnel who contributed significantly to the collection and preparation of data included in this report were: E. R. Cox, S. A. Druse, W. G. Hodson, M. E. Lowry, D. J. O'Connell, G. W. Armentrout, Jr., M.A. Crist, B. H. Ringen, W. B. Borchert, W.R. Glass, G. C. Lines, H.B. Fabricius, P. B. McCollam, C. E. Obert, K. G. Polinoski, T. W. Custis, R. L. Muench, J. O. Ragsdale, M. D. Stevens, R .. C. Baumann, D. W. Brownell, R. V. Foresman, J.M. Johnson, J. L. Lynch, M. L. Smalley, and J. P. Kyner. The Geological Survey has published records of chemical quality, water temperatures, and sediment since 1941 in an annual series of water-supply papers entitled, "Quality of Surface Water of the United States." Beginning with the 1964 water year, water-quality records have been released by the Geological Survey in annual reports on a State-boundary basis. These reports are for limited distribution and are designed primarily for rapid release of data shortly after the end of the water year. These records will be published later in Geological Survey water-supply papers.

Wyoming↗

Water resources data for Wyoming, water year 1973, part 2, water quality records

Water-resources data for the 1973 water year for Wyoming include records of data for the chemical and physical characteristics of surface and ground water. Data on the quality of surface water (chemical, temperature, and sediment) were collected from designated sampling sites at predetermined intervals such as once daily, weekly, monthly or less frequently. At some sites water-temperature data were recorded on charts by recorders. Data are given for 133 sampling stations of which 116 are continuous-record stations and 17 are miscellaneous sites. Chemical analyses are also given for 68 ground-water sites. Locations of surface water-quality stations are shown in figure 1 and locations of ground-water sites are shown in figure 2. These data represent that portion of the National Water Data System collected by the U. S. Geological Survey and cooperating State and Federal agencies in Wyoming. The records were collected and computed by the Water Resources Division of the U. S. Geological Survey under the direction of Robert L. Cushman, district chief. Wyoming district personnel who contributed significantly to the collection and preparation of data included in this report were: E. R. Cox, S. A. Druse, W. G. Hodson, M. E. Lowry, D. J. O'Connell, G. W. Armentrout, Jr., M. A. Crist, B. H. Ringen, W. B. Borchert, W. R. Glass, G. C. Lines, H. B. Fabricius, P. B. McCollam, C. E. Obert, K. G. Polinoski, T. W. Custis, R. L. Muench, J. 0. Ragsdale, M. D. Stevens, R. C. Baumann, D. W. Brownell, J. L. Lynch, S. L. Green, M. L. Smalley, and J. P. Kyner. The Geological Survey has published records of chemical quality, water temperatures, and sediment since 1941 in an annual series of water-supply papers entitled, "Quality of Surface Water of the United States." Beginning with the 1964 water year, water-quality records have been released by the Geological Survey in annual reports on a State-boundary basis. These reports are for limited distribution and are designed primarily for rapid release of data shortly after the end of the water year. These records will be published later in Geological Survey water-supply papers.

Wyoming↗

Water resources data for Kansas, water year 1972; Part 1, Surface water records

Surface-water records for the 1972 water year for Kansas, including records of streamflow or reservoir storage at gaging stations and partial-record stations, are given in this report. The locations of the stations are on figures 1 and 2. Records for a few pertinent gaging stations in bordering States also are included. These data represent that part of the National Water Data System collected by the U. S. Geological Survey and cooperating State and Federal agencies in Kansas. The records were collected and computed by the Water Resources Division of the U. S. Geological Survey under the direction of C. W. Lane, district chief. Kansas district personnel who contributed significantly to the collection and preparation of data included in this report were: J. L. Ebling, C. 0. Geiger, K. D. Medina, L. E. Stuliken, C. 0. Peek, J. D. Craig, L. L. Jones, A. T. Klamm, J. P. Marshall, C. W. Kennedy, W. J. Carswell, D. L. Lacock, G. G. Quy II, J. T. Religa, R. D. Thomas, S. V. Bond, S. T. Green, C. G. Sauer, A. B. Evans, A. F. Browning, M. J. Goetz, M. L. Penny, and M. Pabst. Through September 30, 1960, the records of discharge and stage of streams and canals and contents and stage of lakes or reservoirs were published in an annual series of U. S. Geological Survey water-supply papers entitled "Surface Water Supply of the United States." Beginning with the 1961 water year, surface-water records have been released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these reports is limited; they are designed primarily for rapid release of data shortly after the end of the water year to meet local needs. The discharge and reservoir storage records for 1961-65 also have been published in a Geological Survey water-supply paper series entitled "Surface Water Supply of the United States 1961-65."

Kansas↗

Water resources data for New Mexico, water year 1969; Part 1. Surface water records

Surface-water records for the 1969 water year for New Mexico, including records of streamflow or reservoir storage at gaging stations, partial-record stations, and miscellaneous sites, are given in this report and their locations shown in figures 1, 2. Records for a few pertinent gaging stations in bordering states also are included. The records were collected and computed by the Water Resources Division of the U.S. Geological Survey under the direction of W. E. Hale, district chief. These data represent that portion of the National Water Data System collected by the U.S. Geological Survey and cooperating State and Federal agencies in New Mexico. Through September 30, 1960, the records of discharge and stage of streams and canals and contents and stage of lakes or reservoirs were published in an annual series of U.S. Geological Survey water-supply papers entitled Surface Water Supply of the United States." Beginning with the 1961 water year, surface-water records have been released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these reports is limited; they are designed primarily for rapid release of data shortly after the end of the water year to meet local needs. The discharge and reservoir storage records for 1961-65 also will be published in a Geological Survey water-supply paper series entitled "Surface Water Supply of the United States 1961-65."

New Mexico↗

Water Resources Data for New Mexico; Part 1, Surface Water Records

Surface-water records for the 1970 water year for New Mexico, including records of streamflow or reservoir storage at gaging stations, partial-record stations, and miscellaneous sites, are given in this report and their locations shown in figures 1, 2. Records for a few pertinent gaging stations in bordering States also are included. The records were collected arid computed by the Water Resources Division of the U.S. Geological Survey under the direction of W. E. Hale, district chief. These data represent that portion of the National Water Data System collected by the U.S. Geological Survey and cooperating State and Federal agencies in New Mexico. Through September 30, 1960, the records of discharge and stage of streams and canals and contents and stage of lakes or reservoirs were published in an annual series of U.S. Geological Survey water-supply papers entitled II Surface Water Supply of the United States." Beginning with the 1961 water year, surface-water records have been released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these reports is limited; they are designed primarily for rapid release of data shortly after the end of the water year to meet local needs. The discharge and reservoir storage records for 1961-65 also are published in a Geological Survey water-supply paper series entitled "Surface Water Supply of the United States 1961-65." There will be a similar series of water-supply papers for the water years 1966-70.

New Mexico↗

Water resources data for New Mexico, water year 1973; Part 1. Surface water records

Surface-water records for the 1973 calendar year for New Mexico, including records of streamflow or reservoir storage at gaging stations, partial-record stations, and miscellaneous sites, are given in this report and their locations shown in figures 1, 2. Records for a 'few pertinent gaging stations in bordering States also are included. The records were collected and computed by the Water Resources Division of the US. Geological Survey under the direction of W. E. Hale, district chief. These data represent that portion of the National Water Data System collected by the U.S. Geological Survey and cooperating State and Federal agencies in New Mexico. Through September 30, 1960, the records of discharge and stage of streams and canals and contents and stage of lakes or reservoirs were published in an annual series of U.S. Geological Survey water supply papers entitled "Surface Water Supply of the United States" Beginning with the 1961 water year, surface-water records have been released by the Geological Survey in annual reports on a State boundary basis. Distribution of these reports is limited; they are designed primarily for rapid release of data shortly after the end of the water year to meet local needs. The discharge and reservoir storage records for 1961-65 also are published in a Geological Survey water supply paper series entitled "Surface Water Supply of the United States 1961-65." There will be a similar series of water-supply papers for the water years 1966-70.

New Mexico↗

Water resources data for Arizona, water year 1972: Part 1. Surface water records

Surface-water records for the 1972 water year for Arizona, including records of streamflow or reservoir storage at gaging stations, partial-record stations, and miscellaneous sites, are given in this report and their locations shown in figures 1, 3, and 4. Records for a few pertinent gaging stations in bordering States also are included, The records were collected and computed by the Water Resources Division of the U.S. Geological Survey under the direction of H. M. Babcock, district chief. These data represent that portion of the National Water Data System collected by the U.S. Geological Survey and cooperating State and Federal agencies in Arizona. Through September 30, 1960, the records of discharge and stage of streams and canals and contents and stage of lakes or reservoirs were published in an annual series of U.S. Geological Survey water-supply papers entitled "Surface Water Supply of the United States." Beginning with the 1961 water year, surface-water records have been released by the GeologicalSurvey in annual reports ona State-boundarybasis. Distribution of these reports islimited; theyare designed primarily for rapid release of data shortly after the end of the water year to meet local needs. The discharge and reservoir storage records for 1961-65 also have been published in a Geological Survey water - supply paper series entitled "Surface Water Supply ofthe United States 1961-65. "

Arizona↗

Water resources data for Arizona, 1969: Part 1. Surface water records

Surface-water records for the 1969 water year for Arizona, including records of streamflow or reservoir storage at gaging stations, partial-record stations, and miscellaneous sites, are given in this report and their locations shown in figures 1, 3, and 4. Records for a few pertinent gaging stations in bordering States also are included. The records were collected and computed by the Water Resources Division of the U. S. Geological Survey under the direction of H. M. Babcock, district chief. These data represent that portion of the National Water Data System collected by the U.S. Geological Survey and cooperating State and Federal agencies in Arizona. Through September 30, 1960, the records of discharge and stage of streams and canals and contents and stage of lakes or reservoirs were published in an annual series of U.S. Geological Survey water-supply papers entitled "Surface Water Supply of the United States." Beginning with the 1961 water year, surface-water records have been released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these reports is limited; they are designed primarily for rapid release of data shortly after the end of the water year to meet local needs. The discharge and reservoir storage records for 1961-65 also will be published in a Geological Survey water-supply paper series entitled "Surface Water Supply of the United States 1961-65."

Arizona↗

Water resources data for Arizona, 1970: Part 1. Surface water records

Surface-water records for the 1970 water year for Arizona, including records of streamflow or reservoir storage at gaging stations. partial-record stations. and miscellaneous sites are given in this report and their locations shown in figures 1. 3, and 4. Records for a few pertinent gaging stations in bordering States also are included. The records were collected and computed by the Water Resources Division of the U. S. Geological Survey under the direction of H. M. Babcock, district chief. These data represent that portion of the National Water Data System collected by the U.S. Geological Survey and cooperating State and Federal agencies in Arizona. Through September 30, 1960, the records of discharge and stage of streams and canals and contents and stage of lakes or reservoirs were published in an annual series of U.S. Geological Survey water-supply papers entitled "Surface Water Supply of the United States." Beginning with the 1961 water year, surface-water records have been released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these reports is limited; they are designed primarily for rapid release of data shortly after the end of the water year to meet local needs. The discharge and reservoir storage records for 1961-65 also have been published in a Geological Survey water - supply paper series entitled "Surface Water Supply of the United States 1961-65."

Arizona↗

Water resources data for Kentucky, water year 1972: Part 1. Surface water quality

Surface-water records for the 1972 water year for Kentucky, including records of streamflow or reservoir storage at gaging stations, partial-record stations, and miscellaneous sites, are given in this report. The location of all gaging stations is shown in figures 1 and 2. Records for a few pertinent gaging stations in bordering States also are included. The records were collected and computed by the Water Resources Division of the U.S. Geological Survey under the direction of R. V. Cushman, district chief. These data represent that portion of the National Water Data System collected by the U.S. Geological Survey and cooperating State and Federal agencies in Kentucky. Through September 30, 1960, the records of discharge and stage of streams and canals and contents and stage of lakes or reservoirs were published in an annual series of U.S. Geological Survey water-supply papers entitled "Surface Water Supply of the United States." Since September 30, 1960, the records have been or will be published in a series of Geological Survey water-supply papers on a 5-year basis. Beginning with the 1961 water year, surface-water records have been released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these reports is limited; they are designed primarily for rapid release of data shortly after the end of the water year to meet local needs.

Kentucky↗

Water resources data for Wyoming, water year 1971, part 1, surface water records

Surface-water records for the 1971 water year for Wyoming, including records of streamflow or reservoir storage at gaging stations, partial-record stations, and miscellaneous sites, are given in this report. The locations of the gaging stations and partial-record stations are shown in figures 1 and 2. Records for a few pertinent gaging stations in bordering States also are included. The records were collected and computed by the Water Resources Division of the U.S. Geological Survey under the direction of Robert L. Cushman, district chief. These data represent that portion of the National Water Data System collected by the U.S. Geological Survey and cooperating State and Federal agencies in Wyoming. Through September 30, 1960, the records of discharge and stage of streams and canals, and contents and stage of lakes or reservoirs, were published in an annual series of U.S. Geological Survey water-supply papers entitled "Surface Water Supply of the United States." Beginning with the 1961 water year, surface-water records have been released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these reports is limited; they are designed primarily for rapid release of data shortly after the end of the water year to meet local needs. Records of discharge and reservoir storage for 1961-65 have been published in a Geological Survey water-supply paper series entitled "Surface Water Supply of the United States 1961-65." Records of discharge and reservoir storage for 1966-70 also will be published in a Geological Survey water-supply paper series entitled "Surface Water Supply of the United States 1966-70."

Wyoming↗

Water resources data for Michigan, water year 1973; Part 1, Surface water records

Surface-water records for the 1973 water year for gaging stations, partial-record stations, and miscellaneous sites within the State of Michigan are given in this report. For convenience there are also included records for a few pertinent gaging stations in bordering States. The records were collected and computed by the Water Resources Division of the U.S. Geological Survey, under the direction of T.R. Cummings, district chief. These data represent that portion of the National Water Data System collected by the U.S. Geological Survey and cooperating State and Federal agencies in Michigan. Records of discharge and stage of streams, and contents and stage of lakes or reservoirs are published in a series of U.S. Geological Survey water-supply papers entitled "Surface Water Supply of the United States". Through September 30, 1960, these water-supply papers were in an annual series and since then are in a 5-year series. Since 1951 there have been 20 volumes in the series; each volume covered an area whose boundaries coincided with those of certain natural drainage areas. The records in Michigan are contained in Part 4 of that series. Beginning with the 1961 water year, streamflow records and related data have been released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these basic-data reports is limited and primarily for local needs.

Michigan↗